[Debian-med-packaging] Bug#1058370: python-cogent: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Tue Dec 12 08:21:04 GMT 2023
Source: python-cogent
Version: 2023.2.12a1+dfsg-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20231212 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> sphinx-build -b html -d _build/doctrees . _build/html
> Running Sphinx v7.2.6
> making output directory... done
> WARNING: html_static_path entry '_static' does not exist
> WARNING: The config value `today' has type `date', defaults to `str'.
> [autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_seq.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst
> building [mo]: targets for 0 po files that are out of date
> writing output...
> building [html]: targets for 125 source files that are out of date
> updating environment: [new config] 125 added, 0 changed, 0 removed
> [2Kreading sources... [ 1%] api/__init__/cogent3.__init__.available_apps
> [2Kreading sources... [ 2%] api/__init__/cogent3.__init__.available_codes
> [2Kreading sources... [ 2%] api/__init__/cogent3.__init__.available_models
> [2Kreading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes
> [2Kreading sources... [ 4%] api/__init__/cogent3.__init__.get_code
> [2Kreading sources... [ 5%] api/__init__/cogent3.__init__.get_model
> [2Kreading sources... [ 6%] api/__init__/cogent3.__init__.get_moltype
> [2Kreading sources... [ 6%] api/__init__/cogent3.__init__.load_aligned_seqs
> [2Kreading sources... [ 7%] api/__init__/cogent3.__init__.load_delimited
> [2Kreading sources... [ 8%] api/__init__/cogent3.__init__.load_seq
> [2Kreading sources... [ 9%] api/__init__/cogent3.__init__.load_table
> [2Kreading sources... [ 10%] api/__init__/cogent3.__init__.load_tree
> [2Kreading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs
> [2Kreading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs
> [2Kreading sources... [ 12%] api/__init__/cogent3.__init__.make_seq
> [2Kreading sources... [ 13%] api/__init__/cogent3.__init__.make_table
> [2Kreading sources... [ 14%] api/__init__/cogent3.__init__.make_tree
> [2Kreading sources... [ 14%] api/__init__/cogent3.__init__.make_unaligned_seqs
> [2Kreading sources... [ 15%] api/alignment/alignment
> [2Kreading sources... [ 16%] api/alignment/classes/cogent3.core.alignment.Alignment
> [2Kreading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment
> [2Kreading sources... [ 18%] api/alignment/classes/cogent3.core.alignment.SequenceCollection
> [2Kreading sources... [ 18%] api/alphabet/alphabet
> [2Kreading sources... [ 19%] api/alphabet/classes/cogent3.core.alphabet.Alphabet
> [2Kreading sources... [ 20%] api/apps/composable.define_app
> [2Kreading sources... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode
> [2Kreading sources... [ 22%] api/genetic_code/genetic_code
> [2Kreading sources... [ 22%] api/index
> [2Kreading sources... [ 23%] api/moltype/classes/cogent3.core.moltype.MolType
> [2Kreading sources... [ 24%] api/moltype/moltype
> [2Kreading sources... [ 25%] api/sequence/classes/cogent3.core.sequence.DnaSequence
> [2Kreading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.ProteinSequence
> [2Kreading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.RnaSequence
> [2Kreading sources... [ 27%] api/sequence/sequence
> [2Kreading sources... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser
> [2Kreading sources... [ 29%] api/table/classes/cogent3.util.table.Columns
> [2Kreading sources... [ 30%] api/table/classes/cogent3.util.table.Table
> [2Kreading sources... [ 30%] api/table/table
> [2Kreading sources... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode
> [2Kreading sources... [ 32%] api/tree/tree
> [2Kreading sources... [ 33%] app/align-codon
> [2Kreading sources... [ 34%] app/align-nucleotide
> [2Kreading sources... [ 34%] app/align-protein
> [2Kreading sources... [ 35%] app/app-get
> [2Kreading sources... [ 36%] app/app-help
> [2Kreading sources... [ 37%] app/app-overview
> [2Kreading sources... [ 38%] app/available-apps
> [2Kreading sources... [ 38%] app/dstore
> [2Kreading sources... [ 39%] app/evo-ancestral-states
> [2Kreading sources... [ 40%] app/evo-dt-nuc-model
> [2Kreading sources... [ 41%] app/evo-extract-model-stats
> [2Kreading sources... [ 42%] app/evo-hypothesis
> [2Kreading sources... [ 42%] app/evo-model
> [2Kreading sources... [ 43%] app/evo-model-timehet
> [2Kreading sources... [ 44%] app/evo-model-with-tree
> [2Kreading sources... [ 45%] app/evo-natsel_neutral
> [2Kreading sources... [ 46%] app/evo-natsel_sitehet
> [2Kreading sources... [ 46%] app/evo-natsel_timehet
> [2Kreading sources... [ 47%] app/evo-natsel_zhang
> [2Kreading sources... [ 48%] app/evo-nstat-codon-model
> [2Kreading sources... [ 49%] app/evo-tr-codon-model
> [2Kreading sources... [ 50%] app/evo-tr-nuc-model
> [2Kreading sources... [ 50%] app/index
> [2Kreading sources... [ 51%] app/not-completed
> [2Kreading sources... [ 52%] app/user_function
> [2Kreading sources... [ 53%] cookbook/DNA_and_RNA_sequences
> [2Kreading sources... [ 54%] cookbook/alignments
> [2Kreading sources... [ 54%] cookbook/alphabet
> [2Kreading sources... [ 55%] cookbook/annotations
> [2Kreading sources... [ 56%] cookbook/building_alignments
> [2Kreading sources... [ 57%] cookbook/building_phylogenies
> [2Kreading sources... [ 58%] cookbook/calc_genetic_distance
> [2Kreading sources... [ 58%] cookbook/evo_modelling
> [2Kreading sources... [ 59%] cookbook/genetic_code
> [2Kreading sources... [ 60%] cookbook/index
> [2Kreading sources... [ 61%] cookbook/loading_sequences
> [2Kreading sources... [ 62%] cookbook/loading_tabular
> [2Kreading sources... [ 62%] cookbook/manipulating_biological_data
> [2Kreading sources... [ 63%] cookbook/moltypes
> [2Kreading sources... [ 64%] cookbook/protein_sequences
> [2Kreading sources... [ 65%] cookbook/simple_trees
> [2Kreading sources... [ 66%] cookbook/tables
> [2Kreading sources... [ 66%] cookbook/useful_utilities
> [2Kreading sources... [ 67%] cookbook/what_codes
> [2Kreading sources... [ 68%] data_file_links
> [2Kreading sources... [ 69%] draw/aln/plot_aln-coevolution
> [2Kreading sources... [ 70%] draw/aln/plot_aln-dotplot-1
> [2Kreading sources... [ 70%] draw/aln/plot_aln-dotplot-2
> [2Kreading sources... [ 71%] draw/aln/plot_aln-gaps-per-seq
> [2Kreading sources... [ 72%] draw/aln/plot_aln-info-plot
> [2Kreading sources... [ 73%] draw/aln/plot_aln-seqlogo
> [2Kreading sources... [ 74%] draw/index
> [2Kreading sources... [ 74%] draw/tree/plot_tree-angular
> [2Kreading sources... [ 75%] draw/tree/plot_tree-circular
> [2Kreading sources... [ 76%] draw/tree/plot_tree-radial
> [2Kreading sources... [ 77%] draw/tree/plot_tree-square
> [2Kreading sources... [ 78%] draw/tree/plot_tree-support
> [2Kreading sources... [ 78%] examples/align_codons_to_protein
> [2Kreading sources... [ 79%] examples/calculate_UPGMA_cluster
> [2Kreading sources... [ 80%] examples/calculate_neigbourjoining_tree
> [2Kreading sources... [ 81%] examples/calculate_pairwise_distances
> [2Kreading sources... [ 82%] examples/codon_models
> [2Kreading sources... [ 82%] examples/coevolution
> [2Kreading sources... [ 83%] examples/complete_seq_features
> [2Kreading sources... [ 84%] examples/empirical_protein_models
> [2Kreading sources... [ 85%] examples/hmm_par_heterogeneity
> [2Kreading sources... [ 86%] examples/index
> [2Kreading sources... [ 86%] examples/manipulating_tree_nodes
> [2Kreading sources... [ 87%] examples/neutral_test
> [2Kreading sources... [ 88%] examples/parallel
> [2Kreading sources... [ 89%] examples/parametric_bootstrap
> [2Kreading sources... [ 90%] examples/period_estimation
> [2Kreading sources... [ 90%] examples/phylo_by_ls
> [2Kreading sources... [ 91%] examples/rate_heterogeneity
> [2Kreading sources... [ 92%] examples/relative_rate
> [2Kreading sources... [ 93%] examples/scope_model_params_on_trees
> [2Kreading sources... [ 94%] examples/seq_features
> [2Kreading sources... [ 94%] examples/simple
> [2Kreading sources... [ 95%] examples/simulate_alignment
> [2Kreading sources... [ 96%] examples/testing_multi_loci
> [2Kreading sources... [ 97%] general
> [2Kreading sources... [ 98%] index
> [2Kreading sources... [ 98%] install
> [2Kreading sources... [ 99%] licenses
> [2Kreading sources... [100%] pycogent
>
> /<<PKGBUILDDIR>>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title.
>
> Notes
> -----
> /<<PKGBUILDDIR>>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent.
> /<<PKGBUILDDIR>>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title.
>
> Notes
> -----
> /<<PKGBUILDDIR>>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent.
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_unaligned", format="fasta")
> seqs = loader("data/SCA1-cds.fasta")
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> codon_aligner = get_app("progressive_align", "codon")
> aligned = codon_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> nt_aligner = get_app("progressive_align", "codon", distance="paralinear")
> aligned = nt_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
> codon_aligner = get_app("progressive_align", "codon", guide_tree=tree)
> aligned = codon_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> codon_aligner = get_app("progressive_align",
> "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01
> )
> aligned = codon_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:76: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> codon_aligner = get_app("progressive_align",
> "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3)
> )
> aligned = codon_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-codon.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aligned.info
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_unaligned", format="fasta")
> seqs = loader("data/SCA1-cds.fasta")
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> nt_aligner = get_app("progressive_align", "nucleotide")
> aligned = nt_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93")
> aligned = nt_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
> nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree)
> aligned = nt_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
> nt_aligner = get_app("progressive_align", "F81", guide_tree=tree)
> aligned = nt_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-nucleotide.rst:73: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aligned.info
> /<<PKGBUILDDIR>>/doc/app/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_unaligned", format="fasta")
> to_aa = get_app("translate_seqs")
> process = loader + to_aa
> seqs = process("data/SCA1-cds.fasta")
> /<<PKGBUILDDIR>>/doc/app/align-protein.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> aa_aligner = get_app("progressive_align", "protein")
> aligned = aa_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-protein.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aa_aligner = get_app("progressive_align", "protein", distance="paralinear")
> aligned = aa_aligner(seqs)
> aligned
> /<<PKGBUILDDIR>>/doc/app/align-protein.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aligned.info
> /<<PKGBUILDDIR>>/doc/app/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> just_nucs = get_app("omit_degenerates", moltype="dna")
> just_nucs
> /<<PKGBUILDDIR>>/doc/app/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import app_help
>
> app_help("omit_degenerates")
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from pathlib import Path
> from tempfile import TemporaryDirectory
>
> tmpdir = TemporaryDirectory(dir=".")
> path_to_dir = tmpdir.name
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:89: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app, open_data_store
>
> out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w")
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> cpos3 = get_app("take_codon_positions", 3)
> writer = get_app("write_seqs", out_dstore, format="fasta")
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:102: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data = loader("data/primate_brca1.fasta")
> just3rd = cpos3(data)
> m = writer(just3rd)
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:117: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> process = loader + cpos3 + writer
> m = process("data/primate_brca1.fasta")
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:127: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dstore = open_data_store("data", suffix="fasta", mode="r")
> result = process.apply_to(dstore)
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:142: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> out_dstore.summary_logs
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:151: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> out_dstore.describe
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:157: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> out_dstore.summary_not_completed
> /<<PKGBUILDDIR>>/doc/app/app-overview.rst:164: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result = process.apply_to(dstore, show_progress=True)
> /<<PKGBUILDDIR>>/doc/app/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_apps
>
> available_apps()
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import open_data_store
>
> dstore = open_data_store("data/raw.zip", suffix="fa*", limit=5, mode="r")
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> m = dstore[0]
> m
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:43: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> m.read()[:20] # truncating
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:50: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for m in dstore:
> print(m)
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:69: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dstore = open_data_store("data/demo-locked.sqlitedb")
> dstore.describe
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:76: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dstore.unlock(force=True)
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:85: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dstore.summary_logs
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dstore.logs
> /<<PKGBUILDDIR>>/doc/app/dstore.rst:97: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(dstore.logs[0].read()[:225]) # truncated for clarity
> /<<PKGBUILDDIR>>/doc/app/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta")
> aln = loader("data/primate_brca1.fasta")
> gn = get_app("model", "GN", tree="data/primate_brca1.tree")
> result = gn(aln)
> /<<PKGBUILDDIR>>/doc/app/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> reconstuctor = get_app("ancestral_states")
> states_result = reconstuctor(result)
> states_result
> /<<PKGBUILDDIR>>/doc/app/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> states_result["edge.0"]
> /<<PKGBUILDDIR>>/doc/app/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.tree.get_figure(contemporaneous=True).show(width=500, height=500)
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> model = get_app("model", "BH", tree="data/primate_brca1.tree")
> result = model(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.lf
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = result.tree
> fig = tree.get_figure()
> fig.scale_bar = "top right"
> fig.show(width=500, height=500)
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tabulator = get_app("tabulate_stats")
> stats = tabulator(result)
> stats
> /<<PKGBUILDDIR>>/doc/app/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> stats["edge motif motif2 params"]
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> model = get_app("model", "GN", tree="data/primate_brca1.tree")
> result = model(aln)
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tabulator = get_app("tabulate_stats")
> tabulated = tabulator(result)
> tabulated
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tabulated["edge params"]
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tabulated["global params"]
> /<<PKGBUILDDIR>>/doc/app/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tabulated["motif params"]
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
>
> tree = "data/primate_brca1.tree"
>
> null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True)
> alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True)
> hyp = get_app("hypothesis", null, alt)
> result = hyp(aln)
> type(result)
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.LR, result.df, result.pvalue
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.null
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.null.lf
> /<<PKGBUILDDIR>>/doc/app/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.alt.lf
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago")
> process = loader + select_seqs
> aln = process("data/primate_brca1.fasta")
> aln.names
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> gn = get_app("model", "GN")
> gn
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted = gn(aln)
> type(fitted)
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.lf
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.lnL, fitted.nfp
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.source
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.tree, fitted.alignment
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.total_length(length_as="paralinear")
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> gn = get_app("model", "GN", split_codons=True)
>
> fitted = gn(aln)
> fitted
> /<<PKGBUILDDIR>>/doc/app/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted[3]
> /<<PKGBUILDDIR>>/doc/app/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3 import get_app
>
> tree = load_tree("data/primate_brca1.tree")
> fig = tree.get_figure(contemporaneous=True)
> fig.style_edges(
> "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red")
> )
> fig.show(width=500, height=500)
> /<<PKGBUILDDIR>>/doc/app/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> time_het = get_app("model",
> "GN",
> tree=tree,
> time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")],
> )
> /<<PKGBUILDDIR>>/doc/app/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> loader = get_app("load_aligned", format="fasta")
> aln = loader("data/primate_brca1.fasta")
> result = time_het(aln)
> /<<PKGBUILDDIR>>/doc/app/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.lf
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> aln.names
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3 import get_app
>
> tree = load_tree("data/primate_brca1.tree")
> gn = get_app("model", "GN", tree=tree)
> gn
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> gn = get_app("model", "GN", tree="data/primate_brca1.tree")
> gn
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted = gn(aln)
> fitted
> /<<PKGBUILDDIR>>/doc/app/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fitted.lf
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
>
> omega_eq_1 = get_app("natsel_neutral",
> "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
> )
> result = omega_eq_1(aln)
> type(result)
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.alt.lf
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
>
> sites_differ = get_app("natsel_sitehet",
> "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
> )
>
> result = sites_differ(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.alt.lf
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bprobs = result.alt.lf.get_bin_probs()
> bprobs[:, :20]
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
>
> hc_differ = get_app("natsel_timehet",
> "GNC",
> tree="data/primate_brca1.tree",
> optimise_motif_probs=False,
> tip1="Human",
> tip2="Chimpanzee",
> )
> result = hc_differ(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.alt.lf
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from IPython.core.display import HTML
> from numpy import array
>
> from cogent3 import make_table
>
> header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges']
> data = {'Site Class': array(['0', '1', '2a', '2b'], dtype='<U2'), 'Proportion': array(['p0', 'p1', 'p2', 'p3'], dtype='<U2'), 'Background Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega0 < 1', 'omega1 = 1'],
> dtype='<U14'), 'Foreground Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega2 > 1', '0 < omega0 < 1'],
> dtype='<U14')}
> data = {k: array(data[k], dtype='U') for k in data}
> table = make_table(header, data=data)
> HTML(table.set_repr_policy(show_shape=False))
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:31: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
>
> zhang_test = get_app("natsel_zhang",
> "GNC",
> tree="data/primate_brca1.tree",
> optimise_motif_probs=False,
> tip1="Human",
> tip2="Chimpanzee",
> )
>
> result = zhang_test(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.alt.lf
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:56: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bprobs = result.alt.lf.get_bin_probs()
> bprobs[:, :20]
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:64: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tab = get_app("tabulate_stats")
> stats = tab(result.alt)
> stats
> /<<PKGBUILDDIR>>/doc/app/evo-natsel_zhang.rst:70: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> stats["edge bin params"][:10] # truncating the table
> /<<PKGBUILDDIR>>/doc/app/evo-nstat-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-nstat-codon-model.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> /<<PKGBUILDDIR>>/doc/app/evo-nstat-codon-model.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> model = get_app("model", "GNC", tree="data/primate_brca1.tree")
> result = model(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-nstat-codon-model.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.lf
> /<<PKGBUILDDIR>>/doc/app/evo-nstat-codon-model.rst:37: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = result.tree
> fig = tree.get_figure()
> fig.scale_bar = "top right"
> fig.show(width=500, height=500)
> /<<PKGBUILDDIR>>/doc/app/evo-tr-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-tr-codon-model.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_models
>
> available_models("codon")
> /<<PKGBUILDDIR>>/doc/app/evo-tr-codon-model.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> model = get_app("model",
> "CNFGTR",
> tree="data/primate_brca1.tree",
> optimise_motif_probs=True,
> )
> result = model(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-tr-codon-model.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.lf
> /<<PKGBUILDDIR>>/doc/app/evo-tr-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/evo-tr-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_models
>
> available_models("nucleotide")
> /<<PKGBUILDDIR>>/doc/app/evo-tr-nuc-model.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> loader = get_app("load_aligned", format="fasta", moltype="dna")
> aln = loader("data/primate_brca1.fasta")
> model = get_app("model",
> "GTR", tree="data/primate_brca1.tree", optimise_motif_probs=True
> )
> result = model(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/evo-tr-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result.lf
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_app
>
> reader = get_app("load_aligned", format="fasta")
> select_seqs = get_app("take_named_seqs", "Mouse", "Human")
> aln = reader("data/primate_brca1.fasta")
> result = select_seqs(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> result == False
> result.type
> result.message
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:45: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises:
>
> result = reader("primate_brca1.fasta")
> result
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:54: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> process = reader + select_seqs
> result = process("data/primate_brca1.fasta")
> result
> /<<PKGBUILDDIR>>/doc/app/not-completed.rst:62: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises:
>
> result = process("primate_brca1.fasta")
> result
> /<<PKGBUILDDIR>>/doc/app/user_function.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app.composable import define_app
> from cogent3.app.typing import AlignedSeqsType
>
> @define_app
> def up_to(val: AlignedSeqsType, index=2) -> AlignedSeqsType:
> return val[:index]
> /<<PKGBUILDDIR>>/doc/app/user_function.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> first4 = up_to(index=4)
> first4
> /<<PKGBUILDDIR>>/doc/app/user_function.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna"
> )
> result = first4(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/user_function.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from typing import Union
>
> from cogent3.app.composable import define_app
> from cogent3.app.typing import SeqsCollectionType, SerialisableType
>
> T = Union[SeqsCollectionType, SerialisableType]
>
> @define_app
> def rename_seqs(seqs: SeqsCollectionType) -> T:
> """upper case names"""
> return seqs.rename_seqs(lambda x: x.upper())
>
> renamer = rename_seqs()
> result = renamer(aln)
> result
> /<<PKGBUILDDIR>>/doc/app/user_function.rst:76: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app.composable import define_app
> from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType
>
> @define_app
