[med-svn] [python-biom-format] branch master updated (1c11ad6 -> f3bf690)
Andreas Tille
tille at debian.org
Thu Feb 11 16:02:30 UTC 2016
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 1c11ad6 Adopt changes of package revision 2.1.4+dfsg-2 into current packaging
new bc750a1 Make sure xz compression of repackaged tarball will happen automatically
new a907dbe Do actual changes needed for new version that were mentioned as TODO items
new 20df9f6 Imported Upstream version 2.1.5+dfsg
new ca6e289 Merge tag 'upstream/2.1.5+dfsg'
new f3bf690 Try hard to run all tests but failed
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:
.travis.yml | 29 ++-
ChangeLog.md | 33 ++-
INSTALL | 24 --
MANIFEST.in | 1 -
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/{commands => cli}/table_validator.py | 107 +++++----
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/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 -----
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 +-
debian/changelog | 4 +-
debian/control | 2 +-
debian/rules | 18 +-
debian/watch | 2 +-
doc/conf.py | 4 +-
doc/index.rst | 88 ++-----
scripts/biom | 22 --
scripts/serve-biom | 11 -
setup.py | 40 ++--
.../test_cli/__init__.py | 4 +-
.../test_add_metadata.py} | 47 +---
.../test_data/json_obs_collapsed.biom | 0
.../test_data/json_sample_collapsed.biom | 0
.../test_data/test.biom | Bin
tests/test_cli/test_data/test.json | 1 +
tests/test_cli/test_show_install_info.py | 24 ++
.../test_subset_table.py} | 82 +++----
tests/test_cli/test_summarize_table.py | 122 ++++++++++
.../test_table_converter.py | 256 +++++++++-----------
tests/test_cli/test_table_normalizer.py | 50 ++++
tests/test_cli/test_uc_processor.py | 109 +++++++++
.../test_validate_table.py} | 2 +-
tests/test_commands/__init__.py | 0
tests/test_commands/test_installation_informer.py | 40 ----
tests/test_commands/test_table_normalizer.py | 56 -----
tests/test_commands/test_table_summarizer.py | 132 -----------
tests/test_data/test.json | 2 +-
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 +-
81 files changed, 2235 insertions(+), 2965 deletions(-)
delete mode 100644 INSTALL
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 (89%)
create mode 100644 biom/cli/uc_processor.py
create mode 100644 biom/cli/util.py
delete mode 100644 biom/commands/__init__.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 100755 biom/commands/table_normalizer.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 100755 biom/interfaces/html/config/normalize_table.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 100755 biom/interfaces/optparse/config/normalize_table.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 100755 scripts/biom
delete mode 100644 scripts/serve-biom
rename biom/interfaces/html/output_handler.py => tests/test_cli/__init__.py (78%)
rename tests/{test_commands/test_metadata_adder.py => test_cli/test_add_metadata.py} (80%)
rename tests/{test_commands => test_cli}/test_data/json_obs_collapsed.biom (100%)
rename tests/{test_commands => test_cli}/test_data/json_sample_collapsed.biom (100%)
rename tests/{test_commands => test_cli}/test_data/test.biom (100%)
create mode 100644 tests/test_cli/test_data/test.json
create mode 100644 tests/test_cli/test_show_install_info.py
rename tests/{test_commands/test_table_subsetter.py => test_cli/test_subset_table.py} (65%)
create mode 100644 tests/test_cli/test_summarize_table.py
rename tests/{test_commands => test_cli}/test_table_converter.py (50%)
create mode 100755 tests/test_cli/test_table_normalizer.py
create mode 100644 tests/test_cli/test_uc_processor.py
rename tests/{test_commands/test_table_validator.py => test_cli/test_validate_table.py} (99%)
delete mode 100644 tests/test_commands/__init__.py
delete mode 100644 tests/test_commands/test_installation_informer.py
delete mode 100755 tests/test_commands/test_table_normalizer.py
delete mode 100644 tests/test_commands/test_table_summarizer.py
delete mode 100644 tests/test_interfaces/__init__.py
delete mode 100644 tests/test_interfaces/test_optparse/__init__.py
delete mode 100644 tests/test_interfaces/test_optparse/test_input_handler.py
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