[med-svn] [python-skbio] 02/06: Merge tag 'upstream/0.4.1'
Kevin Murray
daube-guest at moszumanska.debian.org
Mon Dec 21 06:01:21 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository python-skbio.
commit 97ff5686782bf6b9d1c10d19b2ef6e0c52bdb311
Merge: e1c5a00 9f57339
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Mon Dec 21 16:42:22 2015 +1100
Merge tag 'upstream/0.4.1'
Upstream version 0.4.1
.gitignore | 3 +
.travis.yml | 16 +-
CHANGELOG.md | 111 +
CONTRIBUTING.md | 67 +-
MANIFEST.in | 6 +
Makefile | 13 +-
README.rst | 4 +-
RELEASE.md | 28 +-
asv.conf.json | 19 +
benchmarks/__init__.py | 0
benchmarks/benchmarks.py | 64 +
checklist.py | 2 +-
ci/conda_requirements.txt | 14 +
ci/pip_requirements.txt | 11 +
doc/README.md | 23 +-
doc/source/_static/copybutton.js | 44 +-
doc/source/_static/style.css | 27 +-
doc/source/_templates/autosummary/class.rst | 14 +-
doc/source/conf.py | 83 +-
doc/source/draw.rst | 1 -
doc/source/index.rst | 1 -
setup.py | 18 +-
skbio/__init__.py | 10 +-
skbio/_base.py | 834 +++-
skbio/alignment/__init__.py | 152 +-
skbio/alignment/_alignment.py | 1374 ------
skbio/alignment/_exception.py | 19 -
skbio/alignment/_indexing.py | 219 +
skbio/alignment/_pairwise.py | 302 +-
skbio/alignment/_repr.py | 68 +
skbio/alignment/_ssw_wrapper.c | 4514 ++++++++++++--------
skbio/alignment/_ssw_wrapper.pyx | 1 -
skbio/alignment/_tabular_msa.py | 2342 ++++++++++
skbio/alignment/tests/test_alignment.py | 735 ----
skbio/alignment/tests/test_pairwise.py | 666 +--
skbio/alignment/tests/test_ssw.py | 65 +-
skbio/alignment/tests/test_tabular_msa.py | 3676 ++++++++++++++++
skbio/diversity/__init__.py | 382 +-
skbio/diversity/_driver.py | 277 ++
.../__subsample.c => diversity/_phylogenetic.c} | 4053 ++++++++++++------
skbio/diversity/_phylogenetic.pyx | 215 +
skbio/diversity/_util.py | 143 +
skbio/diversity/alpha/__init__.py | 117 +-
skbio/diversity/alpha/_ace.py | 30 +-
skbio/diversity/alpha/_base.py | 331 +-
skbio/diversity/alpha/_chao1.py | 13 +-
skbio/diversity/alpha/_faith_pd.py | 143 +
skbio/diversity/alpha/_gini.py | 12 +-
skbio/diversity/alpha/_lladser.py | 6 +-
.../alpha/tests/data/qiime-191-tt/README.md | 1 +
.../alpha/tests/data/qiime-191-tt/faith-pd.txt | 9 +
.../alpha/tests/data/qiime-191-tt/otu-table.tsv | 12 +
.../alpha/tests/data/qiime-191-tt/tree.nwk | 1 +
skbio/diversity/alpha/tests/test_base.py | 96 +-
skbio/diversity/alpha/tests/test_faith_pd.py | 209 +
skbio/diversity/beta/__init__.py | 166 +-
skbio/diversity/beta/_base.py | 105 -
skbio/diversity/beta/_unifrac.py | 579 +++
.../beta/tests/data/qiime-191-tt/README.md | 26 +
.../beta/tests/data/qiime-191-tt/otu-table.tsv | 12 +
.../beta/tests/data/qiime-191-tt/tree.nwk | 1 +
.../data/qiime-191-tt/unweighted_unifrac_dm.txt | 10 +
.../weighted_normalized_unifrac_dm.txt | 10 +
.../data/qiime-191-tt/weighted_unifrac_dm.txt | 10 +
skbio/diversity/beta/tests/test_base.py | 165 -
skbio/diversity/beta/tests/test_unifrac.py | 690 +++
skbio/{draw => diversity}/tests/__init__.py | 0
skbio/diversity/tests/test_driver.py | 632 +++
skbio/diversity/tests/test_util.py | 240 ++
skbio/draw/__init__.py | 39 -
skbio/draw/_distributions.py | 711 ---
skbio/draw/tests/test_distributions.py | 595 ---
skbio/io/__init__.py | 33 +-
skbio/io/_exception.py | 12 +-
skbio/io/_iosources.py | 15 +-
skbio/io/format/_base.py | 19 +-
skbio/io/format/_blast.py | 44 +
skbio/io/format/blast6.py | 276 ++