> def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType:
> return aln.distance_matrix(calc=calc, show_progress=False)
>
> percent_dist = get_dists(calc="percent")
> result = percent_dist(aln)
> result
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("AGTACACTGGT")
> my_seq
> print(my_seq)
> str(my_seq)
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import RNA
>
> rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("AGTACACTGGT")
> print(my_seq.to_fasta())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import RNA
>
> rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
> rnaseq.to_fasta()
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna")
> my_seq
> type(my_seq)
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:74: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("AGTACACTGGT", moltype="dna")
> my_seq.name = "my_gene"
> print(my_seq.to_fasta())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:85: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("AGTACACTGGT")
> print(my_seq.complement())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:95: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(my_seq.rc())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(my_seq.rc())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("GCTTGGGAAAGTCAAATGGAA", "protein-X")
> pep = my_seq.get_translation()
> type(pep)
> print(pep.to_fasta())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:122: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("ACGTACGTACGTACGT")
> print(my_seq.to_rna())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:132: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import RNA
>
> rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
> print(rnaseq.to_dna())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:142: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> a = DNA.make_seq("AGTACACTGGT")
> a.can_pair(a.complement())
> a.can_pair(a.rc())
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:153: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> my_seq = DNA.make_seq("AGTACACTGGT")
> extra_seq = DNA.make_seq("CTGAC")
> long_seq = my_seq + extra_seq
> long_seq
> str(long_seq)
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> my_seq[1:6]
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:177: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> seq = DNA.make_array_seq("ATGATGATGATG")
> pos3 = seq[2::3]
> assert str(pos3) == "GGGG"
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:190: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> seq = DNA.make_seq("ATGATGATGATG")
> indices = [(i, i + 2) for i in range(len(seq))[::3]]
> pos12 = seq.add_feature("pos12", "pos12", indices)
> pos12 = pos12.get_slice()
> assert str(pos12) == "ATATATAT"
> /<<PKGBUILDDIR>>/doc/cookbook/DNA_and_RNA_sequences.rst:211: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import RNA
>
> s = RNA.make_seq("--AUUAUGCUAU-UAu--")
> print(s.degap())
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs, make_unaligned_seqs
>
> dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
> seqs = make_aligned_seqs(data=dna, moltype="dna")
> print(type(seqs))
> seqs = make_unaligned_seqs(dna, moltype="dna")
> print(type(seqs))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
> seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True)
> print(type(seqs))
> print(seqs)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_unaligned_seqs
>
> seqs = load_unaligned_seqs("data/test.paml")
> print(seqs)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:70: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
> moltype="dna",
> )
> print(aln)
> new_seqs = make_aligned_seqs(
> [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna"
> )
> new_aln = aln.add_seqs(new_seqs)
> print(new_aln)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:92: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> new_aln = aln.add_seqs(new_seqs, before_name="seq2")
> print(new_aln)
> new_aln = aln.add_seqs(new_seqs, after_name="seq2")
> print(new_aln)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:104: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
> moltype="dna",
> )
> ref_aln = make_aligned_seqs(
> [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")],
> moltype="dna",
> )
> new_aln = aln.add_from_ref_aln(ref_aln)
> print(new_aln)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:126: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
> moltype="dna",
> )
> new_aln = aln.get_degapped_relative_to("seq1")
> print(new_aln)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:145: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
> moltype="dna",
> array_align=False,
> )
> seq = aln.get_seq("seq1")
> seq.name
> type(seq)
> seq.is_gapped()
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:161: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq = aln.get_gapped_seq("seq1")
> seq.is_gapped()
> print(seq)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:169: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln.names
> aln.names
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:179: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_unaligned_seqs
>
> fn = "data/long_testseqs.fasta"
> seqs = load_unaligned_seqs(fn, moltype="dna")
> my_seq = seqs.seqs[0]
> my_seq[:24]
> str(my_seq[:24])
> type(my_seq)
> aln = load_aligned_seqs(fn, moltype="dna")
> aln.seqs[0][:24]
> print(aln.seqs[0][:24])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/test.paml", moltype="dna")
> aln.names
> new = aln.take_seqs(["Human", "HowlerMon"])
> new.names
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:207: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/test.paml", array_align=False, moltype="dna")
> seq = aln.get_seq("Human")
> new = aln.take_seqs(["Human", "HowlerMon"])
> id(new.get_seq("Human")) == id(aln.get_seq("Human"))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:222: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_unaligned_seqs
> from cogent3.core.alignment import Alignment
>
> seq = load_unaligned_seqs("data/test.paml")
> aln = Alignment(seq)
> fasta_1 = seq
> fasta_2 = aln
> assert fasta_1 == fasta_2
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:238: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> data = [("a", "ACG---"), ("b", "CCTGGG")]
> aln = make_aligned_seqs(data=data)
> dna = aln.to_dna()
> dna
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:249: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> data = [("a", "ACG---"), ("b", "CCUGGG")]
> aln = make_aligned_seqs(data=data)
> rna = aln.to_rna()
> rna
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:260: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> data = [("x", "TYV"), ("y", "TE-")]
> aln = make_aligned_seqs(data=data)
> prot = aln.to_protein()
> prot
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:277: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
> degapped = aln.degap()
> print(type(degapped))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
> aln = make_aligned_seqs(data=dna, moltype="dna")
> aln.write("sample.fasta")
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:302: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln.write("sample", format="fasta")
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:308: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.io import remove_files
>
> remove_files(["sample", "sample.fasta"], error_on_missing=False)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.core.alignment import Alignment
>
> seq = load_aligned_seqs("data/long_testseqs.fasta")
> aln = Alignment(seq)
> fasta_align = aln
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:329: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.core.alignment import Alignment
>
> seq = load_aligned_seqs("data/test.paml")
> aln = Alignment(seq)
> got = aln.to_phylip()
> print(got)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:342: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.core.alignment import Alignment
>
> seq = load_aligned_seqs("data/test.paml")
> aln = Alignment(seq)
> string_list = aln.to_dict().values()
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:359: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> fn = "data/long_testseqs.fasta"
> aln = load_aligned_seqs(fn, moltype="dna")
> print(aln[:24])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:369: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: TypeError
>
> from cogent3 import load_unaligned_seqs
>
> fn = "data/long_testseqs.fasta"
> seqs = load_unaligned_seqs(fn)
> print(seqs[:24])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:381: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> seq = load_aligned_seqs("data/test.paml")
> column_four = aln[3]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:391: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> region = aln[50:70]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:401: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
> col = aln[113:115].iter_positions()
> type(col)
> list(col)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:415: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False
> )
> list(range(len(aln))[2::3])
> indices = [(i, i + 1) for i in range(len(aln))[2::3]]
> indices
> pos3 = aln.add_feature("pos3", "pos3", indices)
> pos3 = pos3.get_slice()
> print(pos3)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:434: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True
> )
> pos3 = aln[2::3]
> print(pos3)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:454: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"},
> moltype="dna",
> )
> new = aln.trim_stop_codons()
> print(new)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:467: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> data={
> "seq1": "ACGTAA---",
> "seq2": "ACGAC----", # terminal codon incomplete
> "seq3": "ACGCAATGA",
> },
> moltype="dna",
> )
> new = aln.trim_stop_codons(allow_partial=True)
> print(new)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAAGGTG---"),
> ("seq2", "ATGAAGGTGATG"),
> ("seq3", "ATGAAGGNGATG"),
> ],
> moltype="dna",
> )
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:500: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> nucs = aln.no_degenerates()
> print(nucs)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:507: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> trinucs = aln.no_degenerates(motif_length=3)
> print(trinucs)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:515: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> pos = aln.variable_positions()
> just_variable_aln = aln.take_positions(pos)
> print(just_variable_aln[:10])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:527: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> pos = aln.variable_positions()
> just_constant_aln = aln.take_positions(pos, negate=True)
> print(just_constant_aln[:10])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:541: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> variable_codons = aln.filtered(
> lambda x: len(set(map(tuple, x))) > 1, motif_length=3
> )
> print(just_variable_aln[:9])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:553: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = aln.to_type(array_align=False)
> variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3)
> print(just_variable_aln[:9])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:567: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> aln.take_seqs(["Human", "Mouse"])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:576: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln.take_seqs(["Human", "Mouse"], negate=True)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:585: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAAGGTG---"),
> ("seq2", "ATGAAGGTGATG"),
> ("seq3", "ATGAAGGNGATG"),
> ],
> moltype="dna",
> )
>
> def no_N_chars(s):
> return "N" not in s
>
> aln.take_seqs_if(no_N_chars)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:605: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln.take_seqs_if(no_N_chars, negate=True)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:617: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAAGGTG---"),
> ("seq2", "ATGAAGGTGATG"),
> ("seq3", "ATGAAGGNGATG"),
> ],
> moltype="dna",
> )
> counts = aln.counts()
> print(counts)
> counts = aln.counts(motif_length=3)
> print(counts)
> counts = aln.counts(include_ambiguity=True)
> print(counts)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:645: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna")
> motif_probs = aln.get_motif_probs()
> print(motif_probs)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:655: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA, load_aligned_seqs
>
> trinuc_alphabet = DNA.alphabet.get_word_alphabet(3)
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna")
> motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet)
> for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True):
> print("%s %.3f" % (m, motif_probs[m]))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:669: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna")
> motif_probs = aln.get_motif_probs()
> assert motif_probs["T"] == 0.0
> motif_probs = aln.get_motif_probs(pseudocount=1e-6)
> assert 0 < motif_probs["T"] <= 1e-6
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:681: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")]
> aln = make_aligned_seqs(data=seqs, moltype="dna")
> dinuc_alphabet = DNA.alphabet.get_word_alphabet(2)
> motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet)
> assert motif_probs["AA"] == 0.25
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:691: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seqs = [("my_seq", "AAAGTAAG")]
> aln = make_aligned_seqs(data=seqs, moltype="dna")
> my_seq = aln.get_seq("my_seq")
> my_seq.count("AA")
> "AAA".count("AA")
> "AAAA".count("AA")
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:702: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> seq = make_seq(moltype="dna", seq="AAAGTAAG")
> seq
> di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)]
> sum([nn == "AA" for nn in di_nucs])
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:717: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
> col = aln[113:115].iter_positions()
> c1, c2 = list(col)
> c1, c2
> list(filter(lambda x: x == "-", c1))
> list(filter(lambda x: x == "-", c2))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:731: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
> for column in aln[113:150].iter_positions():
> ungapped = list(filter(lambda x: x == "-", column))
> gap_fraction = len(ungapped) * 1.0 / len(column)
> print(gap_fraction)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:746: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAAGG-TG--"),
> ("seq2", "ATG-AGGTGATG"),
> ("seq3", "ATGAAG--GATG"),
> ],
> moltype="dna",
> )
> seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:762: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq_to_aln_map[3]
> seq_to_aln_map[8]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1]
> aln_to_seq_map[3]
> aln_to_seq_map[8]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:779: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: KeyError
>
> seq_pos = aln_to_seq_map[7]
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:793: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAA---TG-"),
> ("seq2", "ATG-AGTGATG"),
> ("seq3", "AT--AG-GATG"),
> ],
> moltype="dna",
> )
> print(aln.omit_gap_runs(2))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:807: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAA---TG-"),
> ("seq2", "ATG-AGTGATG"),
> ("seq3", "AT--AG-GATG"),
> ],
> moltype="dna",
> )
> print(aln.omit_gap_pos(0.40))
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:821: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> data=[
> ("seq1", "ATGAA------"),
> ("seq2", "ATG-AGTGATG"),
> ("seq3", "AT--AG-GATG"),
> ],
> moltype="dna",
> )
> filtered_aln = aln.omit_gap_seqs(0.50)
> print(filtered_aln)
> /<<PKGBUILDDIR>>/doc/cookbook/alignments.rst:836: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(filtered_aln.omit_gap_pos())
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA, PROTEIN
>
> print(DNA.alphabet)
> print(PROTEIN.alphabet)
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> PROTEIN.alphabet.moltype == PROTEIN
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dinuc_alphabet = DNA.alphabet.get_word_alphabet(2)
> print(dinuc_alphabet)
> trinuc_alphabet = DNA.alphabet.get_word_alphabet(3)
> print(trinuc_alphabet)
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq = "TAGT"
> indices = DNA.alphabet.to_indices(seq)
> indices
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq = DNA.alphabet.from_indices([0, 2, 3, 0])
> seq
> /<<PKGBUILDDIR>>/doc/cookbook/alphabet.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0])
> seq
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.genbank import RichGenbankParser
>
> parser = RichGenbankParser(open("data/ST_genome_part.gb"))
> for accession, seq in parser:
> print(accession)
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> cds = seq.get_annotations_matching("CDS")
> print(cds)
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.core.annotation import Feature
>
> def add_annotation(seq, feature, spans):
> type_ = feature["type"]
> if type_ != "CDS":
> return
> name = feature.get("locus_tag", None)
> if name and not isinstance(name, str):
> name = " ".join(name)
> seq.add_annotation(Feature, type_, name, spans)
>
> parser = RichGenbankParser(
> open("data/ST_genome_part.gb"), add_annotation=add_annotation
> )
> for accession, seq in parser: # just reading one accession,sequence
> break
> genes = seq.get_annotations_matching("CDS")
> print(genes)
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
> from cogent3.core.annotation import Feature
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> print(s1[10:15]) # this will be exon 1
> print(s1[30:40]) # this will be exon 2
> print(s1[45:48]) # this will be exon 3
> s2 = DNA.make_seq("CGAAACGTTT", name="seq2")
> s3 = DNA.make_seq("CGAAACGTTT", name="seq3")
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:83: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
> from cogent3.core.annotation import Feature
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)])
> exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:97: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> exon3 = s1.add_feature("exon", "C", [(45, 48)])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:111: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s2 = DNA.make_seq("CGAAACGTTT", name="seq2")
> cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)])
> s3 = DNA.make_seq("CGAAACGTTT", name="seq3")
> cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)])
> cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:126: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> exon1 = s1.add_feature("exon", "A", [(10, 15)])
> exon2 = s1.add_feature("exon", "B", [(30, 40)])
> exon3 = s1.add_feature("exon", "C", [(45, 48)])
> cds = s1.get_region_covering_all([exon1, exon2, exon3])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:143: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> cds.get_coordinates()
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:152: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> not_cds = cds.get_shadow()
> not_cds
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:159: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> cds
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:168: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln1 = make_aligned_seqs(
> data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:182: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.core.annotation import Variable
>
> red_data = aln1.add_annotation(
> Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)]
> )
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:195: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> exon1 = s1.add_feature("exon", "A", [(10, 15)])
> exon2 = s1.add_feature("exon", "B", [(30, 40)])
> s1[exon1]
> s1[10:15]
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:209: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s1[exon2]
> exon2.get_slice()
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:217: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s1 = DNA.make_seq(
> "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
> )
> exon1 = s1.add_feature("exon", "A", [(10, 15)])
> exon2 = s1.add_feature("exon", "B", [(30, 40)])
> exon3 = s1.add_feature("exon", "C", [(45, 48)])
> cds = s1.get_region_covering_all([exon1, exon2, exon3])
> print(s1[cds])
> print(s1[exon1, exon2, exon3])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:233: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s1)
> print(s1[exon1, exon2, exon3])
> print(s1[exon2])
> print(s1[exon3])
> print(s1[exon1, exon3, exon2])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:244: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> s1[1:10, 9:15]
> s1[exon1, exon1]
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:252: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s1.get_region_covering_all([exon3, exon3]).get_slice())
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:259: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s1[exon2])
> ex2_start = exon2[0:3]
> print(s1[ex2_start])
> ex2_end = exon2[-3:]
> print(s1[ex2_end])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:272: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> aln1[seq_exon]
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:282: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln2 = make_aligned_seqs(
> data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
> match_exon = seq.add_feature("exon", "A", [(3, 8)])
> aln2.get_seq("x").copy_annotations(seq)
> copied = list(aln2.get_annotations_from_seq("x", "exon"))
> copied
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:295: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False)
> seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
> match_exon = seq.add_feature("exon", "A", [(5, 8)])
> aln2.get_seq("x").copy_annotations(seq)
> copied = list(aln2.get_annotations_from_seq("x", "exon"))
> copied
> copied[0].get_slice()
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:307: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> # new test
> aln2 = make_aligned_seqs(
> data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
> match_exon = seq.add_feature("exon", "A", [(5, 8)])
> aln2.get_seq("y").copy_annotations(seq)
> copied = list(aln2.get_annotations_from_seq("y", "exon"))
> copied
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:321: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln2 = make_aligned_seqs(
> data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x")
> nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)])
> aln2.get_seq("y").copy_annotations(diff_len_seq)
> copied = list(aln2.get_annotations_from_seq("y", "repeat"))
> copied
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:337: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln_exon = aln1.get_annotations_from_any_seq("exon")
> print(aln1[aln_exon])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:345: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> cpgsite2 = s2.get_annotations_matching("cpgsite")
> print(s2[cpgsite2])
> cpgsite3 = s3.get_annotations_matching("cpgsite")
> s2[cpgsite3]
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:358: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> # this test is new
> dont_exist = s2.get_annotations_matching("dont_exist")
> dont_exist
> s2[dont_exist]
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:370: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln3 = make_aligned_seqs(
> data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False
> )
> exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)])
> print(exon.get_slice())
> aln_exons = list(aln3.get_annotations_from_seq("x", "exon"))
> print(aln_exons)
> print(aln3[aln_exons])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:388: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> unified = aln_exons[0].as_one_span()
> print(aln3[unified])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:398: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG")
> plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)])
> print(plus[plus_rpt])
> minus = plus.rc()
> print(minus)
> minus_rpt = minus.get_annotations_matching("blah")
> print(minus[minus_rpt])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:413: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.genbank import RichGenbankParser
>
> parser = RichGenbankParser(open("data/ST_genome_part.gb"))
> seq = [seq for accession, seq in parser][0]
> no_cds = seq.with_masked_annotations("CDS")
> print(no_cds[150:400])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:429: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]],
> moltype="dna",
> array_align=False,
> )
> exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)])
> print(aln.with_masked_annotations("exon", mask_char="?"))
