[med-svn] [python-skbio] 07/13: Merge tag 'upstream/0.2.3'
Andreas Tille
tille at debian.org
Thu Jul 30 15:46:26 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 c4ed5aeb56fc3f742d7d5ccbb3fa8c593126a795
Merge: a11edb7 639dea5
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 30 17:36:39 2015 +0200
Merge tag 'upstream/0.2.3'
Upstream version 0.2.3
.coveragerc | 20 +
.gitignore | 46 +
.travis.yml | 38 +
CHANGELOG.md | 297 +
CONTRIBUTING.md | 139 +
COPYING.txt | 27 +
MANIFEST.in | 17 +
README.rst | 164 +
RELEASE.md | 124 +
assets/.no.gif | Bin 0 -> 2052678 bytes
assets/horizontal_powered_by.png | Bin 0 -> 15003 bytes
assets/horizontal_powered_by.svg | 152 +
assets/logo.png | Bin 0 -> 12397 bytes
assets/logo.svg | 76 +
assets/logo_and_powered.pdf | Bin 0 -> 63684 bytes
assets/vertical_powered_by.png | Bin 0 -> 15865 bytes
assets/vertical_powered_by.svg | 152 +
checklist.py | 387 +
debian/changelog | 12 -
debian/compat | 1 -
debian/control | 50 -
debian/copyright | 39 -
debian/rules | 20 -
debian/source/format | 1 -
debian/watch | 2 -
doc/Makefile | 183 +
doc/README.md | 244 +
doc/source/_static/copybutton.js | 60 +
doc/source/_static/style.css | 77 +
doc/source/_templates/autosummary/attribute.rst | 9 +
doc/source/_templates/autosummary/class.rst | 27 +
doc/source/_templates/autosummary/method.rst | 9 +
doc/source/_templates/autosummary/module.rst | 2 +
doc/source/_templates/layout.html | 35 +
doc/source/alignment.rst | 1 +
doc/source/conf.py | 442 +
doc/source/development/coding_guidelines.rst | 379 +
doc/source/development/new_module.rst | 49 +
doc/source/development/py3.rst | 366 +
doc/source/diversity.rst | 1 +
doc/source/draw.rst | 1 +
doc/source/format.sequences.rst | 1 +
doc/source/index.rst | 37 +
doc/source/io.rst | 1 +
doc/source/parse.sequences.rst | 1 +
doc/source/sequence.rst | 1 +
doc/source/stats.rst | 1 +
doc/source/tree.rst | 1 +
doc/source/util.rst | 1 +
doc/source/workflow.rst | 1 +
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 +
.../2014.05.13-ElBrogrammer/README.md | 9 +
.../presentations/2014.05.13-ElBrogrammer/dm.txt | 440 +
.../presentations/2014.05.13-ElBrogrammer/map.txt | 466 +
.../scikit-bio presentation.ipynb | 1274 ++
.../2014.05.13-ElBrogrammer/smalldm.txt | 3 +
.../2014.05.13-ElBrogrammer/style.css | 126 +
.../2014.05.13-ElBrogrammer/talktools.py | 41 +
.../caporaso-scipy2014.ipynb | 1470 ++
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.../2014.07.09-gregcaporaso/style.css | 150 +
.../2014.07.09-gregcaporaso/talktools.py | 39 +
licenses/fastq-example-files-readme.txt | 109 +
licenses/ipython.txt | 74 +
licenses/nb-slideshow-template.txt | 30 +
licenses/numpydoc.txt | 1 +
licenses/qiita.txt | 27 +
licenses/scikit-learn.txt | 35 +
licenses/scipy.txt | 31 +
licenses/sphinx-bootstrap-theme.txt | 19 +
licenses/ssw.txt | 46 +
licenses/verman.txt | 27 +
setup.py | 102 +
skbio/__init__.py | 92 +
skbio/_base.py | 25 +
skbio/alignment/__init__.py | 250 +
skbio/alignment/_alignment.py | 2095 +++
