[med-svn] [python-biom-format] branch upstream updated (bbda645 -> 4838a06)
Andreas Tille
tille at debian.org
Tue Oct 27 17:59:00 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-biom-format.
from bbda645 Imported Upstream version 2.1.5+dfsg
new 4838a06 Imported Upstream version 2.1.4+dfsg
The 1 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 +-
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
.../10000x10000x0.010_bench_hdf5.biom.gz | Bin 0 -> 814036 bytes
tests/bench_tables/10000x10000x0.100_bench.biom.gz | Bin 0 -> 23248570 bytes
.../10000x10000x0.100_bench_hdf5.biom.gz | Bin 0 -> 4671830 bytes
tests/bench_tables/10000x1000x0.001_bench.biom.gz | Bin 0 -> 69230 bytes
.../10000x1000x0.001_bench_hdf5.biom.gz | Bin 0 -> 362557 bytes
tests/bench_tables/10000x1000x0.010_bench.biom.gz | Bin 0 -> 320640 bytes
.../10000x1000x0.010_bench_hdf5.biom.gz | Bin 0 -> 485677 bytes
tests/bench_tables/10000x1000x0.100_bench.biom.gz | Bin 0 -> 2659788 bytes
.../10000x1000x0.100_bench_hdf5.biom.gz | Bin 0 -> 1873395 bytes
tests/bench_tables/10000x100x0.001_bench.biom.gz | Bin 0 -> 27854 bytes
.../10000x100x0.001_bench_hdf5.biom.gz | Bin 0 -> 313875 bytes
tests/bench_tables/10000x100x0.010_bench.biom.gz | Bin 0 -> 64621 bytes
.../10000x100x0.010_bench_hdf5.biom.gz | Bin 0 -> 345814 bytes
tests/bench_tables/10000x100x0.100_bench.biom.gz | Bin 0 -> 241263 bytes
.../10000x100x0.100_bench_hdf5.biom.gz | Bin 0 -> 433017 bytes
tests/bench_tables/10000x10x0.001_bench.biom.gz | Bin 0 -> 24427 bytes
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tests/bench_tables/10000x10x0.010_bench.biom.gz | Bin 0 -> 26800 bytes
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tests/bench_tables/10000x10x0.100_bench.biom.gz | Bin 0 -> 50797 bytes
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tests/bench_tables/1000x10000x0.001_bench.biom.gz | Bin 0 -> 62599 bytes
.../1000x10000x0.001_bench_hdf5.biom.gz | Bin 0 -> 362607 bytes
tests/bench_tables/1000x10000x0.010_bench.biom.gz | Bin 0 -> 319000 bytes
.../1000x10000x0.010_bench_hdf5.biom.gz | Bin 0 -> 530288 bytes
tests/bench_tables/1000x10000x0.100_bench.biom.gz | Bin 0 -> 2588217 bytes
.../1000x10000x0.100_bench_hdf5.biom.gz | Bin 0 -> 2485734 bytes
tests/bench_tables/1000x1000x0.001_bench.biom.gz | Bin 0 -> 8166 bytes
.../1000x1000x0.001_bench_hdf5.biom.gz | Bin 0 -> 90203 bytes
tests/bench_tables/1000x1000x0.010_bench.biom.gz | Bin 0 -> 22915 bytes
.../1000x1000x0.010_bench_hdf5.biom.gz | Bin 0 -> 92248 bytes
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
.../bench_tables/1000x100x0.001_bench_hdf5.biom.gz | Bin 0 -> 65803 bytes
tests/bench_tables/1000x100x0.010_bench.biom.gz | Bin 0 -> 6512 bytes
.../bench_tables/1000x100x0.010_bench_hdf5.biom.gz | Bin 0 -> 68066 bytes
tests/bench_tables/1000x100x0.100_bench.biom.gz | Bin 0 -> 29839 bytes
.../bench_tables/1000x100x0.100_bench_hdf5.biom.gz | Bin 0 -> 80553 bytes
tests/bench_tables/1000x10x0.001_bench.biom.gz | Bin 0 -> 2795 bytes
.../bench_tables/1000x10x0.001_bench_hdf5.biom.gz | Bin 46952 -> 65803 bytes
tests/bench_tables/1000x10x0.010_bench.biom.gz | Bin 0 -> 3083 bytes
.../bench_tables/1000x10x0.010_bench_hdf5.biom.gz | Bin 46952 -> 65803 bytes
tests/bench_tables/1000x10x0.100_bench.biom.gz | Bin 0 -> 5583 bytes
.../bench_tables/1000x10x0.100_bench_hdf5.biom.gz | Bin 0 -> 67851 bytes
tests/bench_tables/100x10000x0.001_bench.biom.gz | Bin 0 -> 28147 bytes