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:443: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rc = aln.rc()
> print(rc)
> print(rc.with_masked_annotations("exon", mask_char="?"))
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:452: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s = DNA.make_seq("CCCCAAAAAGGGAA", "x")
> exon = s.add_feature("exon", "norwegian", [(0, 4)])
> rpt = s.add_feature("repeat", "norwegian", [(9, 12)])
> rc = s.rc()
> print(s.with_masked_annotations("exon", shadow=True))
> print(rc.with_masked_annotations("exon", shadow=True))
> print(s.with_masked_annotations(["exon", "repeat"], shadow=True))
> print(rc.with_masked_annotations(["exon", "repeat"], shadow=True))
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:468: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a")
> cds1 = s.add_feature("cds", "cds1", [(0, 12)])
> cds2 = s.add_feature("cds", "cds2", [(15, 24)])
> all_cds = s.get_annotations_matching("cds")
> all_cds
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:483: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.genbank import RichGenbankParser
>
> parser = RichGenbankParser(open("data/ST_genome_part.gb"))
> seq = [seq for accession, seq in parser][0]
> all_cds = seq.get_annotations_matching("CDS")
> coding_seqs = seq.get_region_covering_all(all_cds)
> coding_seqs
> coding_seqs.get_slice()
> noncoding_seqs = coding_seqs.get_shadow()
> noncoding_seqs
> noncoding_seqs.get_slice()
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:502: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> print(aln)
> exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)])
> aln_exons = aln.get_annotations_from_seq("x", "exon")
> aln_exons = aln.get_annotations_from_any_seq("exon")
> aln_exons
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:522: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> seq = DNA.make_seq("aaaccggttt" * 10)
> v = seq.add_feature("exon", "exon", [(20, 35)])
> v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)])
> v = seq.add_feature("repeat_unit", "rep2", [(49, 60)])
> /<<PKGBUILDDIR>>/doc/cookbook/annotations.rst:536: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from cogent3.util.io import remove_files
>
> remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False)
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_unaligned_seqs, make_tree
> from cogent3.align.progressive import TreeAlign
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna")
> aln, tree = TreeAlign("HKY85", seqs, show_progress=False)
> aln
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = make_tree(
> "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)"
> )
> params = {"kappa": 4.0}
> aln, tree = TreeAlign(
> "HKY85", seqs, tree=tree, param_vals=params, show_progress=False
> )
> aln
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_unaligned_seqs, make_tree
> from cogent3.align.progressive import TreeAlign
>
> seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna")
> tree = make_tree(
> "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)"
> )
> params = {"kappa": 4.0, "omega": 1.3}
> aln, tree = TreeAlign(
> "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False
> )
> aln
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_unaligned_seqs
> from cogent3.align.progressive import TreeAlign
> from cogent3.evolve.models import get_model
>
> seqs = [
> (
> "hum",
> "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT",
> ),
> (
> "mus",
> "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG",
> ),
> ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"),
> ]
> unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna")
> print(unaligned_DNA)
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(unaligned_DNA.get_translation())
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aligned_aa_seqs = [
> ("hum", "KQIQESSENGSLAARQERQAQVNLT"),
> ("mus", "KQIQESGESGSLAARQERQAQVNLT"),
> ("rat", "LNKQ------PLS---------NKK"),
> ]
> aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein")
> /<<PKGBUILDDIR>>/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True)
> aligned_DNA
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> tree = aln.quick_tree(calc="TN93", show_progress=False)
> tree = tree.balanced() # purely for display
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> dists = aln.distance_matrix(calc="TN93")
> tree = dists.quick_tree(show_progress=False)
> tree = tree.balanced() # purely for display
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.phylo import nj
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> dists = aln.distance_matrix(calc="TN93")
> tree = nj.nj(dists, show_progress=False)
> tree = tree.balanced() # purely for display
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.phylo import nj
>
> dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73}
> tree = nj.nj(dists, show_progress=False)
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.phylo.least_squares import WLS
> from cogent3.util.deserialise import deserialise_object
>
> dists = deserialise_object("data/dists_for_phylo.json")
> ls = WLS(dists)
> stat, tree = ls.trex(a=5, k=5, show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.evolve.models import F81
> from cogent3.phylo.maximum_likelihood import ML
>
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> ml = ML(F81(), aln)
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_distances
>
> available_distances()
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> dists = aln.distance_matrix(calc="tn93", show_progress=False)
> dists
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_distance_calculator, load_aligned_seqs
>
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> dist_calc = get_distance_calculator("tn93", alignment=aln)
> dist_calc
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dist_calc.run(show_progress=False)
> dists = dist_calc.get_pairwise_distances()
> dists
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dist_calc.stderr
> /<<PKGBUILDDIR>>/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_model, load_aligned_seqs
> from cogent3.evolve import distance
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> d = distance.EstimateDistances(aln, submodel=get_model("F81"))
> d.run(show_progress=False)
> dists = d.get_pairwise_distances()
> dists
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_models
>
> available_models()
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
>
> hky = get_model("HKY85")
> print(hky)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
>
> sub_mod = get_model("GTR", with_rate=True, distribution="gamma")
> print(sub_mod)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
>
> sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma")
> print(sub_mod)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
>
> sub_mod = get_model("JTT92", with_rate=True, distribution="gamma")
> print(sub_mod)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_tree
> from cogent3.evolve.models import get_model
>
> sub_mod = get_model("F81")
> tree = make_tree("(a,b,(c,d))")
> lf = sub_mod.make_likelihood_function(tree)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs, make_tree
> from cogent3.evolve.models import get_model
>
> sub_mod = get_model("F81")
> tree = make_tree("(a,b,(c,d))")
> lf = sub_mod.make_likelihood_function(tree)
> aln = make_aligned_seqs(
> [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")]
> )
> lf.set_alignment(aln)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = get_model("CNFGTR")
> lf = sm.make_likelihood_function(tree, digits=2)
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "Orangutan"],
> outgroup_name="Galago",
> clade=True,
> init=0.5,
> )
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> sm = get_model("CNFGTR")
> lf = sm.make_likelihood_function(tree, digits=2)
> lf.set_param_rule("omega", is_constant=True)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> sm = get_model("CNFGTR")
> lf = sm.make_likelihood_function(tree, digits=2)
> lf.set_param_rule("omega", init=0.1)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> sm = get_model("CNFGTR")
> lf = sm.make_likelihood_function(tree, digits=2)
> lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree)
> lf.set_param_rule("length", upper=1.0)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> sm = get_model("GTR", with_rate=True, distribution="gamma")
> tree = load_tree("data/primate_brca1.tree")
> lf = sm.make_likelihood_function(tree, bins=4, digits=2)
> lf.set_param_rule("bprobs", is_constant=True)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.models import get_model
>
> sm = get_model("GTR", with_rate=True, distribution="gamma")
> tree = load_tree("data/primate_brca1.tree")
> lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2)
> lf.set_param_rule("bprobs", is_constant=True)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree, digits=3, space=2)
> lf.set_alignment(aln)
> lf.optimise(show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(local=True, max_restarts=5, show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(local=False, global_tolerance=1.0, show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree, digits=3, space=2)
> lf.set_alignment(aln)
> try:
> lf.optimise(
> show_progress=False,
> limit_action="raise",
> max_evaluations=10,
> return_calculator=True,
> )
> except ArithmeticError as err:
> print(err)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> sm = get_model("GTR")
> tree = load_tree("data/primate_brca1.tree")
> lf = sm.make_likelihood_function(tree)
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> lf.set_alignment(aln)
> lf.optimise(local=True, show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lnL = lf.lnL
> lnL
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> nfp = lf.nfp
> nfp
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.get_aic()
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.get_aic(second_order=True)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.get_bic()
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> a_g = lf.get_param_value("A/G")
> a_g
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> human = lf.get_param_value("length", "Human")
> human
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mprobs = lf.get_motif_probs()
> mprobs
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tables = lf.get_statistics(with_motif_probs=True, with_titles=True)
> tables[0] # just displaying the first
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree, digits=3, space=2)
> lf.set_alignment(aln)
> lf.set_param_rule(
> "length",
> tip_names=["Human", "Chimpanzee"],
> outgroup_name="Galago",
> clade=True,
> is_independent=False,
> )
> lf.set_name("Null Hypothesis")
> lf.optimise(local=True, show_progress=False)
> null_lnL = lf.lnL
> null_nfp = lf.nfp
> lf
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule("length", is_independent=True)
> lf.set_name("Alt Hypothesis")
> lf.optimise(local=True, show_progress=False)
> alt_lnL = lf.lnL
> alt_nfp = lf.nfp
> lf
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from scipy.stats.distributions import chi2
>
> LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic
> df = alt_nfp - null_nfp # the test degrees of freedom
> p = chi2.sf(LR, df)
> print(f"LR={LR:.4f} ; df={df}; p={df:.4f}")
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
>
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree, digits=3, space=2)
> lf.set_alignment(aln)
> lf.set_param_rule(
> "length",
> tip_names=["Human", "Chimpanzee"],
> outgroup_name="Galago",
> clade=True,
> is_independent=False,
> )
> lf.set_name("Null Hypothesis")
> lf.optimise(local=True, show_progress=False)
> sim_aln = lf.simulate_alignment()
> sim_aln[:60]
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> sm = get_model("HKY85")
> lf = sm.make_likelihood_function(tree)
> lf.set_alignment(aln)
> lf.optimise(local=True, show_progress=False)
> kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa")
> print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}")
> human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human")
> print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}")
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG"))
> tree = make_tree(tip_names=aln.names)
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree)
> lf.set_alignment(aln)
> json = lf.to_json()
> json[:60] # just truncating the displayed string
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.deserialise import deserialise_object
>
> newlf = deserialise_object(json)
> newlf
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
>
> tree = load_tree("data/primate_brca1.tree")
> aln = load_aligned_seqs("data/primate_brca1.fasta")
> sm = get_model("F81")
> lf = sm.make_likelihood_function(tree, digits=3, space=2)
> lf.set_alignment(aln)
> lf.optimise(show_progress=False)
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ancestors = lf.likely_ancestral_seqs()
> ancestors[:60]
> /<<PKGBUILDDIR>>/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ancestral_probs = lf.reconstruct_ancestral_seqs()
> ancestral_probs["root"][:5]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:4: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code
>
> standard_code = get_code(1)
> standard_code.translate("TTTGCAAAC")
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code, make_seq
>
> standard_code = get_code(1)
> seq = make_seq("ATGCTAACATAAA", moltype="dna")
> translations = standard_code.sixframes(seq)
> print(translations)
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code, make_seq
>
> standard_code = get_code(1)
> seq = make_seq("ATGCTAACATAAA", moltype="dna")
> stops_frame1 = standard_code.get_stop_indices(seq, start=0)
> stops_frame1
> stop_index = stops_frame1[0]
> seq[stop_index : stop_index + 3]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code, make_seq
>
> standard_code = get_code(1)
> standard_code["TTT"]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> standard_code["A"]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code
>
> standard_code = get_code(1)
> standard_code["TTT"]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:68: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code
>
> standard_code = get_code(1)
> standard_code["A"]
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> targets = ["A", "C"]
> codons = [standard_code[aa] for aa in targets]
> codons
> flat_list = sum(codons, [])
> flat_list
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:89: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("AGTACACTGGTT", moltype="dna")
> sorted(my_seq.codon_alphabet())
> len(my_seq.codon_alphabet())
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:102: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
> codons = my_seq.get_in_motif_size(3)
> print(codons)
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from cogent3.core.alphabet import AlphabetError
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:120: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: AlphabetError
>
> pep = my_seq.get_translation()
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:128: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
> seq = my_seq.trim_stop_codon()
> pep = seq.get_translation()
> print(pep.to_fasta())
> print(type(pep))
> /<<PKGBUILDDIR>>/doc/cookbook/genetic_code.rst:141: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_seq
>
> my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna")
> pep = my_seq[:-3].get_translation()
> print(pep.to_fasta())
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna")
> type(aln)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln.info.source
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_unaligned_seqs
>
> seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna")
> type(seqs)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
>
> aln = load_aligned_seqs("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna")
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta")
> aln
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> protein_seqs = [">seq1", "DEKQL-RG", ">seq2", "DDK--SRG"]
> proteins_loaded = make_aligned_seqs(protein_seqs)
> proteins_loaded.moltype
> print(proteins_loaded)
> proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein")
> print(proteins_loaded)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:94: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"}
> seqs_loaded = make_aligned_seqs(seqs)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:104: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> seqs = [">seq1", "AATCG-A", ">seq2", "AATCGGA"]
> seqs_loaded = make_aligned_seqs(seqs)
> print(seqs_loaded)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:117: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> DNA_seqs = [
> ">sample1 Mus musculus",
> "AACCTGC--C",
> ">sample2 Gallus gallus",
> "AAC-TGCAAC",
> ]
> loaded_seqs = make_aligned_seqs(
> DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0]
> )
> loaded_seqs
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_unaligned_seqs
>
> seqs = {"seq1": "AATCA", "seq2": "AATCGGA"}
> seqs = make_unaligned_seqs(data=seqs, moltype="dna")
> seqs
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:157: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.fasta import MinimalFastaParser
>
> f = open("data/long_testseqs.fasta")
> seqs = [(name, seq) for name, seq in MinimalFastaParser(f)]
> seqs
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:170: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.fasta import LabelParser
>
> def latin_to_common(latin):
> return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin]
>
> label_parser = LabelParser(
> "%(species)s", [[1, "species", latin_to_common]], split_with=":"
> )
> for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc":
> label = label_parser(label)
> print(label, type(label))
> /<<PKGBUILDDIR>>/doc/cookbook/loading_sequences.rst:186: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.fasta import LabelParser, MinimalFastaParser
>
> fasta_data = [
> ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]",
> "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL",
> "SEIQNIKSELKYVPKAEQ",
> ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]",
> "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY",
> "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD",
> ]
> label_to_name = LabelParser(
> "%(ref)s",
> [[1, "gi", str], [3, "ref", str], [4, "description", str]],
> split_with="|",
> )
> for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name):
> print(name)
> print(name.info.gi)
> print(name.info.description)
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv")
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", sep="\t")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import load_delimited
>
> header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t")
> rows[:4]
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(with_header=False, sep="\t")
> rows = list(reader("data/CerebellumDukeDNaseSeq.pk"))
> rows[:4]
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", limit=2)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(
> lambda line: float(line[2]) <= 10, with_header=True, sep="\t"
> )
> table = load_table("data/stats.tsv", reader=reader, digits=1)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> reader = FilteringParser(
> lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True
> )
> table = load_table("data/stats.tsv", reader=reader, digits=1)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t")
> table = load_table("data/stats.tsv", reader=reader)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t")
> table = load_table("data/stats.tsv", reader=reader)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(with_header=True, sep="\t")
> data = list(reader("data/stats.tsv"))
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data[:2]
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> header = ["A", "B", "C"]
> rows = [range(3), range(3, 6), range(6, 9), range(9, 12)]
> table = make_table(header=["A", "B", "C"], data=rows)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8])
> table = make_table(data=data)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = make_table(header=["C", "A", "B"], data=data)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv", index_name="Locus")
> table["NP_055852"]
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table["NP_055852", "Region"]
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from pandas import DataFrame
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3], b=["a", "c"])
> df = DataFrame(data=data)
> table = make_table(data_frame=df)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]])
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3], b=["a", "c"])
> table = make_table(data=data)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> d2D = {
> "edge.parent": {
> "NineBande": "root",
> "edge.1": "root",
> "DogFaced": "root",
> "Human": "edge.0",
> },
> "x": {
> "NineBande": 1.0,
> "edge.1": 1.0,
> "DogFaced": 1.0,
> "Human": 1.0,
> },
> "length": {
> "NineBande": 4.0,
> "edge.1": 4.0,
> "DogFaced": 4.0,
> "Human": 4.0,
> },
> }
> table = make_table(
> data=d2D,
> )
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table(
> header=["abcd", "data"],
> data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]],
> missing_data="*",
> digits=1,
> )
> table
> /<<PKGBUILDDIR>>/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table()
> table
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_moltypes
>
> available_moltypes()
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_moltype
>
> dna = get_moltype("dna")
> dna
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dna.ambiguities
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dna.degenerates
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dna.complement("AGG")
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seq = dna.make_seq("AGGCTT", name="seq1")
> seq
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rna = get_moltype("rna")
> rna.is_valid("ACGUACGUACGUACGU")
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.core import moltype as mt
>
> DNAgapped = mt.MolType(
> seq_constructor=mt.DnaSequence,
> motifset=mt.IUPAC_DNA_chars,
> ambiguities=mt.IUPAC_DNA_ambiguities,
> complements=mt.IUPAC_DNA_ambiguities_complements,
> pairs=mt.DnaStandardPairs,
> gaps=".",
> )
> seq = DNAgapped.make_seq("ACG.")
