[med-svn] [python-skbio] branch master updated (43d11aa -> bfac25b)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Jun 28 04:26:12 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository python-skbio.
from 43d11aa another change in changelog
new 2cca4ca Imported Upstream version 0.5.0
new b7ad2d8 Merge tag 'upstream/0.5.0'
new eac9a92 Remove python2 package, no longer supported
new bfac25b Bump standards version => 3.9.8
The 4 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:
.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 -
debian/changelog | 9 +
debian/control | 45 +-
debian/python-skbio.lintian-overrides | 6 -
debian/rules | 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 +
..._without_id => stockholm_multi_line_tree_no_id} | 1 +
..._tree_ids => stockholm_multi_line_tree_with_id} | 1 -
...e_trees => stockholm_multiple_multi_line_trees} | 4 +-
.../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 +++---------
skbio/{alignment => 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 +-
209 files changed, 5223 insertions(+), 6733 deletions(-)
delete mode 100644 debian/python-skbio.lintian-overrides
delete mode 100644 doc/source/development/py3.rst
delete mode 100644 licenses/python.txt
create mode 100644 skbio/io/format/tests/data/fastq_single_seq_illumina1.8
create mode 100644 skbio/io/format/tests/data/stockholm_different_padding
create mode 100644 skbio/io/format/tests/data/stockholm_missing_reference_items
create mode 100644 skbio/io/format/tests/data/stockholm_missing_rn_tag
copy skbio/io/format/tests/data/{stockholm_single_tree_without_id => stockholm_multi_line_tree_no_id} (71%)
copy skbio/io/format/tests/data/{stockholm_duplicate_tree_ids => stockholm_multi_line_tree_with_id} (80%)
copy skbio/io/format/tests/data/{stockholm_multiple_trees => stockholm_multiple_multi_line_trees} (86%)
create mode 100644 skbio/io/format/tests/data/stockholm_multiple_references
copy skbio/io/format/tests/data/{stockholm_runon_gf => stockholm_runon_gf_no_whitespace} (98%)
rename skbio/io/format/tests/data/{stockholm_runon_gf => stockholm_runon_gf_with_whitespace} (100%)
delete mode 100644 skbio/io/format/tests/data/stockholm_runon_gs
create mode 100644 skbio/io/format/tests/data/stockholm_runon_gs_no_whitespace
create mode 100644 skbio/io/format/tests/data/stockholm_runon_gs_with_whitespace
create mode 100644 skbio/io/format/tests/data/stockholm_runon_references
create mode 100644 skbio/io/format/tests/data/stockholm_runon_references_mixed
create mode 100644 skbio/io/format/tests/data/stockholm_single_reference
copy skbio/{io/format => metadata}/__init__.py (70%)
create mode 100644 skbio/metadata/_mixin.py
rename skbio/{util/_metadata_repr.py => metadata/_repr.py} (87%)
copy skbio/{util => metadata}/_testing.py (64%)
copy skbio/{alignment => metadata}/tests/__init__.py (84%)
create mode 100644 skbio/metadata/tests/test_mixin.py
copy skbio/{_base.py => stats/ordination/_ordination_results.py} (55%)
copy skbio/{tests/test_base.py => stats/ordination/tests/test_ordination_results.py} (67%)
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