[med-svn] [python-biom-format] branch master updated (bb11697 -> e697787)
Andreas Tille
tille at debian.org
Tue Oct 27 17:58:58 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 bb11697 Merge tag 'upstream/2.1.5+dfsg'
new ee0aee3 Package version 2.1.4 before making the bigger step to 2.1.5
new 4838a06 Imported Upstream version 2.1.4+dfsg
new 65f68e0 Merge tag 'upstream/2.1.4+dfsg'
new b52592e Fix watch file (new upstream version fixes #802867)
new e697787 Upload to unstable
The 5 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:
.coveragerc | 17 +
.travis.yml | 35 +
ChangeLog.md | 33 +-
INSTALL | 24 +
MANIFEST.in | 1 +
PKG-INFO | 30 -
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/cli/uc_processor.py | 85 --
biom/cli/util.py | 35 -
{tests => 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/{cli => commands}/table_validator.py | 107 +-
{tests => biom/interfaces}/__init__.py | 0
{tests => biom/interfaces/html}/__init__.py | 0
{tests => 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 +
.../interfaces/html/output_handler.py | 4 +-
{tests => biom/interfaces/optparse}/__init__.py | 0
.../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 +-
debian/changelog | 6 +-
debian/rules | 1 -
debian/watch | 4 +-
doc/conf.py | 4 +-
doc/index.rst | 88 +-
images/biom-logos.ai | 1124 ++++++++++++++++++++
licenses/numpydoc.txt | 1 +
licenses/scikit-learn.txt | 35 +
licenses/scipy.txt | 31 +
scripts/biom | 22 +
scripts/serve-biom | 11 +
setup.cfg | 5 -
setup.py | 40 +-
tests/bench_tables/10000x10000x0.001_bench.biom.gz | Bin 0 -> 229557 bytes
.../10000x10000x0.001_bench_hdf5.biom.gz | Bin 0 -> 642038 bytes
tests/bench_tables/10000x10000x0.010_bench.biom.gz | Bin 0 -> 2345285 bytes
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tests/bench_tables/10000x10000x0.100_bench.biom.gz | Bin 0 -> 23248570 bytes
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tests/bench_tables/10000x1000x0.001_bench.biom.gz | Bin 0 -> 69230 bytes
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tests/bench_tables/10000x1000x0.010_bench.biom.gz | Bin 0 -> 320640 bytes
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tests/bench_tables/10000x1000x0.100_bench.biom.gz | Bin 0 -> 2659788 bytes
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tests/bench_tables/10000x100x0.001_bench.biom.gz | Bin 0 -> 27854 bytes
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tests/bench_tables/1000x10000x0.010_bench.biom.gz | Bin 0 -> 319000 bytes
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tests/bench_tables/1000x10000x0.100_bench.biom.gz | Bin 0 -> 2588217 bytes
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tests/bench_tables/1000x1000x0.001_bench.biom.gz | Bin 0 -> 8166 bytes
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tests/bench_tables/1000x1000x0.010_bench.biom.gz | Bin 0 -> 22915 bytes
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tests/bench_tables/1000x1000x0.100_bench.biom.gz | Bin 0 -> 234452 bytes
.../1000x1000x0.100_bench_hdf5.biom.gz | Bin 0 -> 113800 bytes
tests/bench_tables/1000x100x0.001_bench.biom.gz | Bin 0 -> 3266 bytes
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tests/bench_tables/1000x100x0.010_bench.biom.gz | Bin 0 -> 6512 bytes
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tests/bench_tables/1000x100x0.100_bench.biom.gz | Bin 0 -> 29839 bytes
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tests/bench_tables/1000x10x0.001_bench.biom.gz | Bin 0 -> 2795 bytes
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tests/bench_tables/1000x10x0.010_bench.biom.gz | Bin 0 -> 3083 bytes
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tests/bench_tables/1000x10x0.100_bench.biom.gz | Bin 0 -> 5583 bytes
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tests/bench_tables/100x10000x0.001_bench.biom.gz | Bin 0 -> 28147 bytes
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tests/bench_tables/100x10000x0.010_bench.biom.gz | Bin 0 -> 59244 bytes
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tests/bench_tables/100x10000x0.100_bench.biom.gz | Bin 0 -> 264503 bytes
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tests/bench_tables/100x1000x0.001_bench.biom.gz | Bin 0 -> 3236 bytes
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tests/bench_tables/100x1000x0.010_bench.biom.gz | Bin 0 -> 6257 bytes
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tests/bench_tables/100x1000x0.100_bench.biom.gz | Bin 0 -> 27986 bytes
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tests/bench_tables/100x100x0.001_bench.biom.gz | Bin 0 -> 590 bytes
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tests/bench_tables/100x100x0.010_bench.biom.gz | Bin 0 -> 952 bytes
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tests/bench_tables/100x100x0.100_bench.biom.gz | Bin 0 -> 2395 bytes
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tests/bench_tables/100x10x0.001_bench.biom.gz | Bin 0 -> 527 bytes
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tests/bench_tables/100x10x0.010_bench.biom.gz | Bin 0 -> 562 bytes
