Andreas Tille pushed to branch master at Debian Med / paleomix
Commits: 48ed3c7f by Andreas Tille at 2018-12-17T11:09:15Z New upstream version 1.2.13.3 - - - - - 4854144a by Andreas Tille at 2018-12-17T11:09:34Z Update upstream source from tag 'upstream/1.2.13.3' Update to upstream version '1.2.13.3' with Debian dir d32c10492e75790dd140c708588b5a5250aa30ca - - - - - da355802 by Andreas Tille at 2018-12-17T11:09:34Z New upstream version - - - - - 03850270 by Andreas Tille at 2018-12-17T11:11:22Z Standards-Version: 4.2.1 - - - - - f89a9ac7 by Andreas Tille at 2018-12-17T11:43:16Z Respect DEB_BUILD_OPTIONS in override_dh_auto_test target - - - - - 3d5326f5 by Andreas Tille at 2018-12-17T12:34:18Z Do not use tox in autopkgtest since it relies on files in full source dir - - - - - 5bd19aa1 by Andreas Tille at 2018-12-17T12:41:51Z Upload to unstable - - - - - 10 changed files: - CHANGES.md - README.rst - debian/changelog - debian/control - debian/rules - debian/tests/control - debian/tests/run-unit-test - docs/bam_pipeline/configuration.rst - paleomix/__init__.py - paleomix/nodes/validation.py Changes: ===================================== CHANGES.md ===================================== @@ -1,5 +1,11 @@ # Changelog +## [1.2.13.3] - 2018-11-01 +### Fixed + - Fixed validation/read counting of pre-trimmed reads not including + the mate 1 files of paired-end reads. This resulted in the + 'seq_retained_reads' count being half the expected value. + ## [1.2.13.2] - 2018-04-22 ### Fixed @@ -575,8 +581,9 @@ the (partially) updated documentation now hosted on ReadTheDocs. - Switching to more traditional version-number tracking. -[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...HEAD -[1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2 +[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD +[1.2.13.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3 +[1.2.13.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2 [1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1 [1.2.13]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.12...v1.2.13 [1.2.12]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.11...v1.2.12 ===================================== README.rst ===================================== @@ -14,4 +14,4 @@ The PALEOMIX pipelines have been published in Nature Protocols; if you make use The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite - Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2007 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. + Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2017 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +paleomix (1.2.13.3-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.2.1 + * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target + * Do not use tox to run full test suite in autopkgtest since it relies + on full source dir + + -- Andreas Tille <[email protected]> Mon, 17 Dec 2018 13:35:27 +0100 + paleomix (1.2.13.2-1) unstable; urgency=medium * Should be architecture any since it build-depends on the amd64-only ===================================== debian/control ===================================== @@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 11~), default-jre-headless, bowtie2, rsync -Standards-Version: 4.1.4 +Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/paleomix Vcs-Git: https://salsa.debian.org/med-team/paleomix.git Homepage: http://geogenetics.ku.dk/publications/paleomix ===================================== debian/rules ===================================== @@ -11,11 +11,13 @@ export PYBUILD_TEST_ARGS = --exclude='(test_requirementobj__version__command_not dh $@ --with python2 --buildsystem=pybuild override_dh_auto_test: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) # apply fix that seems to be needed due to improperly set # time zone in pbuilder sed -i~ 's/"MTime": "2005-07-07 08:50:00"/"MTime": "2005-07-07 06:50:00"/' tests/common_tests/makefile_test.py PATH=$(CURDIR)/bin/:$(PATH) dh_auto_test mv tests/common_tests/makefile_test.py~ tests/common_tests/makefile_test.py +endif override_dh_install: dh_install @@ -43,3 +45,7 @@ override_dh_installdocs: #find debian -name "empty_file*" #find debian -name "timestamp_*" #echo "====== Hope something was printed between these lines ====" + # + # This test tries to execute setup.sh which does not work outside source directory + find debian/$(DEB_SOURCE)/usr/share/doc/ -name fileutils_test.py -delete + find debian/$(DEB_SOURCE)/usr/share/doc/ -name setup.h -delete ===================================== debian/tests/control ===================================== @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @, tox +Depends: @ Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -19,4 +19,7 @@ for gz in `find . -name "*.gz"` ; do fi done -tox \ No newline at end of file +## tox needs to run in source dir and relies on files only available in full source +# tox +## so rather run some test that is part of the tox test suite +nosetests --with-coverage --cover-erase --cover-inclusive --cover-tests --cover-package paleomix . \ No newline at end of file ===================================== docs/bam_pipeline/configuration.rst ===================================== @@ -9,7 +9,7 @@ The BAM pipeline exposes a number options, including the maximum number of threa .. code-block:: bash - $ paleomix bam_pipeline --write-config + $ paleomix bam_pipeline run --write-config The resulting file contains a list of options which can be overwritten:: ===================================== paleomix/__init__.py ===================================== @@ -21,7 +21,7 @@ # SOFTWARE. # -__version_info__ = (1, 2, 13, 2) +__version_info__ = (1, 2, 13, 3) __version__ = '%i.%i.%i.%i' % __version_info__ ===================================== paleomix/nodes/validation.py ===================================== @@ -112,10 +112,10 @@ class ValidateFASTQFilesNode(Node): self._files = set() for (read_type, filename) in input_files.iteritems(): if read_type == "Paired": - filename = filename.format(Pair=1) - filename = filename.format(Pair=2) - - self._files.add((read_type, filename)) + self._files.add((read_type, filename.format(Pair=1))) + self._files.add((read_type, filename.format(Pair=2))) + else: + self._files.add((read_type, filename)) input_files = [filename for _, filename in self._files] Node.__init__(self, View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/fa31afcf165faf4970941e0487f37c905d636b39...5bd19aa1844a1bd9cb0aa6ce3b92e1bf1a4c40a5 -- View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/fa31afcf165faf4970941e0487f37c905d636b39...5bd19aa1844a1bd9cb0aa6ce3b92e1bf1a4c40a5 You're receiving this email because of your account on salsa.debian.org.
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