[med-svn] [snakemake] branch master updated (afcb2de -> 5fb1243)
chrysn
chrysn-guest at moszumanska.debian.org
Mon Dec 4 21:27:33 UTC 2017
This is an automated email from the git hooks/post-receive script.
chrysn-guest pushed a change to branch master
in repository snakemake.
from afcb2de Add d/upstream/metadata
new 06602fe New upstream version 4.3.0
new 2663972 Update upstream source from tag 'upstream/4.3.0'
new d2c7d1c Acknowledge new upstream version in changelog
new 205c70e Refresh patches
new 1147eb7 Add dependency on configargparse
new 5fb1243 Temporarily patch out rate limiter
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CHANGELOG.md | 51 ++
Dockerfile | 14 +-
debian/changelog | 7 +-
debian/control | 1 +
.../0001-Use-the-inbuild-sphinx.ext.napoleon.patch | 8 +-
.../0003-Use-debian-s-mathjax-package.patch | 4 +-
debian/patches/0007-noop-rate-limiter.patch | 36 ++
debian/patches/series | 1 +
docs/_static/sphinx-argparse.css | 6 +
docs/conf.py | 6 +-
docs/executable.rst | 123 +++-
docs/getting_started/installation.rst | 4 +-
docs/index.rst | 26 +-
docs/project_info/faq.rst | 6 +-
docs/project_info/more_resources.rst | 6 +-
docs/requirements.txt | 1 +
docs/snakefiles/deployment.rst | 29 +
docs/snakefiles/modularization.rst | 8 +-
docs/snakefiles/remote_files.rst | 108 +++-
docs/snakefiles/rules.rst | 34 +-
docs/tutorial/tutorial.rst | 2 +-
environment.yml | 15 +-
setup.py | 16 +-
snakemake/__init__.py | 359 ++++++++++--
snakemake/common.py | 9 +
snakemake/conda.py | 23 +-
snakemake/dag.py | 162 ++++--
snakemake/exceptions.py | 4 +
snakemake/executors.py | 619 +++++++++++++++++----
snakemake/io.py | 100 +++-
snakemake/jobs.py | 44 +-
snakemake/logging.py | 53 +-
snakemake/parser.py | 28 +-
snakemake/persistence.py | 222 ++++----
snakemake/remote/FTP.py | 3 +
snakemake/remote/GS.py | 128 ++++-
snakemake/remote/HTTP.py | 3 +
snakemake/remote/NCBI.py | 6 +-
snakemake/remote/S3.py | 225 ++------
snakemake/remote/S3Mocked.py | 13 +-
snakemake/remote/__init__.py | 38 +-
snakemake/remote/dropbox.py | 2 +-
snakemake/remote/gfal.py | 137 +++++
snakemake/remote/gridftp.py | 71 +++
snakemake/remote/webdav.py | 167 ++++++
snakemake/rules.py | 104 ++--
snakemake/scheduler.py | 167 ++++--
snakemake/script.py | 12 +-
snakemake/shell.py | 18 +-
snakemake/singularity.py | 73 +++
snakemake/version.py | 4 +-
snakemake/workflow.py | 123 +++-
snakemake/wrapper.py | 20 +-
test-environment.yml | 19 +-
tests/test_issue612/Snakefile | 11 +
.../expected-results/.gitignore | 0
tests/test_kubernetes/README.md | 11 +
tests/test_kubernetes/Snakefile | 29 +
tests/test_kubernetes/envs/gzip.yaml | 4 +
tests/test_profile/Snakefile | 3 +
tests/test_profile/Snakefile.internal | 5 +
tests/test_profile/config.yaml | 1 +
.../expected-results/test.out | 0
tests/test_profile/workflow-config.yaml | 1 +
tests/test_remote_gs/Snakefile | 15 +
.../expected-results/landsat-data.txt | 218 ++++++++
tests/test_remote_gs/landsat-data.txt | 218 ++++++++
tests/test_remote_log/Snakefile | 17 +
tests/test_remote_log/expected-results/motoState.p | Bin 0 -> 848 bytes
AUTHORS.rst => tests/test_remote_log/test.txt | 0
tests/test_remote_ncbi/Snakefile | 5 +-
tests/test_remote_ncbi/expected-results/sizes.txt | 8 +-
tests/test_remote_ncbi_simple/Snakefile | 4 +-
.../expected-results/sizes.txt | 2 +-
tests/test_restartable_job_cmd_exit_1/Snakefile | 27 +-
.../expected-results/.done | 1 +
tests/test_script/expected-results/test.html | 85 +--
tests/test_singularity/Snakefile | 7 +
tests/test_singularity/expected-results/test.out | 2 +
tests/test_static_remote/S3MockedForStaticTest.py | 7 +-
tests/test_wrapper/Snakefile | 2 +-
tests/tests.py | 103 ++--
wercker.yml | 6 +-
83 files changed, 3408 insertions(+), 852 deletions(-)
create mode 100644 debian/patches/0007-noop-rate-limiter.patch
create mode 100644 docs/_static/sphinx-argparse.css
create mode 100644 snakemake/remote/gfal.py
create mode 100644 snakemake/remote/gridftp.py
create mode 100644 snakemake/remote/webdav.py
create mode 100644 snakemake/singularity.py
create mode 100644 tests/test_issue612/Snakefile
copy tests/{test09 => test_issue612}/expected-results/.gitignore (100%)
create mode 100644 tests/test_kubernetes/README.md
create mode 100644 tests/test_kubernetes/Snakefile
create mode 100644 tests/test_kubernetes/envs/gzip.yaml
create mode 100644 tests/test_profile/Snakefile
create mode 100644 tests/test_profile/Snakefile.internal
create mode 100644 tests/test_profile/config.yaml
copy tests/{test_conditional => test_profile}/expected-results/test.out (100%)
create mode 100644 tests/test_profile/workflow-config.yaml
create mode 100644 tests/test_remote_gs/Snakefile
create mode 100644 tests/test_remote_gs/expected-results/landsat-data.txt
create mode 100644 tests/test_remote_gs/landsat-data.txt
create mode 100644 tests/test_remote_log/Snakefile
create mode 100644 tests/test_remote_log/expected-results/motoState.p
copy AUTHORS.rst => tests/test_remote_log/test.txt (100%)
create mode 100644 tests/test_singularity/Snakefile
create mode 100644 tests/test_singularity/expected-results/test.out
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