skbio/alignment/_exception.py | 26 +
skbio/alignment/_lib/__init__.py | 10 +
skbio/alignment/_lib/ssw.c | 861 ++
skbio/alignment/_lib/ssw.h | 130 +
skbio/alignment/_pairwise.py | 903 ++
skbio/alignment/_ssw_wrapper.c | 14406 +++++++++++++++++++
skbio/alignment/_ssw_wrapper.pyx | 804 ++
skbio/alignment/tests/__init__.py | 7 +
skbio/alignment/tests/test_alignment.py | 1128 ++
skbio/alignment/tests/test_pairwise.py | 585 +
skbio/alignment/tests/test_ssw.py | 739 +
skbio/diversity/__init__.py | 30 +
skbio/diversity/alpha/__init__.py | 161 +
skbio/diversity/alpha/_ace.py | 116 +
skbio/diversity/alpha/_base.py | 913 ++
skbio/diversity/alpha/_chao1.py | 218 +
skbio/diversity/alpha/_gini.py | 124 +
skbio/diversity/alpha/_lladser.py | 605 +
skbio/diversity/alpha/tests/__init__.py | 9 +
skbio/diversity/alpha/tests/test_ace.py | 41 +
skbio/diversity/alpha/tests/test_base.py | 297 +
skbio/diversity/alpha/tests/test_chao1.py | 81 +
skbio/diversity/alpha/tests/test_gini.py | 64 +
skbio/diversity/alpha/tests/test_lladser.py | 242 +
skbio/diversity/beta/__init__.py | 194 +
skbio/diversity/beta/_base.py | 102 +
skbio/diversity/beta/tests/__init__.py | 7 +
skbio/diversity/beta/tests/test_base.py | 165 +
skbio/draw/__init__.py | 37 +
skbio/draw/_distributions.py | 701 +
skbio/draw/tests/__init__.py | 9 +
skbio/draw/tests/test_distributions.py | 576 +
skbio/format/__init__.py | 12 +
skbio/format/sequences/__init__.py | 39 +
skbio/format/sequences/fasta.py | 176 +
skbio/format/sequences/fastq.py | 78 +
skbio/format/sequences/tests/__init__.py | 9 +
skbio/format/sequences/tests/test_fasta.py | 74 +
skbio/format/sequences/tests/test_fastq.py | 39 +
skbio/io/__init__.py | 322 +
skbio/io/_base.py | 187 +
skbio/io/_exception.py | 95 +
skbio/io/_registry.py | 818 ++
skbio/io/_warning.py | 19 +
skbio/io/clustal.py | 328 +
skbio/io/fasta.py | 833 ++
skbio/io/fastq.py | 514 +
skbio/io/lsmat.py | 231 +
skbio/io/newick.py | 485 +
skbio/io/ordination.py | 416 +
skbio/io/phylip.py | 245 +
skbio/io/qseq.py | 253 +
skbio/io/tests/__init__.py | 7 +
skbio/io/tests/data/empty | 0
skbio/io/tests/data/error_diff_ids.fastq | 20 +
skbio/io/tests/data/error_double_qual.fastq | 22 +
skbio/io/tests/data/error_double_seq.fastq | 22 +
skbio/io/tests/data/error_long_qual.fastq | 20 +
skbio/io/tests/data/error_no_qual.fastq | 20 +
skbio/io/tests/data/error_qual_del.fastq | 20 +
skbio/io/tests/data/error_qual_escape.fastq | 20 +
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skbio/io/tests/data/error_qual_space.fastq | 21 +
skbio/io/tests/data/error_qual_tab.fastq | 21 +
skbio/io/tests/data/error_qual_unit_sep.fastq | 20 +
skbio/io/tests/data/error_qual_vtab.fastq | 20 +
skbio/io/tests/data/error_short_qual.fastq | 20 +
skbio/io/tests/data/error_spaces.fastq | 20 +
skbio/io/tests/data/error_tabs.fastq | 21 +
skbio/io/tests/data/error_trunc_at_plus.fastq | 19 +
skbio/io/tests/data/error_trunc_at_qual.fastq | 19 +
skbio/io/tests/data/error_trunc_at_seq.fastq | 18 +
skbio/io/tests/data/error_trunc_in_plus.fastq | 19 +
