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tille pushed a change to branch upstream
in repository snakemake.

      from  a51fb0f   New upstream version 3.9.0+dfsg
      adds  8111782   New upstream version 3.9.1

No new revisions were added by this update.

Summary of changes:
 .dockerignore                                      |      8 +
 .gitignore                                         |      1 +
 examples/cufflinks/hg19.fa => 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 +
 .../dag.png => docs/getting_started/img/c-dag.png  |    Bin
 .../getting_started/img/cufflinks-dag.png          |    Bin
 .../getting_started/img/latex-dag.png              |    Bin
 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 +
 {examples/idea => docs/project_info/img}/idea.png  |    Bin
 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 +-
 .../Snakefile                                      |      0
 .../expected-results/test.out                      |      0
 .../test.in                                        |      0
 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
 .../qsub                                           |      1 +
 .../qsub.py                                        |      0
 tests/test_restartable_job_qsub_exit_1/Snakefile   |     14 +
 .../expected-results/.done                         |      0
 .../qsub                                           |      5 +
 tests/test_restartable_job_qsub_exit_1/qsub.log    |      1 +
 .../qsub.py                                        |      0
 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, 308991 insertions(+), 206 deletions(-)
 create mode 100644 .dockerignore
 copy examples/cufflinks/hg19.fa => AUTHORS.rst (100%)
 create mode 100644 Dockerfile
 delete mode 100755 bin/snakemake
 delete mode 100644 bitbucket-pipelines.yml
 rename docs/{api.rst => api_reference/snakemake.rst} (71%)
 rename docs/{utils.rst => api_reference/snakemake_utils.rst} (83%)
 create mode 100644 docs/executable.rst
 create mode 100644 docs/getting_started/examples.rst
 copy examples/c/src/dag.png => docs/getting_started/img/c-dag.png (100%)
 copy examples/cufflinks/dag.png => docs/getting_started/img/cufflinks-dag.png 
(100%)
 copy examples/latex/dag.png => docs/getting_started/img/latex-dag.png (100%)
 create mode 100644 docs/getting_started/installation.rst
 create mode 100644 docs/project_info/authors.rst
 create mode 100644 docs/project_info/citations.rst
 create mode 100644 docs/project_info/contributing.rst
 create mode 100644 docs/project_info/faq.rst
 create mode 100644 docs/project_info/history.rst
 copy {examples/idea => docs/project_info/img}/idea.png (100%)
 create mode 100644 docs/project_info/license.rst
 create mode 100644 docs/project_info/more_resources.rst
 create mode 100644 docs/snakefiles/configuration.rst
 create mode 100644 docs/snakefiles/deployment.rst
 create mode 100644 docs/snakefiles/modularization.rst
 create mode 100644 docs/snakefiles/remote_files.rst
 create mode 100644 docs/snakefiles/rules.rst
 create mode 100644 docs/snakefiles/utils.rst
 create mode 100644 docs/snakefiles/writing_snakefiles.rst
 create mode 100644 docs/tutorial/additional_features.rst
 create mode 100644 docs/tutorial/advanced.rst
 create mode 100644 docs/tutorial/basics.rst
 create mode 100644 docs/tutorial/welcome.rst
 create mode 100644 docs/tutorial/workflow/.gitignore
 create mode 100644 docs/tutorial/workflow/Snakefile
 create mode 100644 docs/tutorial/workflow/dag_call.png
 create mode 100644 docs/tutorial/workflow/dag_index.png
 create mode 100644 docs/tutorial/workflow/data/genome.fa
 create mode 100644 docs/tutorial/workflow/data/genome.fa.amb
 create mode 100644 docs/tutorial/workflow/data/genome.fa.ann
 create mode 100644 docs/tutorial/workflow/data/genome.fa.bwt
 create mode 100644 docs/tutorial/workflow/data/genome.fa.pac
 create mode 100644 docs/tutorial/workflow/data/genome.fa.sa
 create mode 100644 docs/tutorial/workflow/data/samples/A.fastq
 create mode 100644 docs/tutorial/workflow/data/samples/B.fastq
 create mode 100644 docs/tutorial/workflow/data/samples/C.fastq
 create mode 100755 docs/tutorial/workflow/package.sh
 create mode 100644 docs/tutorial/workflow/requirements.txt
 rename biglogo.pdf => images/biglogo.pdf (100%)
 rename biglogo.png => images/biglogo.png (100%)
 rename biglogo.svg => images/biglogo.svg (100%)
 rename logo.png => images/logo.png (100%)
 rename logo.svg => images/logo.svg (100%)
 create mode 100644 snakemake/__main__.py
 copy tests/{test_shell => test (with parentheses)}/Snakefile (100%)
 copy tests/{test_get_log_both => test (with 
parentheses)}/expected-results/test.out (100%)
 copy tests/{test_get_log_both => test (with parentheses)}/test.in (100%)
 create mode 100644 tests/test_dup_out_patterns/Snakefile
 copy examples/cufflinks/hg19.fa => 
tests/test_dup_out_patterns/expected-results/.gitkeep (100%)
 create mode 100644 tests/test_format_wildcards/Snakefile
 create mode 100644 tests/test_format_wildcards/expected-results/foo.txt
 create mode 100644 tests/test_restartable_job_cmd_exit_1/Snakefile
 copy examples/cufflinks/hg19.fa => 
tests/test_restartable_job_cmd_exit_1/expected-results/.done (100%)
 copy tests/{test14 => test_restartable_job_cmd_exit_1}/qsub (94%)
 copy tests/{test14 => test_restartable_job_cmd_exit_1}/qsub.py (100%)
 create mode 100644 tests/test_restartable_job_qsub_exit_1/Snakefile
 copy examples/cufflinks/hg19.fa => 
tests/test_restartable_job_qsub_exit_1/expected-results/.done (100%)
 copy tests/{test14 => test_restartable_job_qsub_exit_1}/qsub (55%)
 create mode 100644 tests/test_restartable_job_qsub_exit_1/qsub.log
 copy tests/{test14 => test_restartable_job_qsub_exit_1}/qsub.py (100%)
 create mode 100644 tests/test_threads/Snakefile
 create mode 100644 tests/test_threads/expected-results/test.out
 create mode 100644 wercker.yml

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