This is an automated email from the git hooks/post-receive script. daube-guest pushed a change to branch upstream in repository python-skbio.
from c4a696f Imported Upstream version 0.4.0 new 9f57339 Imported Upstream version 0.4.1 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .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 + .../tests/data/empty => 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 + ...unks => phylip_invalid_empty_line_after_header} | 1 + ...nks => phylip_invalid_empty_line_before_header} | 1 + ...unks => phylip_invalid_empty_line_between_seqs} | 1 + ...p_two_chunks => phylip_invalid_header_too_long} | 2 +- ..._two_chunks => phylip_invalid_header_too_short} | 2 +- ...{phylip_two_chunks => phylip_invalid_no_header} | 1 - ...ylip_two_chunks => phylip_invalid_seq_too_long} | 2 +- ...lip_two_chunks => phylip_invalid_seq_too_short} | 2 +- ...ylip_two_chunks => phylip_invalid_too_few_seqs} | 1 - ...lip_two_chunks => phylip_invalid_too_many_seqs} | 2 +- .../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 + ...ip_two_chunks => phylip_whitespace_in_header_1} | 2 +- ...ip_two_chunks => phylip_whitespace_in_header_2} | 2 +- ...ip_two_chunks => phylip_whitespace_in_header_3} | 2 +- ...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, 29477 insertions(+), 14186 deletions(-) create mode 100644 asv.conf.json copy skbio/io/format/tests/data/empty => benchmarks/__init__.py (100%) create mode 100644 benchmarks/benchmarks.py create mode 100644 ci/conda_requirements.txt create mode 100644 ci/pip_requirements.txt delete mode 100644 doc/source/draw.rst delete mode 100644 skbio/alignment/_alignment.py delete mode 100644 skbio/alignment/_exception.py create mode 100644 skbio/alignment/_indexing.py create mode 100644 skbio/alignment/_repr.py create mode 100644 skbio/alignment/_tabular_msa.py delete mode 100644 skbio/alignment/tests/test_alignment.py create mode 100644 skbio/alignment/tests/test_tabular_msa.py create mode 100644 skbio/diversity/_driver.py copy skbio/{stats/__subsample.c => diversity/_phylogenetic.c} (55%) create mode 100644 skbio/diversity/_phylogenetic.pyx create mode 100644 skbio/diversity/_util.py create mode 100644 skbio/diversity/alpha/_faith_pd.py create mode 100644 skbio/diversity/alpha/tests/data/qiime-191-tt/README.md create mode 100644 skbio/diversity/alpha/tests/data/qiime-191-tt/faith-pd.txt create mode 100644 skbio/diversity/alpha/tests/data/qiime-191-tt/otu-table.tsv create mode 100644 skbio/diversity/alpha/tests/data/qiime-191-tt/tree.nwk create mode 100644 skbio/diversity/alpha/tests/test_faith_pd.py delete mode 100644 skbio/diversity/beta/_base.py create mode 100644 skbio/diversity/beta/_unifrac.py create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/README.md create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/otu-table.tsv create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/tree.nwk create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/unweighted_unifrac_dm.txt create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/weighted_normalized_unifrac_dm.txt create mode 100644 skbio/diversity/beta/tests/data/qiime-191-tt/weighted_unifrac_dm.txt delete mode 100644 skbio/diversity/beta/tests/test_base.py create mode 100644 skbio/diversity/beta/tests/test_unifrac.py rename skbio/{draw => diversity}/tests/__init__.py (100%) create mode 100644 skbio/diversity/tests/test_driver.py create mode 100644 skbio/diversity/tests/test_util.py delete mode 100644 skbio/draw/__init__.py delete mode 100644 skbio/draw/_distributions.py delete mode 100644 skbio/draw/tests/test_distributions.py create mode 100644 skbio/io/format/_blast.py create mode 100644 skbio/io/format/blast6.py create mode 100644 skbio/io/format/blast7.py create mode 100644 skbio/io/format/genbank.py create mode 100644 skbio/io/format/tests/data/blast6_custom_minimal create mode 100644 skbio/io/format/tests/data/blast6_custom_mixed_nans create mode 100644 skbio/io/format/tests/data/blast6_custom_multi_line create mode 100644 skbio/io/format/tests/data/blast6_custom_single_line create mode 100644 skbio/io/format/tests/data/blast6_default_multi_line create mode 100644 skbio/io/format/tests/data/blast6_default_single_line create mode 100644 skbio/io/format/tests/data/blast6_invalid_column_types create mode 100644 skbio/io/format/tests/data/blast6_invalid_number_of_columns create mode 100644 skbio/io/format/tests/data/blast6_invalid_type_in_column create mode 100644 skbio/io/format/tests/data/blast7_custom_minimal create mode 100644 skbio/io/format/tests/data/blast7_custom_mixed_nans create mode 100644 skbio/io/format/tests/data/blast7_custom_multi_line create mode 100644 skbio/io/format/tests/data/blast7_custom_single_line create mode 100644 skbio/io/format/tests/data/blast7_default_multi_line