[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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