[med-svn] [python-ruffus] branch master updated (f4f7c9d -> ac9fbf0)
Andreas Tille
tille at debian.org
Thu Mar 12 20:52:31 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository python-ruffus.
from f4f7c9d Fix clean target
new 286459a Add doc-base control files
new 14d47ab Upstream plans a new release based on our hints. This packaging should match the new release
new ac493a8 Imported Upstream version 2.6.2+dfsg
new 96753ba Merge tag 'upstream/2.6.2+dfsg'
new ac9fbf0 Update packaging to new upstream release
The 5 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 +-
debian/changelog | 2 +-
debian/patches/run_test_executable.patch | 174 +
debian/patches/series | 1 +
debian/python-ruffus-doc.doc-base.html | 18 +
debian/python-ruffus-doc.doc-base.pdf | 17 +
debian/python-ruffus-doc.docs | 2 +-
debian/rules | 17 +-
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 +-
122 files changed, 13646 insertions(+), 7191 deletions(-)
create mode 100644 debian/patches/run_test_executable.patch
create mode 100644 debian/patches/series
create mode 100644 debian/python-ruffus-doc.doc-base.html
create mode 100644 debian/python-ruffus-doc.doc-base.pdf
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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