> seq
> /<<PKGBUILDDIR>>/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
> from cogent3.core.sequence import DnaSequence
>
> DnaSequence.moltype = DNA
> /<<PKGBUILDDIR>>/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import PROTEIN
>
> p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein")
> type(p)
> str(p)
> /<<PKGBUILDDIR>>/doc/cookbook/protein_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.core.genetic_code import DEFAULT as standard_code
>
> standard_code.translate("TTTGCAAAC")
> /<<PKGBUILDDIR>>/doc/cookbook/protein_sequences.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> tr.write("data/temp.tree")
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> names = tr.get_node_names()
> names[:4]
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> names[4:]
> names_nodes = tr.get_nodes_dict()
> names_nodes["Human"]
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tr.get_node_matching_name("Mouse")
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> hu = tr.get_node_matching_name("Human")
> tr.name
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> hu.name
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> nodes = tr.get_nodes_dict()
> hu = nodes["Human"]
> type(hu)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> type(tr)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> nodes = tr.get_nodes_dict()
> for n in nodes.items():
> print(n)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for n in tr.iter_tips():
> print(n)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> for n in tr.iter_nontips():
> print(n.get_newick())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> edges = tr.get_connecting_edges("edge.1", "Human")
> for edge in edges:
> print(edge.name)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> nodes = tr.get_nodes_dict()
> hu = nodes["Human"]
> mu = nodes["Mouse"]
> hu.distance(mu)
> hu.is_tip()
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> nodes = tr.get_nodes_dict()
> hu = nodes["Human"]
> mu = nodes["Mouse"]
> lca = hu.last_common_ancestor(mu)
> lca
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> type(lca)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> hu = tr.get_node_matching_name("Human")
> for a in hu.ancestors():
> print(a.name)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> node = tr.get_node_matching_name("edge.1")
> children = list(node.iter_tips()) + list(node.iter_nontips())
> for child in children:
> print(child.name)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> dists = tr.get_distances()
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> human_dists = [names for names in dists if "Human" in names]
> for dist in human_dists:
> print(dist, dists[dist])
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> tr.max_tip_tip_distance()
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> hu = tr.get_node_matching_name("Human")
> tips = hu.tips_within_distance(0.2)
> for t in tips:
> print(t)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.rooted_at("edge.0").ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.root_at_midpoint().ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(tr.rooted_with_tip("Mouse").ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> tr.get_newick()
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tr.get_newick(with_distances=True)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> xml = tr.get_xml()
> for line in xml.splitlines():
> print(line)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> for t in tr.preorder():
> print(t.get_newick())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> for t in tr.postorder():
> print(t.get_newick())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> for tip in tr.iter_nontips():
> tip_names = tip.get_tip_names()
> print(tip_names)
> sub_tree = tr.get_sub_tree(tip_names)
> print(sub_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from cogent3.util.io import remove_files
>
> remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_tree
>
> simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;"
> simple_tree = make_tree(simple_tree_string)
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree.prune()
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(simple_tree)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr1 = load_tree("data/test.tree")
> print(tr1.get_newick())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tr2 = tr1.unrooted_deepcopy()
> print(tr2.get_newick())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;"
> tr = make_tree(tree_string)
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(tr.bifurcating().ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = load_tree("data/test.tree")
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(tr.balanced().ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;")
> tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;")
> tr1.same_topology(tr2)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:452: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;")
> print(tr.ascii_art())
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:459: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tr.set_tip_distances()
> for t in tr.preorder():
> print(t.name, t.TipDistance)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:468: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;")
> print(tr)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:475: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tr.scale_branch_lengths()
> print(tr)
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:485: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr = make_tree("(B:3,(C:2,D:4)F:5)G;")
> d, tips = tr.tip_to_tip_distances()
> for i, t in enumerate(tips):
> print(t.name, d[i])
> /<<PKGBUILDDIR>>/doc/cookbook/simple_trees.rst:505: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
>
> tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;")
> tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;")
> tr1.compare_by_tip_distances(tr2)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> table
> cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv")
> cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", sep="\t")
> table
> cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import load_delimited
>
> header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t")
> rows[:4]
> cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(with_header=False, sep="\t")
> rows = list(reader("data/CerebellumDukeDNaseSeq.pk"))
> rows[:4]
> cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", limit=2)
> table
> cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(
> lambda line: float(line[2]) <= 10, with_header=True, sep="\t"
> )
> table = load_table("data/stats.tsv", reader=reader, digits=1)
> table
> cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> reader = FilteringParser(
> lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True
> )
> table = load_table("data/stats.tsv", reader=reader, digits=1)
> table
> cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t")
> table = load_table("data/stats.tsv", reader=reader)
> table
> cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t")
> table = load_table("data/stats.tsv", reader=reader)
> table
> cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.parse.table import FilteringParser
>
> reader = FilteringParser(with_header=True, sep="\t")
> data = list(reader("data/stats.tsv"))
> cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data[:2]
> cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> header = ["A", "B", "C"]
> rows = [range(3), range(3, 6), range(6, 9), range(9, 12)]
> table = make_table(header=["A", "B", "C"], data=rows)
> table
> cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8])
> table = make_table(data=data)
> table
> cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = make_table(header=["C", "A", "B"], data=data)
> table
> cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv", index_name="Locus")
> table["NP_055852"]
> cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table["NP_055852", "Region"]
> cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from pandas import DataFrame
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3], b=["a", "c"])
> df = DataFrame(data=data)
> table = make_table(data_frame=df)
> table
> cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]])
> table
> cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3], b=["a", "c"])
> table = make_table(data=data)
> table
> cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> d2D = {
> "edge.parent": {
> "NineBande": "root",
> "edge.1": "root",
> "DogFaced": "root",
> "Human": "edge.0",
> },
> "x": {
> "NineBande": 1.0,
> "edge.1": 1.0,
> "DogFaced": 1.0,
> "Human": 1.0,
> },
> "length": {
> "NineBande": 4.0,
> "edge.1": 4.0,
> "DogFaced": 4.0,
> "Human": 4.0,
> },
> }
> table = make_table(
> data=d2D,
> )
> table
> cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table(
> header=["abcd", "data"],
> data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]],
> missing_data="*",
> digits=1,
> )
> table
> cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table()
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table()
> table.columns["a"] = [1, 3, 5]
> table.columns["b"] = [2, 4, 6]
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3], b=["a", "c"])
> table = make_table(data=data, title="Sample title", legend="a legend")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data = dict(a=[0, 3], b=["a", "c"])
> table = make_table(data=data)
> table.title = "My title"
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> for row in table:
> print(row)
> break
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for row in table:
> print(row["Locus"])
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> data = dict(a=[0, 3, 5], b=["a", "c", "d"])
> table = make_table(data=data)
> table.shape[0] == 3
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.shape[1] == 2
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> table.columns
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.columns["Region"]
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for name in table.columns:
> print(name)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table[:2, "Region":]
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table[:2, :1]
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> table.format_column("Ratio", "%.1e")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv", digits=1, space=2)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.space = " "
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> h = ["name", "A/C", "A/G", "A/T", "C/A"]
> rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]]
> wrap_table = make_table(header=h, data=rows, max_width=30)
> wrap_table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name")
> wrap_table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = make_table(data=dict(a=list(range(10)), b=list(range(10))))
> table.head()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.head(2)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.tail()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.tail(1)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.set_repr_policy(random=3)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.set_repr_policy(head=2, tail=3)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> print(table.header)
> table = table.with_new_header("Ratio", "Stat")
> print(table.header)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table()
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.columns["a"] = [1, 3, 5]
> table.columns["b"] = [2, 4, 6]
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table = table.with_new_column(
> "LargeCon",
> lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0,
> columns=["Region", "Ratio"],
> )
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.array
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> locus = table.tolist("Locus")
> locus
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.columns["Locus"].tolist()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:309: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> rows = table.tolist(["Region", "Locus"])
> rows
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:322: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.to_dict()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:332: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.columns.to_dict()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:340: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> df = table.to_dataframe()
> df
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:348: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> df = table.to_dataframe(categories="Region")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:357: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:362: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> contingency = table.to_categorical(["Ts", "Tv"])
> contingency
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:367: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> g_test = contingency.G_independence()
> g_test
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:374: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]})
> contingency = table.to_categorical(["Ts", "Tv"], index_name="")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:386: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table1 = load_table("data/stats.tsv")
> table2 = load_table("data/stats.tsv")
> table = table1.appended(None, table2)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:395: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table1.title = "Data1"
> table2.title = "Data2"
> table = table1.appended("Data#", table2, title="")
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:407: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.summed("Ratio")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:414: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.columns["Ratio"].sum()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:423: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> all_numeric = make_table(
> header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)]
> )
> all_numeric
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:434: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> all_numeric.summed()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:440: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> all_numeric.summed(col_sum=False)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:449: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mixed = make_table(
> header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]]
> )
> mixed
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:458: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mixed.summed(strict=False)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:464: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mixed.summed(col_sum=False, strict=False)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:473: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio")
> sub_table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:481: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sub_table = table.filtered("Ratio < 10.0")
> sub_table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:488: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'")
> sub_table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:498: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20)
> big_numeric
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:506: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.sorted(columns="Ratio")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:514: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.sorted(columns="Ratio", reverse="Ratio")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:521: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.sorted(columns=["Region", "Ratio"], reverse="Ratio")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:528: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> raw = table.tolist("Region")
> raw
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:537: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> raw = table.tolist(["Locus", "Region"])
> raw
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:546: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> assert table.distinct_values("Region") == set(["NonCon", "Con"])
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:554: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> assert table.count("Region == 'NonCon' and Ratio > 1") == 1
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:564: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> table = make_table(
> data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"])
> )
> unique = table.count_unique("A")
> type(unique)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:574: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> unique
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:580: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> unique = table.count_unique(["A", "B"])
> unique
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:585: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> r = unique.to_table()
> r
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:595: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rows = [
> ["NP_004893", True],
> ["NP_005079", True],
> ["NP_005500", False],
> ["NP_055852", False],
> ]
> region_type = make_table(header=["Locus", "LargeCon"], data=rows)
> stats_table = load_table("data/stats.tsv")
> new = stats_table.joined(region_type, columns_self="Locus")
> new
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:615: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_table
>
> header = ["#OTU ID", "14SK041", "14SK802"]
> rows = [
> [-2920, "332", 294],
> [-1606, "302", 229],
> [-393, 141, 125],
> [-2109, 138, 120],
> ]
> table = make_table(header=header, rows=rows)
> table
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:631: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID")
> tp
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:641: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", format="md")
> print(table)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:653: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv", format="tex")
> print(table)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:665: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> print(table.to_markdown(justify="ccr"))
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:673: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table(
> "data/stats.tsv", title="Some stats.", legend="Derived from something."
> )
> print(table.to_latex(justify="ccr", label="tab:table1"))
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:683: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table(
> "data/stats.tsv", title="Some stats.", legend="Derived from something."
> )
> print(table.to_rst(csv_table=True))
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:693: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table(
> "data/stats.tsv", title="Some stats.", legend="Derived from something."
> )
> print(table.to_rst())
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:705: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> print(table.to_string(format="latex"))
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:715: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> rows = [
> ["1", 100, 101, 1.123],
> ["1", 101, 102, 1.123],
> ["1", 102, 103, 1.123],
> ["1", 103, 104, 1.123],
> ["1", 104, 105, 1.123],
> ["1", 105, 106, 1.123],
> ["1", 106, 107, 1.123],
> ["1", 107, 108, 1.123],
> ["1", 108, 109, 1],
> ["1", 109, 110, 1],
> ["1", 110, 111, 1],
> ["1", 111, 112, 1],
> ["1", 112, 113, 1],
> ["1", 113, 114, 1],
> ["1", 114, 115, 1],
> ["1", 115, 116, 1],
> ["1", 116, 117, 1],
> ["1", 117, 118, 1],
> ["1", 118, 119, 2],
> ["1", 119, 120, 2],
> ["1", 120, 121, 2],
> ["1", 150, 151, 2],
> ["1", 151, 152, 2],
> ["1", 152, 153, 2],
> ["1", 153, 154, 2],
> ["1", 154, 155, 2],
> ["1", 155, 156, 2],
> ["1", 156, 157, 2],
> ["1", 157, 158, 2],
> ["1", 158, 159, 2],
> ["1", 159, 160, 2],
> ["1", 160, 161, 2],
> ]
> bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows)
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:754: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bgraph.head()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:760: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(
> bgraph.to_string(
> format="bedgraph",
> name="test track",
> description="test of bedgraph",
> color=(255, 0, 0),
> digits=0,
> )
> )
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:775: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_table
>
> table = load_table("data/stats.tsv")
> straight_html = table.to_html()
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:787: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.format.table import known_formats
>
> known_formats
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:796: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table.write("stats_tab.tex", justify="ccr", label="tab:table1")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:805: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> table = load_table("data/stats.tsv")
> table.write("stats_tab.txt", sep="\t")
> /<<PKGBUILDDIR>>/doc/cookbook/tables.rst:812: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import pathlib
>
> for name in ("stats_tab.txt", "stats_tab.tex"):
> p = pathlib.Path(name)
> if p.exists():
> p.unlink()
> cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.union_dict import UnionDict
>
> data = UnionDict(a=2, b={"c": 24, "d": [25]})
> data.a
> cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data["a"]
> cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data.b.d
> cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.union_dict import UnionDict
>
> data = UnionDict(a=2, b={"c": 24, "d": [25]})
> data.b |= {"d": 25}
> data.b
> cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data.b.union({"d": [25]})
> cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data.b
> {"c": 24, "d": [25]}
> cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: KeyError
>
> from cogent3.util.union_dict import UnionDict
>
> data = UnionDict(a=2, b={"c": 24, "d": [25]})
> data["k"]
> cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: AttributeError
>
> data.k
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import numpy
>
> def DiffOmega(omega):
> def omega_from_S(S):
> omega_est = S / (1 - numpy.e ** (-1 * S))
> return abs(omega - omega_est) ** 2
>
> return omega_from_S
>
> omega = 0.1
> f = DiffOmega(omega)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.optimisers import maximise, minimise
>
> S = minimise(
> f, # the function
> xinit=1.0, # the initial value
> bounds=(-100, 100), # [lower,upper] bounds for the parameter
> local=True, # just local optimisation, not Simulated Annealing
> show_progress=False,
> )
> assert 0.0 <= f(S) < 1e-6
> print("S=%.4f" % S)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: TypeError
>
> from cogent3.util.misc import iterable
>
> my_var = 10
> for i in my_var:
> print("will not work")
>
> for i in iterable(my_var):
> print(i)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import curry
>
> def foo(x, y):
> """Some function"""
> return x + y
>
> bar = curry(foo, 5)
> print(bar.__doc__)
> bar(10)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import is_iterable
>
> can_iter = [1, 2, 3, 4]
> cannot_iter = 1.234
> is_iterable(can_iter)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> is_iterable(cannot_iter)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import is_char
>
> class foo:
> pass
>
> is_char("a")
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> is_char("ab")
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> is_char(foo())
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import recursive_flatten
>
> l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]]
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> recursive_flatten(l)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import not_list_tuple
>
> not_list_tuple(1)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> not_list_tuple([1])
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> not_list_tuple("ab")
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import add_lowercase
>
> d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"}
> add_lowercase(d)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from numpy import array
>
> from cogent3.util.misc import DistanceFromMatrix
>
> m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
> f = DistanceFromMatrix(m)
> f(0, 0)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> f(1, 2)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import ClassChecker
>
> class not_okay(object):
> pass
>
> no = not_okay()
>
> class okay(object):
> pass
>
> o = okay()
>
> class my_dict(dict):
> pass
>
> md = my_dict()
> cc = ClassChecker(str, okay, dict)
> o in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> no in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> 5 in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> {"a": 5} in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> "asasas" in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> md in cc
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import Delegator
>
> class ListAndString(list, Delegator):
> def __init__(self, items, string):
> Delegator.__init__(self, string)
> for i in items:
> self.append(i)
>
> ls = ListAndString([1, 2, 3], "ab_cd")