.../100x10000x0.001_bench_hdf5.biom.gz | Bin 0 -> 315597 bytes
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
.../100x10000x0.100_bench_hdf5.biom.gz | Bin 0 -> 521065 bytes
tests/bench_tables/100x1000x0.001_bench.biom.gz | Bin 0 -> 3236 bytes
.../bench_tables/100x1000x0.001_bench_hdf5.biom.gz | Bin 0 -> 65695 bytes
tests/bench_tables/100x1000x0.010_bench.biom.gz | Bin 0 -> 6257 bytes
.../bench_tables/100x1000x0.010_bench_hdf5.biom.gz | Bin 0 -> 67743 bytes
tests/bench_tables/100x1000x0.100_bench.biom.gz | Bin 0 -> 27986 bytes
.../bench_tables/100x1000x0.100_bench_hdf5.biom.gz | Bin 0 -> 87589 bytes
tests/bench_tables/100x100x0.001_bench.biom.gz | Bin 0 -> 590 bytes
.../bench_tables/100x100x0.001_bench_hdf5.biom.gz | Bin 33800 -> 35080 bytes
tests/bench_tables/100x100x0.010_bench.biom.gz | Bin 0 -> 952 bytes
.../bench_tables/100x100x0.010_bench_hdf5.biom.gz | Bin 33800 -> 35080 bytes
tests/bench_tables/100x100x0.100_bench.biom.gz | Bin 0 -> 2395 bytes
.../bench_tables/100x100x0.100_bench_hdf5.biom.gz | Bin 33800 -> 35080 bytes
tests/bench_tables/100x10x0.001_bench.biom.gz | Bin 0 -> 527 bytes
.../bench_tables/100x10x0.001_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/100x10x0.010_bench.biom.gz | Bin 0 -> 562 bytes
.../bench_tables/100x10x0.010_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/100x10x0.100_bench.biom.gz | Bin 0 -> 808 bytes
.../bench_tables/100x10x0.100_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/10x10000x0.001_bench.biom.gz | Bin 0 -> 24370 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
.../bench_tables/10x1000x0.001_bench_hdf5.biom.gz | Bin 46952 -> 65792 bytes
tests/bench_tables/10x1000x0.010_bench.biom.gz | Bin 0 -> 3046 bytes
.../bench_tables/10x1000x0.010_bench_hdf5.biom.gz | Bin 46952 -> 65792 bytes
tests/bench_tables/10x1000x0.100_bench.biom.gz | Bin 0 -> 5308 bytes
.../bench_tables/10x1000x0.100_bench_hdf5.biom.gz | Bin 0 -> 67839 bytes
tests/bench_tables/10x100x0.001_bench.biom.gz | Bin 0 -> 527 bytes
.../bench_tables/10x100x0.001_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/10x100x0.010_bench.biom.gz | Bin 0 -> 561 bytes
.../bench_tables/10x100x0.010_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/10x100x0.100_bench.biom.gz | Bin 0 -> 770 bytes
.../bench_tables/10x100x0.100_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
tests/bench_tables/10x10x0.001_bench.biom.gz | Bin 0 -> 299 bytes
.../bench_tables/10x10x0.001_bench_hdf5.biom.gz | Bin 33800 -> 30984 bytes
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 +-
183 files changed, 4180 insertions(+), 2243 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
create mode 100644 tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/10000x100x0.100_bench.biom.gz
create mode 100644 tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz
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
create mode 100644 tests/bench_tables/1000x10000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz
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
create mode 100644 tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz
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
create mode 100644 tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz
create mode 100644 tests/bench_tables/100x1000x0.001_bench.biom.gz
create mode 100644 tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz
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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