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tests/bench_tables/100x10x0.100_bench.biom.gz | Bin 0 -> 808 bytes
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tests/bench_tables/10x10000x0.010_bench.biom.gz | Bin 0 -> 26450 bytes
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tests/bench_tables/10x10000x0.100_bench.biom.gz | Bin 0 -> 49427 bytes
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tests/bench_tables/10x1000x0.001_bench.biom.gz | Bin 0 -> 2795 bytes
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tests/bench_tables/10x1000x0.010_bench.biom.gz | Bin 0 -> 3046 bytes
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tests/bench_tables/10x1000x0.100_bench.biom.gz | Bin 0 -> 5308 bytes
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tests/bench_tables/10x100x0.010_bench.biom.gz | Bin 0 -> 561 bytes
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tests/bench_tables/10x10x0.001_bench.biom.gz | Bin 0 -> 299 bytes
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tests/bench_tables/10x10x0.010_bench.biom.gz | Bin 0 -> 301 bytes
.../bench_tables/10x10x0.010_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/10x10x0.100_bench.biom.gz | Bin 0 -> 334 bytes
.../bench_tables/10x10x0.100_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/test_cli/test_show_install_info.py | 24 -
tests/test_cli/test_summarize_table.py | 122 ---
tests/test_cli/test_table_normalizer.py | 50 -
tests/test_cli/test_uc_processor.py | 109 --
tests/{ => test_commands}/__init__.py | 0
.../test_data/json_obs_collapsed.biom | 1 +
.../test_data/json_sample_collapsed.biom | 1 +
.../test_commands/test_data/test.biom | Bin 46952 -> 46952 bytes
tests/test_commands/test_installation_informer.py | 40 +
.../test_metadata_adder.py} | 47 +-
.../test_table_converter.py | 256 +++--
tests/test_commands/test_table_normalizer.py | 56 +
.../test_table_subsetter.py} | 82 +-
tests/test_commands/test_table_summarizer.py | 132 +++
.../test_table_validator.py} | 2 +-
tests/test_data/empty.biom | Bin 0 -> 21224 bytes
tests/{__init__.py => test_data/no-contents.biom} | 0
.../test_data/test.biom | Bin 46952 -> 46952 bytes
tests/test_data/test.json | 1 +
tests/test_data/test.json.gz | Bin 0 -> 678 bytes
tests/{ => test_interfaces}/__init__.py | 0
.../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 +-
186 files changed, 4186 insertions(+), 2248 deletions(-)
create mode 100644 .coveragerc
create mode 100644 .travis.yml
create mode 100644 INSTALL
delete mode 100644 PKG-INFO
delete mode 100644 biom/cli/__init__.py
delete mode 100644 biom/cli/installation_informer.py
delete mode 100644 biom/cli/metadata_adder.py
delete mode 100644 biom/cli/table_converter.py
delete mode 100644 biom/cli/table_head.py
delete mode 100755 biom/cli/table_normalizer.py
delete mode 100644 biom/cli/table_subsetter.py
delete mode 100644 biom/cli/table_summarizer.py
delete mode 100644 biom/cli/uc_processor.py
delete mode 100644 biom/cli/util.py
copy {tests => biom/commands}/__init__.py (100%)
create mode 100644 biom/commands/installation_informer.py
create mode 100644 biom/commands/metadata_adder.py
create mode 100644 biom/commands/table_converter.py
create mode 100755 biom/commands/table_normalizer.py
create mode 100644 biom/commands/table_subsetter.py
create mode 100644 biom/commands/table_summarizer.py
rename biom/{cli => commands}/table_validator.py (89%)
copy {tests => biom/interfaces}/__init__.py (100%)
copy {tests => biom/interfaces/html}/__init__.py (100%)
copy {tests => biom/interfaces/html/config}/__init__.py (100%)
create mode 100644 biom/interfaces/html/config/add_metadata.py
create mode 100644 biom/interfaces/html/config/convert.py
create mode 100755 biom/interfaces/html/config/normalize_table.py
create mode 100644 biom/interfaces/html/config/show_install_info.py
create mode 100644 biom/interfaces/html/config/summarize_table.py
create mode 100644 biom/interfaces/html/config/validate_table.py
create mode 100644 biom/interfaces/html/input_handler.py
rename tests/test_cli/__init__.py => biom/interfaces/html/output_handler.py (78%)
copy {tests => biom/interfaces/optparse}/__init__.py (100%)
copy {tests => biom/interfaces/optparse/config}/__init__.py (100%)
create mode 100644 biom/interfaces/optparse/config/add_metadata.py
create mode 100644 biom/interfaces/optparse/config/convert.py
create mode 100755 biom/interfaces/optparse/config/normalize_table.py
create mode 100644 biom/interfaces/optparse/config/show_install_info.py
create mode 100644 biom/interfaces/optparse/config/subset_table.py
create mode 100644 biom/interfaces/optparse/config/summarize_table.py
create mode 100644 biom/interfaces/optparse/config/validate_table.py
create mode 100644 biom/interfaces/optparse/input_handler.py
create mode 100644 biom/interfaces/optparse/output_handler.py
create mode 100644 images/biom-logos.ai
create mode 100644 licenses/numpydoc.txt
create mode 100644 licenses/scikit-learn.txt
create mode 100644 licenses/scipy.txt
create mode 100755 scripts/biom
create mode 100644 scripts/serve-biom
delete mode 100644 setup.cfg
