[med-svn] [snakemake] 01/02: Merge tag 'debian/3.10.0-1' into debian/jessie-backports

Andreas Tille tille at debian.org
Tue Jul 18 07:13:11 UTC 2017


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

tille pushed a commit to branch debian/jessie-backports
in repository snakemake.

commit 4de9e65b14cc37e7bba164beffd70cff64b5f562
Merge: 282d10c 54f4469
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 9 20:35:12 2017 +0200

    Merge tag 'debian/3.10.0-1' into debian/jessie-backports

 .dockerignore                                      |      8 +
 .gitignore                                         |      1 +
 AUTHORS.rst                                        |      0
 CHANGELOG.md                                       |     22 +
 Dockerfile                                         |      7 +
 LICENSE.md                                         |     18 +-
 bin/snakemake                                      |     20 -
 bitbucket-pipelines.yml                            |      8 -
 debian/changelog                                   |     40 +-
 debian/control                                     |      3 +-
 .../0001-Use-the-inbuild-sphinx.ext.napoleon.patch |      4 +-
 debian/patches/0003-Compat-fix.patch               |      4 +-
 .../0003-Use-debian-s-mathjax-package.patch        |      6 +-
 .../0004-drop_test_symlink_time_handling.patch     |      2 +-
 debian/patches/0005-drop_test_symlink_temp.patch   |      2 +-
 debian/patches/0006-restore-bin.patch              |     14 +
 debian/patches/series                              |      1 +
 debian/rules                                       |      4 +-
 debian/snakemake.lintian-overrides                 |      1 +
 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                          |    736 +
 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                              |     57 +-
 snakemake/__main__.py                              |      3 +
 snakemake/common.py                                |     24 +
 snakemake/conda.py                                 |    128 +-
 snakemake/dag.py                                   |    226 +-
 snakemake/executors.py                             |     86 +-
 snakemake/io.py                                    |     32 +-
 snakemake/jobs.py                                  |     80 +-
 snakemake/logging.py                               |     72 +-
 snakemake/output_index.py                          |      8 +
 snakemake/parser.py                                |      6 +-
 snakemake/persistence.py                           |      4 +-
 snakemake/remote/FTP.py                            |     10 +-
 snakemake/remote/HTTP.py                           |      3 +
 snakemake/remote/S3.py                             |     15 +-
 snakemake/rules.py                                 |     88 +-
 snakemake/scheduler.py                             |     31 +-
 snakemake/script.py                                |     34 +-
 snakemake/utils.py                                 |      7 +-
 snakemake/version.py                               |      2 +-
 snakemake/workflow.py                              |     39 +-
 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_parser/Snakefile                        |      3 +-
 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/test_unpack_dict/Snakefile                   |     27 +
 .../expected-results/prefix.out1.txt               |      1 +
 .../expected-results/prefix.out2.txt               |      1 +
 tests/test_unpack_dict/prefix.in1.txt              |      1 +
 tests/test_unpack_dict/prefix.in2.txt              |      1 +
 tests/test_unpack_list/Snakefile                   |     27 +
 .../expected-results/prefix.out1.txt               |      1 +
 .../expected-results/prefix.out2.txt               |      1 +
 tests/test_unpack_list/prefix.in1.txt              |      1 +
 tests/test_unpack_list/prefix.in2.txt              |      1 +
 tests/testapi.py                                   |     16 +
 tests/tests.py                                     |     74 +-
 wercker.yml                                        |     14 +
 126 files changed, 309643 insertions(+), 339 deletions(-)

diff --cc debian/changelog
index 2e0fe59,14058c1..390e918
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,27 +1,33 @@@
+ snakemake (3.10.0-1) unstable; urgency=medium
+ 
+   * New upstream version 3.10.0
+   * Refresh patches
+ 
+  -- Kevin Murray <kdmfoss at gmail.com>  Thu, 19 Jan 2017 11:41:55 +1100
+ 
+ snakemake (3.9.1-2) unstable; urgency=medium
+ 
+   * Future-proof patch to work-around missing snakemake binary when running
+     tests before installation
+   * Backport fix for crash with dynamic rules (from bitbucket PR #168).
+   * Update my email address
+ 
+  -- Kevin Murray <kdmfoss at gmail.com>  Wed, 18 Jan 2017 00:20:04 +0000
+ 
+ snakemake (3.9.1-1) unstable; urgency=medium
+ 
+   * Team upload
+   * New upstream version
+   * New Build-Depends: python3-sphinx-rtd-theme
+ 
+  -- Andreas Tille <tille at debian.org>  Fri, 13 Jan 2017 15:03:15 +0100
+ 
 +snakemake (3.9.0+dfsg-2~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Andreas Tille <tille at debian.org>  Tue, 17 Jan 2017 16:18:01 +0100
 +
  snakemake (3.9.0+dfsg-2) unstable; urgency=medium
  
    * Team upload.

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