[med-svn] [python-skbio] branch upstream updated (2cca4ca -> 1ee78f3)

[Kevin Murray]

This is an automated email from the git hooks/post-receive script.

daube-guest pushed a change to branch upstream
in repository python-skbio.

      from  2cca4ca   Imported Upstream version 0.5.0
       new  1ee78f3   New upstream version 0.5.1

The 1 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 +
 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 +-
 55 files changed, 15881 insertions(+), 1191 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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