create mode 100644 tests/bench_tables/10000x10000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x10000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x10000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x100x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x100x0.010_bench.biom.gz
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create mode 100644 tests/bench_tables/10000x10x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x10x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x10x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz
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create mode 100644 tests/bench_tables/1000x10000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x10000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/1000x10x0.001_bench.biom.gz
copy examples/rich_sparse_otu_table_hdf5.biom => tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz (50%)
create mode 100644 tests/bench_tables/1000x10x0.010_bench.biom.gz
copy examples/rich_sparse_otu_table_hdf5.biom => tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz (50%)
create mode 100644 tests/bench_tables/1000x10x0.100_bench.biom.gz
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create mode 100644 tests/bench_tables/100x10000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/100x10000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/100x10000x0.100_bench.biom.gz
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create mode 100644 tests/bench_tables/100x1000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/100x1000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/100x100x0.001_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz (69%)
create mode 100644 tests/bench_tables/100x100x0.010_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz (69%)
create mode 100644 tests/bench_tables/100x100x0.100_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz (68%)
create mode 100644 tests/bench_tables/100x10x0.001_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz (68%)
create mode 100644 tests/bench_tables/100x10x0.010_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz (67%)
create mode 100644 tests/bench_tables/100x10x0.100_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz (70%)
create mode 100644 tests/bench_tables/10x10000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10x10000x0.010_bench.biom.gz
create mode 100644 tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10x10000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10x1000x0.001_bench.biom.gz
copy examples/rich_sparse_otu_table_hdf5.biom => tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz (50%)
create mode 100644 tests/bench_tables/10x1000x0.010_bench.biom.gz
copy examples/rich_sparse_otu_table_hdf5.biom => tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz (50%)
create mode 100644 tests/bench_tables/10x1000x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10x100x0.001_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz (69%)
create mode 100644 tests/bench_tables/10x100x0.010_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz (67%)
create mode 100644 tests/bench_tables/10x100x0.100_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz (67%)
create mode 100644 tests/bench_tables/10x10x0.001_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz (75%)
create mode 100644 tests/bench_tables/10x10x0.010_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz (75%)
create mode 100644 tests/bench_tables/10x10x0.100_bench.biom.gz
copy examples/min_sparse_otu_table_hdf5.biom => tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz (73%)
delete mode 100644 tests/test_cli/test_show_install_info.py
delete mode 100644 tests/test_cli/test_summarize_table.py
delete mode 100755 tests/test_cli/test_table_normalizer.py
delete mode 100644 tests/test_cli/test_uc_processor.py
copy tests/{ => test_commands}/__init__.py (100%)
create mode 100644 tests/test_commands/test_data/json_obs_collapsed.biom
create mode 100644 tests/test_commands/test_data/json_sample_collapsed.biom
copy examples/rich_sparse_otu_table_hdf5.biom => tests/test_commands/test_data/test.biom (96%)
create mode 100644 tests/test_commands/test_installation_informer.py
rename tests/{test_cli/test_add_metadata.py => test_commands/test_metadata_adder.py} (80%)
rename tests/{test_cli => test_commands}/test_table_converter.py (50%)
create mode 100755 tests/test_commands/test_table_normalizer.py
rename tests/{test_cli/test_subset_table.py => test_commands/test_table_subsetter.py} (65%)
create mode 100644 tests/test_commands/test_table_summarizer.py
rename tests/{test_cli/test_validate_table.py => test_commands/test_table_validator.py} (99%)
create mode 100644 tests/test_data/empty.biom
copy tests/{__init__.py => test_data/no-contents.biom} (100%)
copy examples/rich_sparse_otu_table_hdf5.biom => tests/test_data/test.biom (96%)
create mode 100644 tests/test_data/test.json
create mode 100644 tests/test_data/test.json.gz
copy tests/{ => test_interfaces}/__init__.py (100%)
copy tests/{ => test_interfaces/test_optparse}/__init__.py (100%)
create mode 100644 tests/test_interfaces/test_optparse/test_input_handler.py
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