skbio/io/tests/data/error_trunc_in_qual.fastq | 20 +
skbio/io/tests/data/error_trunc_in_seq.fastq | 18 +
skbio/io/tests/data/error_trunc_in_title.fastq | 17 +
skbio/io/tests/data/fasta_10_seqs | 24 +
skbio/io/tests/data/fasta_3_seqs_defaults | 6 +
skbio/io/tests/data/fasta_3_seqs_non_defaults | 9 +
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skbio/io/tests/data/fasta_invalid_after_10_seqs | 25 +
skbio/io/tests/data/fasta_invalid_blank_line | 7 +
skbio/io/tests/data/fasta_invalid_legacy_format | 2 +
skbio/io/tests/data/fasta_invalid_missing_header | 2 +
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.../tests/data/fasta_invalid_whitespace_only_line | 7 +
skbio/io/tests/data/fasta_max_width_1 | 11 +
skbio/io/tests/data/fasta_max_width_5 | 20 +
skbio/io/tests/data/fasta_mixed_qual_scores | 4 +
skbio/io/tests/data/fasta_multi_seq | 14 +
skbio/io/tests/data/fasta_multi_seq_roundtrip | 6 +
skbio/io/tests/data/fasta_prot_seqs_odd_labels | 8 +
.../data/fasta_sequence_collection_different_type | 6 +
skbio/io/tests/data/fasta_single_bio_seq_defaults | 2 +
.../tests/data/fasta_single_bio_seq_non_defaults | 5 +
skbio/io/tests/data/fasta_single_dna_seq_defaults | 2 +
.../tests/data/fasta_single_dna_seq_non_defaults | 5 +
skbio/io/tests/data/fasta_single_nuc_seq_defaults | 2 +
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skbio/io/tests/data/fasta_single_prot_seq_defaults | 2 +
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skbio/io/tests/data/fasta_single_rna_seq_defaults | 2 +
.../tests/data/fasta_single_rna_seq_non_defaults | 5 +
skbio/io/tests/data/fasta_single_seq | 2 +
skbio/io/tests/data/fastq_invalid_missing_header | 4 +
skbio/io/tests/data/fastq_invalid_missing_seq_data | 13 +
skbio/io/tests/data/fastq_multi_seq_sanger | 12 +
skbio/io/tests/data/fastq_single_seq_illumina1.3 | 10 +
.../data/fastq_wrapping_as_illumina_no_description | 12 +
.../data/fastq_wrapping_as_sanger_no_description | 12 +
.../fastq_wrapping_original_sanger_no_description | 24 +
.../tests/data/fastq_writer_illumina1.3_defaults | 12 +
skbio/io/tests/data/fastq_writer_sanger_defaults | 12 +
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skbio/io/tests/data/longreads_as_illumina.fastq | 40 +
skbio/io/tests/data/longreads_as_sanger.fastq | 40 +
.../io/tests/data/longreads_original_sanger.fastq | 120 +
skbio/io/tests/data/misc_dna_as_illumina.fastq | 16 +
skbio/io/tests/data/misc_dna_as_sanger.fastq | 16 +
skbio/io/tests/data/misc_dna_original_sanger.fastq | 16 +
skbio/io/tests/data/misc_rna_as_illumina.fastq | 16 +
skbio/io/tests/data/misc_rna_as_sanger.fastq | 16 +
skbio/io/tests/data/misc_rna_original_sanger.fastq | 16 +
skbio/io/tests/data/ordination_L&L_CA_data_scores | 18 +
.../data/ordination_PCoA_sample_data_3_scores | 22 +
skbio/io/tests/data/ordination_error1 | 43 +
skbio/io/tests/data/ordination_error10 | 18 +
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skbio/io/tests/data/ordination_error12 | 22 +
