[med-svn] [python-biom-format] branch upstream updated (4838a06 -> 20df9f6)
Andreas Tille
tille at debian.org
Thu Feb 11 16:02:31 UTC 2016
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 4838a06 Imported Upstream version 2.1.4+dfsg
new 20df9f6 Imported Upstream version 2.1.5+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:
.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 +-
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 +-
77 files changed, 2224 insertions(+), 2950 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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