[med-svn] [snakemake] branch upstream updated (91fdd01 -> 955a326)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Jul 18 08:19:07 UTC 2017
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch upstream
in repository snakemake.
from 91fdd01 New upstream version 3.10.0
adds 955a326 New upstream version 3.13.3
No new revisions were added by this update.
Summary of changes:
CHANGELOG.md | 65 +++
Dockerfile | 17 +-
README.md | 13 +-
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 +
99 files changed, 3558 insertions(+), 671 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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