skbio/io/format/blast7.py | 384 ++
skbio/io/format/clustal.py | 155 +-
skbio/io/format/fasta.py | 402 +-
skbio/io/format/fastq.py | 141 +-
skbio/io/format/genbank.py | 890 ++++
skbio/io/format/newick.py | 6 +-
skbio/io/format/ordination.py | 54 +-
skbio/io/format/phylip.py | 255 +-
skbio/io/format/qseq.py | 96 +-
skbio/io/format/tests/data/blast6_custom_minimal | 1 +
.../io/format/tests/data/blast6_custom_mixed_nans | 2 +
.../io/format/tests/data/blast6_custom_multi_line | 3 +
.../io/format/tests/data/blast6_custom_single_line | 1 +
.../io/format/tests/data/blast6_default_multi_line | 3 +
.../format/tests/data/blast6_default_single_line | 1 +
.../format/tests/data/blast6_invalid_column_types | 3 +
.../tests/data/blast6_invalid_number_of_columns | 1 +
.../tests/data/blast6_invalid_type_in_column | 2 +
skbio/io/format/tests/data/blast7_custom_minimal | 6 +
.../io/format/tests/data/blast7_custom_mixed_nans | 16 +
.../io/format/tests/data/blast7_custom_multi_line | 16 +
.../io/format/tests/data/blast7_custom_single_line | 15 +
.../io/format/tests/data/blast7_default_multi_line | 12 +
.../format/tests/data/blast7_default_single_line | 10 +
.../tests/data/blast7_invalid_differing_fields | 21 +
.../format/tests/data/blast7_invalid_for_sniffer | 4 +
.../format/tests/data/blast7_invalid_for_sniffer_2 | 4 +
.../io/format/tests/data/blast7_invalid_gibberish | 3 +
skbio/io/format/tests/data/blast7_invalid_no_data | 24 +
.../tests/data/blast7_invalid_too_many_columns | 21 +
.../tests/data/blast7_invalid_unrecognized_field | 10 +
...erent_type => fasta_tabular_msa_different_type} | 0
.../tests/data/genbank_5_blanks_start_of_file | 6 +
.../tests/data/genbank_6_blanks_start_of_file | 7 +
.../format/tests/data/genbank_missing_locus_name | 1 +
skbio/io/format/tests/data/genbank_multi_records | 46 +
skbio/io/format/tests/data/genbank_single_record | 27 +
.../format/tests/data/genbank_single_record_lower | 4 +
.../format/tests/data/genbank_single_record_upper | 4 +
.../tests/data/genbank_w_beginning_whitespace | 1 +
.../format/tests/data/legacy9_and_blast7_default | 12 +
.../tests/data/legacy9_invalid_differing_fields | 20 +
.../tests/data/legacy9_invalid_too_many_columns | 6 +
skbio/io/format/tests/data/legacy9_mixed_nans | 7 +
skbio/io/format/tests/data/legacy9_multi_line | 8 +
skbio/io/format/tests/data/legacy9_single_line | 6 +
.../data/phylip_invalid_empty_line_after_header | 4 +
.../data/phylip_invalid_empty_line_before_header | 4 +
.../data/phylip_invalid_empty_line_between_seqs | 4 +
.../tests/data/phylip_invalid_header_too_long | 3 +
.../tests/data/phylip_invalid_header_too_short | 3 +
.../io/format/tests/data/phylip_invalid_no_header | 2 +
.../format/tests/data/phylip_invalid_seq_too_long | 3 +
.../format/tests/data/phylip_invalid_seq_too_short | 3 +
.../format/tests/data/phylip_invalid_too_few_seqs | 2 +
.../format/tests/data/phylip_invalid_too_many_seqs | 3 +
.../format/tests/data/phylip_invalid_zero_seq_len | 2 +
.../io/format/tests/data/phylip_invalid_zero_seqs | 1 +
.../format/tests/data/phylip_variable_length_ids | 10 +-
.../tests/data/phylip_varied_whitespace_in_seqs | 3 +
.../tests/data/phylip_whitespace_in_header_1 | 3 +
.../tests/data/phylip_whitespace_in_header_2 | 3 +
.../tests/data/phylip_whitespace_in_header_3 | 3 +
...ferent_type => qual_tabular_msa_different_type} | 0
skbio/io/format/tests/test_blast6.py | 123 +
skbio/io/format/tests/test_blast7.py | 212 +
