[med-svn] [python-skbio] 13/13: Merge tag 'upstream/0.4.0'
Andreas Tille
tille at debian.org
Thu Jul 30 15:46:28 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-skbio.
commit c15a5800a63117ffeced0f801b81f71c8ee33d7d
Merge: c2740a6 c4a696f
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 30 17:42:47 2015 +0200
Merge tag 'upstream/0.4.0'
Upstream version 0.4.0
.coveragerc | 2 -
.travis.yml | 32 +-
CHANGELOG.md | 68 +
CONTRIBUTING.md | 157 +-
MANIFEST.in | 3 +-
skbio/format/__init__.py => Makefile | 15 +-
README.rst | 137 +-
RELEASE.md | 11 +-
assets/logo-inverted.svg | 76 +
checklist.py | 108 +-
doc/README.md | 58 +-
doc/source/_static/style.css | 1 +
doc/source/_templates/autosummary/class.rst | 4 +-
doc/source/conf.py | 58 +-
doc/source/development/coding_guidelines.rst | 11 +-
doc/source/development/new_module.rst | 6 +-
doc/source/development/py3.rst | 4 +-
doc/source/format.sequences.rst | 1 -
doc/source/index.rst | 16 +-
doc/source/parse.sequences.rst | 1 -
doc/source/user/api_stability.rst | 69 +
doc/source/user/assets/api-lifecycle.png | Bin 0 -> 40262 bytes
doc/sphinxext/numpydoc/LICENSE.txt | 94 -
doc/sphinxext/numpydoc/README.rst | 54 -
doc/sphinxext/numpydoc/numpydoc/__init__.py | 3 -
doc/sphinxext/numpydoc/numpydoc/comment_eater.py | 169 -
.../numpydoc/numpydoc/compiler_unparse.py | 865 ---
doc/sphinxext/numpydoc/numpydoc/docscrape.py | 525 --
.../numpydoc/numpydoc/docscrape_sphinx.py | 274 -
doc/sphinxext/numpydoc/numpydoc/linkcode.py | 83 -
doc/sphinxext/numpydoc/numpydoc/numpydoc.py | 187 -
doc/sphinxext/numpydoc/numpydoc/phantom_import.py | 167 -
doc/sphinxext/numpydoc/numpydoc/plot_directive.py | 642 ---
.../numpydoc/numpydoc/tests/test_docscrape.py | 767 ---
.../numpydoc/numpydoc/tests/test_linkcode.py | 5 -
.../numpydoc/numpydoc/tests/test_phantom_import.py | 12 -
.../numpydoc/numpydoc/tests/test_plot_directive.py | 11 -
.../numpydoc/numpydoc/tests/test_traitsdoc.py | 11 -
doc/sphinxext/numpydoc/numpydoc/traitsdoc.py | 142 -
.../README.md | 0
.../dm.txt | 0
.../map.txt | 0
.../scikit-bio presentation.ipynb | 0
.../smalldm.txt | 0
.../style.css | 0
.../talktools.py | 0
licenses/flask.txt | 33 +
licenses/numpydoc.txt | 1 -
licenses/python.txt | 270 +
setup.py | 53 +-
skbio/__init__.py | 43 +-
skbio/alignment/__init__.py | 75 +-
skbio/alignment/_alignment.py | 1411 ++---
skbio/alignment/_exception.py | 9 +-
skbio/alignment/_lib/__init__.py | 6 +-
skbio/alignment/_pairwise.py | 158 +-
skbio/alignment/_ssw_wrapper.c | 5948 +++++++++-----------
skbio/alignment/_ssw_wrapper.pyx | 97 +-
skbio/alignment/tests/__init__.py | 2 +
skbio/alignment/tests/test_alignment.py | 707 +--
skbio/alignment/tests/test_pairwise.py | 138 +-
skbio/alignment/tests/test_ssw.py | 25 +-
skbio/diversity/__init__.py | 6 +-
skbio/diversity/alpha/__init__.py | 6 +-
skbio/diversity/alpha/_ace.py | 7 +-
skbio/diversity/alpha/_base.py | 25 +
skbio/diversity/alpha/_chao1.py | 8 +-
skbio/diversity/alpha/_gini.py | 7 +-
skbio/diversity/alpha/_lladser.py | 11 +-
skbio/diversity/alpha/tests/__init__.py | 4 +-
skbio/diversity/alpha/tests/test_ace.py | 5 +-
