[med-svn] [python-biom-format] 04/05: Merge tag 'upstream/2.1.5+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository python-biom-format.

commit ca6e289faf9c9958d8850211ee849db947757171
Merge: a907dbe 20df9f6
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 11 12:44:04 2016 +0100

    Merge tag 'upstream/2.1.5+dfsg'
    
    Upstream version 2.1.5+dfsg

 .travis.yml                                        |  29 ++-
 ChangeLog.md                                       |  33 ++-
 INSTALL                                            |  24 --
 MANIFEST.in                                        |   1 -
 README.md                                          |   3 +-
 biom/__init__.py                                   |   5 +-
 biom/cli/__init__.py                               |  31 +++
 biom/cli/installation_informer.py                  | 121 ++++++++++
 biom/cli/metadata_adder.py                         | 186 +++++++++++++++
 biom/cli/table_converter.py                        | 209 +++++++++++++++++
 biom/cli/table_head.py                             |  46 ++++
 biom/cli/table_normalizer.py                       |  74 ++++++
 biom/cli/table_subsetter.py                        | 139 +++++++++++
 biom/cli/table_summarizer.py                       | 136 +++++++++++
 biom/{commands => cli}/table_validator.py          | 107 +++++----
 biom/cli/uc_processor.py                           |  85 +++++++
 biom/cli/util.py                                   |  35 +++
 biom/commands/__init__.py                          |   0
 biom/commands/installation_informer.py             | 123 ----------
 biom/commands/metadata_adder.py                    | 165 -------------
 biom/commands/table_converter.py                   | 221 -----------------
 biom/commands/table_normalizer.py                  |  91 -------
 biom/commands/table_subsetter.py                   | 122 ----------
 biom/commands/table_summarizer.py                  | 168 -------------
 biom/interfaces/__init__.py                        |   0
 biom/interfaces/html/__init__.py                   |   0
 biom/interfaces/html/config/__init__.py            |   0
 biom/interfaces/html/config/add_metadata.py        |  99 --------
 biom/interfaces/html/config/convert.py             |  74 ------
 biom/interfaces/html/config/normalize_table.py     |  56 -----
 biom/interfaces/html/config/show_install_info.py   |  36 ---
 biom/interfaces/html/config/summarize_table.py     |  53 -----
 biom/interfaces/html/config/validate_table.py      |  55 -----
 biom/interfaces/html/input_handler.py              |  56 -----
 biom/interfaces/optparse/__init__.py               |   0
 biom/interfaces/optparse/config/__init__.py        |   0
 biom/interfaces/optparse/config/add_metadata.py    | 114 ---------
 biom/interfaces/optparse/config/convert.py         |  81 -------
 biom/interfaces/optparse/config/normalize_table.py |  84 -------
 .../optparse/config/show_install_info.py           |  39 ---
 biom/interfaces/optparse/config/subset_table.py    |  77 ------
 biom/interfaces/optparse/config/summarize_table.py |  64 -----
 biom/interfaces/optparse/config/validate_table.py  |  65 -----
 biom/interfaces/optparse/input_handler.py          |  79 -------
 biom/interfaces/optparse/output_handler.py         |  80 -------
 biom/parse.py                                      | 114 ++++++++-
 biom/table.py                                      | 261 +++++++++++++--------
 biom/util.py                                       |  26 +-
 doc/conf.py                                        |   4 +-
 doc/index.rst                                      |  88 ++-----
 scripts/biom                                       |  22 --
 scripts/serve-biom                                 |  11 -
 setup.py                                           |  40 ++--
 .../test_cli/__init__.py                           |   4 +-
 .../test_add_metadata.py}                          |  47 +---
 .../test_data/json_obs_collapsed.biom              |   0
 .../test_data/json_sample_collapsed.biom           |   0
 .../test_data/test.biom                            | Bin
 tests/test_cli/test_data/test.json                 |   1 +
 tests/test_cli/test_show_install_info.py           |  24 ++
 .../test_subset_table.py}                          |  82 +++----
 tests/test_cli/test_summarize_table.py             | 122 ++++++++++
 .../test_table_converter.py                        | 256 +++++++++-----------
 tests/test_cli/test_table_normalizer.py            |  50 ++++
 tests/test_cli/test_uc_processor.py                | 109 +++++++++
 .../test_validate_table.py}                        |   2 +-
 tests/test_commands/__init__.py                    |   0
 tests/test_commands/test_installation_informer.py  |  40 ----
 tests/test_commands/test_table_normalizer.py       |  56 -----
 tests/test_commands/test_table_summarizer.py       | 132 -----------
 tests/test_data/test.json                          |   2 +-
 tests/test_interfaces/__init__.py                  |   0
 tests/test_interfaces/test_optparse/__init__.py    |   0
 .../test_optparse/test_input_handler.py            | 118 ----------
 tests/test_parse.py                                | 143 ++++++++++-
 tests/test_table.py                                | 152 ++++++++----
 tests/test_util.py                                 |   2 +-
 77 files changed, 2224 insertions(+), 2950 deletions(-)

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