[med-svn] [python-ruffus] 02/03: Merge tag 'upstream/2.6.3+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository python-ruffus.

commit c3e0b980fc7af1a021d37e7902fbea76bee7a8b9
Merge: 38a066a 65b49ab
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 17 22:03:57 2015 +0200

    Merge tag 'upstream/2.6.3+dfsg'
    
    Upstream version 2.6.3+dfsg

 PKG-INFO                                           |   2 +-
 README.rst                                         | 127 ++++
 doc/_build/latex/ruffus.pdf                        | Bin 4688129 -> 4690982 bytes
 doc/history.rst                                    |  22 +-
 doc/implementation_notes.rst                       |  27 -
 doc/static_data/ruffus.pdf                         | Bin 4688129 -> 4690982 bytes
 doc/todo.rst                                       |  50 +-
 doc/tutorials/new_syntax_worked_example_code.rst   | 186 ++++--
 ruffus/drmaa_wrapper.py                            |  87 ++-
 ruffus/file_name_parameters.py                     |  35 +-
 ruffus/proxy_logger.py                             |  45 --
 ruffus/ruffus_exceptions.py                        |   4 +
 ruffus/ruffus_utility.py                           |  64 +-
 ruffus/ruffus_version.py                           |   2 +-
 ruffus/task.py                                     | 642 ++++++++++++---------
 .../auto_generated_pipeline_examples/parallel.py   | 228 --------
 .../auto_generated_pipeline_examples/simple.py     | 253 --------
 .../auto_generated_pipeline_examples/simpler.py    | 269 ---------
 ruffus/test/complicated_example.py                 |   6 +-
 .../create_test_script_from_dependency_tree.py     |   3 +-
 ruffus/test/manual_test_ctrl_c_exceptions.py       |   2 +-
 ruffus/test/play_with_colours.py                   |   3 +-
 ruffus/test/run_all_unit_tests.cmd                 |  93 +++
 ruffus/test/run_all_unit_tests3.cmd                |  93 +++
 ruffus/test/simpler.py                             | 234 --------
 ruffus/test/simpler_with_shared_logging.py         |   9 +-
 ruffus/test/slow_process_for_testing.py            |  22 +
 ruffus/test/test_N_x_M_and_collate.py              |  27 +-
 ruffus/test/test_active_if.py                      |  23 +-
 ruffus/test/test_branching_dependencies.py         |  22 +-
 ruffus/test/test_cmdline.py                        |  20 +-
 ruffus/test/test_collate.py                        |  17 +-
 ruffus/test/test_combinatorics.py                  | 160 +++--
 ruffus/test/test_drmaa_wrapper_run_job_locally.py  |  86 +++
 ruffus/test/test_empty_files_decorator.py          |  14 +-
 ruffus/test/test_exceptions.py                     |   9 +-
 ruffus/test/test_file_name_parameters.py           | 510 ++++++++--------
 ruffus/test/test_files_decorator.py                |  28 +-
 ruffus/test/test_filesre_combine.py                |  21 +-
 ruffus/test/test_filesre_split_and_combine.py      |  21 +-
 ruffus/test/test_follows_mkdir.py                  |  32 +-
 ruffus/test/test_graphviz.py                       |  18 +-
 ..._inputs_with_multiple_args_raising_exception.py |  31 +-
 ruffus/test/test_job_completion_checksums.py       |  86 ++-
 ruffus/test/test_job_history_with_exceptions.py    |  57 +-
 ruffus/test/test_mkdir.py                          |  43 +-
 ruffus/test/test_newstyle_combinatorics.py         | 125 ++--
 ruffus/test/test_newstyle_proxy.py                 |  39 +-
 ruffus/test/test_newstyle_regex_error_messages.py  |  37 +-
 ruffus/test/test_pausing.py                        |  18 +-
 ruffus/test/test_pipeline_printout_graph.py        |  19 +-
 ruffus/test/test_posttask_merge.py                 |  21 +-
 ruffus/test/test_proxy_logger.py                   |  78 +++
 ruffus/test/test_regex_error_messages.py           |  39 +-
 ruffus/test/test_ruffus_utility.py                 |  20 +-
 .../test_ruffus_utility_parse_task_arguments.py    |  51 +-
 ruffus/test/test_runtime_data.py                   |  35 +-
 ruffus/test/test_softlink_uptodate.py              |  24 +-
 ruffus/test/test_split_and_combine.py              |  13 +-
 ruffus/test/test_split_regex_and_collate.py        |  25 +-
 ruffus/test/test_split_subdivide_checkpointing.py  |  24 +-
 ruffus/test/test_subpipeline.py                    |  33 +-
 ..._subpipeline.py => test_subpipeline_cmdline.py} | 134 +++--
 ruffus/test/test_suffix_output_dir.py              | 204 ++++---
 ruffus/test/test_task_file_dependencies.py         |  16 +-
 ruffus/test/test_task_misc.py                      |   7 +-
 ruffus/test/test_transform_add_inputs.py           |   8 +-
 ruffus/test/test_transform_formatter.py            | 147 +++++
 ruffus/test/test_transform_inputs.py               |  19 +-
 ruffus/test/test_transform_with_no_re_matches.py   |  33 +-
 ruffus/test/test_tutorial7.py                      |  44 +-
 ruffus/test/test_unicode_filenames.py              |  59 +-
 ruffus/test/test_verbosity.py                      |  55 +-
 ruffus/test/test_with_logger.py                    | 214 +++++++
 74 files changed, 2665 insertions(+), 2609 deletions(-)

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