[med-svn] [Git][med-team/snakemake][debian_for_upstream_5.14.0_which_requires_conda] 3 commits: Update d/copyright.
Rebecca N. Palmer
gitlab at salsa.debian.org
Fri Apr 10 13:08:06 BST 2020
Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda at Debian Med / snakemake
Commits:
bf14fd40 by Rebecca N. Palmer at 2020-04-10T13:05:16+01:00
Update d/copyright.
- - - - -
12901587 by Rebecca N. Palmer at 2020-04-10T13:07:02+01:00
Enable verbose test output.
- - - - -
8fa5ce30 by Rebecca N. Palmer at 2020-04-10T13:07:47+01:00
Update dependencies, add minimal-Depends test.
- - - - -
7 changed files:
- debian/README.source
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/README.source
=====================================
@@ -19,11 +19,13 @@ Missing (optional) dependencies:
- conda
- gfal-copy and other gfal-* commands for gfal/gridftp (missing from gfal2?)
-Missing (optional) Python dependencies:
+- setup.py-declared optional depends:
+slacker
+crc32c, oauth2client, google-api-python-client, google-cloud-storage (google.cloud)
-- moto https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=777089
-- google.cloud (google-cloud-sdk)
-- ftputil
-- pysftp
-- XRootD
-- aioeasywebdav
+- imports in snakemake directory (not tests/doc/examples) other than setup.py-declared depends:
+XRootD
+aioeasywebdav
+moto (RFP #777089)
+pysftp
+tibanna
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -16,6 +16,8 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
* Reproducibility: don't ship (timestamped) test logs.
* Add self to Uploaders.
* Update d/copyright, remove no longer needed Files-Excluded.
+ * Enable verbose test output.
+ * Update dependencies, add minimal-Depends test.
-- Rebecca N. Palmer <rebecca_palmer at zoho.com> Thu, 09 Apr 2020 14:57:00 +0100
=====================================
debian/control
=====================================
@@ -9,11 +9,13 @@ Build-Depends: ca-certificates,
dh-python,
imagemagick,
python3,
+ python3-appdirs,
python3-biopython,
python3-boto3,
python3-botocore,
python3-configargparse,
python3-datrie,
+ python3-docutils,
python3-dropbox,
python3-flask,
python3-git,
@@ -21,8 +23,8 @@ Build-Depends: ca-certificates,
python3-jsonschema,
python3-nbformat,
python3-networkx,
- python3-nose,
python3-pandas,
+ python3-pkg-resources,
python3-psutil,
python3-pygments,
python3-pygraphviz,
@@ -30,13 +32,14 @@ Build-Depends: ca-certificates,
python3-pytest-xdist,
python3-pytools,
python3-ratelimiter,
- python3-recommonmark,
+ python3-recommonmark <!nodoc>,
+ python3-requests,
python3-rpy2,
python3-setuptools,
- python3-sphinx,
- python3-sphinx-argparse,
- python3-sphinx-bootstrap-theme,
- python3-sphinx-rtd-theme,
+ python3-sphinx <!nodoc>,
+ python3-sphinx-argparse <!nodoc>,
+ python3-sphinx-bootstrap-theme <!nodoc>,
+ python3-sphinx-rtd-theme <!nodoc>,
python3-toposort,
python3-wrapt,
python3-yaml,
@@ -53,16 +56,18 @@ Architecture: all
Depends: ca-certificates,
libjs-d3,
libjs-mathjax,
+ python3-appdirs,
+ python3-configargparse,
python3-datrie,
python3-docutils,
- python3-networkx,
+ python3-git,
+ python3-jsonschema,
+ python3-nbformat,
+ python3-pkg-resources,
python3-psutil,
- python3-pygraphviz,
- python3-pytools,
python3-ratelimiter,
- python3-recommonmark,
- python3-rpy2,
- python3-setuptools,
+ python3-requests,
+ python3-toposort,
python3-wrapt,
python3-yaml,
${misc:Depends},
@@ -70,12 +75,25 @@ Depends: ca-certificates,
${sphinxdoc:Depends}
Recommends: cwltool,
imagemagick,
+ python3-tz,
+ python3-yappi,
+# for the reports feature
+ python3-jinja2,
+ python3-networkx,
+ python3-pygments,
+ python3-pygraphviz,
+# for distributed / cloud setups or online data access
+ python3-azure-storage,
python3-biopython,
python3-boto3,
python3-botocore,
+ python3-drmaa,
python3-dropbox,
python3-flask,
- r-cran-rmarkdown
+ python3-ftputil,
+ python3-irodsclient,
+ python3-kubernetes,
+ python3-urllib3
Description: pythonic workflow management system
Build systems like GNU Make are frequently used to create complicated
workflows, e.g. in bioinformatics. This project aims to reduce the
=====================================
debian/copyright
=====================================
@@ -16,7 +16,22 @@ Copyright: 2005, 2015 jQuery Foundation, Inc. (jquery)
2013 Greg Franko (jquery Tocify)
2014 Aidan Lister and Ruben Arslan (jQuery Plugin: Sticky Tabs)
License: Expat
-Comment: This is a test reference, we don't actually run this code. For source code of these modules, see r-cran-rmarkdown (0.8 for this version) and dependencies.
