[med-svn] [python-skbio] 02/04: Merge tag 'upstream/0.5.0'
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Jun 28 04:26:22 UTC 2016
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 b7ad2d83d01eb01e05dd0bb227822ea3d31606eb
Merge: 43d11aa 2cca4ca
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Tue Jun 28 13:53:53 2016 +1000
Merge tag 'upstream/0.5.0'
Upstream version 0.5.0
.travis.yml | 1 -
CHANGELOG.md | 54 ++
CONTRIBUTING.md | 11 +-
README.rst | 37 +-
RELEASE.md | 16 +-
asv.conf.json | 5 +-
benchmarks/benchmarks.py | 3 +-
checklist.py | 37 +-
ci/conda_requirements.txt | 2 -
ci/pip_requirements.txt | 2 -
doc/README.md | 2 +-
doc/source/conf.py | 18 +-
doc/source/development/coding_guidelines.rst | 17 +-
doc/source/development/new_module.rst | 4 -
doc/source/development/py3.rst | 366 --------
doc/source/index.rst | 3 +-
licenses/python.txt | 270 ------
setup.py | 35 +-
skbio/__init__.py | 5 +-
skbio/_base.py | 803 +----------------
skbio/alignment/__init__.py | 2 -
skbio/alignment/_indexing.py | 10 +-
skbio/alignment/_lib/__init__.py | 2 -
skbio/alignment/_pairwise.py | 44 +-
skbio/alignment/_repr.py | 3 +-
skbio/alignment/_tabular_msa.py | 400 ++++++---
skbio/alignment/tests/__init__.py | 2 -
skbio/alignment/tests/test_pairwise.py | 173 ++--
skbio/alignment/tests/test_ssw.py | 11 +-
skbio/alignment/tests/test_tabular_msa.py | 997 +++++++++++++--------
skbio/diversity/__init__.py | 15 +-
skbio/diversity/_driver.py | 109 ++-
skbio/diversity/_util.py | 10 +-
skbio/diversity/alpha/__init__.py | 2 -
skbio/diversity/alpha/_ace.py | 2 -
skbio/diversity/alpha/_base.py | 2 -
skbio/diversity/alpha/_chao1.py | 2 -
skbio/diversity/alpha/_faith_pd.py | 8 +-
skbio/diversity/alpha/_gini.py | 2 -
skbio/diversity/alpha/_lladser.py | 2 -
skbio/diversity/alpha/tests/__init__.py | 2 -
skbio/diversity/alpha/tests/test_ace.py | 2 -
skbio/diversity/alpha/tests/test_base.py | 12 +-
skbio/diversity/alpha/tests/test_chao1.py | 2 -
skbio/diversity/alpha/tests/test_faith_pd.py | 48 +-
skbio/diversity/alpha/tests/test_gini.py | 2 -
skbio/diversity/alpha/tests/test_lladser.py | 2 -
skbio/diversity/beta/__init__.py | 2 -
skbio/diversity/beta/_unifrac.py | 24 +-
skbio/diversity/beta/tests/__init__.py | 2 -
skbio/diversity/beta/tests/test_unifrac.py | 50 +-
skbio/diversity/tests/__init__.py | 2 -
skbio/diversity/tests/test_driver.py | 249 +++--
skbio/diversity/tests/test_util.py | 61 +-
skbio/io/__init__.py | 2 -
skbio/io/_exception.py | 2 -
skbio/io/_fileobject.py | 94 +-
skbio/io/_iosources.py | 57 +-
skbio/io/_warning.py | 2 -
skbio/io/format/__init__.py | 2 -
skbio/io/format/_base.py | 4 -
skbio/io/format/_blast.py | 3 -
skbio/io/format/blast6.py | 19 +-
skbio/io/format/blast7.py | 27 +-
skbio/io/format/clustal.py | 3 -
skbio/io/format/emptyfile.py | 3 -
skbio/io/format/fasta.py | 15 +-
skbio/io/format/fastq.py | 16 +-
skbio/io/format/genbank.py | 8 +-
skbio/io/format/lsmat.py | 3 -