skbio/diversity/alpha/tests/test_base.py | 5 +-
skbio/diversity/alpha/tests/test_chao1.py | 5 +-
skbio/diversity/alpha/tests/test_gini.py | 5 +-
skbio/diversity/beta/__init__.py | 13 +-
skbio/diversity/beta/_base.py | 17 +-
skbio/diversity/beta/tests/__init__.py | 2 +
skbio/diversity/beta/tests/test_base.py | 4 +-
skbio/draw/__init__.py | 6 +-
skbio/draw/_distributions.py | 16 +-
skbio/draw/tests/__init__.py | 4 +-
skbio/draw/tests/test_distributions.py | 45 +-
skbio/format/sequences/__init__.py | 39 -
skbio/format/sequences/fasta.py | 176 -
skbio/format/sequences/fastq.py | 78 -
skbio/format/sequences/tests/test_fasta.py | 74 -
skbio/format/sequences/tests/test_fastq.py | 39 -
skbio/io/__init__.py | 325 +-
skbio/io/_exception.py | 33 +-
skbio/io/_fileobject.py | 139 +
skbio/io/_iosources.py | 237 +
skbio/io/_registry.py | 818 ---
skbio/io/_warning.py | 4 +-
skbio/{parse => io/format}/__init__.py | 9 +-
skbio/io/{ => format}/_base.py | 88 +-
skbio/io/{ => format}/clustal.py | 113 +-
skbio/io/format/emptyfile.py | 43 +
skbio/io/{ => format}/fasta.py | 662 ++-
skbio/io/{ => format}/fastq.py | 300 +-
skbio/io/{ => format}/lsmat.py | 37 +-
skbio/io/{ => format}/newick.py | 25 +-
skbio/io/{ => format}/ordination.py | 21 +-
skbio/io/{ => format}/phylip.py | 42 +-
skbio/io/{ => format}/qseq.py | 105 +-
.../sequences => io/format}/tests/__init__.py | 4 +-
skbio/io/{ => format}/tests/data/empty | 0
.../{ => format}/tests/data/error_diff_ids.fastq | 0
.../tests/data/error_double_qual.fastq | 0
.../{ => format}/tests/data/error_double_seq.fastq | 0
.../{ => format}/tests/data/error_long_qual.fastq | 0
.../io/{ => format}/tests/data/error_no_qual.fastq | 0
.../{ => format}/tests/data/error_qual_del.fastq | 0
.../tests/data/error_qual_escape.fastq | 0
.../{ => format}/tests/data/error_qual_null.fastq | Bin
.../{ => format}/tests/data/error_qual_space.fastq | 0
.../{ => format}/tests/data/error_qual_tab.fastq | 0
.../tests/data/error_qual_unit_sep.fastq | 0
.../{ => format}/tests/data/error_qual_vtab.fastq | 0
.../{ => format}/tests/data/error_short_qual.fastq | 0
.../io/{ => format}/tests/data/error_spaces.fastq | 0
skbio/io/{ => format}/tests/data/error_tabs.fastq | 0
.../tests/data/error_trunc_at_plus.fastq | 0
.../tests/data/error_trunc_at_qual.fastq | 0
.../tests/data/error_trunc_at_seq.fastq | 0
.../tests/data/error_trunc_in_plus.fastq | 0
.../tests/data/error_trunc_in_qual.fastq | 0
.../tests/data/error_trunc_in_seq.fastq | 0
.../tests/data/error_trunc_in_title.fastq | 0
skbio/io/{ => format}/tests/data/fasta_10_seqs | 0
.../{ => format}/tests/data/fasta_3_seqs_defaults | 0
.../tests/data/fasta_3_seqs_non_defaults | 0
.../tests/data/fasta_5_blanks_start_of_file} | 7 +-
.../tests/data/fasta_5_ws_lines_start_of_file} | 7 +-
.../tests/data/fasta_6_blanks_start_of_file} | 8 +-
.../tests/data/fasta_6_ws_lines_start_of_file} | 8 +-
.../tests/data/fasta_blank_lines_between_records} | 14 +-
.../tests/data/fasta_blanks_end_of_file} | 9 +-
...fasta_description_newline_replacement_empty_str | 0
...asta_description_newline_replacement_multi_char | 0