skbio/io/format/tests/test_clustal.py | 77 +-
skbio/io/format/tests/test_fasta.py | 274 +-
skbio/io/format/tests/test_fastq.py | 116 +-
skbio/io/format/tests/test_genbank.py | 503 +++
skbio/io/format/tests/test_ordination.py | 174 +-
skbio/io/format/tests/test_phylip.py | 212 +-
skbio/io/format/tests/test_qseq.py | 47 +-
skbio/io/registry.py | 18 +-
skbio/io/tests/test_registry.py | 3 +-
skbio/io/tests/test_util.py | 13 +-
skbio/io/util.py | 6 +-
skbio/sequence/__init__.py | 58 +-
skbio/sequence/_base.py | 43 -
skbio/sequence/_dna.py | 25 +-
skbio/sequence/_genetic_code.py | 6 +-
skbio/sequence/_iupac_sequence.py | 150 +-
skbio/sequence/_nucleotide_mixin.py | 8 +-
skbio/sequence/_protein.py | 18 +-
skbio/sequence/_repr.py | 108 +
skbio/sequence/_rna.py | 85 +-
skbio/sequence/_sequence.py | 1056 +++--
skbio/sequence/tests/test_base.py | 48 -
skbio/sequence/tests/test_iupac_sequence.py | 45 +-
skbio/sequence/tests/test_rna.py | 45 +
skbio/sequence/tests/test_sequence.py | 993 ++---
skbio/stats/__init__.py | 1 -
skbio/stats/__subsample.c | 1733 +++++---
skbio/stats/composition.py | 640 ++-
skbio/stats/distance/__init__.py | 4 +-
skbio/stats/distance/_base.py | 102 +-
skbio/stats/distance/_mantel.py | 6 +-
skbio/stats/distance/tests/test_base.py | 76 +
skbio/stats/gradient.py | 10 +-
skbio/stats/ordination/__init__.py | 95 +-
skbio/stats/ordination/_base.py | 402 --
.../_canonical_correspondence_analysis.py | 345 +-
skbio/stats/ordination/_correspondence_analysis.py | 295 +-
.../ordination/_principal_coordinate_analysis.py | 181 +-
skbio/stats/ordination/_redundancy_analysis.py | 364 +-
skbio/stats/ordination/_utils.py | 60 +-
skbio/stats/ordination/tests/data/example2_Y | 22 +-
.../ordination/tests/data/example2_biplot_scaling1 | 4 +
.../ordination/tests/data/example2_biplot_scaling2 | 4 +
.../data/example2_sample_constraints_scaling1 | 10 +
.../data/example2_sample_constraints_scaling2 | 10 +
.../ordination/tests/data/example3_biplot_scaling1 | 3 +
.../ordination/tests/data/example3_biplot_scaling2 | 3 +
.../data/example3_sample_constraints_scaling1 | 10 +
.../data/example3_sample_constraints_scaling2 | 10 +
.../test_canonical_correspondence_analysis.py | 174 +
.../tests/test_correspondence_analysis.py | 194 +
skbio/stats/ordination/tests/test_ordination.py | 887 ----
.../tests/test_principal_coordinate_analysis.py | 132 +
.../ordination/tests/test_redundancy_analysis.py | 171 +
skbio/stats/ordination/tests/test_util.py | 69 +
skbio/stats/power.py | 141 +-
skbio/stats/spatial.py | 201 -
skbio/stats/tests/test_composition.py | 666 ++-
skbio/stats/tests/test_gradient.py | 12 +-
skbio/stats/tests/test_power.py | 18 -
skbio/stats/tests/test_spatial.py | 146 -
skbio/tests/test_base.py | 377 +-
skbio/tree/__init__.py | 93 +-
skbio/tree/_majority_rule.py | 75 +-
skbio/tree/_tree.py | 313 +-
skbio/tree/_trie.py | 266 --
skbio/tree/tests/test_tree.py | 242 +-
skbio/tree/tests/test_trie.py | 216 -
skbio/util/__init__.py | 25 +-
skbio/util/_decorator.py | 34 +-
skbio/util/_metadata_repr.py | 168 +
skbio/util/_misc.py | 64 +-
skbio/util/_testing.py | 1069 ++++-
skbio/util/_warning.py | 12 +
skbio/util/tests/test_decorator.py | 60 +-
skbio/util/tests/test_misc.py | 37 +-
skbio/util/tests/test_testing.py | 179 +-
skbio/workflow.py | 26 +-
222 files changed, 29506 insertions(+), 14176 deletions(-)
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