+Comment: These are test references, we don't actually run this code. For source code of these modules, see r-cran-rmarkdown (0.8 for this version) and dependencies.
+
+Files: tests/test_report/expected-results/report.html
+ tests/test_report_zip/expected-results/report.zip
+ tests/test_issue635/expected-results/report.html
+Copyright: 2005-2018 JS Foundation and other contributors (jquery)
+ 2018 Federico Zivolo (Popper.js)
+ 2011-2018 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
+ 2009-2018 The MathJax Consortium
+ 2016 Jed Watson (http://jedwatson.github.io/classnames)
+ Eli Grey (FileSaver.js https://github.com/eligrey/FileSaver.js)
+ 2008-2019 SpryMedia Ltd. (DataTables, Responsive, Select)
+ 2007-2015 Ariel Flesler (scrollTo)
+ and some unidentified pieces
+License: Expat and Apache-2.0
+Comment: These are test references, we don't actually run this code. For source code of these modules, see r-cran-rmarkdown (0.8 for this version) and dependencies.
Files: debian/*
Copyright: 2015-2020 Kevin Murray <spam at kdmurray.id.au> and Debian Med Team
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export HOME=$(CURDIR)/fakehome
export PYBUILD_NAME=snakemake
export PYBUILD_DESTDIR_python3=debian/snakemake
export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir}
-export PYBUILD_TEST_ARGS=python{version} -m pytest tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
# test_report
# test_ancient
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,9 @@
+# minimal Depends smoke test
+Test-Command: cp tests/test_bash/Snakefile $AUTOPKGTEST_TMP && cd $AUTOPKGTEST_TMP && snakemake --cores 1 && grep -e bash test.out
+Depends: snakemake
+Restrictions: allow-stderr
+
+# upstream's tests
Tests: run-unit-test
-Depends: @, python3-pandas, python3-pytest-xdist, stress
+Depends: snakemake, python3-pandas, python3-pytest-xdist, python3-pygraphviz, stress
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -17,5 +17,5 @@ cd "${AUTOPKGTEST_TMP}"
export HOME="${AUTOPKGTEST_TMP}"
-python3 -m pytest ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
+python3 -m pytest -v ${ROOT}/tests/test*.py -n auto -k 'not report and not ancient and not test_script and not default_remote and not issue635 and not convert_to_cwl and not issue1083 and not issue1092 and not issue1093 and not test_remote and not test_default_resources and not test_singularity and not test_singularity_conda and not test_cwl_singularity and not test_cwl and not test_url_include and not test_tibanna and not test_github_issue78 and not test_output_file_cache_remote and not test_env_modules and not test_archive and not test_container and not test_cluster_sync'
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/e5cc7980fc0ee227c5e7fcb907ec558de2474671...8fa5ce30bcd58ef663597421c2b8f26535051991
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/e5cc7980fc0ee227c5e7fcb907ec558de2474671...8fa5ce30bcd58ef663597421c2b8f26535051991
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