.../fasta_description_newline_replacement_none | 0
.../data/fasta_id_whitespace_replacement_empty_str | 0
.../fasta_id_whitespace_replacement_multi_char | 0
.../data/fasta_id_whitespace_replacement_none | 0
.../tests/data/fasta_invalid_after_10_seqs | 0
.../data/fasta_invalid_blank_line_after_header} | 2 +-
.../data/fasta_invalid_blank_line_within_sequence} | 3 +-
.../tests/data/fasta_invalid_blank_sequence} | 1 +
.../tests/data/fasta_invalid_legacy_format | 0
.../tests/data/fasta_invalid_missing_header | 0
.../data/fasta_invalid_missing_seq_data_first | 0
.../tests/data/fasta_invalid_missing_seq_data_last | 0
.../data/fasta_invalid_missing_seq_data_middle | 0
.../fasta_invalid_whitespace_line_after_header} | 2 +-
...a_invalid_whitespace_only_line_within_sequence} | 1 +
.../data/fasta_invalid_whitespace_only_sequence} | 1 -
skbio/io/{ => format}/tests/data/fasta_max_width_1 | 0
skbio/io/{ => format}/tests/data/fasta_max_width_5 | 3 -
.../tests/data/fasta_mixed_qual_scores | 0
skbio/io/{ => format}/tests/data/fasta_multi_seq | 2 -
.../tests/data/fasta_multi_seq_roundtrip | 0
.../tests/data/fasta_prot_seqs_odd_labels | 0
.../data/fasta_sequence_collection_different_type | 6 +-
.../tests/data/fasta_single_bio_seq_defaults | 2 +-
.../tests/data/fasta_single_bio_seq_non_defaults | 4 +-
.../tests/data/fasta_single_dna_seq_defaults | 2 +-
.../tests/data/fasta_single_dna_seq_non_defaults | 4 +-
.../tests/data/fasta_single_prot_seq_defaults | 2 +-
.../tests/data/fasta_single_prot_seq_non_defaults | 2 +-
.../tests/data/fasta_single_rna_seq_defaults | 2 +-
.../tests/data/fasta_single_rna_seq_non_defaults | 4 +-
skbio/io/{ => format}/tests/data/fasta_single_seq | 0
.../tests/data/fasta_ws_lines_between_records} | 13 +-
.../tests/data/fasta_ws_lines_end_of_file} | 10 +-
.../tests/data/fastq_5_blanks_start_of_file} | 5 +
.../tests/data/fastq_5_ws_lines_start_of_file} | 5 +
.../tests/data/fastq_blank_lines} | 3 +
.../tests/data/fastq_invalid_blank_after_header} | 1 +
.../tests/data/fastq_invalid_blank_after_plus} | 1 +
.../tests/data/fastq_invalid_blank_after_seq} | 1 +
.../data/fastq_invalid_blank_in_seq_at_symbol} | 4 +-
.../tests/data/fastq_invalid_blank_within_qual} | 4 +-
.../tests/data/fastq_invalid_blank_within_seq} | 4 +-
.../tests/data/fastq_invalid_missing_header | 0
.../tests/data/fastq_invalid_missing_seq_data | 0
.../tests/data/fastq_invalid_ws_line_after_header} | 1 +
.../tests/data/fastq_invalid_ws_line_after_plus} | 1 +
.../tests/data/fastq_invalid_ws_line_after_seq} | 1 +
.../tests/data/fastq_invalid_ws_line_within_qual} | 4 +-
.../tests/data/fastq_invalid_ws_line_within_seq} | 4 +-
.../tests/data/fastq_multi_blank_between_records} | 8 +
.../tests/data/fastq_multi_blank_end_of_file} | 7 +
.../tests/data/fastq_multi_blank_start_of_file} | 6 +
.../{ => format}/tests/data/fastq_multi_seq_sanger | 0
.../tests/data/fastq_multi_whitespace_stripping | 14 +
.../data/fastq_multi_ws_lines_between_records} | 6 +
.../tests/data/fastq_multi_ws_lines_end_of_file | 20 +
.../tests/data/fastq_multi_ws_lines_start_of_file} | 6 +
