[med-svn] [snakemake] branch master updated (48f7e7d -> c0dfa18)
Andreas Tille
tille at debian.org
Fri Jan 13 14:21:00 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository snakemake.
from 48f7e7d Upload to unstable
adds 8111782 New upstream version 3.9.1
adds 4b3f401 Merge tag 'upstream/3.9.1'
adds a3171d8 New upstream version
adds ca552f3 Refresh patches
adds eae0392 New Build-Depends: python3-sphinx-rtd-theme
adds 1ca7ec8 ersion 3.9.1 is lacking snakemake executable - using copy from 3.9.0 created via this quilt patch to enable running build time tests
adds 745fd19 Remove duplicated license file in doc
adds a0c4e18 Ignore extra license file
adds 07179f5 Rather than using copy of old version use what we get inside the release as the executable for testing
adds c0dfa18 Upload to unstable
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 -
debian/changelog | 8 +
debian/control | 1 +
.../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 | 20 +
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 +
.../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 +
110 files changed, 309030 insertions(+), 220 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
create mode 100644 debian/patches/0006-restore-bin.patch
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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