[med-svn] [snakemake] branch master updated (11f9056 -> bdb3192)
Kevin Murray
daube-guest at moszumanska.debian.org
Sun Nov 13 11:17:02 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 11f9056 fix git link URL
new b2416e5 Update d/watch with bitbucket's new tag page
new 1881744 New upstream version 3.8.2+dfsg
new 39f71be Merge tag 'upstream/3.8.2+dfsg'
new bdb3192 Update changelog
The 4 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:
.gitignore | 1 +
CHANGELOG.md | 23 ++
bitbucket-pipelines.yml | 9 +
debian/changelog | 7 +
debian/watch | 2 +-
environment.yml | 2 +
setup.py | 15 +-
snakemake/__init__.py | 37 ++-
snakemake/dag.py | 138 ++++++----
snakemake/executors.py | 108 ++++----
snakemake/io.py | 120 ++++++--
snakemake/jobs.py | 108 ++++++--
snakemake/logging.py | 30 +-
snakemake/parser.py | 25 +-
snakemake/remote/FTP.py | 76 +++---
snakemake/remote/SFTP.py | 18 +-
snakemake/remote/__init__.py | 35 ++-
snakemake/rules.py | 304 ++++++++++++++-------
snakemake/scheduler.py | 11 +-
snakemake/script.py | 49 ++++
snakemake/stats.py | 2 +-
snakemake/utils.py | 107 ++++++--
snakemake/version.py | 2 +-
snakemake/workflow.py | 37 ++-
tests/test_deferred_func_eval/Snakefile | 22 ++
.../expected-results/test.out | 1 +
.../test_deferred_func_eval/test1.in | 0
.../test_deferred_func_eval/test2.in | 0
tests/test_delete_output/Snakefile | 23 ++
.../expected-results/foo/output.foo.file | 0
.../expected-results/output.file | 0
tests/test_format_params/Snakefile | 5 +
.../expected-results/test.out | 0
tests/test_get_log_both/Snakefile | 6 +
tests/test_get_log_both/expected-results/test.log | 2 +
.../expected-results/test.out | 0
tests/{test_shell => test_get_log_both}/test.in | 0
.../test.out | 0
tests/test_get_log_both/wrapper.py | 7 +
tests/test_get_log_complex/Snakefile | 6 +
.../test_get_log_complex/expected-results/test.log | 3 +
.../expected-results/test.out | 0
tests/{test_shell => test_get_log_complex}/test.in | 0
.../test.out | 0
tests/test_get_log_complex/wrapper.py | 11 +
tests/test_get_log_none/Snakefile | 5 +
.../expected-results/test.out | 0
tests/{test_shell => test_get_log_none}/test.in | 0
tests/test_get_log_none/wrapper.py | 7 +
tests/test_get_log_stderr/Snakefile | 6 +
.../test_get_log_stderr/expected-results/test.log | 1 +
.../expected-results/test.out | 0
tests/{test_shell => test_get_log_stderr}/test.in | 0
.../test.out | 0
tests/test_get_log_stderr/wrapper.py | 7 +
tests/test_get_log_stdout/Snakefile | 6 +
.../test_get_log_stdout/expected-results/test.log | 1 +
.../expected-results/test.out | 0
tests/{test_shell => test_get_log_stdout}/test.in | 0
.../test.out | 0
tests/test_get_log_stdout/wrapper.py | 7 +
tests/test_io.py | 33 +++
tests/test_issue328/Snakefile | 26 ++
.../test_issue328/expected-results/out.txt | 0
.../hg19.fa => tests/test_issue328/in.txt | 0
tests/test_remote_sftp/Snakefile | 10 +
tests/test_remote_sftp/expected-results/readme.txt | 10 +
tests/test_shadow/Snakefile | 68 ++++-
.../{test_temp => test_spaces_in_fnames}/Snakefile | 8 +-
.../expected-results/test bam file realigned.bam | 0
tests/{test_temp => test_spaces_in_fnames}/qsub | 0
.../test_spaces_in_fnames/test bam file.bam | 0
.../S3MockedForStaticTest.py} | 24 +-
tests/test_static_remote/Snakefile | 42 +++
tests/{ => test_static_remote}/__init__.py | 0
tests/test_static_remote/expected-results/out1.txt | 1 +
tests/test_static_remote/expected-results/out2.txt | 1 +
tests/test_static_remote/out1.txt | 1 +
tests/test_static_remote/out2.txt | 1 +
tests/test_static_remote/test.txt | 1 +
tests/test_subworkflows/Snakefile | 1 +
tests/test_subworkflows/subconfig.yaml | 2 +
tests/test_symlink_time_handling/Snakefile | 68 +++++
.../expected-results/time_diff.txt | 1 +
tests/test_wildcard_keyword/Snakefile | 35 +++
.../expected-results/globalbar.log | 0
.../expected-results/globalbar.txt | 1 +
.../expected-results/localbar.log | 0
.../expected-results/localbar.txt | 1 +
.../expected-results/stringbar.log | 0
.../expected-results/stringbar.txt | 1 +
tests/tests.py | 81 +++++-
92 files changed, 1439 insertions(+), 370 deletions(-)
create mode 100644 bitbucket-pipelines.yml
create mode 100644 tests/test_deferred_func_eval/Snakefile
create mode 100644 tests/test_deferred_func_eval/expected-results/test.out
copy examples/cufflinks/hg19.fa => tests/test_deferred_func_eval/test1.in (100%)
