[med-svn] [python-skbio] 03/06: Merge tag 'upstream/0.4.2'

[Kevin Murray]

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

commit 889e71f08c34a22a23a2d5b1a5286e96f315140e
Merge: b29f34f 76aae4f
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Wed Feb 17 16:23:36 2016 -0800

    Merge tag 'upstream/0.4.2'
    
    Upstream version 0.4.2

 CHANGELOG.md                                       |  33 +-
 RELEASE.md                                         |   4 +-
 ci/pip_requirements.txt                            |   2 +-
 doc/source/_static/style.css                       |   4 +
 doc/source/conf.py                                 |   7 +-
 skbio/__init__.py                                  |   2 +-
 skbio/alignment/_pairwise.py                       |  26 +-
 skbio/alignment/_tabular_msa.py                    |  45 +-
 skbio/alignment/tests/test_pairwise.py             |  18 +-
 skbio/alignment/tests/test_tabular_msa.py          |  36 +-
 skbio/diversity/alpha/_lladser.py                  |   2 +-
 skbio/io/__init__.py                               |   9 +-
 skbio/io/_exception.py                             |   5 +
 skbio/io/format/_base.py                           |   2 +-
 skbio/io/format/clustal.py                         |  12 +-
 skbio/io/format/fasta.py                           |   9 +-
 skbio/io/format/fastq.py                           |   9 +-
 skbio/io/format/genbank.py                         |   8 +-
 skbio/io/format/phylip.py                          |   8 +-
 skbio/io/format/stockholm.py                       | 710 +++++++++++++++++++++
 .../io/format/tests/data/stockholm_all_data_types  |  15 +
 skbio/io/format/tests/data/stockholm_blank_lines   |   6 +
 skbio/io/format/tests/data/stockholm_data_only     |   5 +
 .../tests/data/stockholm_differing_gc_data_length  |   4 +
 .../tests/data/stockholm_differing_gr_data_length  |   4 +
 .../tests/data/stockholm_differing_seq_lengths     |   4 +
 skbio/io/format/tests/data/stockholm_duplicate_gc  |   7 +
 skbio/io/format/tests/data/stockholm_duplicate_gr  |   8 +
 .../tests/data/stockholm_duplicate_sequence_names  |   6 +
 .../format/tests/data/stockholm_duplicate_tree_ids |   6 +
 skbio/io/format/tests/data/stockholm_extensive     |  15 +
 .../io/format/tests/data/stockholm_extensive_mixed |  15 +
 .../format/tests/data/stockholm_invalid_data_type  |   4 +
 .../tests/data/stockholm_invalid_nonexistent_gr    |   7 +
 .../tests/data/stockholm_invalid_nonexistent_gs    |   5 +
 .../tests/data/stockholm_malformed_data_line       |   3 +
 .../format/tests/data/stockholm_malformed_gc_line  |   4 +
 .../format/tests/data/stockholm_malformed_gf_line  |   3 +
 .../format/tests/data/stockholm_malformed_gr_line  |   4 +
 .../format/tests/data/stockholm_malformed_gs_line  |   4 +
 skbio/io/format/tests/data/stockholm_metadata_only |   4 +
 skbio/io/format/tests/data/stockholm_minimal       |   3 +
 .../io/format/tests/data/stockholm_missing_footer  |   4 +
 .../io/format/tests/data/stockholm_missing_header  |   4 +
 skbio/io/format/tests/data/stockholm_multiple_msa  |  18 +
 .../io/format/tests/data/stockholm_multiple_trees  |   8 +
 skbio/io/format/tests/data/stockholm_no_data       |   2 +
 .../format/tests/data/stockholm_nonstring_labels   |   7 +
 skbio/io/format/tests/data/stockholm_rna           |   9 +
 skbio/io/format/tests/data/stockholm_runon_gf      |   5 +
 skbio/io/format/tests/data/stockholm_runon_gs      |   5 +
 .../tests/data/stockholm_single_tree_with_id       |   4 +
 .../tests/data/stockholm_single_tree_without_id    |   3 +
 .../tests/data/stockholm_two_of_each_metadata      |  11 +
 .../tests/data/stockholm_whitespace_only_lines     |   5 +
 skbio/io/format/tests/test_base.py                 |   4 +-
 skbio/io/format/tests/test_clustal.py              |  15 +-
 skbio/io/format/tests/test_fasta.py                |  17 +-
 skbio/io/format/tests/test_fastq.py                |  17 +-
 skbio/io/format/tests/test_genbank.py              |  15 +-
 skbio/io/format/tests/test_stockholm.py            | 701 ++++++++++++++++++++
 skbio/io/registry.py                               |  28 +-
 skbio/io/tests/test_registry.py                    |  36 +-
 skbio/io/tests/test_util.py                        |  36 +-
 skbio/sequence/__init__.py                         |  13 +-
 skbio/sequence/_dna.py                             |  33 +-
 .../{_iupac_sequence.py => _grammared_sequence.py} | 189 +++++-
 skbio/sequence/_nucleotide_mixin.py                |   2 +-
 skbio/sequence/_protein.py                         |  39 +-
 skbio/sequence/_rna.py                             |  33 +-
 skbio/sequence/_sequence.py                        |  90 ++-
 skbio/sequence/distance.py                         | 115 ++++
 skbio/sequence/tests/test_distance.py              | 130 ++++
 skbio/sequence/tests/test_dna.py                   |   6 +
 skbio/sequence/tests/test_grammared_sequence.py    | 613 ++++++++++++++++++
 skbio/sequence/tests/test_iupac_sequence.py        | 506 ---------------
 skbio/sequence/tests/test_nucleotide_sequences.py  |  27 +-
 skbio/sequence/tests/test_protein.py               |   6 +
 skbio/sequence/tests/test_rna.py                   |   5 +
 skbio/sequence/tests/test_sequence.py              | 216 +++++--
 skbio/stats/composition.py                         |  28 +-
 skbio/stats/distance/_base.py                      |   4 +-
 skbio/stats/distance/tests/test_base.py            |  53 +-
 .../ordination/tests/test_redundancy_analysis.py   |   2 +
 skbio/stats/power.py                               |  14 +-
 skbio/stats/tests/test_composition.py              |  20 +-
 skbio/stats/tests/test_gradient.py                 |  42 +-
 skbio/tree/_tree.py                                |  67 +-
 skbio/tree/tests/test_tree.py                      |  13 +
 skbio/util/__init__.py                             |  15 +-
 skbio/util/_decorator.py                           |   3 +-
 skbio/util/_misc.py                                |  22 +-
 skbio/util/_testing.py                             |  27 +-
 skbio/util/_warning.py                             |  14 +-
 skbio/util/tests/test_decorator.py                 |   9 +-
 skbio/util/tests/test_misc.py                      |   2 +-
 96 files changed, 3529 insertions(+), 870 deletions(-)

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