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.../tests/data/ordination_exp_Ordination_CCA_site | 10 +
.../ordination_exp_Ordination_CCA_site_constraints | 10 +
.../data/ordination_exp_Ordination_CCA_species | 9 +
.../tests/data/ordination_exp_Ordination_PCoA_site | 9 +
.../tests/data/ordination_exp_Ordination_RDA_site | 10 +
.../ordination_exp_Ordination_RDA_site_constraints | 10 +
.../data/ordination_exp_Ordination_RDA_species | 6 +
skbio/io/tests/data/phylip_dna_3_seqs | 4 +
skbio/io/tests/data/phylip_single_seq_long | 2 +
skbio/io/tests/data/phylip_single_seq_short | 2 +
skbio/io/tests/data/phylip_two_chunks | 3 +
skbio/io/tests/data/phylip_variable_length_ids | 7 +
skbio/io/tests/data/qseq_invalid_filter | 1 +
skbio/io/tests/data/qseq_invalid_lane | 1 +
skbio/io/tests/data/qseq_invalid_read | 1 +
skbio/io/tests/data/qseq_invalid_tile | 1 +
skbio/io/tests/data/qseq_invalid_x | 1 +
skbio/io/tests/data/qseq_invalid_y | 1 +
skbio/io/tests/data/qseq_multi_seq_illumina1.3 | 4 +
skbio/io/tests/data/qseq_single_seq_sanger | 1 +
skbio/io/tests/data/qual_2_seqs_defaults | 4 +
skbio/io/tests/data/qual_3_seqs_defaults | 8 +
.../tests/data/qual_3_seqs_defaults_desc_mismatch | 8 +
skbio/io/tests/data/qual_3_seqs_defaults_extra | 10 +
.../io/tests/data/qual_3_seqs_defaults_id_mismatch | 8 +
.../data/qual_3_seqs_defaults_length_mismatch | 8 +
skbio/io/tests/data/qual_3_seqs_non_defaults | 14 +
.../qual_description_newline_replacement_empty_str | 4 +
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.../data/qual_description_newline_replacement_none | 15 +
.../data/qual_id_whitespace_replacement_empty_str | 4 +
.../data/qual_id_whitespace_replacement_multi_char | 4 +
.../tests/data/qual_id_whitespace_replacement_none | 7 +
skbio/io/tests/data/qual_invalid_blank_line | 9 +
skbio/io/tests/data/qual_invalid_legacy_format | 2 +
skbio/io/tests/data/qual_invalid_missing_header | 2 +
.../data/qual_invalid_missing_qual_scores_first | 7 +
.../data/qual_invalid_missing_qual_scores_last | 5 +
.../data/qual_invalid_missing_qual_scores_middle | 7 +
skbio/io/tests/data/qual_invalid_qual_scores_float | 8 +
.../tests/data/qual_invalid_qual_scores_negative | 8 +
.../io/tests/data/qual_invalid_qual_scores_string | 8 +
.../tests/data/qual_invalid_whitespace_only_line | 9 +
skbio/io/tests/data/qual_max_width_1 | 11 +
skbio/io/tests/data/qual_max_width_5 | 34 +
skbio/io/tests/data/qual_multi_seq | 14 +
skbio/io/tests/data/qual_multi_seq_roundtrip | 6 +
skbio/io/tests/data/qual_prot_seqs_odd_labels | 8 +
.../data/qual_sequence_collection_different_type | 6 +
.../io/tests/data/qual_single_bio_seq_non_defaults | 5 +
.../io/tests/data/qual_single_dna_seq_non_defaults | 5 +
.../io/tests/data/qual_single_nuc_seq_non_defaults | 6 +
.../tests/data/qual_single_prot_seq_non_defaults | 4 +
.../io/tests/data/qual_single_rna_seq_non_defaults | 5 +
skbio/io/tests/data/qual_single_seq | 2 +
skbio/io/tests/data/real_file | 5 +
skbio/io/tests/data/real_file_2 | 6 +
.../tests/data/sanger_full_range_as_illumina.fastq | 8 +
