[med-svn] [python-skbio] branch master updated (e1c5a00 -> c30a63e)
Kevin Murray
daube-guest at moszumanska.debian.org
Mon Dec 21 06:01:19 UTC 2015
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 e1c5a00 Remove unused build-dep, add doc-base
new 9f57339 Imported Upstream version 0.4.1
new 97ff568 Merge tag 'upstream/0.4.1'
new be0c95f Refresh patches after new upstream imported
new b10589e Add new upstream to d/ch
new 8d04508 Refresh another patch I missed
new c30a63e Fix changelog to remove unreleased version 0.4.0-4
The 6 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 +
debian/changelog | 6 +-
debian/patches/0001-Use-stock-debian-sphinx.patch | 24 -
debian/patches/0002-Disable-intersphinx.patch | 44 -
...ce-use-of-Agg-backend-no-X-for-matplotlib.patch | 14 +-
.../0005-Set-mathjax-path-to-debian-s-copy.patch | 6 +-
debian/patches/series | 2 -
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 +-
228 files changed, 29489 insertions(+), 14270 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 debian/patches/0001-Use-stock-debian-sphinx.patch
delete mode 100644 debian/patches/0002-Disable-intersphinx.patch
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
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