[med-svn] [python-ruffus] 04/05: Merge tag 'upstream/2.6.2+dfsg'
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 commit to branch master
in repository python-ruffus.
commit 96753bab54398142c4c3235a99b497970b4ce214
Merge: 14d47ab ac493a8
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 12 21:50:36 2015 +0100
Merge tag 'upstream/2.6.2+dfsg'
Upstream version 2.6.2+dfsg
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(-)
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