[med-svn] [python-biom-format] branch master updated (3f6d6c9 -> bb11697)
Andreas Tille
tille at debian.org
Mon Oct 26 21:33:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository python-biom-format.
from 3f6d6c9 cme fix dpkg-control
new bbda645 Imported Upstream version 2.1.5+dfsg
new bb11697 Merge tag 'upstream/2.1.5+dfsg'
The 2 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 | 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(-)
mode change 100644 => 100755 biom/__init__.py
create mode 100644 biom/cli/__init__.py
create mode 100644 biom/cli/installation_informer.py
create mode 100644 biom/cli/metadata_adder.py
create mode 100644 biom/cli/table_converter.py
create mode 100644 biom/cli/table_head.py
create mode 100755 biom/cli/table_normalizer.py
create mode 100644 biom/cli/table_subsetter.py
create mode 100644 biom/cli/table_summarizer.py
rename biom/{commands => cli}/table_validator.py (88%)
create mode 100644 biom/cli/uc_processor.py
create mode 100644 biom/cli/util.py
delete mode 100644 biom/commands/installation_informer.py
delete mode 100644 biom/commands/metadata_adder.py
delete mode 100644 biom/commands/table_converter.py
delete mode 100644 biom/commands/table_subsetter.py
delete mode 100644 biom/commands/table_summarizer.py
delete mode 100644 biom/interfaces/__init__.py
delete mode 100644 biom/interfaces/html/__init__.py
delete mode 100644 biom/interfaces/html/config/__init__.py
delete mode 100644 biom/interfaces/html/config/add_metadata.py
delete mode 100644 biom/interfaces/html/config/convert.py
delete mode 100644 biom/interfaces/html/config/show_install_info.py
delete mode 100644 biom/interfaces/html/config/summarize_table.py
delete mode 100644 biom/interfaces/html/config/validate_table.py
delete mode 100644 biom/interfaces/html/input_handler.py
delete mode 100644 biom/interfaces/optparse/__init__.py
delete mode 100644 biom/interfaces/optparse/config/__init__.py
delete mode 100644 biom/interfaces/optparse/config/add_metadata.py
delete mode 100644 biom/interfaces/optparse/config/convert.py
delete mode 100644 biom/interfaces/optparse/config/show_install_info.py
delete mode 100644 biom/interfaces/optparse/config/subset_table.py
delete mode 100644 biom/interfaces/optparse/config/summarize_table.py
delete mode 100644 biom/interfaces/optparse/config/validate_table.py
delete mode 100644 biom/interfaces/optparse/input_handler.py
delete mode 100644 biom/interfaces/optparse/output_handler.py
delete mode 100644 doc/documentation/generated/biom.load_table.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__eq__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__format__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__getitem__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__init__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__iter__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__ne__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__new__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__reduce__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__reduce_ex__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__repr__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__sizeof__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__str__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.__subclasshook__.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._axis_to_num.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._cast_metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._conv_to_self_type.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._data_equality.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._extract_data_from_tsv.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._get_col.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._get_row.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._get_sparse_data.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._index.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._index_ids.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._intersect_id_order.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._invert_axis.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._iter_obs.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._iter_samp.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._to_dense.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._to_sparse.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._union_id_order.rst
delete mode 100644 doc/documentation/generated/biom.table.Table._verify_metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.add_group_metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.add_metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.collapse.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.copy.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.data.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.delimited_self.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.descriptive_equality.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.dtype.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.exists.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.filter.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.from_hdf5.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.from_json.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.from_tsv.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.get_table_density.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.get_value_by_ids.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.group_metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.ids.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.index.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.is_empty.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.iter.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.iter_data.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.iter_pairwise.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.matrix_data.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.max.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.merge.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.metadata.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.min.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.nnz.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.nonzero.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.nonzero_counts.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.norm.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.pa.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.partition.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.reduce.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.shape.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.sort.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.sort_order.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.subsample.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.sum.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.to_hdf5.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.to_json.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.to_tsv.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.transform.rst
delete mode 100644 doc/documentation/generated/biom.table.Table.transpose.rst
delete mode 100644 examples/asasd
delete mode 100644 examples/asd.hdf5
delete mode 100644 examples/asdasdsd
delete mode 100644 examples/bar_hdf5
delete mode 100644 examples/bar_json
delete mode 100644 examples/bar_tsv
delete mode 100644 examples/foo_hdf5
delete mode 100644 examples/foo_json
delete mode 100644 examples/foo_tsv
delete mode 100644 examples/foobar_hdf5
delete mode 100644 examples/foobar_json
delete mode 100644 examples/foobar_json2
delete mode 100644 examples/foobar_tsv
delete mode 100644 examples/qweqweqwasd
delete mode 100644 examples/rich_sparse_otu_table.biom.gz
delete mode 100644 examples/wtf
delete mode 100644 examples/wtf2
delete mode 100755 scripts/biom
delete mode 100644 scripts/serve-biom
rename {biom/commands => tests}/__init__.py (100%)
rename biom/interfaces/html/output_handler.py => tests/test_cli/__init__.py (78%)
create mode 100644 tests/test_cli/test_add_metadata.py
create mode 100644 tests/test_cli/test_show_install_info.py
create mode 100644 tests/test_cli/test_subset_table.py
create mode 100644 tests/test_cli/test_summarize_table.py
create mode 100644 tests/test_cli/test_table_converter.py
create mode 100755 tests/test_cli/test_table_normalizer.py
create mode 100644 tests/test_cli/test_uc_processor.py
create mode 100644 tests/test_cli/test_validate_table.py
create mode 100644 tests/test_err.py
create mode 100644 tests/test_parse.py
create mode 100644 tests/test_table.py
create mode 100644 tests/test_util.py
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