.../tests/data/fastq_single_seq_illumina1.3 | 2 +-
.../tests/data/fastq_whitespace_only_lines} | 3 +
.../data/fastq_wrapping_as_illumina_no_description | 0
.../data/fastq_wrapping_as_sanger_no_description | 0
.../fastq_wrapping_original_sanger_no_description | 0
.../tests/data/fastq_writer_illumina1.3_defaults | 6 +-
.../tests/data/fastq_writer_sanger_defaults | 6 +-
.../tests/data/fastq_writer_sanger_non_defaults | 6 +-
.../data/illumina_full_range_as_illumina.fastq | 0
.../tests/data/illumina_full_range_as_sanger.fastq | 0
.../illumina_full_range_original_illumina.fastq | 0
.../tests/data/longreads_as_illumina.fastq | 0
.../tests/data/longreads_as_sanger.fastq | 0
.../tests/data/longreads_original_sanger.fastq | 0
.../tests/data/misc_dna_as_illumina.fastq | 0
.../tests/data/misc_dna_as_sanger.fastq | 0
.../tests/data/misc_dna_original_sanger.fastq | 0
.../tests/data/misc_rna_as_illumina.fastq | 0
.../tests/data/misc_rna_as_sanger.fastq | 0
.../tests/data/misc_rna_original_sanger.fastq | 0
.../tests/data/ordination_L&L_CA_data_scores | 0
.../data/ordination_PCoA_sample_data_3_scores | 0
skbio/io/{ => format}/tests/data/ordination_error1 | 0
.../io/{ => format}/tests/data/ordination_error10 | 0
.../io/{ => format}/tests/data/ordination_error11 | 0
.../io/{ => format}/tests/data/ordination_error12 | 0
.../io/{ => format}/tests/data/ordination_error13 | 0
.../io/{ => format}/tests/data/ordination_error14 | 0
.../io/{ => format}/tests/data/ordination_error15 | 0
.../io/{ => format}/tests/data/ordination_error16 | 0
.../io/{ => format}/tests/data/ordination_error17 | 0
.../io/{ => format}/tests/data/ordination_error18 | 0
.../io/{ => format}/tests/data/ordination_error19 | 0
skbio/io/{ => format}/tests/data/ordination_error2 | 0
.../io/{ => format}/tests/data/ordination_error20 | 0
.../io/{ => format}/tests/data/ordination_error21 | 0
.../io/{ => format}/tests/data/ordination_error22 | 0
.../io/{ => format}/tests/data/ordination_error23 | 0
.../io/{ => format}/tests/data/ordination_error24 | 0
skbio/io/{ => format}/tests/data/ordination_error3 | 0
skbio/io/{ => format}/tests/data/ordination_error4 | 0
skbio/io/{ => format}/tests/data/ordination_error5 | 0
skbio/io/{ => format}/tests/data/ordination_error6 | 0
skbio/io/{ => format}/tests/data/ordination_error7 | 0
skbio/io/{ => format}/tests/data/ordination_error8 | 0
skbio/io/{ => format}/tests/data/ordination_error9 | 0
.../tests/data/ordination_example2_scores | 0
.../tests/data/ordination_example3_scores | 0
.../tests/data/ordination_exp_Ordination_CCA_site | 0
.../ordination_exp_Ordination_CCA_site_constraints | 0
.../data/ordination_exp_Ordination_CCA_species | 0
.../tests/data/ordination_exp_Ordination_PCoA_site | 0
.../tests/data/ordination_exp_Ordination_RDA_site | 0
.../ordination_exp_Ordination_RDA_site_constraints | 0
.../data/ordination_exp_Ordination_RDA_species | 0
skbio/io/{ => format}/tests/data/phylip_dna_3_seqs | 0
.../{ => format}/tests/data/phylip_single_seq_long | 0
.../tests/data/phylip_single_seq_short | 0
skbio/io/{ => format}/tests/data/phylip_two_chunks | 0
.../tests/data/phylip_variable_length_ids | 0