.../tests/data/sanger_full_range_as_sanger.fastq | 8 +
.../data/sanger_full_range_original_sanger.fastq | 8 +
.../data/solexa_full_range_original_solexa.fastq | 8 +
skbio/io/tests/data/tsv_10_fields | 6 +
skbio/io/tests/data/tsv_8_fields | 6 +
skbio/io/tests/data/whitespace_only | 17 +
skbio/io/tests/data/wrapping_as_illumina.fastq | 12 +
skbio/io/tests/data/wrapping_as_sanger.fastq | 12 +
skbio/io/tests/data/wrapping_original_sanger.fastq | 24 +
skbio/io/tests/test_base.py | 359 +
skbio/io/tests/test_clustal.py | 265 +
skbio/io/tests/test_fasta.py | 893 ++
skbio/io/tests/test_fastq.py | 551 +
skbio/io/tests/test_lsmat.py | 251 +
skbio/io/tests/test_newick.py | 371 +
skbio/io/tests/test_ordination.py | 228 +
skbio/io/tests/test_phylip.py | 102 +
skbio/io/tests/test_qseq.py | 294 +
skbio/io/tests/test_registry.py | 1228 ++
skbio/io/tests/test_util.py | 123 +
skbio/io/util.py | 99 +
skbio/parse/__init__.py | 12 +
skbio/parse/record.py | 491 +
skbio/parse/record_finder.py | 193 +
skbio/parse/sequences/__init__.py | 201 +
skbio/parse/sequences/_exception.py | 16 +
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 +
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skbio/parse/sequences/tests/data/fq1.fq | 8 +
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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 | 163 +
skbio/sequence/_exception.py | 29 +
skbio/sequence/_genetic_code.py | 620 +
skbio/sequence/_sequence.py | 1969 +++
skbio/sequence/tests/__init__.py | 9 +
skbio/sequence/tests/test_genetic_code.py | 377 +
skbio/sequence/tests/test_sequence.py | 1418 ++
skbio/stats/__init__.py | 49 +
skbio/stats/__subsample.c | 6415 +++++++++
skbio/stats/__subsample.pyx | 36 +
skbio/stats/_misc.py | 74 +
skbio/stats/_subsample.py | 325 +
skbio/stats/distance/__init__.py | 206 +
skbio/stats/distance/_anosim.py | 275 +
skbio/stats/distance/_base.py | 1232 ++
skbio/stats/distance/_bioenv.py | 243 +
skbio/stats/distance/_mantel.py | 490 +
skbio/stats/distance/_permanova.py | 221 +
skbio/stats/distance/tests/__init__.py | 9 +
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skbio/stats/distance/tests/data/df.txt | 8 +
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.../tests/data/pwmantel_exp_results_all_dms.txt | 7 +
.../tests/data/pwmantel_exp_results_dm_dm2.txt | 2 +
.../data/pwmantel_exp_results_duplicate_dms.txt | 4 +
.../tests/data/pwmantel_exp_results_minimal.txt | 4 +
.../pwmantel_exp_results_minimal_with_labels.txt | 4 +
.../tests/data/pwmantel_exp_results_na_p_value.txt | 2 +
...tel_exp_results_reordered_distance_matrices.txt | 4 +
skbio/stats/distance/tests/test_anosim.py | 202 +
skbio/stats/distance/tests/test_base.py | 766 +
skbio/stats/distance/tests/test_bioenv.py | 222 +
skbio/stats/distance/tests/test_mantel.py | 569 +
skbio/stats/distance/tests/test_permanova.py | 200 +
skbio/stats/gradient.py | 852 ++
skbio/stats/ordination/__init__.py | 123 +
skbio/stats/ordination/_base.py | 472 +
