[med-svn] [snakemake] branch master updated (54f4469 -> 7d85877)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Jul 18 01:06:11 UTC 2017
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository snakemake.
from 54f4469 Upload to unstable
new 955a326 New upstream version 3.13.3
new 4cce424 Updated version 3.13.3 from 'upstream/3.13.3'
new faae86a bump changelog
new 31d58de refresh patches
new 7d85877 Add missing dependencies for newer snakemake
The 5 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 | 65 +++
Dockerfile | 17 +-
README.md | 13 +-
debian/changelog | 6 +
debian/control | 4 +
debian/patches/0003-Compat-fix.patch | 18 +-
docs/getting_started/examples.rst | 5 +-
docs/getting_started/installation.rst | 35 +-
docs/index.rst | 34 +-
docs/project_info/authors.rst | 1 +
docs/project_info/citations.rst | 4 +-
docs/project_info/contributing.rst | 4 +-
docs/project_info/faq.rst | 25 +
docs/project_info/more_resources.rst | 4 +
docs/snakefiles/configuration.rst | 32 ++
docs/snakefiles/deployment.rst | 38 +-
docs/snakefiles/modularization.rst | 79 ++-
docs/snakefiles/remote_files.rst | 119 ++++-
docs/snakefiles/rules.rst | 190 ++++++-
docs/tutorial/additional_features.rst | 120 ++++-
docs/tutorial/advanced.rst | 51 +-
docs/tutorial/basics.rst | 100 +++-
docs/tutorial/{welcome.rst => setup.rst} | 46 +-
docs/tutorial/tutorial.rst | 37 ++
environment.yml | 12 +-
examples/c/src/Snakefile | 2 +-
misc/vim/syntax/snakemake.vim | 2 +-
setup.py | 6 +-
snakemake/__init__.py | 116 ++++-
snakemake/benchmark.py | 259 ++++++++++
snakemake/common.py | 6 +
snakemake/conda.py | 262 ++++++----
snakemake/dag.py | 118 +++--
snakemake/exceptions.py | 20 +-
snakemake/executors.py | 203 +++++---
snakemake/io.py | 32 +-
snakemake/jobs.py | 60 ++-
snakemake/logging.py | 16 +-
snakemake/parser.py | 9 +-
snakemake/persistence.py | 13 +-
snakemake/remote/FTP.py | 89 +++-
snakemake/remote/GS.py | 23 +-
snakemake/remote/HTTP.py | 65 ++-
snakemake/remote/NCBI.py | 574 +++++++++++++++++++++
snakemake/remote/S3.py | 52 +-
.../test_remote => snakemake/remote}/S3Mocked.py | 14 +-
snakemake/remote/SFTP.py | 28 +-
snakemake/remote/XRootD.py | 197 +++++++
snakemake/remote/__init__.py | 114 ++--
snakemake/remote/dropbox.py | 47 +-
snakemake/report.py | 4 +-
snakemake/rules.py | 38 +-
snakemake/scheduler.py | 39 +-
snakemake/script.py | 55 +-
snakemake/shell.py | 12 +-
snakemake/utils.py | 9 +
snakemake/version.py | 2 +-
snakemake/workflow.py | 43 +-
snakemake/wrapper.py | 10 +-
environment.yml => test-environment.yml | 11 +-
tests/test_benchmark/Snakefile | 30 +-
.../{test.benchmark.txt => test.benchmark_run.txt} | 0
.../expected-results/test.benchmark_run_shell.txt} | 0
.../expected-results/test.benchmark_script.txt | 0
.../expected-results/test.benchmark_shell.txt | 0
tests/test_benchmark/script.py | 7 +
tests/test_conda/Snakefile | 4 +-
tests/test_conda_custom_prefix/Snakefile | 12 +
.../expected-results/test0.out | 1 +
.../expected-results/test1.out | 1 +
.../expected-results/test2.out | 1 +
.../test-env.yaml | 0
tests/test_default_remote/Snakefile | 40 ++
.../expected-results/.gitignore | 0
.../test_test.out => test_default_remote/test.txt} | 0
tests/test_dynamic_temp/Snakefile | 30 ++
.../expected-results/out.txt | 0
tests/test_dynamic_temp/test1.txt | 8 +
tests/test_dynamic_temp/test2.txt | 8 +
tests/test_ftp_immediate_close/Snakefile | 11 +
.../expected-results/size.txt | 1 +
tests/test_get_log_none/Snakefile | 2 +-
tests/test_issue260/Snakefile | 32 ++
.../test_issue260/expected-results/output/done.txt | 1 +
