[med-svn] [python-skbio] 02/03: Merge tag 'upstream/0.5.1'

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository python-skbio.

commit 1178635148834235ae175c4e03634cc9fc2f3fb1
Merge: da78527 1ee78f3
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Tue Nov 15 18:56:30 2016 +1100

    Merge tag 'upstream/0.5.1'
    
    Upstream version 0.5.1

 CHANGELOG.md                                       |    39 +-
 checklist.py                                       |    26 +-
 ci/matplotlibrc                                    |     1 +
 doc/source/index.rst                               |     1 +
 doc/source/metadata.rst                            |     1 +
 licenses/bx_python.txt                             |    20 +
 setup.py                                           |    15 +-
 skbio/__init__.py                                  |     5 +-
 skbio/alignment/_pairwise.py                       |     2 +-
 skbio/diversity/__init__.py                        |     5 +-
 skbio/diversity/_block.py                          |   319 +
 skbio/diversity/_driver.py                         |     2 +-
 skbio/diversity/tests/test_block.py                |   207 +
 skbio/io/__init__.py                               |     1 +
 skbio/io/format/_blast.py                          |    29 +-
 skbio/io/format/_sequence_feature_vocabulary.py    |   351 +
 skbio/io/format/genbank.py                         |   557 +-
 skbio/io/format/tests/data/genbank_multi_records   |     8 +-
 skbio/io/format/tests/data/genbank_single_record   |     6 +-
 skbio/io/format/tests/test_fasta.py                |     5 +-
 skbio/io/format/tests/test_genbank.py              |   305 +-
 .../tests/test_sequence_feature_vocabulary.py      |   102 +
 skbio/metadata/__init__.py                         |    14 +
 skbio/metadata/_intersection.c                     | 10555 +++++++++++++++++++
 skbio/metadata/_intersection.pyx                   |   529 +
 skbio/metadata/_interval.py                        |   978 ++
 skbio/metadata/_mixin.py                           |   135 +-
 skbio/metadata/_repr.py                            |    21 +-
 skbio/metadata/_testing.py                         |   315 +
 skbio/metadata/tests/test_intersection.py          |   241 +
 skbio/metadata/tests/test_interval.py              |   718 ++
 skbio/metadata/tests/test_mixin.py                 |    42 +-
 skbio/sequence/_dna.py                             |    14 +-
 skbio/sequence/_grammared_sequence.py              |     9 +-
 skbio/sequence/_nucleotide_mixin.py                |    17 +-
 skbio/sequence/_protein.py                         |     4 +
 skbio/sequence/_rna.py                             |     9 +
 skbio/sequence/_sequence.py                        |   237 +-
 skbio/sequence/tests/test_dna.py                   |    10 +-
 skbio/sequence/tests/test_grammared_sequence.py    |     9 +-
 skbio/sequence/tests/test_nucleotide_sequences.py  |    35 +-
 skbio/sequence/tests/test_rna.py                   |    10 +-
 skbio/sequence/tests/test_sequence.py              |   325 +-
 skbio/stats/composition.py                         |    47 +-
 skbio/stats/distance/_base.py                      |   132 +-
 skbio/stats/distance/tests/test_base.py            |   203 +-
 skbio/stats/power.py                               |     6 +-
 skbio/stats/tests/test_composition.py              |    72 +
 skbio/stats/tests/test_power.py                    |    15 +-
 skbio/tree/_tree.py                                |    44 +-
 skbio/tree/tests/test_tree.py                      |    26 +
 skbio/util/__init__.py                             |     9 +-
 skbio/util/_decorator.py                           |    23 +-
 skbio/util/_misc.py                                |   196 +-
 skbio/util/tests/test_misc.py                      |    82 +-
 55 files changed, 15899 insertions(+), 1190 deletions(-)

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