.../io/{ => format}/tests/data/qseq_invalid_filter | 0
skbio/io/{ => format}/tests/data/qseq_invalid_lane | 0
skbio/io/{ => format}/tests/data/qseq_invalid_read | 0
skbio/io/{ => format}/tests/data/qseq_invalid_tile | 0
skbio/io/{ => format}/tests/data/qseq_invalid_x | 0
skbio/io/{ => format}/tests/data/qseq_invalid_y | 0
.../tests/data/qseq_multi_seq_illumina1.3 | 0
.../{ => format}/tests/data/qseq_single_seq_sanger | 0
.../{ => format}/tests/data/qual_2_seqs_defaults | 0
.../{ => format}/tests/data/qual_3_seqs_defaults | 0
.../tests/data/qual_3_seqs_defaults_desc_mismatch | 0
.../tests/data/qual_3_seqs_defaults_extra | 0
.../tests/data/qual_3_seqs_defaults_id_mismatch | 0
.../data/qual_3_seqs_defaults_length_mismatch | 0
.../tests/data/qual_3_seqs_non_defaults | 0
.../tests/data/qual_5_blanks_start_of_file} | 13 +-
.../tests/data/qual_5_ws_lines_start_of_file | 17 +
.../tests/data/qual_6_blanks_start_of_file} | 14 +-
.../tests/data/qual_6_ws_lines_start_of_file | 18 +
.../tests/data/qual_blank_lines_between_records} | 18 +-
.../tests/data/qual_blanks_end_of_file} | 15 +-
.../qual_description_newline_replacement_empty_str | 2 +-
...qual_description_newline_replacement_multi_char | 2 +-
.../data/qual_description_newline_replacement_none | 2 +-
.../data/qual_id_whitespace_replacement_empty_str | 0
.../data/qual_id_whitespace_replacement_multi_char | 0
.../tests/data/qual_id_whitespace_replacement_none | 0
.../data/qual_invalid_blank_line_after_header} | 2 +-
.../tests/data/qual_invalid_blank_line_within_seq} | 3 +-
.../tests/data/qual_invalid_blank_sequence} | 1 +
.../tests/data/qual_invalid_legacy_format | 0
.../tests/data/qual_invalid_missing_header | 0
.../data/qual_invalid_missing_qual_scores_first | 0
.../data/qual_invalid_missing_qual_scores_last | 0
.../data/qual_invalid_missing_qual_scores_middle | 0
.../tests/data/qual_invalid_qual_scores_float | 0
.../tests/data/qual_invalid_qual_scores_negative | 0
.../tests/data/qual_invalid_qual_scores_over_255} | 2 +-
.../tests/data/qual_invalid_qual_scores_string | 0
.../data/qual_invalid_whitespace_line_in_seq} | 3 +-
.../data/qual_invalid_whitespace_only_sequence} | 1 +
.../tests/data/qual_invalid_ws_line_after_header} | 2 +-
skbio/io/{ => format}/tests/data/qual_max_width_1 | 4 +-
skbio/io/{ => format}/tests/data/qual_max_width_5 | 21 +-
skbio/io/{ => format}/tests/data/qual_multi_seq | 8 +-
.../tests/data/qual_multi_seq_roundtrip | 0
.../tests/data/qual_prot_seqs_odd_labels | 2 +-
.../data/qual_sequence_collection_different_type | 2 +-
.../tests/data/qual_single_bio_seq_non_defaults | 0
.../tests/data/qual_single_dna_seq_non_defaults | 0
.../tests/data/qual_single_nuc_seq_non_defaults | 0
.../tests/data/qual_single_prot_seq_non_defaults | 0
.../tests/data/qual_single_rna_seq_non_defaults | 0
skbio/io/format/tests/data/qual_single_seq | 2 +
.../tests/data/qual_ws_lines_between_records | 22 +
.../io/format/tests/data/qual_ws_lines_end_of_file | 20 +
.../tests/data/sanger_full_range_as_illumina.fastq | 0
.../tests/data/sanger_full_range_as_sanger.fastq | 0
