[med-svn] [python-biom-format] 02/02: Merge tag 'upstream/2.1.5+dfsg'

Andreas Tille tille at debian.org
Mon Oct 26 21:33:25 UTC 2015


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

commit bb116975486e8783b9b34c0ed55cac06f39004fb
Merge: 3f6d6c9 bbda645
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 26 22:32:59 2015 +0100

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

 ChangeLog.md                                       |  132 +-
 MANIFEST.in                                        |    1 -
 PKG-INFO                                           |    4 +-
 README.md                                          |    9 +-
 biom/__init__.py                                   |   17 +-
 biom/_filter.pyx                                   |    2 +-
 biom/_subsample.pyx                                |   26 +-
 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          |  121 +-
 biom/cli/uc_processor.py                           |   85 +
 biom/cli/util.py                                   |   35 +
 biom/commands/installation_informer.py             |  123 -
 biom/commands/metadata_adder.py                    |  165 -
 biom/commands/table_converter.py                   |  221 --
 biom/commands/table_subsetter.py                   |  122 -
 biom/commands/table_summarizer.py                  |  159 -
 biom/err.py                                        |    1 -
 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/show_install_info.py   |   36 -
 biom/interfaces/html/config/summarize_table.py     |   53 -
 biom/interfaces/html/config/validate_table.py      |   57 -
 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    |  112 -
 biom/interfaces/optparse/config/convert.py         |   81 -
 .../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  |   69 -
 biom/interfaces/optparse/input_handler.py          |   79 -
 biom/interfaces/optparse/output_handler.py         |   80 -
 biom/parse.py                                      |  166 +-
 biom/table.py                                      |  728 +++--
 biom/util.py                                       |   77 +-
 doc/conf.py                                        |    6 +-
 doc/documentation/biom_conversion.rst              |    2 +-
 doc/documentation/generated/biom.load_table.rst    |    6 -
 .../generated/biom.table.Table.__eq__.rst          |    8 -
 .../generated/biom.table.Table.__format__.rst      |    8 -
 .../generated/biom.table.Table.__getitem__.rst     |    8 -
 .../generated/biom.table.Table.__init__.rst        |    8 -
 .../generated/biom.table.Table.__iter__.rst        |    8 -
 .../generated/biom.table.Table.__ne__.rst          |    8 -
 .../generated/biom.table.Table.__new__.rst         |    8 -
 .../generated/biom.table.Table.__reduce__.rst      |    8 -
 .../generated/biom.table.Table.__reduce_ex__.rst   |    8 -
 .../generated/biom.table.Table.__repr__.rst        |    8 -
 .../generated/biom.table.Table.__sizeof__.rst      |    8 -
 .../generated/biom.table.Table.__str__.rst         |    8 -
 .../biom.table.Table.__subclasshook__.rst          |    8 -
 .../generated/biom.table.Table._axis_to_num.rst    |    8 -
 .../generated/biom.table.Table._cast_metadata.rst  |    8 -
 .../biom.table.Table._conv_to_self_type.rst        |    8 -
 .../generated/biom.table.Table._data_equality.rst  |    8 -
 .../biom.table.Table._extract_data_from_tsv.rst    |    8 -
 .../generated/biom.table.Table._get_col.rst        |    8 -
 .../generated/biom.table.Table._get_row.rst        |    8 -
 .../biom.table.Table._get_sparse_data.rst          |    8 -
 .../generated/biom.table.Table._index.rst          |    8 -
 .../generated/biom.table.Table._index_ids.rst      |    8 -
 .../biom.table.Table._intersect_id_order.rst       |    8 -
 .../generated/biom.table.Table._invert_axis.rst    |    8 -
 .../generated/biom.table.Table._iter_obs.rst       |    8 -
 .../generated/biom.table.Table._iter_samp.rst      |    8 -
 .../generated/biom.table.Table._to_dense.rst       |    8 -
 .../generated/biom.table.Table._to_sparse.rst      |    8 -
 .../generated/biom.table.Table._union_id_order.rst |    8 -
 .../biom.table.Table._verify_metadata.rst          |    8 -
 .../biom.table.Table.add_group_metadata.rst        |    8 -
 .../generated/biom.table.Table.add_metadata.rst    |    8 -
 .../generated/biom.table.Table.collapse.rst        |    8 -
 .../generated/biom.table.Table.copy.rst            |    8 -
 .../generated/biom.table.Table.data.rst            |    8 -
 .../generated/biom.table.Table.delimited_self.rst  |    8 -
 .../biom.table.Table.descriptive_equality.rst      |    8 -
 .../generated/biom.table.Table.dtype.rst           |    8 -
