[med-svn] [python-ruffus] branch upstream updated (1cce2f7 -> ac493a8)
Andreas Tille
tille at debian.org
Thu Mar 12 20:52:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-ruffus.
from 1cce2f7 Imported Upstream version 2.5+dfsg
new ac493a8 Imported Upstream version 2.6.2+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:
CHANGES.TXT | 78 +
PKG-INFO | 2 +-
doc/Makefile | 2 +-
doc/_build/latex/ruffus.pdf | Bin 4513083 -> 4688129 bytes
doc/_templates/index.html | 23 +-
doc/_templates/layout.html | 2 +-
doc/contents.rst | 3 +
doc/decorators/active_if.rst | 2 +-
doc/decorators/check_if_uptodate.rst | 1 +
doc/decorators/collate.rst | 105 +-
doc/decorators/collate_ex.rst | 105 +-
doc/decorators/combinations.rst | 239 +-
doc/decorators/combinations_with_replacement.rst | 238 +-
doc/decorators/files.rst | 6 +-
doc/decorators/files_ex.rst | 2 +-
doc/decorators/follows.rst | 2 +-
doc/decorators/graphviz.rst | 1 +
doc/decorators/indicator_objects.rst | 5 +-
doc/decorators/jobs_limit.rst | 2 +-
doc/decorators/merge.rst | 46 +-
doc/decorators/mkdir.rst | 59 +-
doc/decorators/originate.rst | 40 +-
doc/decorators/parallel.rst | 2 +-
doc/decorators/permutations.rst | 232 +-
doc/decorators/posttask.rst | 1 +
doc/decorators/product.rst | 295 +-
doc/decorators/split.rst | 68 +-
doc/decorators/subdivide.rst | 45 +-
doc/decorators/transform.rst | 72 +-
doc/decorators/transform_ex.rst | 136 +-
doc/examples/bioinformatics/part2.rst | 2 +-
doc/faq.rst | 36 +-
doc/global.inc | 11 +-
doc/history.rst | 174 +-
doc/images/small_logo.png | Bin 0 -> 14521 bytes
doc/images/subpipeline_example.png | Bin 0 -> 65279 bytes
doc/implementation_notes.rst | 434 +-
doc/installation.rst | 61 +-
.../example_scripts/play_with_colours.py | 2 +-
doc/static_data/example_scripts/simpler.py | 46 +-
doc/static_data/ruffus.pdf | Bin 4513083 -> 4688129 bytes
doc/static_data/small_logo.png | Bin 0 -> 14521 bytes
doc/todo.rst | 226 +-
doc/tutorials/new_syntax.rst | 485 ++
doc/tutorials/new_syntax_worked_example.rst | 355 ++
doc/tutorials/new_syntax_worked_example_code.rst | 222 +
doc/tutorials/new_tutorial/checkpointing_code.rst | 36 +-
.../new_tutorial/flowchart_colours_code.rst | 2 +-
doc/tutorials/new_tutorial/parallel.rst | 1 +
.../new_tutorial/pipeline_printout_graph.rst | 3 +
ruffus/__init__.py | 23 +-
ruffus/cmdline.py | 6 +-
ruffus/drmaa_wrapper.py | 50 +-
ruffus/file_name_parameters.py | 218 +-
ruffus/graph.py | 299 +-
ruffus/parse_old_style_ruffus.py | 268 +
ruffus/print_dependencies.py | 37 +-
ruffus/proxy_logger.py | 2 +
ruffus/ruffus_exceptions.py | 42 +-
ruffus/ruffus_utility.py | 456 +-
ruffus/ruffus_version.py | 2 +-
ruffus/task.py | 5968 +++++++++++++-------
.../auto_generated_pipeline_examples/parallel.py | 4 +-
.../auto_generated_pipeline_examples/simple.py | 4 +-
.../auto_generated_pipeline_examples/simpler.py | 4 +-
.../create_test_script_from_dependency_tree.py | 78 +-
ruffus/test/draw_specified_dependency_tree.py | 40 +-
...eptions.py => manual_test_ctrl_c_exceptions.py} | 0
.../test/{test_drmaa.py => manual_test_drmaa.py} | 0
ruffus/test/play_with_colours.py | 2 +-
ruffus/test/simpler_at_runtime.py | 253 -
ruffus/test/simpler_with_shared_logging.py | 2 +-
ruffus/test/test_N_x_M_and_collate.py | 223 +-
ruffus/test/test_active_if.py | 165 +-
ruffus/test/test_branching_dependencies.py | 392 +-
