[med-svn] [python-biom-format] 03/05: Merge tag 'upstream/2.1.4+dfsg'
Andreas Tille
tille at debian.org
Tue Oct 27 17:58:59 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-biom-format.
commit 65f68e05a5f94a639795232329848a59689f060d
Merge: ee0aee3 4838a06
Author: Andreas Tille <tille at debian.org>
Date: Tue Oct 27 18:32:00 2015 +0100
Merge tag 'upstream/2.1.4+dfsg'
Upstream version 2.1.4+dfsg
.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 -
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 +-
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/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 +-
biom/interfaces/optparse/__init__.py | 0
biom/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
.../bench_tables/10000x10x0.001_bench_hdf5.biom.gz | Bin 0 -> 311609 bytes
tests/bench_tables/10000x10x0.010_bench.biom.gz | Bin 0 -> 26800 bytes
.../bench_tables/10000x10x0.010_bench_hdf5.biom.gz | Bin 0 -> 313657 bytes
tests/bench_tables/10000x10x0.100_bench.biom.gz | Bin 0 -> 50797 bytes
.../bench_tables/10000x10x0.100_bench_hdf5.biom.gz | Bin 0 -> 340159 bytes
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 0 -> 65803 bytes
tests/bench_tables/1000x10x0.010_bench.biom.gz | Bin 0 -> 3083 bytes
.../bench_tables/1000x10x0.010_bench_hdf5.biom.gz | Bin 0 -> 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
.../100x10000x0.010_bench_hdf5.biom.gz | Bin 0 -> 345664 bytes
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 0 -> 35080 bytes
tests/bench_tables/100x100x0.010_bench.biom.gz | Bin 0 -> 952 bytes
.../bench_tables/100x100x0.010_bench_hdf5.biom.gz | Bin 0 -> 35080 bytes
tests/bench_tables/100x100x0.100_bench.biom.gz | Bin 0 -> 2395 bytes
.../bench_tables/100x100x0.100_bench_hdf5.biom.gz | Bin 0 -> 35080 bytes
tests/bench_tables/100x10x0.001_bench.biom.gz | Bin 0 -> 527 bytes
tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/100x10x0.010_bench.biom.gz | Bin 0 -> 562 bytes
tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/100x10x0.100_bench.biom.gz | Bin 0 -> 808 bytes
tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x10000x0.001_bench.biom.gz | Bin 0 -> 24370 bytes
.../bench_tables/10x10000x0.001_bench_hdf5.biom.gz | Bin 0 -> 311616 bytes
tests/bench_tables/10x10000x0.010_bench.biom.gz | Bin 0 -> 26450 bytes
.../bench_tables/10x10000x0.010_bench_hdf5.biom.gz | Bin 0 -> 313659 bytes
tests/bench_tables/10x10000x0.100_bench.biom.gz | Bin 0 -> 49427 bytes
.../bench_tables/10x10000x0.100_bench_hdf5.biom.gz | Bin 0 -> 340204 bytes
tests/bench_tables/10x1000x0.001_bench.biom.gz | Bin 0 -> 2795 bytes
.../bench_tables/10x1000x0.001_bench_hdf5.biom.gz | Bin 0 -> 65792 bytes
tests/bench_tables/10x1000x0.010_bench.biom.gz | Bin 0 -> 3046 bytes
.../bench_tables/10x1000x0.010_bench_hdf5.biom.gz | Bin 0 -> 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
tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x100x0.010_bench.biom.gz | Bin 0 -> 561 bytes
tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x100x0.100_bench.biom.gz | Bin 0 -> 770 bytes
tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x10x0.001_bench.biom.gz | Bin 0 -> 299 bytes
tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x10x0.010_bench.biom.gz | Bin 0 -> 301 bytes
tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz | Bin 0 -> 30984 bytes
tests/bench_tables/10x10x0.100_bench.biom.gz | Bin 0 -> 334 bytes
tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz | Bin 0 -> 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 +
tests/test_commands/test_data/test.biom | Bin 0 -> 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/test_data/no-contents.biom | 0
tests/test_data/test.biom | Bin 0 -> 46952 bytes
tests/test_data/test.json | 1 +
tests/test_data/test.json.gz | Bin 0 -> 678 bytes
tests/test_interfaces/__init__.py | 0
tests/test_interfaces/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(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biom-format.git
More information about the debian-med-commit
mailing list