[med-svn] [Git][med-team/snakemake][master] Testing.
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Tue Oct 19 00:53:06 BST 2021
Steffen Möller pushed to branch master at Debian Med / snakemake
Commits:
5f7a3d5b by Steffen Moeller at 2021-10-19T01:51:22+02:00
Testing.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix_test_pytest.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -14,8 +14,11 @@ snakemake (6.9.1-1) UNRELEASED; urgency=medium
* d/control:
+ Add versioned Dep on pulp (>= 2.0)
+ Add B-D on python3-smart-open
-TODO: pulp new version is needed, which has a dep on amply. Mail sent to -openstack mailing list
-to update this one.
+
+ [ Steffen Moeller ]
+ * Unselected tests needing internet access
+ * fixing one calling pytest -> pytest-3
+ * d/rules: Allowing consecutive builds with better cleaning
-- Nilesh Patra <nilesh at debian.org> Sun, 17 Oct 2021 14:19:21 +0000
=====================================
debian/control
=====================================
@@ -10,35 +10,35 @@ Build-Depends: ca-certificates,
environment-modules,
imagemagick,
python3,
- python3-appdirs,
- python3-biopython,
- python3-boto3,
- python3-botocore,
+ python3-appdirs <!nocheck>,
+ python3-biopython <!nocheck>,
+ python3-boto3 <!nocheck>,
+ python3-botocore <!nocheck>,
python3-configargparse,
python3-datrie,
python3-docutils,
- python3-dropbox,
+ python3-dropbox <!nocheck>,
python3-filelock,
- python3-flask,
+ python3-flask <!nocheck>,
python3-git,
python3-jinja2,
python3-jsonschema,
python3-nbformat,
- python3-networkx,
- python3-pandas,
+ python3-networkx <!nocheck>,
+ python3-pandas <!nocheck>,
python3-pkg-resources,
python3-psutil,
python3-pulp (>= 2.0),
- python3-pygments,
- python3-pygraphviz,
- python3-pytest,
+ python3-pygments <!nocheck>,
+ python3-pygraphviz <!nocheck>,
+ python3-pytest <!nocheck>,
# sometimes fails tests https://github.com/pytest-dev/pytest-xdist/issues/469 python3-pytest-xdist,
- python3-pytools,
+ python3-pytools <!nocheck>,
python3-ratelimiter,
python3-recommonmark <!nodoc>,
python3-requests,
python3-requests-mock <!nocheck>,
- python3-rpy2,
+ python3-rpy2 <!nocheck>,
python3-setuptools,
python3-smart-open (>= 3.0),
python3-sphinx <!nodoc>,
@@ -47,11 +47,11 @@ Build-Depends: ca-certificates,
python3-sphinx-rtd-theme <!nodoc>,
python3-stopit,
python3-tabulate,
- python3-toposort,
+ python3-toposort <!nocheck>,
python3-wrapt,
python3-yaml,
r-cran-rmarkdown,
- stress
+ stress <!nocheck>
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/snakemake
Vcs-Git: https://salsa.debian.org/med-team/snakemake.git
=====================================
debian/patches/fix_test_pytest.patch
=====================================
@@ -0,0 +1,17 @@
+Author: Steffen Moeller <moeller at debian.org>
+Description: pytest has the -3 suffix on Debian
+Forwarded: Not required since Debian-specific
+
+Index: snakemake/tests/tests.py
+===================================================================
+--- snakemake.orig/tests/tests.py
++++ snakemake/tests/tests.py
+@@ -1173,7 +1173,7 @@ def test_generate_unit_tests():
+ check_md5=False,
+ cleanup=False,
+ )
+- sp.check_call(["pytest", ".tests", "-vs"], cwd=tmpdir)
++ sp.check_call(["pytest-3", ".tests", "-vs"], cwd=tmpdir)
+
+
+ @skip_on_windows
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ local_javascript.patch
python3.patch
workaround_sphinx_issue.patch
remove_ccbysa_snippets.patch
+fix_test_pytest.patch
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@
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 -v tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_ancient'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -v tests/test*.py -k 'not test_cwl and not test_cwl_singularity and not test_url_include and not test_wrapper and not test_issue1083 and not test_github_issue78 and not test_container and not test_singularity and not test_singularity_conda and not test_convert_to_cwl and not test_report and not test_report_zip and not test_archive and not test_jupyter_notebook and not test_conda and not test_upstream_conda and not test_conda_custom_prefix and not test_script and not test_issue635 and not test_issue1093 and not test_default_resources and not test_default_remote and not test_remote and not test_output_file_cache_remote and not test_tibanna and not test_ancient and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_github_issue1062 and not test_env_modules and not test_modules_meta_wrapper'
# Skipped because they download executables (which is forbidden in Debian buildd and debci)
# Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper
@@ -49,3 +49,14 @@ override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
. /etc/profile.d/modules.sh && PYBUILD_SYSTEM=custom dh_auto_test
endif
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f tests/test_filegraph/fg.pdf
+ rm -f tests/test_filegraph/fg.dot
+ rm -rf tests/test_github_issue413/.snakemake
+ rm -f tests/test_github_issue413/stats.txt
+ find tests/test_metadata_migration -name "path.txt" -delete
+ find tests -name "*.log" | grep -v expected-results | xargs -r rm -f
+ rm -rf .snakemake
+ rm -rf tests/test_metadata_migration/.snakemake
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/5f7a3d5be84d259e365a6e6da34b2abeedc3833f
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