> len(ls)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls[0]
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls.upper()
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls.split("_")
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import FunctionWrapper
>
> f = FunctionWrapper(str)
> f
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> f(123)
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from cogent3.util.misc import ConstraintError
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.util.misc import ConstrainedDict
>
> d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc")
> d
> /<<PKGBUILDDIR>>/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ConstraintError
>
> d["d"] = 5
> /<<PKGBUILDDIR>>/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import available_codes
>
> available_codes()
> /<<PKGBUILDDIR>>/doc/cookbook/what_codes.rst:20: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
> nt_seqs[:21]
> /<<PKGBUILDDIR>>/doc/cookbook/what_codes.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True)
> aa_seqs[:20]
> /<<PKGBUILDDIR>>/doc/cookbook/what_codes.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import get_code
>
> gc = get_code(4)
> gc
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/brca1.fasta", moltype="dna")
> aln = aln.no_degenerates(motif_length=3)
> aln = aln.get_translation()
> aln = aln[:100] # for compute speed in testing the documentation
> coevo = aln.coevolution(show_progress=False, drawable="heatmap")
> coevo.drawable.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png"
>
> coevo.drawable.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> coevo = aln.coevolution(show_progress=False, drawable="violin")
> coevo.drawable.show(width=300)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> coevo = aln.coevolution(show_progress=False, drawable="box")
> coevo.drawable.show(width=300)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import os
>
> from cogent3 import load_unaligned_seqs
>
> seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna")
> draw = seqs.dotplot()
> draw.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png"
>
> draw.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8)
> draw.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True)
> draw.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-1.rst:59: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400)
> draw.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app.io import get_data_store, load_json
>
> loader = load_json()
> seqs = loader("data/tp53.json")
> dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600)
> dp.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png"
>
> dp.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> help(dp.remove_track)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dp.remove_track(left_track=True)
> dp.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
>
> aln = load_aligned_seqs("data/brca1.fasta", moltype="dna")
>
> counts = aln.count_gaps_per_seq(unique=True)
> counts[10: 20] # limiting the width of the displayed output
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> counts = aln.count_gaps_per_seq(unique=True, drawable="bar")
> counts.drawable.show(width=500)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png"
>
> counts.drawable.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> counts = aln.count_gaps_per_seq(unique=True, drawable="violin")
> counts.drawable.show(width=300, height=500)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> counts = aln.count_gaps_per_seq(unique=True, drawable="box")
> counts.drawable.show(width=300, height=500)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq
>
> s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna")
> s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna")
>
> seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna")
> draw = seqs.information_plot(window=2, include_gap=True)
> draw.show(width=500, height=400)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = load_aligned_seqs("data/brca1.fasta", moltype="protein")
>
> fig = aln.information_plot(stat="median")
> fig.show(width=500, height=400)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.parse import jaspar
>
> _, pwm = jaspar.read("data/tbp.jaspar")
> freqarr = pwm.to_freq_array()
> freqarr[:5] # illustrating the contents of the MotifFreqsArray
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> logo = freqarr.logo()
> logo.show(height=250, width=500)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png"
>
> logo.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
> l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05)
> l.show()
> /<<PKGBUILDDIR>>/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aa = aln.get_translation(incomplete_ok=True)[:120]
> logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1)
> logo.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app import io
>
> reader = io.load_json()
>
> ens_tree = reader("data/GN-tree.json")
> fig = ens_tree.get_figure(style="angular", width=600, height=600)
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.contemporaneous = True
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app import io
>
> reader = io.load_json()
>
> ens_tree = reader("data/GN-tree.json")
> fig = ens_tree.get_figure("circular", width=600, height=600)
> fig.scale_bar = "top right"
> fig.label_pad = 0.1
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.style_edges(
> "AfricanEl",
> tip2="Manatee",
> legendgroup="Afrotheria",
> line=dict(color="magenta", width=2),
> )
> fig.show(width=650, height=600)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.contemporaneous = True
> fig.label_pad = 0.3
> fig.show(width=650, height=600)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app import io
>
> reader = io.load_json()
>
> ens_tree = reader("data/GN-tree.json")
> fig = ens_tree.get_figure("radial", width=600, height=600)
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.contemporaneous = True
> fig.label_pad = 0.23
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app import io
>
> reader = io.load_json()
>
> ens_tree = reader("data/GN-tree.json")
> fig = ens_tree.get_figure(width=600, height=600)
> fig.scale_bar = "top right"
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.style_edges(
> "AfricanEl",
> tip2="Manatee",
> legendgroup="Afrotheria",
> line=dict(color="magenta"),
> )
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.contemporaneous = True
> fig.show()
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.app import io
>
> reader = io.load_json()
>
> tree = reader("data/tree-with-support.json")
> fig = tree.get_figure(show_support=True, threshold=0.8)
> fig.scale_bar = None
> fig.show(width=500, height=400)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> fig.support_xshift = 15
> fig.support_yshift = 0
> fig.show(width=500, height=400)
> /<<PKGBUILDDIR>>/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png"
>
> fig.write(outpath)
> /<<PKGBUILDDIR>>/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs, make_unaligned_seqs
> /<<PKGBUILDDIR>>/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> seqs = {
> "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT",
> "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG",
> "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA",
> }
> unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna")
> print(unaligned_DNA.to_fasta())
> /<<PKGBUILDDIR>>/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> unaligned_aa = unaligned_DNA.get_translation()
> print(unaligned_aa.to_fasta())
> /<<PKGBUILDDIR>>/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aligned_aa_seqs = {
> "hum": "KQIQESSENGSLAARQERQAQVNLT",
> "mus": "KQIQESGESGSLAARQERQAQVNLT",
> "rat": "LNKQ------PLS---------NKK",
> }
> aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein")
> aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA)
> aligned_DNA
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.cluster.UPGMA import upgma
> from cogent3.evolve import distance
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import HKY85
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> al = load_aligned_seqs("data/test.paml")
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> d = distance.EstimateDistances(al, submodel=HKY85())
> d.run(show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mycluster = upgma(d.get_pairwise_distances())
> print(mycluster.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mycluster.write("test_upgma.tree")
> /<<PKGBUILDDIR>>/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import os
>
> os.remove("test_upgma.tree")
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.evolve import distance
> from cogent3.phylo import nj
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> al = load_aligned_seqs("data/long_testseqs.fasta")
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> d = distance.EstimateDistances(al, submodel=get_model("HKY85"))
> d.run(show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mytree = nj.nj(d.get_pairwise_distances(), show_progress=False)
> print(mytree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> mytree.write("test_nj.tree")
> /<<PKGBUILDDIR>>/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import os
>
> os.remove("test_nj.tree")
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs
> from cogent3.evolve import distance
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import HKY85
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> al = load_aligned_seqs("data/long_testseqs.fasta")
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> d = distance.EstimateDistances(al, submodel=HKY85())
> d.run(show_progress=False)
> d.get_pairwise_distances()
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> d.write("dists_for_phylo.phylip", format="phylip")
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import pickle
>
> with open("dists_for_phylo.pickle", "wb") as f:
> pickle.dump(d.get_pairwise_distances(), f)
> /<<PKGBUILDDIR>>/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import os
>
> for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle":
> os.remove(file_name)
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.models import get_model
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tf = get_model("GY94")
> nf = get_model("MG94GTR")
> cnf = get_model("CNFGTR")
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
>
> aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
> tree = load_tree("data/primate_brca1.tree")
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = cnf.make_likelihood_function(tree, digits=2, space=3)
> lf.set_param_rule("omega", is_constant=True, value=1.0)
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> optimiser_args = dict(
> local=True, max_restarts=5, tolerance=1e-8, show_progress=False
> )
> lf.set_alignment(aln)
> lf.optimise(**optimiser_args)
> lf
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> neutral_lnL = lf.get_log_likelihood()
> neutral_nfp = lf.get_num_free_params()
> lf.set_param_rule("omega", is_constant=False)
> lf.optimise(**optimiser_args)
> non_neutral_lnL = lf.get_log_likelihood()
> non_neutral_nfp = lf.get_num_free_params()
> lf
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from scipy.stats.distributions import chi2
>
> LR = 2 * (non_neutral_lnL - neutral_lnL)
> df = non_neutral_nfp - neutral_nfp
> print(chi2.sf(LR, df))
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True
> )
> lf.optimise(**optimiser_args)
> lf
> chimp_human_clade_lnL = lf.get_log_likelihood()
> chimp_human_clade_nfp = lf.get_num_free_params()
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL)
> df = chimp_human_clade_nfp - non_neutral_nfp
> print(chi2.sf(LR, df))
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = cnf.make_likelihood_function(tree, digits=2, space=3)
> lf.set_alignment(aln)
> lf.optimise(**optimiser_args)
> non_neutral_lnL = lf.get_log_likelihood()
> non_neutral_nfp = lf.get_num_free_params()
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> annot_tree = lf.get_annotated_tree()
> omega_mle = lf.get_param_value("omega")
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_lf = cnf.make_likelihood_function(
> annot_tree, bins=["neutral", "adaptive"], digits=2, space=3
> )
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> epsilon = 1e-6
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle)
> rate_lf.set_param_rule(
> "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon
> )
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon])
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_lf.set_alignment(aln)
> rate_lf.optimise(**optimiser_args)
> rate_lnL = rate_lf.get_log_likelihood()
> rate_nfp = rate_lf.get_num_free_params()
> LR = 2 * (rate_lnL - non_neutral_lnL)
> df = rate_nfp - non_neutral_nfp
> rate_lf
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(chi2.sf(LR, df))
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> pp = rate_lf.get_bin_probs()
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> from IPython.core.display import HTML
> from numpy import array
>
> from cogent3 import make_table
>
> header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges']
> data = {'Site Class': array(['0', '1', '2a', '2b'], dtype='<U2'), 'Proportion': array(['p0', 'p1', 'p2', 'p3'], dtype='<U2'), 'Background Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega0 < 1', 'omega1 = 1'],
> dtype='<U14'), 'Foreground Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega2 > 1', '0 < omega0 < 1'],
> dtype='<U14')}
> data = {k: array(data[k], dtype='U') for k in data}
> table = make_table(header, data=data)
> HTML(table.set_repr_policy(show_shape=False))
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:232: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_lf = cnf.make_likelihood_function(tree, bins=["0", "1"], digits=2, space=3)
> rate_lf.set_param_rule("omega", bin="0", upper=1.0 - epsilon, init=1 - epsilon)
> rate_lf.set_param_rule("omega", bins="1", is_constant=True, value=1.0)
> rate_lf.set_alignment(aln)
> rate_lf.optimise(**optimiser_args)
> tables = rate_lf.get_statistics(with_titles=True)
> for table in tables:
> if "bin" in table.title:
> print(table)
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:246: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> globals = [t for t in tables if "global" in t.title][0]
> globals = dict(zip(globals.header, globals.tolist()[0]))
> bin_params = [t for t in tables if "bin" in t.title][0]
> rate_class_omegas = dict(bin_params.tolist(["bin", "omega"]))
> rate_class_probs = dict(bin_params.tolist(["bin", "bprobs"]))
> lengths = [t for t in tables if "edge" in t.title][0]
> lengths = dict(lengths.tolist(["edge", "length"]))
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:258: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_branch_lf = cnf.make_likelihood_function(
> tree, bins=["0", "1", "2a", "2b"], digits=2, space=3
> )
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:266: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for branch, length in lengths.items():
> rate_branch_lf.set_param_rule("length", edge=branch, init=length)
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:273: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for param, mle in globals.items():
> rate_branch_lf.set_param_rule(param, init=mle)
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:280: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_branch_lf.set_param_rule(
> "omega", bins=["0", "2a"], upper=1.0, init=rate_class_omegas["0"]
> )
> rate_branch_lf.set_param_rule(
> "omega", bins=["1", "2b"], is_constant=True, value=1.0
> )
> rate_branch_lf.set_param_rule(
> "omega",
> bins=["2a", "2b"],
> edges=["Chimpanzee", "Human"],
> init=99,
> lower=1.0,
> upper=100.0,
> is_constant=False,
> )
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:300: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_branch_lf.set_param_rule(
> "bprobs",
> init=[
> rate_class_probs["0"] - epsilon,
> rate_class_probs["1"] - epsilon,
> epsilon,
> epsilon,
> ],
> )
> /<<PKGBUILDDIR>>/doc/examples/codon_models.rst:314: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> rate_branch_lf.set_alignment(aln)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:10: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
> from cogent3.core.alignment import ArrayAlignment
> from cogent3.evolve.coevolution import validate_alignment
>
> aln = make_aligned_seqs(
> {"1": "GAA", "2": "CTA", "3": "CTC", "4": "-TC"},
> moltype="protein",
> array_align=True,
> )
> validate_alignment(aln)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:25: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
> from cogent3.core.alignment import ArrayAlignment
>
> aln = make_aligned_seqs(
> {"1": "AAA", "2": "CTA", "3": "CTC", "4": "-TC"},
> moltype="protein",
> array_align=True,
> )
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:38: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.coevolution import (
> coevolve_pair,
> coevolve_pair_functions,
> )
>
> coevolve_pair(coevolve_pair_functions["mi"], aln, pos1=1, pos2=2)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.coevolution import (
> coevolve_pair,
> coevolve_pair_functions,
> )
>
> coevolve_pair(coevolve_pair_functions["sca"], aln, pos1=1, pos2=2, cutoff=0.5)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.coevolution import (
> coevolve_position,
> coevolve_position_functions,
> )
>
> coevolve_position(coevolve_position_functions["mi"], aln, position=1)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:71: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.coevolution import (
> coevolve_alignment,
> coevolve_alignment_functions,
> )
>
> coevolve_alignment(coevolve_alignment_functions["mi"], aln)
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:82: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(coevolve_pair_functions.keys())
> /<<PKGBUILDDIR>>/doc/examples/coevolution.rst:88: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.evolve.coevolution import (
> coevolve_alignment_functions,
> coevolve_alignments,
> )
>
> aln1 = make_aligned_seqs(
> {
> "human+protein1": "AAA",
> "pig+protein1": "CTA",
> "chicken+protein1": "CTC",
> "echidna+weird_db_identifier": "-TC",
> },
> moltype="protein",
> array_align=True,
> )
> aln2 = make_aligned_seqs(
> {
> "pig+protein2": "AAAY",
> "chicken+protein2": "CTAY",
> "echidna+protein2": "CTCF",
> "human+protein2": "-TCF",
> },
> moltype="protein",
> array_align=True,
> )
> coevolve_alignments(coevolve_alignment_functions["mi"], aln1, aln2)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
> from cogent3.core.annotation import Feature
>
> s = DNA.make_seq("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", name="Orig")
> exon1 = s.add_annotation(Feature, "exon", "fred", [(10, 15)])
> exon2 = s.add_annotation(Feature, "exon", "trev", [(30, 40)])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:19: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s[exon1]
> exon1.get_slice()
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exons = s.get_annotations_matching("exon")
> print(exons)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> dont_exist = s.get_annotations_matching("dont_exist")
> dont_exist
> s[dont_exist]
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s.get_region_covering_all(exons))
> print(s.get_region_covering_all(exons).get_shadow())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s.get_region_covering_all(exons).get_slice()
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:54: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s[exon1, exon2]
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> print(s.get_region_covering_all(exons + exons))
> s[exon1, exon1, exon1, exon1, exon1]
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:68: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> s[15:20, 5:16]
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:75: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exon1[0:3].get_slice()
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:81: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> c = s[exon1[4:]] + s
> print(len(c))
> for feat in c.annotations:
> print(feat)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:90: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :raises: ValueError
>
> print(c[exon1])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:97: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> len(s.annotations)
> region = s.get_region_covering_all(exons)
> len(s.annotations)
> region.attach()
> len(s.annotations)
> region.detach()
> len(s.annotations)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:109: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> plus = DNA.make_seq("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="plus")
> plus_cds = plus.add_annotation(Feature, "CDS", "gene", [(2, 6), (10, 15), (25, 35)])
> print(plus_cds.get_slice())
> minus = plus.rc()
> minus_cds = minus.get_annotations_matching("CDS")[0]
> print(minus_cds.get_slice())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:120: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_aligned_seqs
>
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> print(aln)
> exon = aln.get_seq("x").add_annotation(Feature, "exon", "fred", [(3, 8)])
> aln_exons = aln.get_annotations_from_seq("x", "exon")
> aln_exons = aln.get_annotations_from_any_seq("exon")
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:134: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(exon)
> print(aln_exons[0])
> print(aln_exons[0].get_slice())
> aln_exons[0].attach()
> len(aln.annotations)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:144: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exons = aln.get_projected_annotations("y", "exon")
> print(exons)
> print(aln.get_seq("y")[exons[0].map.without_gaps()])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:152: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "TTTT--CCCC"]], array_align=False
> )
> s = DNA.make_seq("AAAAAAAAA", name="x")
> exon = s.add_annotation(Feature, "exon", "fred", [(3, 8)])
> exon = aln.get_seq("x").copy_annotations(s)
> aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
> print(aln_exons)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:165: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exon = aln.get_seq("y").copy_annotations(s)
> aln_exons = list(aln.get_annotations_from_seq("y", "exon"))
> print(aln_exons)
> print(aln[aln_exons])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:174: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs([["x", "-AAAA"], ["y", "TTTTT"]], array_align=False)
> seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
> exon = seq.add_feature("exon", "A", [(5, 8)])
> aln.get_seq("x").copy_annotations(seq)
> copied = list(aln.get_annotations_from_seq("x", "exon"))
> copied
> copied[0].get_slice()
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:186: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
> match_exon = seq.add_feature("exon", "A", [(5, 8)])
> aln.get_seq("y").copy_annotations(seq)
> copied = list(aln.get_annotations_from_seq("y", "exon"))
> copied
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:199: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
> )
> diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x")
> nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)])
> aln.get_seq("y").copy_annotations(diff_len_seq)
> copied = list(aln.get_annotations_from_seq("y", "repeat"))
> copied
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:212: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "------TTTT"]], array_align=False
> )
> exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)])
> aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
> print(aln_exons)
> print(aln_exons[0].get_slice())
> aln = make_aligned_seqs(
> [["x", "-AAAAAAAAA"], ["y", "TTTT--T---"]], array_align=False
> )
> exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)])
> aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
> print(aln_exons[0].get_slice())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:230: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], moltype="dna", array_align=False
> )
> print(aln)
> exon = aln.get_seq("x").add_feature("exon", "ex1", [(0, 4)])
> print(exon)
> print(exon.get_slice())
> aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
> print(aln_exons)
> print(aln_exons[0].get_slice())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:245: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(aln_exons[0].as_one_span().get_slice())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:251: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln_rc = aln.rc()
> rc_exons = list(aln_rc.get_annotations_from_any_seq("exon"))
> print(aln_rc[rc_exons]) # not using as_one_span, so gap removed from x
> print(aln_rc[rc_exons[0].as_one_span()])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:260: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> all_exons = aln.get_region_covering_all(aln_exons)
> coords = all_exons.get_coordinates()
> assert coords == [(0, 1), (2, 5)]
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:270: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = make_aligned_seqs(
> [["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], array_align=False
> )
> print(aln)
> exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)])
> print(exon.get_slice())
> repeat = aln.get_seq("x").add_feature("repeat", "blue", [(9, 12)])
> print(repeat.get_slice())
> repeat = aln.get_seq("y").add_feature("repeat", "frog", [(5, 7)])
> print(repeat.get_slice())
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:285: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?"))