create mode 100644 skbio/io/format/tests/data/blast7_default_single_line create mode 100644 skbio/io/format/tests/data/blast7_invalid_differing_fields create mode 100644 skbio/io/format/tests/data/blast7_invalid_for_sniffer create mode 100644 skbio/io/format/tests/data/blast7_invalid_for_sniffer_2 create mode 100644 skbio/io/format/tests/data/blast7_invalid_gibberish create mode 100644 skbio/io/format/tests/data/blast7_invalid_no_data create mode 100644 skbio/io/format/tests/data/blast7_invalid_too_many_columns create mode 100644 skbio/io/format/tests/data/blast7_invalid_unrecognized_field rename skbio/io/format/tests/data/{fasta_sequence_collection_different_type => fasta_tabular_msa_different_type} (100%) create mode 100644 skbio/io/format/tests/data/genbank_5_blanks_start_of_file create mode 100644 skbio/io/format/tests/data/genbank_6_blanks_start_of_file create mode 100644 skbio/io/format/tests/data/genbank_missing_locus_name create mode 100644 skbio/io/format/tests/data/genbank_multi_records create mode 100644 skbio/io/format/tests/data/genbank_single_record create mode 100644 skbio/io/format/tests/data/genbank_single_record_lower create mode 100644 skbio/io/format/tests/data/genbank_single_record_upper create mode 100644 skbio/io/format/tests/data/genbank_w_beginning_whitespace create mode 100644 skbio/io/format/tests/data/legacy9_and_blast7_default create mode 100644 skbio/io/format/tests/data/legacy9_invalid_differing_fields create mode 100644 skbio/io/format/tests/data/legacy9_invalid_too_many_columns create mode 100644 skbio/io/format/tests/data/legacy9_mixed_nans create mode 100644 skbio/io/format/tests/data/legacy9_multi_line create mode 100644 skbio/io/format/tests/data/legacy9_single_line copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_empty_line_after_header} (98%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_empty_line_before_header} (98%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_empty_line_between_seqs} (98%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_header_too_long} (80%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_header_too_short} (92%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_no_header} (92%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_seq_too_long} (52%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_seq_too_short} (53%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_too_few_seqs} (53%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_invalid_too_many_seqs} (92%) create mode 100644 skbio/io/format/tests/data/phylip_invalid_zero_seq_len create mode 100644 skbio/io/format/tests/data/phylip_invalid_zero_seqs create mode 100644 skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_whitespace_in_header_1} (60%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_whitespace_in_header_2} (74%) copy skbio/io/format/tests/data/{phylip_two_chunks => phylip_whitespace_in_header_3} (62%) rename skbio/io/format/tests/data/{qual_sequence_collection_different_type => qual_tabular_msa_different_type} (100%) create mode 100644 skbio/io/format/tests/test_blast6.py create mode 100644 skbio/io/format/tests/test_blast7.py create mode 100644 skbio/io/format/tests/test_genbank.py delete mode 100644 skbio/sequence/_base.py create mode 100644 skbio/sequence/_repr.py delete mode 100644 skbio/sequence/tests/test_base.py create mode 100644 skbio/sequence/tests/test_rna.py delete mode 100644 skbio/stats/ordination/_base.py create mode 100644 skbio/stats/ordination/tests/data/example2_biplot_scaling1 create mode 100644 skbio/stats/ordination/tests/data/example2_biplot_scaling2 create mode 100644 skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 create mode 100644 skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 create mode 100644 skbio/stats/ordination/tests/data/example3_biplot_scaling1 create mode 100644 skbio/stats/ordination/tests/data/example3_biplot_scaling2 create mode 100644 skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 create mode 100644 skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 create mode 100644 skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py create mode 100644 skbio/stats/ordination/tests/test_correspondence_analysis.py delete mode 100644 skbio/stats/ordination/tests/test_ordination.py create mode 100644 skbio/stats/ordination/tests/test_principal_coordinate_analysis.py create mode 100644 skbio/stats/ordination/tests/test_redundancy_analysis.py create mode 100644 skbio/stats/ordination/tests/test_util.py delete mode 100644 skbio/stats/spatial.py delete mode 100644 skbio/stats/tests/test_spatial.py delete mode 100644 skbio/tree/_trie.py delete mode 100644 skbio/tree/tests/test_trie.py create mode 100644 skbio/util/_metadata_repr.py -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit