[med-svn] [Git][med-team/python-cogent][upstream] New upstream version 2026.9.10

[Karsten Schöke (@karso)]

Karsten Schöke pushed to branch upstream at Debian Med / python-cogent


Commits:
298f79b1 by Karsten Schöke at 2026-10-14T10:05:35+02:00
New upstream version 2026.9.10
- - - - -


404 changed files:

- + .codacy.yml
- .github/dependabot.yml
- .github/workflows/codeql.yml
- .github/workflows/linters.yml
- .github/workflows/release.yml
- .github/workflows/testing_develop.yml
- .gitignore
- README.md
- changelog.md
- + doc/.gitignore
- − doc/Makefile
- doc/COGENT3_LICENSE.rst → doc/_COGENT3_LICENSE.qmd
- + doc/_quarto.yml
- − doc/api/__init__/cogent3.__init__.available_apps.rst
- − doc/api/__init__/cogent3.__init__.available_codes.rst
- − doc/api/__init__/cogent3.__init__.available_models.rst
- − doc/api/__init__/cogent3.__init__.available_moltypes.rst
- − doc/api/__init__/cogent3.__init__.get_code.rst
- − doc/api/__init__/cogent3.__init__.get_model.rst
- − doc/api/__init__/cogent3.__init__.get_moltype.rst
- − doc/api/__init__/cogent3.__init__.load_aligned_seqs.rst
- − doc/api/__init__/cogent3.__init__.load_annotations.rst
- − doc/api/__init__/cogent3.__init__.load_delimited.rst
- − doc/api/__init__/cogent3.__init__.load_seq.rst
- − doc/api/__init__/cogent3.__init__.load_table.rst
- − doc/api/__init__/cogent3.__init__.load_tree.rst
- − doc/api/__init__/cogent3.__init__.load_unaligned_seqs.rst
- − doc/api/__init__/cogent3.__init__.make_aligned_seqs.rst
- − doc/api/__init__/cogent3.__init__.make_seq.rst
- − doc/api/__init__/cogent3.__init__.make_table.rst
- − doc/api/__init__/cogent3.__init__.make_tree.rst
- − doc/api/__init__/cogent3.__init__.make_unaligned_seqs.rst
- − doc/api/__init__/cogent3.__init__.open_.rst
- − doc/api/__init__/cogent3.__init__.open_data_store.rst
- − doc/api/alignment/alignment.rst
- − doc/api/alignment/classes/cogent3.core.alignment.Aligned.rst
- − doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst
- − doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst
- − doc/api/alphabet/alphabet.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.CharAlphabet.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.KmerAlphabet.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.PhredEncoding.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.SenseCodonAlphabet.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.bytes_to_array.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.make_qual_converter.rst
- − doc/api/alphabet/classes/cogent3.core.alphabet.make_text_to_array_converter.rst
- − doc/api/annotation/annotation.rst
- − doc/api/annotation/classes/cogent3.core.annotation.Feature.rst
- − doc/api/annotation_db/annotation_db.rst
- − doc/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.rst
- − doc/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.rst
- − doc/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.rst
- − doc/api/app/data_store/classes/cogent3.app.data_store.DataMember.rst
- − doc/api/app/data_store/classes/cogent3.app.data_store.DataStoreDirectory.rst
- − doc/api/app/data_store/classes/cogent3.app.data_store.ReadOnlyDataStoreZipped.rst
- − doc/api/app/sqlite_data_store/classes/cogent3.app.sqlite_data_store.DataStoreSqlite.rst
- − doc/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.rst
- − doc/api/genetic_code/genetic_code.rst
- − doc/api/index.rst
- − doc/api/moltype/classes/cogent3.core.moltype.MolType.rst
- − doc/api/moltype/moltype.rst
- − doc/api/seq_storage/classes/cogent3.core.seq_storage.AlignedSeqsData.rst
- − doc/api/seq_storage/classes/cogent3.core.seq_storage.SeqsData.rst
- − doc/api/seq_storage/seq_storage.rst
- − doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst
- − doc/api/sequence/classes/cogent3.core.sequence.ProteinSequence.rst
- − doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst
- − doc/api/sequence/sequence.rst
- − doc/api/seqview/classes/cogent3.core.seqview.AlignedDataView.rst
- − doc/api/seqview/classes/cogent3.core.seqview.SeqDataView.rst
- − doc/api/seqview/classes/cogent3.core.seqview.SeqView.rst
- − doc/api/seqview/seqview.rst
- − doc/api/slice_record/classes/cogent3.core.slice_record.SliceRecord.rst
- − doc/api/slice_record/slice_record.rst
- − doc/api/table/classes/cogent3.core.table.Columns.rst
- − doc/api/table/classes/cogent3.core.table.Table.rst
- − doc/api/table/classes/cogent3.parse.table.FilteringParser.rst
- − doc/api/table/table.rst
- − doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst
- − doc/api/tree/tree.rst
- + doc/app/app_cookbook/align-codon.qmd
- − doc/app/app_cookbook/align-codon.rst
- + doc/app/app_cookbook/align-nucleotide.qmd
- − doc/app/app_cookbook/align-nucleotide.rst
- + doc/app/app_cookbook/align-protein.qmd
- − doc/app/app_cookbook/align-protein.rst
- + doc/app/app_cookbook/index-align.qmd
- − doc/app/app_cookbook/index-align.rst
- + doc/app/app_cookbook/index-loaders.qmd
- − doc/app/app_cookbook/index-loaders.rst
- + doc/app/app_cookbook/index-sample.qmd
- − doc/app/app_cookbook/index-sample.rst
- + doc/app/app_cookbook/index-writers.qmd
- − doc/app/app_cookbook/index-writers.rst
- + doc/app/app_cookbook/load-aligned.qmd
- − doc/app/app_cookbook/load-aligned.rst
- + doc/app/app_cookbook/load-json.qmd
- − doc/app/app_cookbook/load-json.rst
- + doc/app/app_cookbook/load-tabular.qmd
- − doc/app/app_cookbook/load-tabular.rst
- + doc/app/app_cookbook/load-unaligned.qmd
- − doc/app/app_cookbook/load-unaligned.rst
- + doc/app/app_cookbook/sample-concat.qmd
- − doc/app/app_cookbook/sample-concat.rst
- + doc/app/app_cookbook/sample-fixed-len.qmd
- − doc/app/app_cookbook/sample-fixed-len.rst
- + doc/app/app_cookbook/sample-min-len.qmd
- − doc/app/app_cookbook/sample-min-len.rst
- + doc/app/app_cookbook/sample-omit-bad.qmd
- − doc/app/app_cookbook/sample-omit-bad.rst
- + doc/app/app_cookbook/sample-omit-degen.qmd
- − doc/app/app_cookbook/sample-omit-degen.rst
- + doc/app/app_cookbook/sample-omit-duplicated.qmd
- − doc/app/app_cookbook/sample-omit-duplicated.rst
- + doc/app/app_cookbook/sample-omit-gap.qmd
- − doc/app/app_cookbook/sample-omit-gap.rst
- + doc/app/app_cookbook/sample-take-n-seqs.qmd
- − doc/app/app_cookbook/sample-take-n-seqs.rst
- + doc/app/app_cookbook/sample-take-pos.qmd
- − doc/app/app_cookbook/sample-take-pos.rst
- + doc/app/app_cookbook/sample-take-seqs.qmd
- − doc/app/app_cookbook/sample-take-seqs.rst
- + doc/app/app_cookbook/sample-trim-stops.qmd
- − doc/app/app_cookbook/sample-trim-stops.rst
- + doc/app/app_cookbook/write-db.qmd
- − doc/app/app_cookbook/write-db.rst
- + doc/app/app_cookbook/write-json.qmd
- − doc/app/app_cookbook/write-json.rst
- + doc/app/app_cookbook/write-seqs.qmd
- − doc/app/app_cookbook/write-seqs.rst
- + doc/app/app_cookbook/write-tabular.qmd
- − doc/app/app_cookbook/write-tabular.rst
- + doc/app/app_overview/app-get.qmd
- − doc/app/app_overview/app-get.rst
- doc/app/app_overview/app-help.rst → doc/app/app_overview/app-help.qmd
- + doc/app/app_overview/app-overview.qmd
- − doc/app/app_overview/app-overview.rst
- + doc/app/app_overview/available-apps.qmd
