[med-svn] [python-skbio] branch master updated (da78527 -> 6efca22)

[Kevin Murray]

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  da78527   dch
       new  1ee78f3   New upstream version 0.5.1
       new  1178635   Merge tag 'upstream/0.5.1'
       new  6efca22   Update changelog, and email

The 3 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:
 CHANGELOG.md                                       |    39 +-
 checklist.py                                       |    26 +-
 ci/matplotlibrc                                    |     1 +
 debian/changelog                                   |    13 +-
 debian/control                                     |     2 +-
 doc/source/index.rst                               |     1 +
 doc/source/metadata.rst                            |     1 +
 .../{sphinx-bootstrap-theme.txt => bx_python.txt}  |     3 +-
 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 +-
 57 files changed, 15889 insertions(+), 1198 deletions(-)
 create mode 100644 ci/matplotlibrc
 create mode 100644 doc/source/metadata.rst
 copy licenses/{sphinx-bootstrap-theme.txt => bx_python.txt} (90%)
 create mode 100644 skbio/diversity/_block.py
 create mode 100644 skbio/diversity/tests/test_block.py
 create mode 100644 skbio/io/format/_sequence_feature_vocabulary.py
 create mode 100644 skbio/io/format/tests/test_sequence_feature_vocabulary.py
 create mode 100644 skbio/metadata/_intersection.c
 create mode 100644 skbio/metadata/_intersection.pyx
 create mode 100644 skbio/metadata/_interval.py
 create mode 100644 skbio/metadata/tests/test_intersection.py
 create mode 100644 skbio/metadata/tests/test_interval.py

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