.../data/sanger_full_range_original_sanger.fastq | 0
.../data/solexa_full_range_original_solexa.fastq | 0
skbio/io/{ => format}/tests/data/tsv_10_fields | 0
skbio/io/{ => format}/tests/data/tsv_8_fields | 0
skbio/io/{ => format}/tests/data/whitespace_only | 0
.../tests/data/wrapping_as_illumina.fastq | 0
.../tests/data/wrapping_as_sanger.fastq | 0
.../tests/data/wrapping_original_sanger.fastq | 0
skbio/io/{ => format}/tests/test_base.py | 92 +-
skbio/io/{ => format}/tests/test_clustal.py | 120 +-
skbio/io/format/tests/test_emptyfile.py | 38 +
skbio/io/{ => format}/tests/test_fasta.py | 671 ++-
skbio/io/{ => format}/tests/test_fastq.py | 365 +-
skbio/io/{ => format}/tests/test_lsmat.py | 9 +-
skbio/io/{ => format}/tests/test_newick.py | 8 +-
skbio/io/{ => format}/tests/test_ordination.py | 15 +-
skbio/io/{ => format}/tests/test_phylip.py | 48 +-
skbio/io/{ => format}/tests/test_qseq.py | 210 +-
skbio/io/registry.py | 1145 ++++
skbio/io/tests/__init__.py | 2 +
skbio/io/tests/data/big5_file | 1 +
skbio/io/tests/data/big5_file.bz2 | Bin 0 -> 46 bytes
skbio/io/tests/data/big5_file.gz | Bin 0 -> 35 bytes
skbio/io/tests/data/example_file | 2 +
skbio/io/tests/data/example_file.bz2 | Bin 0 -> 84 bytes
skbio/io/tests/data/example_file.gz | Bin 0 -> 83 bytes
skbio/io/tests/data/fasta_single_nuc_seq_defaults | 2 -
.../tests/data/fasta_single_nuc_seq_non_defaults | 6 -
skbio/io/tests/data/qual_single_seq | 2 -
skbio/io/tests/test_iosources.py | 53 +
skbio/io/tests/test_registry.py | 1554 +++--
skbio/io/tests/test_util.py | 643 ++-
skbio/io/util.py | 276 +-
skbio/parse/record.py | 491 --
skbio/parse/record_finder.py | 193 -
skbio/parse/sequences/__init__.py | 201 -
skbio/parse/sequences/clustal.py | 100 -
skbio/parse/sequences/factory.py | 147 -
skbio/parse/sequences/fasta.py | 240 -
skbio/parse/sequences/fastq.py | 176 -
skbio/parse/sequences/iterator.py | 206 -
skbio/parse/sequences/tests/__init__.py | 9 -
skbio/parse/sequences/tests/data/fna1.fasta | 4 -
skbio/parse/sequences/tests/data/fna1.fna.gz | Bin 49 -> 0 bytes
skbio/parse/sequences/tests/data/fna1.qual | 4 -
skbio/parse/sequences/tests/data/fq1.fastq.gz | Bin 60 -> 0 bytes
skbio/parse/sequences/tests/data/fq1.fq | 8 -
skbio/parse/sequences/tests/data/noextensionfasta | 4 -
skbio/parse/sequences/tests/data/qs1.qseq.gz | Bin 91 -> 0 bytes
skbio/parse/sequences/tests/test_clustal.py | 155 -
skbio/parse/sequences/tests/test_factory.py | 201 -
skbio/parse/sequences/tests/test_fasta.py | 196 -
skbio/parse/sequences/tests/test_fastq.py | 223 -
skbio/parse/sequences/tests/test_iterator.py | 336 --
skbio/parse/tests/__init__.py | 9 -
skbio/parse/tests/test_record.py | 550 --
skbio/parse/tests/test_record_finder.py | 257 -
skbio/sequence/__init__.py | 369 +-
skbio/sequence/_base.py | 43 +
skbio/sequence/_dna.py | 410 ++
skbio/sequence/_exception.py | 29 -
skbio/sequence/_genetic_code.py | 1184 ++--
skbio/sequence/_iupac_sequence.py | 601 ++
skbio/sequence/_nucleotide_mixin.py | 363 ++
skbio/sequence/_protein.py | 215 +
skbio/sequence/_rna.py | 351 ++
skbio/sequence/_sequence.py | 3311 ++++++-----