- − doc/app/app_overview/available-apps.rst
- + doc/app/app_overview/dstore.qmd
- − doc/app/app_overview/dstore.rst
- + doc/app/app_overview/not-completed.qmd
- − doc/app/app_overview/not-completed.rst
- + doc/app/app_overview/user_function.qmd
- − doc/app/app_overview/user_function.rst
- + doc/app/app_tutorials/evo-ancestral-states.qmd
- − doc/app/app_tutorials/evo-ancestral-states.rst
- + doc/app/app_tutorials/evo-dt-nuc-model.qmd
- − doc/app/app_tutorials/evo-dt-nuc-model.rst
- + doc/app/app_tutorials/evo-extract-model-stats.qmd
- − doc/app/app_tutorials/evo-extract-model-stats.rst
- + doc/app/app_tutorials/evo-hypothesis.qmd
- − doc/app/app_tutorials/evo-hypothesis.rst
- doc/app/app_tutorials/evo-model-timehet.rst → doc/app/app_tutorials/evo-model-timehet.qmd
- + doc/app/app_tutorials/evo-model-with-tree.qmd
- − doc/app/app_tutorials/evo-model-with-tree.rst
- + doc/app/app_tutorials/evo-model.qmd
- − doc/app/app_tutorials/evo-model.rst
- + doc/app/app_tutorials/evo-natsel_neutral.qmd
- − doc/app/app_tutorials/evo-natsel_neutral.rst
- doc/app/app_tutorials/evo-natsel_sitehet.rst → doc/app/app_tutorials/evo-natsel_sitehet.qmd
- + doc/app/app_tutorials/evo-natsel_timehet.qmd
- − doc/app/app_tutorials/evo-natsel_timehet.rst
- + doc/app/app_tutorials/evo-natsel_zhang.qmd
- − doc/app/app_tutorials/evo-natsel_zhang.rst
- + doc/app/app_tutorials/evo-nstat-codon-model.qmd
- − doc/app/app_tutorials/evo-nstat-codon-model.rst
- + doc/app/app_tutorials/evo-tr-codon-model.qmd
- − doc/app/app_tutorials/evo-tr-codon-model.rst
- + doc/app/app_tutorials/evo-tr-nuc-model.qmd
- − doc/app/app_tutorials/evo-tr-nuc-model.rst
- + doc/app/app_tutorials/index-evo-hypothesis.qmd
- − doc/app/app_tutorials/index-evo-hypothesis.rst
- + doc/app/app_tutorials/index-evo-model.qmd
- − doc/app/app_tutorials/index-evo-model.rst
- doc/app/app_tutorials/index-evo-natsel.rst → doc/app/app_tutorials/index-evo-natsel.qmd
- + doc/app/index-app.qmd
- − doc/app/index-app.rst
- + doc/app/index-cookbook.qmd
- − doc/app/index-cookbook.rst
- − doc/app/index-help.rst
- doc/app/index-tutorials.rst → doc/app/index-tutorials.qmd
- + doc/app/index.qmd
- − doc/app/index.rst
- + doc/community.qmd
- − doc/community.rst
- − doc/conf.py
- + doc/cookbook/DNA_and_RNA_sequences.qmd
- − doc/cookbook/DNA_and_RNA_sequences.rst
- + doc/cookbook/_loading_tabular.qmd
- + doc/cookbook/_union_dict.qmd
- + doc/cookbook/alignments.qmd
- − doc/cookbook/alignments.rst
- + doc/cookbook/alphabet.qmd
- − doc/cookbook/alphabet.rst
- + doc/cookbook/annotation_db.qmd
- − doc/cookbook/annotation_db.rst
- + doc/cookbook/building_alignments.qmd
- − doc/cookbook/building_alignments.rst
- + doc/cookbook/building_phylogenies.qmd
- − doc/cookbook/building_phylogenies.rst
- + doc/cookbook/calc_genetic_distance.qmd
- − doc/cookbook/calc_genetic_distance.rst
- + doc/cookbook/evo_modelling.qmd
- − doc/cookbook/evo_modelling.rst
- + doc/cookbook/features.qmd
- − doc/cookbook/features.rst
- + doc/cookbook/genetic_code.qmd
- − doc/cookbook/genetic_code.rst
- + doc/cookbook/index.qmd
- − doc/cookbook/index.rst
- + doc/cookbook/loading_sequences.qmd
- − doc/cookbook/loading_sequences.rst
- − doc/cookbook/loading_tabular.rst
- + doc/cookbook/manipulating_biological_data.qmd
- − doc/cookbook/manipulating_biological_data.rst
- + doc/cookbook/moltypes.qmd
- − doc/cookbook/moltypes.rst
- + doc/cookbook/protein_sequences.qmd
- − doc/cookbook/protein_sequences.rst
- + doc/cookbook/simple_trees.qmd
- − doc/cookbook/simple_trees.rst
- + doc/cookbook/tables.qmd
