[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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