[med-svn] [Git][med-team/paleomix][master] 7 commits: New upstream version 1.2.13.3
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 17 12:46:35 GMT 2018
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 <tille at debian.org> 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
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