- − doc/cookbook/tables.rst
- − doc/cookbook/union_dict.rst
- doc/cookbook/useful_utilities.rst → doc/cookbook/useful_utilities.qmd
- + doc/cookbook/what_codes.qmd
- − doc/cookbook/what_codes.rst
- + doc/custom.css
- doc/data/fastq.txt
- + doc/data_file_links.qmd
- − doc/data_file_links.rst
- − doc/doctest_rsts.py
- + doc/draw/aln/plot_aln-coevolution.qmd
- − doc/draw/aln/plot_aln-coevolution.rst
- + doc/draw/aln/plot_aln-dotplot-1.qmd
- − doc/draw/aln/plot_aln-dotplot-1.rst
- + doc/draw/aln/plot_aln-dotplot-2.qmd
- − doc/draw/aln/plot_aln-dotplot-2.rst
- doc/draw/aln/plot_aln-dotplot-3.rst → doc/draw/aln/plot_aln-dotplot-3.qmd
- + doc/draw/aln/plot_aln-gaps-per-seq.qmd
- − doc/draw/aln/plot_aln-gaps-per-seq.rst
- + doc/draw/aln/plot_aln-info-plot.qmd
- − doc/draw/aln/plot_aln-info-plot.rst
- + doc/draw/aln/plot_aln-seqlogo.qmd
- − doc/draw/aln/plot_aln-seqlogo.rst
- doc/draw/annotations/plot_annotation-db.rst → doc/draw/annotations/plot_annotation-db.qmd
- doc/draw/annotations/plot_seq-features.rst → doc/draw/annotations/plot_seq-features.qmd
- + doc/draw/index.qmd
- − doc/draw/index.rst
- + doc/draw/tree/plot_tree-angular.qmd
- − doc/draw/tree/plot_tree-angular.rst
- + doc/draw/tree/plot_tree-circular.qmd
- − doc/draw/tree/plot_tree-circular.rst
- + doc/draw/tree/plot_tree-iplotx.qmd
- − doc/draw/tree/plot_tree-iplotx.rst
- + doc/draw/tree/plot_tree-radial.qmd
- − doc/draw/tree/plot_tree-radial.rst
- + doc/draw/tree/plot_tree-square.qmd
- − doc/draw/tree/plot_tree-square.rst
- + doc/draw/tree/plot_tree-support.qmd
- − doc/draw/tree/plot_tree-support.rst
- doc/examples/align_codons_to_protein.rst → doc/examples/align_codons_to_protein.qmd
- + doc/examples/calculate_UPGMA_cluster.qmd
- − doc/examples/calculate_UPGMA_cluster.rst
- + doc/examples/calculate_neigbourjoining_tree.qmd
- − doc/examples/calculate_neigbourjoining_tree.rst
- doc/examples/calculate_pairwise_distances.rst → doc/examples/calculate_pairwise_distances.qmd
- doc/examples/codon_models.rst → doc/examples/codon_models.qmd
- doc/examples/empirical_protein_models.rst → doc/examples/empirical_protein_models.qmd
- doc/examples/hmm_par_heterogeneity.rst → doc/examples/hmm_par_heterogeneity.qmd
- + doc/examples/index.qmd
- − doc/examples/index.rst
- doc/examples/neutral_test.rst → doc/examples/neutral_test.qmd
- doc/examples/nonstationary_inference.rst → doc/examples/nonstationary_inference.qmd
- − doc/examples/parallel.rst
- doc/examples/parametric_bootstrap.rst → doc/examples/parametric_bootstrap.qmd
- + doc/examples/period_estimation.qmd
- − doc/examples/period_estimation.rst
- + doc/examples/phylo_by_ls.qmd
- − doc/examples/phylo_by_ls.rst
- + doc/examples/rate_heterogeneity.qmd
- − doc/examples/rate_heterogeneity.rst
- doc/examples/relative_rate.rst → doc/examples/relative_rate.qmd
- + doc/examples/scope_model_params_on_trees.qmd
- − doc/examples/scope_model_params_on_trees.rst
- + doc/examples/simple.qmd
- − doc/examples/simple.rst
- doc/examples/simulate_alignment.rst → doc/examples/simulate_alignment.qmd
- doc/examples/testing_multi_loci.rst → doc/examples/testing_multi_loci.qmd
- + doc/images/c3-logo.svg
- + doc/images/c3-square.svg
- + doc/index.qmd
- − doc/index.rst
- + doc/install.qmd
- − doc/install.rst
- doc/licenses.rst → doc/licenses.qmd
- doc/pycogent.rst → doc/pycogent.qmd
- − doc/rst2script.py
- − doc/set_working_directory.py
- − doc/templates/class.rst
- noxfile.py
- pyproject.toml
- ruff.toml
- src/cogent3/__init__.py
- src/cogent3/_plugin.py
- src/cogent3/_version.py