> print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?", shadow=True))
> print(aln.get_seq("x").with_masked_annotations(["exon", "repeat"], mask_char="?"))
> print(
> aln.get_seq("x").with_masked_annotations(
> ["exon", "repeat"], mask_char="?", shadow=True
> )
> )
> print(aln.get_seq("y").with_masked_annotations("exon", mask_char="?"))
> print(aln.get_seq("y").with_masked_annotations("repeat", mask_char="?"))
> print(
> aln.get_seq("y").with_masked_annotations("repeat", mask_char="?", shadow=True)
> )
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:303: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(aln.with_masked_annotations("exon", mask_char="?"))
> print(aln.with_masked_annotations("exon", mask_char="?", shadow=True))
> print(aln.with_masked_annotations("repeat", mask_char="?"))
> print(aln.with_masked_annotations("repeat", mask_char="?", shadow=True))
> print(aln.with_masked_annotations(["repeat", "exon"], mask_char="?"))
> print(aln.with_masked_annotations(["repeat", "exon"], shadow=True))
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:314: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> data = [["human", "CGAAACGTTT"], ["mouse", "CTAAACGTCG"]]
> as_series = make_aligned_seqs(data, array_align=False)
> as_items = make_aligned_seqs(data, array_align=False)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:322: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> as_series.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2), (5, 7)])
> as_series.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7), (8, 10)])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:329: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> as_items.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2)])
> as_items.get_seq("human").add_feature("cpgsite", "cpg", [(5, 7)])
> as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7)])
> as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(8, 10)])
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:338: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> serial = as_series.with_masked_annotations(["cpgsite"])
> print(serial)
> itemwise = as_items.with_masked_annotations(["cpgsite"])
> print(itemwise)
> /<<PKGBUILDDIR>>/doc/examples/complete_seq_features.rst:347: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(plus.with_masked_annotations("CDS"))
> print(minus.with_masked_annotations("CDS"))
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, make_tree
> from cogent3.evolve.substitution_model import EmpiricalProteinMatrix
> from cogent3.parse.paml_matrix import PamlMatrixParser
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> treestring = "(((rabbit,rat),human),goat-cow,marsupial);"
> t = make_tree(treestring)
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> al = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> matrix_file = open("data/dayhoff.dat")
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> empirical_matrix, empirical_frequencies = PamlMatrixParser(matrix_file)
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = EmpiricalProteinMatrix(empirical_matrix, empirical_frequencies)
> /<<PKGBUILDDIR>>/doc/examples/empirical_protein_models.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = sm.make_likelihood_function(t)
> lf.set_alignment(al)
> lf.optimise(show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.substitution_model import (
> TimeReversibleNucleotide,
> predicate,
> )
> from scipy.stats.distributions import chi2
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> tree = load_tree("data/test.tree")
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:42: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> MotifChange = predicate.MotifChange
> treat_gap = dict(recode_gaps=True, model_gaps=False)
> kappa = (~MotifChange("R", "Y")).aliased("kappa")
> model = TimeReversibleNucleotide(predicates=[kappa], **treat_gap)
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:51: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf_one = model.make_likelihood_function(tree, digits=2, space=3)
> lf_one.set_alignment(aln)
> lf_one.optimise(show_progress=False)
> lnL_one = lf_one.get_log_likelihood()
> df_one = lf_one.get_num_free_params()
> lf_one
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bin_submod = TimeReversibleNucleotide(
> predicates=[kappa], ordered_param="rate", distribution="gamma", **treat_gap
> )
> lf_bins = bin_submod.make_likelihood_function(
> tree, bins=2, sites_independent=True, digits=2, space=3
> )
> lf_bins.set_param_rule("bprobs", is_constant=True)
> lf_bins.set_alignment(aln)
> lf_bins.optimise(local=True, show_progress=False)
> lnL_bins = lf_bins.get_log_likelihood()
> df_bins = lf_bins.get_num_free_params()
> assert df_bins == 9
> lf_bins
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:86: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf_patches = bin_submod.make_likelihood_function(
> tree, bins=2, sites_independent=False, digits=2, space=3
> )
> lf_patches.set_param_rule("bprobs", is_constant=True)
> lf_patches.set_alignment(aln)
> lf_patches.optimise(local=True, show_progress=False)
> lnL_patches = lf_patches.get_log_likelihood()
> df_patches = lf_patches.get_num_free_params()
> lf_patches
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:100: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> LR = lambda alt, null: 2 * (alt - null)
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:106: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lr = LR(lnL_bins, lnL_one)
> lr
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:111: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print("%.4f" % chi2.sf(lr, df_patches - df_bins))
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:117: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bprobs = lf_patches.get_param_value("bprobs")
> print("%.1f : %.1f" % tuple(bprobs))
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:124: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> pp = lf_patches.get_bin_probs()
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:130: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(pp["bin0"][20])
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:143: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from numpy import array
>
> single_kappa = lf_one.get_param_value("kappa")
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:151: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> kappa_bin_submod = TimeReversibleNucleotide(predicates=[kappa], **treat_gap)
> lf_kappa = kappa_bin_submod.make_likelihood_function(
> tree, bins=["slow", "fast"], sites_independent=False, digits=1, space=3
> )
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:160: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> epsilon = 1e-6
> lf_kappa.set_param_rule(
> kappa, init=single_kappa - epsilon, upper=single_kappa, bin="slow"
> )
> lf_kappa.set_param_rule(
> kappa, init=single_kappa + epsilon, lower=single_kappa, bin="fast"
> )
> /<<PKGBUILDDIR>>/doc/examples/hmm_par_heterogeneity.rst:172: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf_kappa.set_param_rule("bprobs", init=array([1.0 - epsilon, 0.0 + epsilon]))
> lf_kappa.set_alignment(aln)
> lf_kappa.optimise(local=True, show_progress=False)
> lf_kappa
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree, make_tree
> from cogent3.core.tree import PhyloNode
> from cogent3.parse.tree import DndParser
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:24: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree_string = "(B:0.2,(C:0.3,D:0.4)E:0.5)F;"
> complex_tree_string = "(((363564 AB294167.1 Alkalibacterium putridalgicola:0.0028006,55874 AB083411.1 Marinilactibacillus psychrotolerans:0.0022089):0.40998,(15050 Y10772.1 Facklamia hominis:0.32304,(132509 AY707780.1 Aerococcus viridans:0.58815,((143063 AY879307.1 Abiotrophia defectiva:0.5807,83619 AB042060.1 Bacillus schlegelii:0.23569):0.03586,169722 AB275483.1 Fibrobacter succinogenes:0.38272):0.06516):0.03492):0.14265):0.63594,(3589 M62687.1 Fibrobacter intestinalis:0.65866,314063 CP001146.1 Dictyoglomus thermophilum:0.38791):0.32147,276579 EU652053.1 Thermus scotoductus:0.57336);"
> simple_tree = make_tree(simple_tree_string)
> complex_tree = DndParser(complex_tree_string, PhyloNode)
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> A_node = PhyloNode(name="A", Length=0.1)
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:47: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(simple_tree.children)
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree.children[1].remove("C")
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:59: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree.children[1].insert(0, A_node)
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:71: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree.children[1].remove("A")
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simple_tree.prune()
> print(simple_tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:90: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for n in complex_tree.iter_tips():
> n.name = n.name.split()[2] + " " + n.name.split()[3]
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:97: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(complex_tree.ascii_art(show_internal=False))
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:105: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tips = complex_tree.tips()
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:111: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> tips_to_delete = []
> AEROCOCCUS_INDEX = 3
> for n in tips:
> if tips[AEROCOCCUS_INDEX].distance(n) > 1.8:
> tips_to_delete.append(n)
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> for n in tips_to_delete:
> n.parent.remove(n)
> complex_tree.prune()
> /<<PKGBUILDDIR>>/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(complex_tree.ascii_art(show_internal=False))
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
> from scipy.stats.distributions import chi2
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> al = load_aligned_seqs("data/long_testseqs.fasta")
> t = load_tree("data/test.tree")
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = get_model("MG94GTR")
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = sm.make_likelihood_function(t, digits=2, space=2)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_alignment(al)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(global_tolerance=1.0, show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> null_lnL = lf.get_log_likelihood()
> null_nfp = lf.get_num_free_params()
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule("omega", is_independent=True)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(local=True, show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> at = lf.get_annotated_tree()
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> LR = 2 * (lf.get_log_likelihood() - null_lnL)
> df = lf.get_num_free_params() - null_nfp
> P = chi2.sf(LR, df)
> /<<PKGBUILDDIR>>/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(f"Likelihood ratio statistic = {LR}")
> print(f"degrees-of-freedom = {df}")
> print(f"probability = {P}")
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve import bootstrap
> from cogent3.evolve.models import HKY85
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> def create_alt_function():
> t = load_tree("data/test.tree")
> sm = HKY85()
> return sm.make_likelihood_function(t)
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> def create_null_function():
> lf = create_alt_function()
> # set the local clock for humans & howler monkey
> lf.set_local_clock("Human", "HowlerMon")
> return lf
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> estimateP = bootstrap.EstimateProbability(
> create_null_function(), create_alt_function(), aln
> )
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> estimateP.set_num_replicates(5)
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> estimateP.run(show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> p = estimateP.get_estimated_prob()
> /<<PKGBUILDDIR>>/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print("%.2f, %.2f" % estimateP.get_observed_lnL())
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import numpy
>
> numpy.random.seed(11)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import numpy
>
> t = numpy.arange(0, 10, 0.1)
> n = numpy.random.randn(len(t))
> nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1
> nse = nse[: len(t)]
> sig = numpy.sin(2 * numpy.pi * t) + nse
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import dft
>
> pwr, period = dft(sig)
> print(period)
> print(pwr)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> pwr = abs(pwr)
> max_pwr, max_period = sorted(zip(pwr, period))[-1]
> print(max_pwr, max_period)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import auto_corr
>
> pwr, period = auto_corr(sig)
> print(period)
> print(pwr)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> max_pwr, max_period = sorted(zip(pwr, period))[-1]
> print(max_pwr, max_period)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s = (
> "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG"
> "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT"
> "AATTTTTAACCGCGGAATTGCGTC"
> )
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.stats.period import SeqToSymbols
>
> seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"])
> symbols = seq_to_symbols(s)
> len(symbols) == len(s)
> symbols
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import ipdft
>
> powers, periods = ipdft(symbols)
> powers
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> periods
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import auto_corr, hybrid
>
> powers, periods = auto_corr(symbols)
> powers
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> periods
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> powers, periods = hybrid(symbols)
> powers
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> periods
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import goertzel
>
> pwr = goertzel(sig, 10)
> print(pwr)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> powers, periods = auto_corr(symbols)
> llim = 2
> period5 = 5 - llim
> periods[period5]
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> powers[period5]
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import goertzel
>
> period = 4
> power = goertzel(symbols, period)
> ipdft_powers, periods = ipdft(symbols)
> ipdft_power = abs(ipdft_powers[period - llim])
> round(power, 6) == round(ipdft_power, 6)
> power
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> power = hybrid(symbols, period=period)
> power
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import Goertzel
>
> goertzel_calc = Goertzel(len(sig), period=10)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.stats.period import blockwise_bootstrap
>
> obs_stat, p = blockwise_bootstrap(
> sig, calc=goertzel_calc, block_size=10, num_reps=1000
> )
> print(obs_stat)
> print(p)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.period import Hybrid
>
> hybrid_calculator = Hybrid(len(s), period=4)
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.stats.period import SeqToSymbols
>
> seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s))
> /<<PKGBUILDDIR>>/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.maths.stats.period import blockwise_bootstrap
>
> stat, p = blockwise_bootstrap(
> s,
> calc=hybrid_calculator,
> block_size=10,
> num_reps=1000,
> seq_to_symbols=seq_to_symbols,
> )
> print(stat)
> p < 0.1
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import pickle
>
> from cogent3 import load_aligned_seqs
> from cogent3.evolve import distance
> from cogent3.evolve.fast_distance import DistanceMatrix
> from cogent3.evolve.models import HKY85
>
> al = load_aligned_seqs("data/long_testseqs.fasta")
> d = distance.EstimateDistances(al, submodel=HKY85())
> d.run(show_progress=False)
>
> with open("dists_for_phylo.pickle", "wb") as f:
> pickle.dump(d.get_pairwise_distances(), f)
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import pickle
>
> from cogent3.phylo import least_squares
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> with open("dists_for_phylo.pickle", "rb") as f:
> dists = pickle.load(f)
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls = least_squares.WLS(dists)
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists))
> ls_pairwise_matrix = least_squares.WLS(dists.to_dict())
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> score, tree = ls.trex(a=5, k=1, show_progress=False)
> assert score < 1e-4
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> trees = ls.trex(a=5, k=5, return_all=True, show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(len(trees))
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> wls_stats = [tree[0] for tree in trees]
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> t1 = trees[0][1].balanced()
> t2 = trees[1][1].balanced()
> print(t1.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(t2.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import make_tree
>
> query_tree = make_tree(
> "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)"
> )
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> ls.evaluate_tree(query_tree)
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> wls, t = ls.evaluate_topology(query_tree)
> assert "%.4f" % wls == "0.0084"
> /<<PKGBUILDDIR>>/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import os
>
> os.remove("dists_for_phylo.pickle")
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_tree
> from cogent3.evolve.substitution_model import TimeReversibleNucleotide
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> model = TimeReversibleNucleotide(equal_motif_probs=True)
> tree = load_tree("data/test.tree")
> lf = model.make_likelihood_function(tree)
> lf.set_param_rule("length", value=0.6, is_constant=True)
> aln1 = lf.simulate_alignment(sequence_length=10000)
> lf.set_param_rule("length", value=0.2, is_constant=True)
> aln2 = lf.simulate_alignment(sequence_length=10000)
> aln3 = aln1 + aln2
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> model = TimeReversibleNucleotide(
> equal_motif_probs=True, ordered_param="rate", distribution="free"
> )
> lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3)
> lf.set_alignment(aln3)
> lf.optimise(local=True, max_restarts=2, show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0]
> bprobs
> /<<PKGBUILDDIR>>/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> model = TimeReversibleNucleotide(
> equal_motif_probs=True, ordered_param="rate", distribution="gamma"
> )
> lf = model.make_likelihood_function(tree, bins=4)
> lf.set_param_rule("bprobs", is_constant=True)
> lf.set_alignment(aln3)
> lf.optimise(local=True, max_restarts=2, show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import get_model
> from scipy.stats.distributions import chi2
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> t = load_tree(filename="data/test.tree")
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = get_model("HKY85")
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = sm.make_likelihood_function(t, digits=2, space=3)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_local_clock("Human", "HowlerMon")
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_alignment(aln)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_name("clock")
> lf
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> null_lnL = lf.get_log_likelihood()
> null_nfp = lf.get_num_free_params()
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule("length", is_independent=True)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.optimise(show_progress=False)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_name("non clock")
> lf
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> LR = 2 * (lf.get_log_likelihood() - null_lnL)
> df = lf.get_num_free_params() - null_nfp
> P = chi2.sf(LR, df)
> /<<PKGBUILDDIR>>/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print("Likelihood ratio statistic = ", LR)
> print("degrees-of-freedom = ", df)
> print("probability = ", P)
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, load_tree
> from cogent3.evolve.models import MG94HKY
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> tree = load_tree("data/test.tree")
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = MG94HKY()
> lf = sm.make_likelihood_function(tree, digits=2, space=3)
> lf.set_alignment(aln)
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(tree.ascii_art())
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega",
> tip_names=["DogFaced", "Mouse"],
> outgroup_name="Human",
> init=2.0,
> clade=True,
> )
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule("omega", init=1.0)
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "HowlerMon"],
> outgroup_name="Mouse",
> init=2.0,
> stem=True,
> clade=False,
> )
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> lf.set_param_rule("omega", init=1.0)
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "HowlerMon"],
> outgroup_name="Mouse",
> init=2.0,
> stem=True,
> clade=True,
> )
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> lf.set_param_rule("omega", init=1.0)
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "HowlerMon"],
> outgroup_name="Mouse",
> clade=True,
> value=1.0,
> is_constant=True,
> )
> lf.optimise(local=True, show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "HowlerMon"],
> outgroup_name="Mouse",
> clade=True,
> is_constant=False,
> )
> lf.optimise(local=True, show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule(
> "omega",
> tip_names=["Human", "HowlerMon"],
> outgroup_name="Mouse",
> clade=True,
> is_independent=True,
> )
> lf.optimise(local=True, show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf.set_param_rule("omega", is_independent=True)
> lf.optimise(local=True, show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:14: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import DNA
>
> s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig")
> exon1 = s.add_feature("exon", "exon1", [(10, 15)])
> exon2 = s.add_feature("exon", "exon2", [(30, 40)])
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3.core.annotation import Feature
>
> s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2")
> exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)])
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:35: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> s[exon1]
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exons = s.get_annotations_matching("exon")
> print(exons)
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s.get_region_covering_all(exons))
> s.get_region_covering_all(exons).get_slice()
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:55: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> print(s.get_region_covering_all(exons).get_shadow().get_slice())
> /<<PKGBUILDDIR>>/doc/examples/seq_features.rst:63: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> exon1[0:3].get_slice()
> /<<PKGBUILDDIR>>/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, make_tree
> from cogent3.evolve.models import get_model
>
> model = get_model("HKY85")
> aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
> tree = make_tree(tip_names=aln.names)
> lf = model.make_likelihood_function(tree)
> lf.set_alignment(aln)
> lf.optimise(show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> import sys
>
> from cogent3 import make_tree
> from cogent3.evolve.models import get_model
> /<<PKGBUILDDIR>>/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);")
> /<<PKGBUILDDIR>>/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> sm = get_model("F81")
> lf = sm.make_likelihood_function(t)
> lf.set_constant_lengths()
> lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4))
> lf
> /<<PKGBUILDDIR>>/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> simulated = lf.simulate_alignment(sequence_length=1000)
> simulated
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
> :hide-code:
>
> import set_working_directory
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> from cogent3 import load_aligned_seqs, make_table, make_tree
> from cogent3.evolve.models import HKY85
> from scipy.stats.distributions import chi2
> from cogent3.recalculation.scope import ALL, EACH
>
> aln = load_aligned_seqs("data/long_testseqs.fasta")
> half = len(aln) // 2
> aln1 = aln[:half]
> aln2 = aln[half:]
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> loci_names = ["1st-half", "2nd-half"]
> loci = [aln1, aln2]
> tree = make_tree(tip_names=aln.names)
> mod = HKY85()
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3)
> lf.set_param_rule("length", is_independent=False)
> lf.set_param_rule("kappa", loci=ALL)
> lf.set_alignment(loci)
> lf.optimise(show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> all_lnL = lf.lnL
> all_nfp = lf.nfp
> lf.set_param_rule("kappa", loci=EACH)
> lf.optimise(show_progress=False)
> lf
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> each_lnL = lf.lnL
> each_nfp = lf.nfp
> LR = 2 * (each_lnL - all_lnL)
> df = each_nfp - all_nfp
> /<<PKGBUILDDIR>>/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute".