skbio/sequence/tests/__init__.py | 4 +-
skbio/sequence/tests/test_base.py | 48 +
skbio/sequence/tests/test_dna.py | 45 +
skbio/sequence/tests/test_genetic_code.py | 834 +--
skbio/sequence/tests/test_iupac_sequence.py | 509 ++
skbio/sequence/tests/test_nucleotide_sequences.py | 474 ++
skbio/sequence/tests/test_protein.py | 124 +
skbio/sequence/tests/test_sequence.py | 3726 +++++++-----
skbio/stats/__init__.py | 16 +-
skbio/stats/__subsample.c | 1929 +++----
skbio/stats/_misc.py | 50 -
skbio/stats/_subsample.py | 62 +-
skbio/stats/composition.py | 389 ++
skbio/stats/distance/__init__.py | 24 +-
skbio/stats/distance/_anosim.py | 75 +-
skbio/stats/distance/_base.py | 379 +-
skbio/stats/distance/_bioenv.py | 14 +-
skbio/stats/distance/_mantel.py | 16 +-
skbio/stats/distance/_permanova.py | 89 +-
skbio/stats/distance/tests/__init__.py | 4 +-
skbio/stats/distance/tests/test_anosim.py | 99 +-
skbio/stats/distance/tests/test_base.py | 119 +-
skbio/stats/distance/tests/test_bioenv.py | 25 +-
skbio/stats/distance/tests/test_mantel.py | 37 +-
skbio/stats/distance/tests/test_permanova.py | 101 +-
skbio/stats/evolve/__init__.py | 41 +
skbio/stats/evolve/_hommola.py | 268 +
skbio/{draw => stats/evolve}/tests/__init__.py | 4 +-
skbio/stats/evolve/tests/test_hommola.py | 188 +
skbio/stats/gradient.py | 19 +-
skbio/stats/ordination/__init__.py | 9 +-
skbio/stats/ordination/_base.py | 82 +-
.../_canonical_correspondence_analysis.py | 3 +
skbio/stats/ordination/_correspondence_analysis.py | 3 +
.../ordination/_principal_coordinate_analysis.py | 3 +
skbio/stats/ordination/_redundancy_analysis.py | 3 +
skbio/stats/ordination/_utils.py | 7 +
skbio/stats/ordination/tests/__init__.py | 2 +
skbio/stats/ordination/tests/test_ordination.py | 35 +-
skbio/stats/power.py | 792 ++-
skbio/stats/spatial.py | 8 +-
skbio/stats/tests/__init__.py | 4 +-
skbio/stats/tests/test_composition.py | 222 +
skbio/stats/tests/test_gradient.py | 63 +-
skbio/stats/tests/test_misc.py | 41 -
skbio/stats/tests/test_power.py | 305 +-
skbio/stats/tests/test_spatial.py | 5 +-
skbio/stats/tests/test_subsample.py | 20 +-
skbio/{parse/sequences/_exception.py => test.py} | 17 +-
skbio/tests/__init__.py | 4 +-
skbio/tests/test_workflow.py | 4 +-
skbio/tree/__init__.py | 54 +-
skbio/tree/_exception.py | 4 +-
skbio/tree/_majority_rule.py | 33 +-
skbio/tree/_nj.py | 8 +-
skbio/tree/_tree.py | 717 +--
skbio/tree/_trie.py | 48 +-
skbio/tree/tests/__init__.py | 2 +
skbio/tree/tests/test_majority_rule.py | 6 +-
skbio/tree/tests/test_nj.py | 6 +-
skbio/tree/tests/test_tree.py | 445 +-
skbio/util/__init__.py | 17 +-
skbio/util/_decorator.py | 338 ++
skbio/util/_exception.py | 9 +-
skbio/util/_misc.py | 96 +-
skbio/util/_testing.py | 112 +
skbio/util/_warning.py | 4 +-
skbio/util/tests/__init__.py | 4 +-
skbio/util/tests/test_decorator.py | 275 +
skbio/util/tests/test_misc.py | 150 +-
skbio/util/tests/test_testing.py | 84 +-
skbio/workflow.py | 41 +-
454 files changed, 23828 insertions(+), 23698 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-skbio.git
More information about the debian-med-commit
mailing list