copy examples/cufflinks/hg19.fa => tests/test_deferred_func_eval/test2.in (100%)
create mode 100644 tests/test_delete_output/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_delete_output/expected-results/foo/output.foo.file (100%)
copy examples/cufflinks/hg19.fa => tests/test_delete_output/expected-results/output.file (100%)
create mode 100644 tests/test_format_params/Snakefile
copy tests/{test_script => test_format_params}/expected-results/test.out (100%)
create mode 100644 tests/test_get_log_both/Snakefile
create mode 100644 tests/test_get_log_both/expected-results/test.log
copy tests/{test_shell => test_get_log_both}/expected-results/test.out (100%)
copy tests/{test_shell => test_get_log_both}/test.in (100%)
copy tests/{test_shell/expected-results => test_get_log_both}/test.out (100%)
create mode 100644 tests/test_get_log_both/wrapper.py
create mode 100644 tests/test_get_log_complex/Snakefile
create mode 100644 tests/test_get_log_complex/expected-results/test.log
copy tests/{test_shell => test_get_log_complex}/expected-results/test.out (100%)
copy tests/{test_shell => test_get_log_complex}/test.in (100%)
copy tests/{test_shell/expected-results => test_get_log_complex}/test.out (100%)
create mode 100644 tests/test_get_log_complex/wrapper.py
create mode 100644 tests/test_get_log_none/Snakefile
copy tests/{test_shell => test_get_log_none}/expected-results/test.out (100%)
copy tests/{test_shell => test_get_log_none}/test.in (100%)
create mode 100644 tests/test_get_log_none/wrapper.py
create mode 100644 tests/test_get_log_stderr/Snakefile
create mode 100644 tests/test_get_log_stderr/expected-results/test.log
copy tests/{test_shell => test_get_log_stderr}/expected-results/test.out (100%)
copy tests/{test_shell => test_get_log_stderr}/test.in (100%)
copy tests/{test_shell/expected-results => test_get_log_stderr}/test.out (100%)
create mode 100644 tests/test_get_log_stderr/wrapper.py
create mode 100644 tests/test_get_log_stdout/Snakefile
create mode 100644 tests/test_get_log_stdout/expected-results/test.log
copy tests/{test_shell => test_get_log_stdout}/expected-results/test.out (100%)
copy tests/{test_shell => test_get_log_stdout}/test.in (100%)
copy tests/{test_shell/expected-results => test_get_log_stdout}/test.out (100%)
create mode 100644 tests/test_get_log_stdout/wrapper.py
create mode 100644 tests/test_io.py
create mode 100644 tests/test_issue328/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_issue328/expected-results/out.txt (100%)
copy examples/cufflinks/hg19.fa => tests/test_issue328/in.txt (100%)
create mode 100644 tests/test_remote_sftp/Snakefile
create mode 100644 tests/test_remote_sftp/expected-results/readme.txt
copy tests/{test_temp => test_spaces_in_fnames}/Snakefile (77%)
copy examples/cufflinks/hg19.fa => tests/test_spaces_in_fnames/expected-results/test bam file realigned.bam (100%)
copy tests/{test_temp => test_spaces_in_fnames}/qsub (100%)
copy examples/cufflinks/hg19.fa => tests/test_spaces_in_fnames/test bam file.bam (100%)
copy tests/{test_remote/S3Mocked.py => test_static_remote/S3MockedForStaticTest.py} (82%)
create mode 100644 tests/test_static_remote/Snakefile
copy tests/{ => test_static_remote}/__init__.py (100%)
create mode 100644 tests/test_static_remote/expected-results/out1.txt
create mode 100644 tests/test_static_remote/expected-results/out2.txt
create mode 100644 tests/test_static_remote/out1.txt
create mode 100644 tests/test_static_remote/out2.txt
create mode 100644 tests/test_static_remote/test.txt
create mode 100644 tests/test_subworkflows/subconfig.yaml
create mode 100644 tests/test_symlink_time_handling/Snakefile
create mode 100644 tests/test_symlink_time_handling/expected-results/time_diff.txt
create mode 100644 tests/test_wildcard_keyword/Snakefile
copy examples/cufflinks/hg19.fa => tests/test_wildcard_keyword/expected-results/globalbar.log (100%)
create mode 100644 tests/test_wildcard_keyword/expected-results/globalbar.txt
copy examples/cufflinks/hg19.fa => tests/test_wildcard_keyword/expected-results/localbar.log (100%)
create mode 100644 tests/test_wildcard_keyword/expected-results/localbar.txt
copy examples/cufflinks/hg19.fa => tests/test_wildcard_keyword/expected-results/stringbar.log (100%)
create mode 100644 tests/test_wildcard_keyword/expected-results/stringbar.txt
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