[med-svn] [Git][med-team/python-pybedtools][master] 12 commits: Mark the -doc package Multi-Arch: foreign
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Nov 14 12:34:40 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / python-pybedtools
Commits:
898f6d22 by Michael R. Crusoe at 2019-11-13T18:13:59Z
Mark the -doc package Multi-Arch: foreign
- - - - -
9e499bd8 by Michael R. Crusoe at 2019-11-13T18:14:39Z
debhelper-compat 12
- - - - -
cfa9da81 by Michael R. Crusoe at 2019-11-13T18:18:14Z
Testsuite: autopkgtest-pkg-python
- - - - -
4244abf5 by Michael R. Crusoe at 2019-11-13T18:18:14Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
64ced1c6 by Michael R. Crusoe at 2019-11-13T18:18:14Z
Remove trailing whitespace in debian/control
- - - - -
5a551d55 by Michael R. Crusoe at 2019-11-13T18:18:14Z
Set upstream metadata fields: Repository.
- - - - -
bc826416 by Michael R. Crusoe at 2019-11-13T18:18:14Z
Remove obsolete fields Name from debian/upstream/metadata.
- - - - -
d9f0d7b4 by Michael R. Crusoe at 2019-11-13T18:26:29Z
manual pages seem missing
- - - - -
b70f3cc4 by Michael R. Crusoe at 2019-11-13T18:31:53Z
add patch description
- - - - -
d667affc by Michael R. Crusoe at 2019-11-14T08:16:13Z
-doc: add ${sphinxdoc:Built-Using}
- - - - -
da492640 by Michael R. Crusoe at 2019-11-14T12:16:23Z
try the tests
- - - - -
b920999b by Michael R. Crusoe at 2019-11-14T12:16:45Z
release to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- − debian/manpages
- debian/patches/parseDebianVersions.patch
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+python-pybedtools (0.8.0-3) unstable; urgency=medium
+
+ * Mark the -doc package Multi-Arch: foreign
+ * debhelper-compat 12
+ * Testsuite: autopkgtest-pkg-python
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/control
+ * Set upstream metadata fields: Repository.
+ * Remove obsolete fields Name from debian/upstream/metadata.
+ * -doc: add ${sphinxdoc:Built-Using}
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 14 Nov 2019 13:16:33 +0100
+
python-pybedtools (0.8.0-2) unstable; urgency=medium
* Improved parsing of version of bedtool binary
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-10
=====================================
debian/control
=====================================
@@ -3,8 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Steffen Moeller <moeller at debian.org>
Section: python
+Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper-compat (= 12),
dh-python,
bedtools,
cython3,
@@ -16,9 +17,11 @@ Build-Depends: debhelper (>= 10),
python3-numpy,
python3-numpydoc,
python3-pandas,
+ python3-psutil,
+ python3-pytest,
python3-yaml,
python3-tk,
- python3-sphinx,
+ python3-sphinx,
r-base-core,
zlib1g-dev
Standards-Version: 4.4.0
@@ -55,6 +58,8 @@ Description: Python 3 wrapper around BEDTools for bioinformatics work
Package: python-pybedtools-doc
Architecture: all
Section: doc
+Multi-Arch: foreign
+Built-Using: ${sphinxdoc:Built-Using}
Depends: ${misc:Depends},
${sphinxdoc:Depends}
Suggests: python3-pybedtools|python-pybedtools
=====================================
debian/manpages deleted
=====================================
@@ -1 +0,0 @@
-debian/*.1
=====================================
debian/patches/parseDebianVersions.patch
=====================================
@@ -1,3 +1,5 @@
+Author: Steffen Moeller <moeller at debian.org>
+Description: Fixed incompatibility with latest bedtools package
Index: python-pybedtools/pybedtools/helpers.py
===================================================================
--- python-pybedtools.orig/pybedtools/helpers.py
=====================================
debian/rules
=====================================
@@ -5,10 +5,13 @@ DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export PYBUILD_NAME=pybedtools
export MATPLOTLIBRC=$(CURDIR)/debian/
-# Add back test_issue_178 after upstream provided a patch https://github.com/daler/pybedtools/pull/228
-export PYBUILD_TEST_ARGS=--attr '!url' # --exclude='(test_issue_178)'
-export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/
-export HOME=$(shell echo $$PWD"/fakehome")
+#export PYBUILD_TEST_ARGS=--attr '!url'
+export PYBUILD_BEFORE_TEST=cp {dir}/debian/mpl-expected.png {build_dir}/pybedtools/test/ ; python3 {dir}/setup.py install --user ; export HOME=$(CURDIR)/fakehome
+export PYBUILD_TEST_ARGS=-v --doctest-modules
+export PYBUILD_AFTER_TEST=cd {dir}/docs ; make clean doctest
+export PYBUILD_DISABLE=test # tests aren't passing upstream
+export HOME=$(CURDIR)/fakehome
+export PATH:=$(PATH):$(HOME)/.local/bin
%:
dh $@ --with python3,sphinxdoc --buildsystem=pybuild
@@ -27,11 +30,6 @@ override_dh_auto_install:
rm -fr debian/python-pybedtools/usr/bin
rm -fr debian/python3-pybedtools/usr/bin
-override_dh_auto_test:
- @echo
- @echo *** NOT TESTING ***
- @echo
-
override_dh_auto_clean:
/bin/rm -rf fakehome .eggs .pybuild
/bin/rm -rf debian/python3-pybedtools debian/files
=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,24 @@
-Name: pybedtools
Reference:
- - Author: R. K. Dale and B. S. Pedersen and A. R. Quinlan
- Title: >
- Pybedtools: a flexible Python library for manipulating genomic
- datasets and annotations"
- Journal: Bioinformatics
- Publisher: Oxford University Press (OUP)
- Volume: 27
- Number: 24
- Pages: 3423-3424
- Year: 2011
- Month: sep
- DOI: 10.1093/bioinformatics/btr539
- URL: https://doi.org/10.1093%2Fbioinformatics%2Fbtr539
- Type: article
+- Author: R. K. Dale and B. S. Pedersen and A. R. Quinlan
+ Title: "Pybedtools: a flexible Python library for manipulating genomic datasets\
+ \ and annotations\"\n"
+ Journal: Bioinformatics
+ Publisher: Oxford University Press (OUP)
+ Volume: 27
+ Number: 24
+ Pages: 3423-3424
+ Year: 2011
+ Month: sep
+ DOI: 10.1093/bioinformatics/btr539
+ URL: https://doi.org/10.1093%2Fbioinformatics%2Fbtr539
+ Type: article
Registry:
- - Name: bio.tools
- Entry: pybedtools
- - Name: SciCrunch
- Entry: NA
- - Name: OMICtools
- Entry: OMICS_09508
- - Name: conda:bioconda
- Entry: pybedtools
+- Name: bio.tools
+ Entry: pybedtools
+- Name: SciCrunch
+ Entry: NA
+- Name: OMICtools
+ Entry: OMICS_09508
+- Name: conda:bioconda
+ Entry: pybedtools
+Repository: https://github.com/daler/pybedtools
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/compare/830343ac70d391058526eff11827b6efa95c7c31...b920999b74040b9c96af14770b42e23a6a2e8b98
--
View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/compare/830343ac70d391058526eff11827b6efa95c7c31...b920999b74040b9c96af14770b42e23a6a2e8b98
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