.../_canonical_correspondence_analysis.py | 250 +
skbio/stats/ordination/_correspondence_analysis.py | 187 +
.../ordination/_principal_coordinate_analysis.py | 171 +
skbio/stats/ordination/_redundancy_analysis.py | 233 +
skbio/stats/ordination/_utils.py | 223 +
skbio/stats/ordination/tests/__init__.py | 7 +
skbio/stats/ordination/tests/data/L&L_CA_data | 3 +
skbio/stats/ordination/tests/data/PCoA_sample_data | 14 +
.../stats/ordination/tests/data/PCoA_sample_data_2 | 6 +
.../stats/ordination/tests/data/PCoA_sample_data_3 | 10 +
skbio/stats/ordination/tests/data/example2_X | 10 +
skbio/stats/ordination/tests/data/example2_Y | 12 +
.../tests/data/example2_site_scaling1_from_vegan | 10 +
.../tests/data/example2_site_scaling2_from_vegan | 10 +
.../data/example2_species_scaling1_from_vegan | 6 +
.../data/example2_species_scaling2_from_vegan | 6 +
skbio/stats/ordination/tests/data/example3_X | 10 +
skbio/stats/ordination/tests/data/example3_Y | 13 +
.../tests/data/example3_site_scaling1_from_vegan | 10 +
.../tests/data/example3_site_scaling2_from_vegan | 10 +
.../data/example3_species_scaling1_from_vegan | 9 +
.../data/example3_species_scaling2_from_vegan | 9 +
.../tests/data/exp_PCoAEigenResults_site | 9 +
.../stats/ordination/tests/data/exp_PCoAzeros_site | 14 +
skbio/stats/ordination/tests/test_ordination.py | 896 ++
skbio/stats/power.py | 994 ++
skbio/stats/spatial.py | 197 +
skbio/stats/tests/__init__.py | 9 +
skbio/stats/tests/data/cr_data_out | 6 +
skbio/stats/tests/data/cr_data_raw | 8 +
skbio/stats/tests/data/cr_no_data_out | 1 +
skbio/stats/tests/data/cr_no_data_raw | 0
skbio/stats/tests/data/gr_w_msg_out | 3 +
skbio/stats/tests/data/gr_w_msg_raw | 4 +
skbio/stats/tests/data/gr_wo_msg_out | 2 +
skbio/stats/tests/data/gr_wo_msg_raw | 3 +
skbio/stats/tests/data/vr_out | 12 +
skbio/stats/tests/data/vr_raw | 13 +
skbio/stats/tests/data/vr_real_out | 14 +
skbio/stats/tests/data/vr_real_raw | 13 +
skbio/stats/tests/test_gradient.py | 1033 ++
skbio/stats/tests/test_misc.py | 99 +
skbio/stats/tests/test_power.py | 398 +
skbio/stats/tests/test_spatial.py | 147 +
skbio/stats/tests/test_subsample.py | 262 +
skbio/tests/__init__.py | 9 +
skbio/tests/test_base.py | 26 +
skbio/tests/test_workflow.py | 407 +
skbio/tree/__init__.py | 260 +
skbio/tree/_exception.py | 34 +
skbio/tree/_majority_rule.py | 309 +
skbio/tree/_nj.py | 286 +
skbio/tree/_tree.py | 3294 +++++
skbio/tree/_trie.py | 264 +
skbio/tree/tests/__init__.py | 7 +
skbio/tree/tests/test_majority_rule.py | 171 +
skbio/tree/tests/test_nj.py | 207 +
skbio/tree/tests/test_tree.py | 1350 ++
skbio/tree/tests/test_trie.py | 216 +
skbio/util/__init__.py | 76 +
skbio/util/_exception.py | 14 +
skbio/util/_misc.py | 334 +
skbio/util/_testing.py | 47 +
skbio/util/_warning.py | 22 +
skbio/util/tests/__init__.py | 9 +
skbio/util/tests/test_misc.py | 160 +
skbio/util/tests/test_testing.py | 28 +
skbio/workflow.py | 550 +
488 files changed, 86105 insertions(+), 125 deletions(-)
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