skbio/io/format/newick.py | 5 -
skbio/io/format/ordination.py | 6 +-
skbio/io/format/phylip.py | 5 +-
skbio/io/format/qseq.py | 5 -
skbio/io/format/stockholm.py | 134 ++-
skbio/io/format/tests/__init__.py | 2 -
.../format/tests/data/fastq_single_seq_illumina1.8 | 4 +
.../format/tests/data/stockholm_different_padding | 8 +
.../tests/data/stockholm_missing_reference_items | 5 +
.../io/format/tests/data/stockholm_missing_rn_tag | 3 +
.../tests/data/stockholm_multi_line_tree_no_id | 4 +
.../tests/data/stockholm_multi_line_tree_with_id | 5 +
.../tests/data/stockholm_multiple_multi_line_trees | 8 +
.../tests/data/stockholm_multiple_references | 20 +
...m_runon_gf => stockholm_runon_gf_no_whitespace} | 2 +-
...runon_gf => stockholm_runon_gf_with_whitespace} | 0
skbio/io/format/tests/data/stockholm_runon_gs | 5 -
.../tests/data/stockholm_runon_gs_no_whitespace | 5 +
.../tests/data/stockholm_runon_gs_with_whitespace | 5 +
.../format/tests/data/stockholm_runon_references | 10 +
.../tests/data/stockholm_runon_references_mixed | 10 +
.../format/tests/data/stockholm_single_reference | 8 +
skbio/io/format/tests/test_base.py | 24 +-
skbio/io/format/tests/test_blast6.py | 20 +-
skbio/io/format/tests/test_blast7.py | 44 +-
skbio/io/format/tests/test_clustal.py | 72 +-
skbio/io/format/tests/test_emptyfile.py | 8 +-
skbio/io/format/tests/test_fasta.py | 48 +-
skbio/io/format/tests/test_fastq.py | 27 +-
skbio/io/format/tests/test_genbank.py | 16 +-
skbio/io/format/tests/test_lsmat.py | 41 +-
skbio/io/format/tests/test_newick.py | 22 +-
skbio/io/format/tests/test_ordination.py | 9 +-
skbio/io/format/tests/test_phylip.py | 12 +-
skbio/io/format/tests/test_qseq.py | 4 -
skbio/io/format/tests/test_stockholm.py | 377 ++++++--
skbio/io/registry.py | 46 +-
skbio/io/tests/__init__.py | 2 -
skbio/io/tests/test_iosources.py | 2 -
skbio/io/tests/test_registry.py | 164 ++--
skbio/io/tests/test_util.py | 97 +-
skbio/io/util.py | 57 +-
skbio/{io/format => metadata}/__init__.py | 12 +-
skbio/metadata/_mixin.py | 408 +++++++++
.../{util/_metadata_repr.py => metadata/_repr.py} | 31 +-
skbio/{util => metadata}/_testing.py | 565 +++---------
.../alpha => metadata}/tests/__init__.py | 2 -
skbio/metadata/tests/test_mixin.py | 80 ++
skbio/sequence/__init__.py | 76 +-
skbio/sequence/_dna.py | 83 +-
skbio/sequence/_genetic_code.py | 67 +-
skbio/sequence/_grammared_sequence.py | 221 +++--
skbio/sequence/_nucleotide_mixin.py | 30 +-
skbio/sequence/_protein.py | 22 +-
skbio/sequence/_repr.py | 4 +-
skbio/sequence/_rna.py | 83 +-
skbio/sequence/_sequence.py | 235 +++--
skbio/sequence/distance.py | 87 +-
skbio/sequence/tests/__init__.py | 2 -
skbio/sequence/tests/test_distance.py | 126 ++-
skbio/sequence/tests/test_dna.py | 5 +-
skbio/sequence/tests/test_genetic_code.py | 72 +-
skbio/sequence/tests/test_grammared_sequence.py | 160 ++--
skbio/sequence/tests/test_nucleotide_sequences.py | 24 +-
skbio/sequence/tests/test_protein.py | 12 +-