>
> .. jupyter-execute::
>
> make_table(
> header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3,
> )
> /<<PKGBUILDDIR>>/doc/index.rst:8: ERROR: Unknown directive type "dropdown".
>
> .. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process.
>
> .. raw:: html
>
> <object type="image/gif" data="../_static/gif/demo-fit-ns.gif" style="height: 400px; width: auto;"></object>
> /<<PKGBUILDDIR>>/doc/index.rst:16: ERROR: Unknown directive type "dropdown".
>
> .. dropdown:: Click to see an animation showing defining and using sequence annotations.
>
> .. raw:: html
>
> <object type="image/gif" data="../_static/gif/demo-annotate.gif" style="height: 400px; width: auto;"></object>
> /<<PKGBUILDDIR>>/doc/index.rst:22: ERROR: Unknown directive type "panels".
>
> .. panels::
> :header: bg-primary
> :footer: text-right
>
> ---
>
> ``cogent3`` apps
> ^^^^^^^^^^^^^^^^
>
> ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines.
>
> +++++++++++
>
> .. link-button:: app/index
> :type: ref
> :text: …
> :classes: stretched-link
>
> ---
>
> Cookbook
> ^^^^^^^^
>
> The cookbook presents short code recipes targeted at specific problems.
>
> +++++++++++
>
> .. link-button:: cookbook/index
> :type: ref
> :text: …
> :classes: stretched-link
>
> ---
>
> Tutorials
> ^^^^^^^^^
>
> The tutorials present code for solving more extensive problems.
>
> +++++++++++
>
> .. link-button:: examples/index
> :type: ref
> :text: …
> :classes: stretched-link
>
> ---
>
> API
> ^^^
>
> The API for major ``cogent3`` objects
>
> +++++++++++
>
> .. link-button:: api/index
> :type: ref
> :text: …
> :classes: stretched-link
> looking for now-outdated files... none found
> pickling environment... done
> checking consistency... /<<PKGBUILDDIR>>/doc/data_file_links.rst: WARNING: document isn't included in any toctree
> /<<PKGBUILDDIR>>/doc/draw/index.rst: WARNING: document isn't included in any toctree
> /<<PKGBUILDDIR>>/doc/general.rst: WARNING: document isn't included in any toctree
> /<<PKGBUILDDIR>>/doc/install.rst: WARNING: document isn't included in any toctree
> /<<PKGBUILDDIR>>/doc/licenses.rst: WARNING: document isn't included in any toctree
> /<<PKGBUILDDIR>>/doc/pycogent.rst: WARNING: document isn't included in any toctree
> done
> preparing documents... done
> copying assets... [2Kcopying downloadable files... [ 4%] data/abglobin_aa.phylip
> [2Kcopying downloadable files... [ 8%] data/dists_for_phylo.json
> [2Kcopying downloadable files... [ 12%] data/long_testseqs.fasta
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> [2Kcopying downloadable files... [ 24%] data/primate_cdx2_promoter.fasta
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> [2Kcopying downloadable files... [ 32%] data/test.tree
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> [2Kcopying downloadable files... [ 60%] data/SCA1-cds.fasta
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> [2Kcopying downloadable files... [ 84%] data/F9-demo.fa
> [2Kcopying downloadable files... [ 88%] data/BRCA1-demo.fasta
> [2Kcopying downloadable files... [ 92%] data/tbp.jaspar
> [2Kcopying downloadable files... [ 96%] data/stats.tsv
> [2Kcopying downloadable files... [100%] data/CerebellumDukeDNaseSeq.pk
>
> copying static files... done
> copying extra files... done
> done
> [2Kwriting output... [ 1%] api/__init__/cogent3.__init__.available_apps
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> [2Kwriting output... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs
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> [2Kwriting output... [ 20%] api/apps/composable.define_app
> [2Kwriting output... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode
> [2Kwriting output... [ 22%] api/genetic_code/genetic_code
> [2Kwriting output... [ 22%] api/index
> [2Kwriting output... [ 23%] api/moltype/classes/cogent3.core.moltype.MolType
> [2Kwriting output... [ 24%] api/moltype/moltype
> [2Kwriting output... [ 25%] api/sequence/classes/cogent3.core.sequence.DnaSequence
> [2Kwriting output... [ 26%] api/sequence/classes/cogent3.core.sequence.ProteinSequence
> [2Kwriting output... [ 26%] api/sequence/classes/cogent3.core.sequence.RnaSequence
> [2Kwriting output... [ 27%] api/sequence/sequence
> [2Kwriting output... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser
> [2Kwriting output... [ 29%] api/table/classes/cogent3.util.table.Columns
> [2Kwriting output... [ 30%] api/table/classes/cogent3.util.table.Table
> [2Kwriting output... [ 30%] api/table/table
> [2Kwriting output... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode
> [2Kwriting output... [ 32%] api/tree/tree
> [2Kwriting output... [ 33%] app/align-codon
> [2Kwriting output... [ 34%] app/align-nucleotide
> [2Kwriting output... [ 34%] app/align-protein
> [2Kwriting output... [ 35%] app/app-get
> [2Kwriting output... [ 36%] app/app-help
> [2Kwriting output... [ 37%] app/app-overview
> [2Kwriting output... [ 38%] app/available-apps
> [2Kwriting output... [ 38%] app/dstore
> [2Kwriting output... [ 39%] app/evo-ancestral-states
> [2Kwriting output... [ 40%] app/evo-dt-nuc-model
> [2Kwriting output... [ 41%] app/evo-extract-model-stats
> [2Kwriting output... [ 42%] app/evo-hypothesis
> [2Kwriting output... [ 42%] app/evo-model
> [2Kwriting output... [ 43%] app/evo-model-timehet
> [2Kwriting output... [ 44%] app/evo-model-with-tree
> [2Kwriting output... [ 45%] app/evo-natsel_neutral
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> [2Kwriting output... [ 47%] app/evo-natsel_zhang
> [2Kwriting output... [ 48%] app/evo-nstat-codon-model
> [2Kwriting output... [ 49%] app/evo-tr-codon-model
> [2Kwriting output... [ 50%] app/evo-tr-nuc-model
> [2Kwriting output... [ 50%] app/index
> [2Kwriting output... [ 51%] app/not-completed
> [2Kwriting output... [ 52%] app/user_function
> [2Kwriting output... [ 53%] cookbook/DNA_and_RNA_sequences
> [2Kwriting output... [ 54%] cookbook/alignments
> [2Kwriting output... [ 54%] cookbook/alphabet
> [2Kwriting output... [ 55%] cookbook/annotations
> [2Kwriting output... [ 56%] cookbook/building_alignments
> [2Kwriting output... [ 57%] cookbook/building_phylogenies
> [2Kwriting output... [ 58%] cookbook/calc_genetic_distance
> [2Kwriting output... [ 58%] cookbook/evo_modelling
> [2Kwriting output... [ 59%] cookbook/genetic_code
> [2Kwriting output... [ 60%] cookbook/index
> [2Kwriting output... [ 61%] cookbook/loading_sequences
> [2Kwriting output... [ 62%] cookbook/loading_tabular
> [2Kwriting output... [ 62%] cookbook/manipulating_biological_data
> [2Kwriting output... [ 63%] cookbook/moltypes
> [2Kwriting output... [ 64%] cookbook/protein_sequences
> [2Kwriting output... [ 65%] cookbook/simple_trees
> [2Kwriting output... [ 66%] cookbook/tables
> [2Kwriting output... [ 66%] cookbook/useful_utilities
> [2Kwriting output... [ 67%] cookbook/what_codes
> [2Kwriting output... [ 68%] data_file_links
> [2Kwriting output... [ 69%] draw/aln/plot_aln-coevolution
> [2Kwriting output... [ 70%] draw/aln/plot_aln-dotplot-1
> [2Kwriting output... [ 70%] draw/aln/plot_aln-dotplot-2
> [2Kwriting output... [ 71%] draw/aln/plot_aln-gaps-per-seq
> [2Kwriting output... [ 72%] draw/aln/plot_aln-info-plot
> [2Kwriting output... [ 73%] draw/aln/plot_aln-seqlogo
> [2Kwriting output... [ 74%] draw/index
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> [2Kwriting output... [ 78%] draw/tree/plot_tree-support
> [2Kwriting output... [ 78%] examples/align_codons_to_protein
> [2Kwriting output... [ 79%] examples/calculate_UPGMA_cluster
> [2Kwriting output... [ 80%] examples/calculate_neigbourjoining_tree
> [2Kwriting output... [ 81%] examples/calculate_pairwise_distances
> [2Kwriting output... [ 82%] examples/codon_models
> [2Kwriting output... [ 82%] examples/coevolution
> [2Kwriting output... [ 83%] examples/complete_seq_features
> [2Kwriting output... [ 84%] examples/empirical_protein_models
> [2Kwriting output... [ 85%] examples/hmm_par_heterogeneity
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> [2Kwriting output... [ 89%] examples/parametric_bootstrap
> [2Kwriting output... [ 90%] examples/period_estimation
> [2Kwriting output... [ 90%] examples/phylo_by_ls
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> [2Kwriting output... [ 94%] examples/simple
> [2Kwriting output... [ 95%] examples/simulate_alignment
> [2Kwriting output... [ 96%] examples/testing_multi_loci
> [2Kwriting output... [ 97%] general
> [2Kwriting output... [ 98%] index
> [2Kwriting output... [ 98%] install
> [2Kwriting output... [ 99%] licenses
> [2Kwriting output... [100%] pycogent
>
> generating indices... genindex done
> /usr/lib/python3/dist-packages/nbsphinx.py:2094: RemovedInSphinx80Warning: The alias 'sphinx.util.status_iterator' is deprecated, use 'sphinx.util.display.status_iterator' instead. Check CHANGES for Sphinx API modifications.
> status_iterator = sphinx.util.status_iterator
> copying linked files...
> copying notebooks ...
> writing additional pages... search done
> dumping search index in English (code: en)... done
> dumping object inventory... done
> build succeeded, 925 warnings.
>
> The HTML pages are in _build/html.
>
> Build finished. The HTML pages are in _build/html.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> # remove superfluous files and dirs
> find doc/_build -name "*.doctree*" -delete
> rm -f doc/_build/html/_sources/COGENT_LICENSE.txt
> rm -f doc/_build/html/_static/jquery.js
> rm -f doc/_build/html/_static/underscore.js
> rm -rf doc/_build/html/_images/math/
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild pybuild:314: cp -r /<<PKGBUILDDIR>>/tests/data /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
> ============================= test session starts ==============================
> platform linux -- Python 3.12.1, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build
> configfile: pyproject.toml
> testpaths: tests
> plugins: cov-4.1.0, xdist-3.4.0, anyio-3.7.0
> collected 0 items / 105 errors
>
> ==================================== ERRORS ====================================
> _____________________ ERROR collecting tests/test_phylo.py _____________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_phylo.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_recalculation.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_recalculation.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_align/test_align.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_align/test_align.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_align/test_compare.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_align/test_compare.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_app/test_align.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_align.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_align.py:3: in <module>
> from cogent3 import (
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_app/test_app_mpi.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_app_mpi.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_app_mpi.py:5: in <module>
> from cogent3 import get_app, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_app/test_composable.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_composable.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_composable.py:17: in <module>
> from cogent3 import get_app, make_aligned_seqs, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_app/test_data_store_new.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_data_store_new.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_data_store_new.py:12: in <module>
> import cogent3.app.io_new as io_app
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_app/test_dist.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_dist.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_dist.py:8: in <module>
> from cogent3 import DNA, PROTEIN, get_app, make_unaligned_seqs, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_app/test_evo.py __________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_evo.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_evo.py:11: in <module>
> from cogent3 import (
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_app/test_init.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_init.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_init.py:10: in <module>
> from cogent3 import app_help, available_apps, get_app, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_app/test_io_new.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_io_new.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_io_new.py:17: in <module>
> from cogent3 import DNA, get_app, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_app/test_result.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_result.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_result.py:5: in <module>
> from cogent3 import make_aligned_seqs, make_table
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_app/test_sample.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_sample.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_sample.py:3: in <module>
> from cogent3 import DNA, make_aligned_seqs, make_unaligned_seqs
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_app/test_sqlite_data_store.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_sqlite_data_store.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_sqlite_data_store.py:9: in <module>
> from cogent3 import get_app, open_data_store
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_app/test_translate.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_translate.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_translate.py:3: in <module>
> from cogent3 import DNA, make_aligned_seqs, make_unaligned_seqs
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_app/test_tree.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_tree.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_tree.py:5: in <module>
> from cogent3 import DNA, load_aligned_seqs, make_aligned_seqs, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_app/test_typing.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_app/test_typing.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_app/test_typing.py:7: in <module>
> from cogent3.app.typing import (
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_cluster/test_UPGMA.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_cluster/test_UPGMA.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_core/test_alignment.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_alignment.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_core/test_alphabet.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_alphabet.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_core/test_annotation.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_annotation.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___________ ERROR collecting tests/test_core/test_core_standalone.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_core_standalone.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_core/test_features.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_features.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_core/test_genetic_code.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_genetic_code.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_core/test_info.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_info.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_core/test_location.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_location.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_core/test_maps.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_maps.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_core/test_moltype.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_moltype.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_core/test_profile.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_profile.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________ ERROR collecting tests/test_core/test_seq_aln_integration.py _________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_seq_aln_integration.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_core/test_sequence.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_sequence.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_core/test_tree.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_core/test_tree.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_data/test_molecular_weight.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_data/test_molecular_weight.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_draw/test_dendrogram.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_draw/test_dendrogram.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_draw/test_dendrogram.py:5: in <module>
> from cogent3 import make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_draw/test_dotplot.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_draw/test_dotplot.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_draw/test_dotplot.py:3: in <module>
> from cogent3 import DNA, make_unaligned_seqs
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_draw/test_draw_integration.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_draw/test_draw_integration.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_draw/test_draw_integration.py:6: in <module>
> from cogent3 import load_aligned_seqs, make_aligned_seqs, make_table
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_draw/test_logo.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_draw/test_logo.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_draw/test_logo.py:3: in <module>
> from cogent3.draw.letter import get_character
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_draw/test_shapes.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_draw/test_shapes.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> test_draw/test_shapes.py:5: in <module>
> from cogent3.draw import drawable
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_evolve/test_best_likelihood.py __________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_best_likelihood.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_evolve/test_bootstrap.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_bootstrap.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_evolve/test_coevolution.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_coevolution.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_evolve/test_distance.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_distance.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________ ERROR collecting tests/test_evolve/test_likelihood_function.py ________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_likelihood_function.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_evolve/test_models.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_models.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_evolve/test_motifchange.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_motifchange.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_evolve/test_newq.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_newq.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______ ERROR collecting tests/test_evolve/test_ns_substitution_model.py _______
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_ns_substitution_model.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______ ERROR collecting tests/test_evolve/test_parameter_controller.py ________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_parameter_controller.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_evolve/test_scale_rules.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_scale_rules.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_evolve/test_simulation.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_simulation.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________ ERROR collecting tests/test_evolve/test_substitution_model.py _________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_evolve/test_substitution_model.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_format/test_bedgraph.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_format/test_bedgraph.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_format/test_clustal.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_format/test_clustal.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_format/test_fasta.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_format/test_fasta.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________ ERROR collecting tests/test_maths/test_distance_transform.py _________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_distance_transform.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_maths/test_geometry.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_geometry.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___ ERROR collecting tests/test_maths/test_matrix_exponential_integration.py ___
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_matrix_exponential_integration.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_maths/test_matrix_logarithm.py __________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_matrix_logarithm.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_maths/test_measure.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_measure.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_maths/test_optimisers.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_optimisers.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_maths/test_period.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_period.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_maths/test_util.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_util.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______ ERROR collecting tests/test_maths/test_stats/test_contingency.py _______
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_contingency.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______ ERROR collecting tests/test_maths/test_stats/test_distribution.py _______
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_distribution.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __ ERROR collecting tests/test_maths/test_stats/test_information_criteria.py ___
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_information_criteria.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________ ERROR collecting tests/test_maths/test_stats/test_jackknife.py ________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_jackknife.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___________ ERROR collecting tests/test_maths/test_stats/test_ks.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_ks.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________ ERROR collecting tests/test_maths/test_stats/test_number.py __________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_number.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________ ERROR collecting tests/test_maths/test_stats/test_period.py __________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_period.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________ ERROR collecting tests/test_maths/test_stats/test_special.py _________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_special.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_maths/test_stats/test_test.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_maths/test_stats/test_test.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_blast.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_blast.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_parse/test_blast_xml.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_blast_xml.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_cigar.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_cigar.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_parse/test_clustal.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_clustal.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_parse/test_dialign.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_dialign.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_parse/test_ebi.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_ebi.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_fasta.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_fasta.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_gbseq.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_gbseq.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_parse/test_genbank.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_genbank.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_parse/test_gff.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_gff.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_parse/test_greengenes.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_greengenes.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_parse/test_locuslink.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_locuslink.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___________ ERROR collecting tests/test_parse/test_ncbi_taxonomy.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_ncbi_taxonomy.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_nexus.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_nexus.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_parse/test_pamlmatrix.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_pamlmatrix.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_phylip.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_phylip.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_parse/test_psl.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_psl.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ____________ ERROR collecting tests/test_parse/test_pwm_parsers.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_pwm_parsers.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_parse/test_rdb.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_rdb.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _______________ ERROR collecting tests/test_parse/test_record.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_record.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___________ ERROR collecting tests/test_parse/test_record_finder.py ____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_record_finder.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_parse/test_tinyseq.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_tinyseq.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_parse/test_tree.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_tree.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_parse/test_unigene.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_parse/test_unigene.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_util/test_deserialise.py _____________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_deserialise.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_util/test_dictarray.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_dictarray.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _________________ ERROR collecting tests/test_util/test_io.py __________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_io.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_util/test_misc.py _________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_misc.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_util/test_parallel.py _______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_parallel.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> __________ ERROR collecting tests/test_util/test_recode_alignment.py ___________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_recode_alignment.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ________________ ERROR collecting tests/test_util/test_table.py ________________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_table.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ______________ ERROR collecting tests/test_util/test_transform.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_transform.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _____________ ERROR collecting tests/test_util/test_union_dict.py ______________
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/tests/test_util/test_union_dict.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> __init__.py:11: in <module>
> exec(f"from {__name__} import {sub_module}")
> test_phylo.py:11: in <module>
> from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
> ../cogent3/__init__.py:13: in <module>
> from cogent3.app import app_help, available_apps, get_app, open_data_store
> ../cogent3/app/__init__.py:9: in <module>
> from .io_new import open_data_store
> ../cogent3/app/io_new.py:21: in <module>
> from cogent3.evolve.fast_distance import DistanceMatrix
> ../cogent3/evolve/fast_distance.py:14: in <module>
> from .pairwise_distance_numba import fill_diversity_matrix
> ../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
> from numba import njit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> =========================== short test summary info ============================
> ERROR tests/test_phylo.py
> ERROR tests/test_recalculation.py
> ERROR tests/test_align/test_align.py
> ERROR tests/test_align/test_compare.py
> ERROR tests/test_app/test_align.py
> ERROR tests/test_app/test_app_mpi.py
> ERROR tests/test_app/test_composable.py
> ERROR tests/test_app/test_data_store_new.py
> ERROR tests/test_app/test_dist.py
> ERROR tests/test_app/test_evo.py
> ERROR tests/test_app/test_init.py
> ERROR tests/test_app/test_io_new.py
> ERROR tests/test_app/test_result.py
> ERROR tests/test_app/test_sample.py
> ERROR tests/test_app/test_sqlite_data_store.py
> ERROR tests/test_app/test_translate.py
> ERROR tests/test_app/test_tree.py
> ERROR tests/test_app/test_typing.py
> ERROR tests/test_cluster/test_UPGMA.py
> ERROR tests/test_core/test_alignment.py
> ERROR tests/test_core/test_alphabet.py
> ERROR tests/test_core/test_annotation.py
> ERROR tests/test_core/test_core_standalone.py
> ERROR tests/test_core/test_features.py
> ERROR tests/test_core/test_genetic_code.py
> ERROR tests/test_core/test_info.py
> ERROR tests/test_core/test_location.py
> ERROR tests/test_core/test_maps.py
> ERROR tests/test_core/test_moltype.py
> ERROR tests/test_core/test_profile.py
> ERROR tests/test_core/test_seq_aln_integration.py
> ERROR tests/test_core/test_sequence.py
> ERROR tests/test_core/test_tree.py
> ERROR tests/test_data/test_molecular_weight.py
> ERROR tests/test_draw/test_dendrogram.py
> ERROR tests/test_draw/test_dotplot.py
> ERROR tests/test_draw/test_draw_integration.py
> ERROR tests/test_draw/test_logo.py
> ERROR tests/test_draw/test_shapes.py
> ERROR tests/test_evolve/test_best_likelihood.py
> ERROR tests/test_evolve/test_bootstrap.py
> ERROR tests/test_evolve/test_coevolution.py
> ERROR tests/test_evolve/test_distance.py
> ERROR tests/test_evolve/test_likelihood_function.py
> ERROR tests/test_evolve/test_models.py
> ERROR tests/test_evolve/test_motifchange.py
> ERROR tests/test_evolve/test_newq.py
> ERROR tests/test_evolve/test_ns_substitution_model.py
> ERROR tests/test_evolve/test_parameter_controller.py
> ERROR tests/test_evolve/test_scale_rules.py
> ERROR tests/test_evolve/test_simulation.py
> ERROR tests/test_evolve/test_substitution_model.py
> ERROR tests/test_format/test_bedgraph.py
> ERROR tests/test_format/test_clustal.py
> ERROR tests/test_format/test_fasta.py
> ERROR tests/test_maths/test_distance_transform.py
> ERROR tests/test_maths/test_geometry.py
> ERROR tests/test_maths/test_matrix_exponential_integration.py
> ERROR tests/test_maths/test_matrix_logarithm.py
> ERROR tests/test_maths/test_measure.py
> ERROR tests/test_maths/test_optimisers.py
> ERROR tests/test_maths/test_period.py
> ERROR tests/test_maths/test_util.py
> ERROR tests/test_maths/test_stats/test_contingency.py
> ERROR tests/test_maths/test_stats/test_distribution.py
> ERROR tests/test_maths/test_stats/test_information_criteria.py
> ERROR tests/test_maths/test_stats/test_jackknife.py
> ERROR tests/test_maths/test_stats/test_ks.py
> ERROR tests/test_maths/test_stats/test_number.py
> ERROR tests/test_maths/test_stats/test_period.py
> ERROR tests/test_maths/test_stats/test_special.py
> ERROR tests/test_maths/test_stats/test_test.py
> ERROR tests/test_parse/test_blast.py
> ERROR tests/test_parse/test_blast_xml.py
> ERROR tests/test_parse/test_cigar.py
> ERROR tests/test_parse/test_clustal.py
> ERROR tests/test_parse/test_dialign.py
> ERROR tests/test_parse/test_ebi.py
> ERROR tests/test_parse/test_fasta.py
> ERROR tests/test_parse/test_gbseq.py
> ERROR tests/test_parse/test_genbank.py
> ERROR tests/test_parse/test_gff.py
> ERROR tests/test_parse/test_greengenes.py
> ERROR tests/test_parse/test_locuslink.py
> ERROR tests/test_parse/test_ncbi_taxonomy.py
> ERROR tests/test_parse/test_nexus.py
> ERROR tests/test_parse/test_pamlmatrix.py
> ERROR tests/test_parse/test_phylip.py
> ERROR tests/test_parse/test_psl.py
> ERROR tests/test_parse/test_pwm_parsers.py
> ERROR tests/test_parse/test_rdb.py
> ERROR tests/test_parse/test_record.py
> ERROR tests/test_parse/test_record_finder.py
> ERROR tests/test_parse/test_tinyseq.py
> ERROR tests/test_parse/test_tree.py
> ERROR tests/test_parse/test_unigene.py
> ERROR tests/test_util/test_deserialise.py
> ERROR tests/test_util/test_dictarray.py
> ERROR tests/test_util/test_io.py
> ERROR tests/test_util/test_misc.py
> ERROR tests/test_util/test_parallel.py
> ERROR tests/test_util/test_recode_alignment.py
> ERROR tests/test_util/test_table.py
> ERROR tests/test_util/test_transform.py
> ERROR tests/test_util/test_union_dict.py
> !!!!!!!!!!!!!!!!!! Interrupted: 105 errors during collection !!!!!!!!!!!!!!!!!!!
> ============================= 105 errors in 11.70s =============================
> E: pybuild pybuild:395: test: plugin pyproject failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
> I: pybuild pybuild:314: cp -r /<<PKGBUILDDIR>>/tests/data /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build; python3.11 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
> ============================= test session starts ==============================
> platform linux -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build
> configfile: pyproject.toml
> testpaths: tests
> plugins: cov-4.1.0, xdist-3.4.0, anyio-3.7.0
> collected 2873 items / 4 deselected / 2869 selected
>
> tests/test_phylo.py ................ [ 0%]
> tests/test_recalculation.py . [ 0%]
> tests/test_align/test_align.py ............................... [ 1%]
> tests/test_align/test_compare.py ....................................... [ 3%]
> .... [ 3%]
> tests/test_app/test_align.py ....................... [ 3%]
> tests/test_app/test_app_mpi.py s [ 4%]
> tests/test_app/test_composable.py .............xX....................... [ 5%]
> ........................................... [ 6%]
> tests/test_app/test_data_store_new.py .................................. [ 8%]
> ....................... [ 8%]
> tests/test_app/test_dist.py ....... [ 9%]
> tests/test_app/test_evo.py ......................................... [ 10%]
> tests/test_app/test_init.py ............. [ 10%]
> tests/test_app/test_io_new.py .......................................... [ 12%]
> ...... [ 12%]
> tests/test_app/test_result.py ............................ [ 13%]
> tests/test_app/test_sample.py ................. [ 14%]
> tests/test_app/test_sqlite_data_store.py ............................... [ 15%]
> .................. [ 15%]
> tests/test_app/test_translate.py ...... [ 16%]
> tests/test_app/test_tree.py ..... [ 16%]
> tests/test_app/test_typing.py ..................... [ 17%]
> tests/test_cluster/test_UPGMA.py ....... [ 17%]
> tests/test_core/test_alignment.py ...................................... [ 18%]
> ........................................................................ [ 21%]
> ........................................................................ [ 23%]
> ........................................................................ [ 26%]
> ........................................................................ [ 28%]
> ................................................................... [ 30%]
> tests/test_core/test_alphabet.py ........................ [ 31%]
> tests/test_core/test_annotation.py ......... [ 32%]
> tests/test_core/test_core_standalone.py ................................ [ 33%]
> .......................... [ 34%]
> tests/test_core/test_features.py ............................. [ 35%]
> tests/test_core/test_genetic_code.py ................... [ 35%]
> tests/test_core/test_info.py ............ [ 36%]
> tests/test_core/test_location.py ................................... [ 37%]
> tests/test_core/test_maps.py .... [ 37%]
> tests/test_core/test_moltype.py ........................................ [ 38%]
> ......................... [ 39%]
> tests/test_core/test_profile.py ................................ [ 40%]
> tests/test_core/test_seq_aln_integration.py .............. [ 41%]
> tests/test_core/test_sequence.py ....................................... [ 42%]
> ........................................................................ [ 45%]
> ........................................................................ [ 47%]
> ........................................... [ 49%]
> tests/test_core/test_tree.py ........................................... [ 50%]
> ........................................................................ [ 53%]
> ......................... [ 54%]
> tests/test_data/test_molecular_weight.py . [ 54%]
> tests/test_draw/test_dendrogram.py .......... [ 54%]
> tests/test_draw/test_dotplot.py ........... [ 54%]
> tests/test_draw/test_draw_integration.py ........................ [ 55%]
> tests/test_draw/test_logo.py ..... [ 55%]
> tests/test_draw/test_shapes.py ... [ 56%]
> tests/test_evolve/test_best_likelihood.py ....... [ 56%]
> tests/test_evolve/test_bootstrap.py .. [ 56%]
> tests/test_evolve/test_coevolution.py .................................. [ 57%]
> ........................................................................ [ 60%]
> .............. [ 60%]
> tests/test_evolve/test_distance.py ..................................... [ 61%]
> ..... [ 62%]
> tests/test_evolve/test_likelihood_function.py .......................... [ 62%]
> .............................................. [ 64%]
> tests/test_evolve/test_models.py ........... [ 64%]
> tests/test_evolve/test_motifchange.py ............. [ 65%]
> tests/test_evolve/test_newq.py ............. [ 65%]
> tests/test_evolve/test_ns_substitution_model.py .............. [ 66%]
> tests/test_evolve/test_parameter_controller.py .......... [ 66%]
> tests/test_evolve/test_scale_rules.py .... [ 66%]
> tests/test_evolve/test_substitution_model.py ...................... [ 67%]
> tests/test_format/test_bedgraph.py ........ [ 67%]
> tests/test_format/test_clustal.py ... [ 67%]
> tests/test_format/test_fasta.py . [ 68%]
> tests/test_maths/test_distance_transform.py ............................ [ 68%]
> ....... [ 69%]
> tests/test_maths/test_geometry.py .......... [ 69%]
> tests/test_maths/test_matrix_exponential_integration.py .... [ 69%]
> tests/test_maths/test_matrix_logarithm.py ... [ 69%]
> tests/test_maths/test_measure.py ........ [ 70%]
> tests/test_maths/test_optimisers.py ...... [ 70%]
> tests/test_maths/test_period.py ....... [ 70%]
> tests/test_maths/test_util.py ....... [ 70%]
> tests/test_maths/test_stats/test_contingency.py .................... [ 71%]
> tests/test_maths/test_stats/test_distribution.py ....................... [ 72%]
> . [ 72%]
> tests/test_maths/test_stats/test_information_criteria.py ... [ 72%]
> tests/test_maths/test_stats/test_jackknife.py .... [ 72%]
> tests/test_maths/test_stats/test_ks.py ...... [ 72%]
> tests/test_maths/test_stats/test_number.py ...................... [ 73%]
> tests/test_maths/test_stats/test_period.py .......... [ 73%]
> tests/test_maths/test_stats/test_special.py ....................... [ 74%]
> tests/test_maths/test_stats/test_test.py ............................... [ 75%]
> ...................................................................... [ 78%]
> tests/test_parse/test_blast.py .............. [ 78%]
> tests/test_parse/test_blast_xml.py ............... [ 79%]
> tests/test_parse/test_cigar.py ..... [ 79%]
> tests/test_parse/test_clustal.py ......... [ 79%]
> tests/test_parse/test_dialign.py ... [ 79%]
> tests/test_parse/test_ebi.py ........................................... [ 81%]
> ............ [ 81%]
> tests/test_parse/test_fasta.py ..................... [ 82%]
> tests/test_parse/test_gbseq.py . [ 82%]
> tests/test_parse/test_genbank.py ................ [ 83%]
> tests/test_parse/test_gff.py ...... [ 83%]
> tests/test_parse/test_greengenes.py .... [ 83%]
> tests/test_parse/test_locuslink.py ............. [ 83%]
> tests/test_parse/test_ncbi_taxonomy.py .................. [ 84%]
> tests/test_parse/test_nexus.py ............... [ 85%]
> tests/test_parse/test_pamlmatrix.py . [ 85%]
> tests/test_parse/test_phylip.py ... [ 85%]
> tests/test_parse/test_psl.py ... [ 85%]
> tests/test_parse/test_pwm_parsers.py .. [ 85%]
> tests/test_parse/test_rdb.py .................. [ 85%]
> tests/test_parse/test_record.py ........................................ [ 87%]
> .. [ 87%]
> tests/test_parse/test_record_finder.py ................. [ 88%]
> tests/test_parse/test_tinyseq.py . [ 88%]
> tests/test_parse/test_tree.py ............... [ 88%]
> tests/test_parse/test_unigene.py .... [ 88%]
> tests/test_util/test_deserialise.py ............................ [ 89%]
> tests/test_util/test_dictarray.py ............................... [ 90%]
> tests/test_util/test_io.py ...................................ssss.sss [ 92%]
> tests/test_util/test_misc.py ........................................... [ 93%]
> .......................................... [ 95%]
> tests/test_util/test_parallel.py ... [ 95%]
> tests/test_util/test_recode_alignment.py ............... [ 95%]
> tests/test_util/test_table.py .......................................... [ 97%]
> ............................................................. [ 99%]
> tests/test_util/test_transform.py ..... [ 99%]
> tests/test_util/test_union_dict.py ........... [100%]
>
> =============================== warnings summary ===============================
> tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/sequence.py:1123: UserWarning: Dropped remainder "GA" from end of sequence
> warnings.warn(
>
> tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_repr_policy_valid_input
> /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (<bound method SequenceCollectionBaseTests.test_set_repr_policy_valid_input of <tests.test_core.test_alignment.SequenceCollectionTests testMethod=test_set_repr_policy_valid_input>>)
> return self.run(*args, **kwds)
>
> tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_wrap_affects_repr_html
> /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (<bound method SequenceCollectionBaseTests.test_set_wrap_affects_repr_html of <tests.test_core.test_alignment.SequenceCollectionTests testMethod=test_set_wrap_affects_repr_html>>)
> return self.run(*args, **kwds)
>
> tests/test_core/test_core_standalone.py::TestConstructorFunctions::test_load_seq
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/info.py:208: UserWarning: Keys overwritten by other sequence: source
> warn("Keys overwritten by other sequence: " + "".join(overwrites))
>
> tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_get_param_rules_multilocus
> tests/test_util/test_deserialise.py::TestDeserialising::test_deserialise_likelihood_function_multilocus
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning:
>
> Used mean of 12 mprobs values
>
> tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_make_discrete_markov
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py:808: UserWarning:
>
> Ignoring tree edge lengths
>
> tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_set_param_rule_adjust_bounds
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning:
>
> Used mean of 7 beta values
>
> tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/maths/optimisers.py:189: UserWarning:
>
> Unused arg for local alignment: results
>
> tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch
> /usr/lib/python3/dist-packages/numpy/core/_methods.py:269: RuntimeWarning:
>
> Degrees of freedom <= 0 for slice
>
> tests/test_util/test_misc.py::UtilsTests::test_get_setting_from_environ
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_cogent3/build/cogent3/util/misc.py:1034: UserWarning:
>
> could not cast name=blah to type <class 'float'>, skipping
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> SKIPPED [1] tests/test_app/test_app_mpi.py:26: Not using MPI
> SKIPPED [4] tests/test_util/test_io.py:320: Do not test in Debian since offline
> SKIPPED [1] tests/test_util/test_io.py:361: Do not test in Debian since offline
> SKIPPED [1] tests/test_util/test_io.py:378: Do not test in Debian since offline
> SKIPPED [1] tests/test_util/test_io.py:388: Do not test in Debian since offline
> XFAIL tests/test_app/test_composable.py::test_as_completed_progress[True] - passes except when run in full test suite
> XPASS tests/test_app/test_composable.py::test_as_completed_progress[False] passes except when run in full test suite
> = 2859 passed, 8 skipped, 4 deselected, 1 xfailed, 1 xpassed, 11 warnings in 240.97s (0:04:00) =
> dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/12/12/python-cogent_2023.2.12a1+dfsg-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231212;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231212&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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