.../expected-results/output/result.n1 | 1 +
.../expected-results/output/result.n2 | 1 +
.../expected-results/output/result.n3 | 1 +
tests/test_remote/Snakefile | 21 +-
tests/test_remote_ncbi/Snakefile | 26 +
tests/test_remote_ncbi/expected-results/sizes.txt | 4 +
tests/test_remote_ncbi_simple/Snakefile | 14 +
.../expected-results/sizes.txt | 1 +
tests/test_run_namedlist/Snakefile | 5 +
.../test_run_namedlist/expected-results/file.txt | 0
tests/test_script/Snakefile | 13 +
tests/test_script/expected-results/test.html | 234 +++++++++
tests/test_script/scripts/test.Rmd | 22 +
tests/test_subworkflows/Snakefile | 7 +-
tests/test_symlink_time_handling/Snakefile | 22 +-
tests/test_xrootd/Snakefile | 27 +
tests/tests.py | 56 +-
wercker.yml | 4 +
102 files changed, 3578 insertions(+), 679 deletions(-)
rename docs/tutorial/{welcome.rst => setup.rst} (71%)
create mode 100644 docs/tutorial/tutorial.rst
create mode 100644 snakemake/benchmark.py
create mode 100644 snakemake/remote/NCBI.py
rename {tests/test_remote => snakemake/remote}/S3Mocked.py (95%)
create mode 100644 snakemake/remote/XRootD.py
copy environment.yml => test-environment.yml (71%)
rename tests/test_benchmark/expected-results/{test.benchmark.txt => test.benchmark_run.txt} (100%)
rename tests/{test_remote/__init__.py => test_benchmark/expected-results/test.benchmark_run_shell.txt} (100%)
copy AUTHORS.rst => tests/test_benchmark/expected-results/test.benchmark_script.txt (100%)
copy AUTHORS.rst => tests/test_benchmark/expected-results/test.benchmark_shell.txt (100%)
create mode 100755 tests/test_benchmark/script.py
create mode 100644 tests/test_conda_custom_prefix/Snakefile
create mode 100644 tests/test_conda_custom_prefix/expected-results/test0.out
create mode 100644 tests/test_conda_custom_prefix/expected-results/test1.out
create mode 100644 tests/test_conda_custom_prefix/expected-results/test2.out
copy tests/{test_conda => test_conda_custom_prefix}/test-env.yaml (100%)
create mode 100644 tests/test_default_remote/Snakefile
copy tests/{test09 => test_default_remote}/expected-results/.gitignore (100%)
copy tests/{test_same_wildcard/expected-results/test_test.out => test_default_remote/test.txt} (100%)
create mode 100644 tests/test_dynamic_temp/Snakefile
copy tests/{test_issue328 => test_dynamic_temp}/expected-results/out.txt (100%)
create mode 100644 tests/test_dynamic_temp/test1.txt
create mode 100644 tests/test_dynamic_temp/test2.txt
create mode 100644 tests/test_ftp_immediate_close/Snakefile
create mode 100644 tests/test_ftp_immediate_close/expected-results/size.txt
create mode 100644 tests/test_issue260/Snakefile
create mode 100644 tests/test_issue260/expected-results/output/done.txt
create mode 100644 tests/test_issue260/expected-results/output/result.n1
create mode 100644 tests/test_issue260/expected-results/output/result.n2
create mode 100644 tests/test_issue260/expected-results/output/result.n3
create mode 100644 tests/test_remote_ncbi/Snakefile
create mode 100644 tests/test_remote_ncbi/expected-results/sizes.txt
create mode 100644 tests/test_remote_ncbi_simple/Snakefile
create mode 100644 tests/test_remote_ncbi_simple/expected-results/sizes.txt
create mode 100644 tests/test_run_namedlist/Snakefile
copy AUTHORS.rst => tests/test_run_namedlist/expected-results/file.txt (100%)
create mode 100644 tests/test_script/expected-results/test.html
create mode 100644 tests/test_script/scripts/test.Rmd
create mode 100644 tests/test_xrootd/Snakefile
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