[med-svn] [snakemake] 01/09: Merge tag 'upstream/3.9.1'

[Andreas Tille]

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tille pushed a commit to tag debian/3.9.1-1
in repository snakemake.

commit 4b3f40158a954678daeb273b173f84e698efa9ad
Merge: 48f7e7d 8111782
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 9 14:12:51 2017 +0100

    Merge tag 'upstream/3.9.1'
    
    Upstream version 3.9.1

 .dockerignore                                      |      8 +
 .gitignore                                         |      1 +
 AUTHORS.rst                                        |      0
 CHANGELOG.md                                       |     10 +
 Dockerfile                                         |      7 +
 LICENSE.md                                         |     18 +-
 bin/snakemake                                      |     20 -
 bitbucket-pipelines.yml                            |      8 -
 docs/{api.rst => api_reference/snakemake.rst}      |      2 +
 .../snakemake_utils.rst}                           |      2 +
 docs/conf.py                                       |      9 +-
 docs/executable.rst                                |    176 +
 docs/getting_started/examples.rst                  |    301 +
 docs/getting_started/img/c-dag.png                 |    Bin 0 -> 8155 bytes
 docs/getting_started/img/cufflinks-dag.png         |    Bin 0 -> 26777 bytes
 docs/getting_started/img/latex-dag.png             |    Bin 0 -> 9527 bytes
 docs/getting_started/installation.rst              |     70 +
 docs/index.rst                                     |    211 +-
 docs/project_info/authors.rst                      |     58 +
 docs/project_info/citations.rst                    |     51 +
 docs/project_info/contributing.rst                 |    205 +
 docs/project_info/faq.rst                          |    413 +
 docs/project_info/history.rst                      |      8 +
 docs/project_info/img/idea.png                     |    Bin 0 -> 43456 bytes
 docs/project_info/license.rst                      |     10 +
 docs/project_info/more_resources.rst               |     34 +
 docs/requirements.txt                              |      4 +-
 docs/snakefiles/configuration.rst                  |    111 +
 docs/snakefiles/deployment.rst                     |     81 +
 docs/snakefiles/modularization.rst                 |     99 +
 docs/snakefiles/remote_files.rst                   |    409 +
 docs/snakefiles/rules.rst                          |    695 +
 docs/snakefiles/utils.rst                          |     81 +
 docs/snakefiles/writing_snakefiles.rst             |     55 +
 docs/tutorial/additional_features.rst              |    249 +
 docs/tutorial/advanced.rst                         |    365 +
 docs/tutorial/basics.rst                           |    476 +
 docs/tutorial/welcome.rst                          |    178 +
 docs/tutorial/workflow/.gitignore                  |      1 +
 docs/tutorial/workflow/Snakefile                   |     70 +
 docs/tutorial/workflow/dag_call.png                |    Bin 0 -> 23038 bytes
 docs/tutorial/workflow/dag_index.png               |    Bin 0 -> 13781 bytes
 docs/tutorial/workflow/data/genome.fa              |   3838 +
 docs/tutorial/workflow/data/genome.fa.amb          |    228 +
 docs/tutorial/workflow/data/genome.fa.ann          |      3 +
 docs/tutorial/workflow/data/genome.fa.bwt          |    Bin 0 -> 230320 bytes
 docs/tutorial/workflow/data/genome.fa.pac          |    Bin 0 -> 57556 bytes
 docs/tutorial/workflow/data/genome.fa.sa           |    Bin 0 -> 115160 bytes
 docs/tutorial/workflow/data/samples/A.fastq        | 100000 ++++++++++++++++++
 docs/tutorial/workflow/data/samples/B.fastq        | 100000 ++++++++++++++++++
 docs/tutorial/workflow/data/samples/C.fastq        | 100000 ++++++++++++++++++
 docs/tutorial/workflow/package.sh                  |      1 +
 docs/tutorial/workflow/requirements.txt            |      9 +
 environment.yml                                    |      7 +-
 biglogo.pdf => images/biglogo.pdf                  |    Bin
 biglogo.png => images/biglogo.png                  |    Bin
 biglogo.svg => images/biglogo.svg                  |      0
 logo.png => images/logo.png                        |    Bin
 logo.svg => images/logo.svg                        |      0
 setup.py                                           |      1 -
 snakemake/__init__.py                              |     35 +-
 snakemake/__main__.py                              |      3 +
 snakemake/conda.py                                 |     19 +-
 snakemake/dag.py                                   |    127 +-
 snakemake/executors.py                             |     73 +-
 snakemake/jobs.py                                  |     15 +-
 snakemake/output_index.py                          |      8 +
 snakemake/parser.py                                |      6 +-
 snakemake/remote/FTP.py                            |     10 +-
 snakemake/remote/S3.py                             |     15 +-
 snakemake/rules.py                                 |     31 +-
 snakemake/scheduler.py                             |     31 +-
 snakemake/script.py                                |     21 +-
 snakemake/utils.py                                 |      7 +-
 snakemake/version.py                               |      2 +-
 snakemake/workflow.py                              |     28 +-
 snakemake/wrapper.py                               |      4 +-
 tests/test (with parentheses)/Snakefile            |     10 +
 .../expected-results/test.out                      |      2 +
 tests/test (with parentheses)/test.in              |      2 +
 tests/test_conda/Snakefile                         |     13 +-
 tests/test_dup_out_patterns/Snakefile              |     12 +
 .../expected-results/.gitkeep                      |      0
 tests/test_format_wildcards/Snakefile              |      9 +
 .../test_format_wildcards/expected-results/foo.txt |      1 +
 tests/test_restartable_job_cmd_exit_1/Snakefile    |     19 +
 .../expected-results/.done                         |      0
 tests/test_restartable_job_cmd_exit_1/qsub         |      7 +
 tests/test_restartable_job_cmd_exit_1/qsub.py      |     14 +
 tests/test_restartable_job_qsub_exit_1/Snakefile   |     14 +
 .../expected-results/.done                         |      0
 tests/test_restartable_job_qsub_exit_1/qsub        |     11 +
 tests/test_restartable_job_qsub_exit_1/qsub.log    |      1 +
 tests/test_restartable_job_qsub_exit_1/qsub.py     |     14 +
 tests/test_threads/Snakefile                       |      7 +
 tests/test_threads/expected-results/test.out       |      1 +
 tests/testapi.py                                   |     16 +
 tests/tests.py                                     |     66 +-
 wercker.yml                                        |     14 +
 99 files changed, 309045 insertions(+), 206 deletions(-)

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