[med-svn] [python-ruffus] branch upstream updated (ac493a8 -> 65b49ab)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository python-ruffus.

      from  ac493a8   Imported Upstream version 2.6.2+dfsg
       new  65b49ab   Imported Upstream version 2.6.3+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:
 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(-)
 create mode 100644 README.rst
 delete mode 100644 ruffus/test/auto_generated_pipeline_examples/parallel.py
 delete mode 100644 ruffus/test/auto_generated_pipeline_examples/simple.py
 delete mode 100644 ruffus/test/auto_generated_pipeline_examples/simpler.py
 create mode 100755 ruffus/test/run_all_unit_tests.cmd
 create mode 100755 ruffus/test/run_all_unit_tests3.cmd
 delete mode 100644 ruffus/test/simpler.py
 create mode 100644 ruffus/test/slow_process_for_testing.py
 create mode 100755 ruffus/test/test_drmaa_wrapper_run_job_locally.py
 create mode 100755 ruffus/test/test_proxy_logger.py
 copy ruffus/test/{test_subpipeline.py => test_subpipeline_cmdline.py} (57%)
 create mode 100755 ruffus/test/test_transform_formatter.py
 create mode 100755 ruffus/test/test_with_logger.py

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-ruffus.git