 .../generated/biom.table.Table.exists.rst          |    8 -
 .../generated/biom.table.Table.filter.rst          |    8 -
 .../generated/biom.table.Table.from_hdf5.rst       |    8 -
 .../generated/biom.table.Table.from_json.rst       |    8 -
 .../generated/biom.table.Table.from_tsv.rst        |    8 -
 .../biom.table.Table.get_table_density.rst         |    8 -
 .../biom.table.Table.get_value_by_ids.rst          |    8 -
 .../generated/biom.table.Table.group_metadata.rst  |    8 -
 .../generated/biom.table.Table.ids.rst             |    8 -
 .../generated/biom.table.Table.index.rst           |    8 -
 .../generated/biom.table.Table.is_empty.rst        |    8 -
 .../generated/biom.table.Table.iter.rst            |    8 -
 .../generated/biom.table.Table.iter_data.rst       |    8 -
 .../generated/biom.table.Table.iter_pairwise.rst   |    8 -
 .../generated/biom.table.Table.matrix_data.rst     |    8 -
 .../generated/biom.table.Table.max.rst             |    8 -
 .../generated/biom.table.Table.merge.rst           |    8 -
 .../generated/biom.table.Table.metadata.rst        |    8 -
 .../generated/biom.table.Table.min.rst             |    8 -
 .../generated/biom.table.Table.nnz.rst             |    8 -
 .../generated/biom.table.Table.nonzero.rst         |    8 -
 .../generated/biom.table.Table.nonzero_counts.rst  |    8 -
 .../generated/biom.table.Table.norm.rst            |    8 -
 .../generated/biom.table.Table.pa.rst              |    8 -
 .../generated/biom.table.Table.partition.rst       |    8 -
 .../generated/biom.table.Table.reduce.rst          |    8 -
 doc/documentation/generated/biom.table.Table.rst   |   98 -
 .../generated/biom.table.Table.shape.rst           |    8 -
 .../generated/biom.table.Table.sort.rst            |    8 -
 .../generated/biom.table.Table.sort_order.rst      |    8 -
 .../generated/biom.table.Table.subsample.rst       |    8 -
 .../generated/biom.table.Table.sum.rst             |    8 -
 .../generated/biom.table.Table.to_hdf5.rst         |    8 -
 .../generated/biom.table.Table.to_json.rst         |    8 -
 .../generated/biom.table.Table.to_tsv.rst          |    8 -
 .../generated/biom.table.Table.transform.rst       |    8 -
 .../generated/biom.table.Table.transpose.rst       |    8 -
 doc/index.rst                                      |   88 +-
 examples/asasd                                     |    7 -
 examples/asd.hdf5                                  |  Bin 28920 -> 0 bytes
 examples/asdasdsd                                  |  Bin 35720 -> 0 bytes
 examples/bar_hdf5                                  |  Bin 35720 -> 0 bytes
 examples/bar_json                                  |    1 -
 examples/bar_tsv                                   |    7 -
 examples/foo_hdf5                                  |  Bin 35720 -> 0 bytes
 examples/foo_json                                  |    1 -
 examples/foo_tsv                                   |    7 -
 examples/foobar_hdf5                               |  Bin 33352 -> 0 bytes
 examples/foobar_json                               |    1 -
 examples/foobar_json2                              |    1 -
 examples/foobar_tsv                                |    7 -
 examples/qweqweqwasd                               |    1 -
 examples/rich_sparse_otu_table.biom.gz             |  Bin 735 -> 0 bytes
 examples/wtf                                       |  Bin 35720 -> 0 bytes
 examples/wtf2                                      |    1 -
 scripts/biom                                       |   22 -
 scripts/serve-biom                                 |   11 -
 setup.cfg                                          |    4 +-
 setup.py                                           |   41 +-
 {biom/commands => tests}/__init__.py               |    0
 .../test_cli/__init__.py                           |    4 +-
 tests/test_cli/test_add_metadata.py                |  134 +
 tests/test_cli/test_show_install_info.py           |   24 +
 tests/test_cli/test_subset_table.py                |  122 +
 tests/test_cli/test_summarize_table.py             |  122 +
 tests/test_cli/test_table_converter.py             |  292 ++
 tests/test_cli/test_table_normalizer.py            |   50 +
 tests/test_cli/test_uc_processor.py                |  109 +
 tests/test_cli/test_validate_table.py              |  718 +++++
 tests/test_err.py                                  |  218 ++
 tests/test_parse.py                                | 1692 ++++++++++
 tests/test_table.py                                | 3376 ++++++++++++++++++++
 tests/test_util.py                                 |  384 +++
 161 files changed, 9276 insertions(+), 2993 deletions(-)

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