[med-svn] [snakemake] branch master updated (2343b29 -> 350cf7b)
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Dec 6 22:06:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository snakemake.
from 2343b29 Upload to unstable
new a51fb0f New upstream version 3.9.0+dfsg
new 189bb92 Merge branch 'upstream'
new 350cf7b Bump changelog
The 3 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 | 15 ++
biglogo.pdf | Bin 0 -> 3806 bytes
biglogo.png | Bin 0 -> 17334 bytes
biglogo.svg | 141 +++++++++++
bitbucket-pipelines.yml | 1 -
debian/changelog | 6 +
environment.yml | 4 +
setup.py | 12 +-
snakemake/__init__.py | 47 +++-
snakemake/common.py | 10 +
snakemake/conda.py | 50 ++++
snakemake/dag.py | 22 +-
snakemake/exceptions.py | 8 +
snakemake/executors.py | 131 ++++++----
snakemake/futures.py | 36 ---
snakemake/io.py | 98 ++++++--
snakemake/jobs.py | 56 ++++-
snakemake/logging.py | 53 ++--
snakemake/parser.py | 110 ++++----
snakemake/persistence.py | 20 +-
snakemake/remote/HTTP.py | 14 +-
snakemake/remote/__init__.py | 4 +-
snakemake/report.py | 46 ++--
snakemake/rules.py | 53 +++-
snakemake/scheduler.py | 18 +-
snakemake/script.py | 160 +++++++-----
snakemake/shell.py | 8 +-
snakemake/version.py | 4 +-
snakemake/workflow.py | 45 +++-
snakemake/wrapper.py | 38 ++-
tests/test01/Snakefile | 2 +-
tests/test05/Snakefile | 4 +
tests/test09/Snakefile | 3 +
tests/test13/Snakefile | 4 +
tests/test14/Snakefile.nonstandard | 4 +
tests/test_ancient/Snakefile | 28 +++
.../test_ancient/expected-results/A | 0
.../test_ancient/expected-results/B | 0
tests/test_ancient/expected-results/C | 1 +
tests/test_ancient/expected-results/D | 1 +
tests/test_conda/Snakefile | 11 +
tests/test_conda/expected-results/test0.out | 279 +++++++++++++++++++++
tests/test_conda/expected-results/test1.out | 279 +++++++++++++++++++++
tests/test_conda/expected-results/test2.out | 279 +++++++++++++++++++++
tests/test_conda/test-env.yaml | 4 +
tests/test_delete_output/Snakefile | 52 +++-
.../hg19.fa => tests/test_delete_output/nosuchfile | 0
tests/test_get_log_both/test.out | 2 -
tests/test_get_log_complex/test.out | 2 -
tests/test_get_log_stderr/test.out | 2 -
tests/test_get_log_stdout/test.out | 2 -
tests/test_issue381/Snakefile | 21 ++
.../cufflinks/hg19.fa => tests/test_issue381/a.in | 0
.../test_issue381/expected-results/b.out | 0
tests/test_persistent_dict/Snakefile | 44 ++--
tests/test_rule_defined_in_for_loop/Snakefile | 12 +
.../expected-results/iteration-01.txt | 0
.../expected-results/iteration-02.txt | 0
.../test_rule_defined_in_for_loop/iteration-01.txt | 0
tests/test_wrapper/Snakefile | 7 +
tests/test_wrapper/expected-results/test.vcf.gz | Bin 0 -> 438 bytes
tests/test_wrapper/test.vcf | 15 ++
tests/tests.py | 44 +++-
63 files changed, 1921 insertions(+), 391 deletions(-)
create mode 100644 biglogo.pdf
create mode 100644 biglogo.png
create mode 100644 biglogo.svg
create mode 100644 snakemake/conda.py
delete mode 100644 snakemake/futures.py
create mode 100644 tests/test_ancient/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_ancient/expected-results/A (100%)
copy examples/cufflinks/hg19.fa => tests/test_ancient/expected-results/B (100%)
create mode 100644 tests/test_ancient/expected-results/C
create mode 100644 tests/test_ancient/expected-results/D
create mode 100644 tests/test_conda/Snakefile
create mode 100644 tests/test_conda/expected-results/test0.out
create mode 100644 tests/test_conda/expected-results/test1.out
create mode 100644 tests/test_conda/expected-results/test2.out
create mode 100644 tests/test_conda/test-env.yaml
copy examples/cufflinks/hg19.fa => tests/test_delete_output/nosuchfile (100%)
delete mode 100644 tests/test_get_log_both/test.out
delete mode 100644 tests/test_get_log_complex/test.out
delete mode 100644 tests/test_get_log_stderr/test.out
delete mode 100644 tests/test_get_log_stdout/test.out
create mode 100644 tests/test_issue381/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_issue381/a.in (100%)
copy examples/cufflinks/hg19.fa => tests/test_issue381/expected-results/b.out (100%)
create mode 100644 tests/test_rule_defined_in_for_loop/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/expected-results/iteration-01.txt (100%)
copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/expected-results/iteration-02.txt (100%)
copy examples/cufflinks/hg19.fa => tests/test_rule_defined_in_for_loop/iteration-01.txt (100%)
create mode 100644 tests/test_wrapper/Snakefile
create mode 100644 tests/test_wrapper/expected-results/test.vcf.gz
create mode 100644 tests/test_wrapper/test.vcf
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