[med-svn] [snakemake] branch upstream updated (a51fb0f -> 8111782)
Andreas Tille
tille at debian.org
Fri Jan 13 14:21:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
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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