- src/cogent3/align/dp_calculation.py
- src/cogent3/align/indel_model.py
- src/cogent3/align/pairwise.py
- src/cogent3/align/pycompare.py
- − src/cogent3/app/composable.py
- − src/cogent3/app/data_store.py
- src/cogent3/app/io.py
- − src/cogent3/app/sqlite_data_store.py
- src/cogent3/app/tree.py
- src/cogent3/app/typing.py
- src/cogent3/core/alignment.py
- src/cogent3/core/alphabet.py
- src/cogent3/core/annotation_db.py
- src/cogent3/core/genetic_code.py
- src/cogent3/core/location.py
- src/cogent3/core/moltype.py
- src/cogent3/core/sequence.py
- src/cogent3/core/slice_record.py
- src/cogent3/core/table.py
- src/cogent3/core/tree.py
- src/cogent3/data/molecular_weight.py
- src/cogent3/draw/drawable.py
- src/cogent3/evolve/bootstrap.py
- src/cogent3/evolve/coevolution.py
- src/cogent3/evolve/fast_distance.py
- src/cogent3/evolve/likelihood_tree.py
- src/cogent3/evolve/motif_prob_model.py
- src/cogent3/evolve/ns_substitution_model.py
- src/cogent3/evolve/parameter_controller.py
- src/cogent3/evolve/simulate.py
- src/cogent3/evolve/substitution_model.py
- src/cogent3/format/table.py
- src/cogent3/maths/markov.py
- src/cogent3/maths/matrix_exponentiation.py
- src/cogent3/maths/stats/ks.py
- src/cogent3/parse/blast_xml.py
- src/cogent3/parse/cogent3_json.py
- src/cogent3/parse/ebi.py
- src/cogent3/parse/genbank.py
- src/cogent3/parse/gff.py
- src/cogent3/parse/nexus.py
- src/cogent3/parse/phylip.py
- src/cogent3/parse/record_finder.py
- src/cogent3/parse/sequence.py
- src/cogent3/recalculation/calculation.py
- src/cogent3/recalculation/definition.py
- src/cogent3/recalculation/scope.py
- src/cogent3/recalculation/setting.py
- − src/cogent3/util/deserialise.py
- src/cogent3/util/dict_array.py
- − src/cogent3/util/io.py
- src/cogent3/util/misc.py
- − src/cogent3/util/parallel.py
- − src/cogent3/util/progress_display.py
- tests/__init__.py
- tests/benchmark.py
- tests/conftest.py
- + tests/data/01_basic_dna.nex
- + tests/data/02_non_consecutive_sites.nex
- + tests/data/03_mixed_dna_protein.nex
- + tests/data/04_codon_models_genetic_code.nex
- + tests/data/05_comprehensive_mixed.nex
- + tests/data/07_model_free.nex
- + tests/data/08_data_and_partition.nex
- tests/test_app/test_align.py
- tests/test_app/test_data_store.py
- tests/test_app/test_init.py
- tests/test_app/test_io.py
- tests/test_app/test_plugins.py
- tests/test_core/test_alignment.py
- tests/test_core/test_annotation_db.py
- tests/test_core/test_features.py
- tests/test_core/test_info.py
- tests/test_core/test_location.py
- tests/test_core/test_profile.py
- tests/test_core/test_sequence.py
- tests/test_core/test_table.py
- tests/test_core/test_tree.py
- tests/test_draw/test_draw_integration.py
- tests/test_evolve/test_coevolution.py
- tests/test_evolve/test_distance.py
- tests/test_evolve/test_newq.py
- tests/test_evolve/test_ns_substitution_model.py
- tests/test_evolve/test_substitution_model.py
- tests/test_format/test_bedgraph.py
- tests/test_maths/test_optimisers.py
- tests/test_maths/test_util.py
- tests/test_parse/test_ebi.py
- tests/test_parse/test_gff.py
- tests/test_parse/test_nexus.py
- tests/test_parse/test_phylip.py
- tests/test_phylo.py
- tests/test_recalculation.py
- tests/test_top_level_imports.py
- tests/test_util/test_dictarray.py
- − tests/test_util/test_io.py
- + uv.lock


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View it on GitLab: https://salsa.debian.org/med-team/python-cogent/-/commit/298f79b16903d7acd587b23adaf9565f242d1aab

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