ruffus/test/test_cmdline.py | 47 +-
ruffus/test/test_collate.py | 223 +-
ruffus/test/test_combinatorics.py | 75 +-
ruffus/test/test_empty_files_decorator.py | 184 +-
ruffus/test/test_exceptions.py | 69 +-
ruffus/test/test_file_name_parameters.py | 387 +-
ruffus/test/test_files_decorator.py | 186 +-
ruffus/test/test_files_post_merge.py | 299 -
ruffus/test/test_filesre_combine.py | 191 +-
ruffus/test/test_filesre_split_and_combine.py | 257 +-
ruffus/test/test_follows_mkdir.py | 180 +-
ruffus/test/test_graphviz.py | 138 +-
..._inputs_with_multiple_args_raising_exception.py | 198 +-
ruffus/test/test_job_completion_checksums.py | 404 +-
ruffus/test/test_job_history_with_exceptions.py | 170 +-
ruffus/test/test_mkdir.py | 66 +-
...inatorics.py => test_newstyle_combinatorics.py} | 306 +-
ruffus/test/test_newstyle_proxy.py | 181 +
...es.py => test_newstyle_regex_error_messages.py} | 197 +-
ruffus/test/test_pausing.py | 294 +-
ruffus/test/test_pipeline_printout_graph.py | 205 +
ruffus/test/test_posttask_merge.py | 244 +
ruffus/test/test_regex_error_messages.py | 48 +-
ruffus/test/test_ruffus_utility.py | 170 +-
.../test_ruffus_utility_parse_task_arguments.py | 713 +++
ruffus/test/test_runtime_data.py | 187 +
ruffus/test/test_softlink_uptodate.py | 151 +-
ruffus/test/test_split_and_combine.py | 287 +-
ruffus/test/test_split_regex_and_collate.py | 115 +-
ruffus/test/test_split_subdivide_checkpointing.py | 239 +
ruffus/test/test_subpipeline.py | 201 +
ruffus/test/test_suffix_output_dir.py | 259 +
ruffus/test/test_task_file_dependencies.py | 130 +-
ruffus/test/test_task_misc.py | 63 +-
ruffus/test/test_transform_add_inputs.py | 234 +-
ruffus/test/test_transform_inputs.py | 207 +-
ruffus/test/test_transform_with_no_re_matches.py | 194 +-
ruffus/test/test_tutorial7.py | 137 +-
ruffus/test/test_unicode_filenames.py | 185 +-
ruffus/test/test_verbosity.py | 137 +-
115 files changed, 13423 insertions(+), 7183 deletions(-)
create mode 100644 doc/images/small_logo.png
create mode 100644 doc/images/subpipeline_example.png
create mode 100644 doc/static_data/small_logo.png
create mode 100644 doc/tutorials/new_syntax.rst
create mode 100644 doc/tutorials/new_syntax_worked_example.rst
create mode 100644 doc/tutorials/new_syntax_worked_example_code.rst
create mode 100755 ruffus/parse_old_style_ruffus.py
rename ruffus/test/{test_ctrl_c_exceptions.py => manual_test_ctrl_c_exceptions.py} (100%)
rename ruffus/test/{test_drmaa.py => manual_test_drmaa.py} (100%)
delete mode 100755 ruffus/test/simpler_at_runtime.py
delete mode 100755 ruffus/test/test_files_post_merge.py
copy ruffus/test/{test_combinatorics.py => test_newstyle_combinatorics.py} (56%)
create mode 100755 ruffus/test/test_newstyle_proxy.py
copy ruffus/test/{test_regex_error_messages.py => test_newstyle_regex_error_messages.py} (68%)
create mode 100755 ruffus/test/test_pipeline_printout_graph.py
create mode 100755 ruffus/test/test_posttask_merge.py
create mode 100755 ruffus/test/test_ruffus_utility_parse_task_arguments.py
create mode 100755 ruffus/test/test_runtime_data.py
create mode 100755 ruffus/test/test_split_subdivide_checkpointing.py
create mode 100755 ruffus/test/test_subpipeline.py
create mode 100755 ruffus/test/test_suffix_output_dir.py
mode change 100644 => 100755 ruffus/test/test_transform_inputs.py
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