skbio/sequence/tests/test_rna.py | 5 +-
skbio/sequence/tests/test_sequence.py | 406 ++++-----
skbio/stats/__init__.py | 2 -
skbio/stats/__subsample.c | 122 +--
skbio/stats/__subsample.pyx | 2 -
skbio/stats/_misc.py | 2 -
skbio/stats/_subsample.py | 30 +-
skbio/stats/composition.py | 175 +++-
skbio/stats/distance/__init__.py | 2 -
skbio/stats/distance/_anosim.py | 2 -
skbio/stats/distance/_base.py | 15 +-
skbio/stats/distance/_bioenv.py | 2 -
skbio/stats/distance/_mantel.py | 8 +-
skbio/stats/distance/_permanova.py | 3 -
skbio/stats/distance/tests/__init__.py | 2 -
skbio/stats/distance/tests/test_anosim.py | 8 +-
skbio/stats/distance/tests/test_base.py | 19 +-
skbio/stats/distance/tests/test_bioenv.py | 1 -
skbio/stats/distance/tests/test_mantel.py | 7 +-
skbio/stats/distance/tests/test_permanova.py | 8 +-
skbio/stats/evolve/__init__.py | 2 -
skbio/stats/evolve/_hommola.py | 3 -
skbio/stats/evolve/tests/__init__.py | 2 -
skbio/stats/evolve/tests/test_hommola.py | 1 -
skbio/stats/gradient.py | 10 +-
skbio/stats/ordination/__init__.py | 14 +-
.../_canonical_correspondence_analysis.py | 22 +-
skbio/stats/ordination/_correspondence_analysis.py | 14 +-
.../ordination/_ordination_results.py} | 450 +---------
.../ordination/_principal_coordinate_analysis.py | 23 +-
skbio/stats/ordination/_redundancy_analysis.py | 25 +-
skbio/stats/ordination/_utils.py | 2 -
skbio/stats/ordination/tests/__init__.py | 2 -
.../test_canonical_correspondence_analysis.py | 31 +-
.../tests/test_correspondence_analysis.py | 2 -
.../ordination/tests/test_ordination_results.py} | 160 +---
.../tests/test_principal_coordinate_analysis.py | 2 -
.../ordination/tests/test_redundancy_analysis.py | 43 +-
skbio/stats/ordination/tests/test_util.py | 3 -
skbio/stats/power.py | 11 +-
skbio/stats/tests/__init__.py | 2 -
skbio/stats/tests/test_composition.py | 387 ++++++--
skbio/stats/tests/test_gradient.py | 37 +-
skbio/stats/tests/test_misc.py | 1 -
skbio/stats/tests/test_power.py | 2 -
skbio/stats/tests/test_subsample.py | 55 +-
skbio/test.py | 2 -
skbio/tests/__init__.py | 2 -
skbio/tests/test_base.py | 348 +------
skbio/tests/test_workflow.py | 3 -
skbio/tree/__init__.py | 2 -
skbio/tree/_exception.py | 2 -
skbio/tree/_majority_rule.py | 34 +-
skbio/tree/_nj.py | 5 +-
skbio/tree/_tree.py | 51 +-
skbio/tree/tests/__init__.py | 2 -
skbio/tree/tests/test_majority_rule.py | 77 +-
skbio/tree/tests/test_nj.py | 13 +-
skbio/tree/tests/test_tree.py | 246 ++---
skbio/util/__init__.py | 2 -
skbio/util/_decorator.py | 3 +-
skbio/util/_exception.py | 2 -
skbio/util/_misc.py | 49 +-
skbio/util/_testing.py | 859 +-----------------
skbio/util/_warning.py | 2 -
skbio/util/tests/__init__.py | 2 -
skbio/util/tests/test_decorator.py | 59 +-
skbio/util/tests/test_misc.py | 22 +-
skbio/util/tests/test_testing.py | 2 -
skbio/workflow.py | 22 +-
205 files changed, 5219 insertions(+), 6686 deletions(-)
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