[med-svn] r18116 - trunk/packages/python-biopython/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Wed Sep 24 12:18:44 UTC 2014
Author: tille
Date: 2014-09-24 12:18:43 +0000 (Wed, 24 Sep 2014)
New Revision: 18116
Modified:
trunk/packages/python-biopython/trunk/debian/changelog
trunk/packages/python-biopython/trunk/debian/control
trunk/packages/python-biopython/trunk/debian/rules
Log:
Several changes in one rush - main important one is not testing samtools
* Exclude samtools test from unit testing for the moment since this
package is in flux and it is not clear what architectures will be
supported finally
* Do not suggest python3 packages in python-biopython and no
python package sin python3-biopython
* cme fix dpkg-control
Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog 2014-09-24 11:56:51 UTC (rev 18115)
+++ trunk/packages/python-biopython/trunk/debian/changelog 2014-09-24 12:18:43 UTC (rev 18116)
@@ -1,3 +1,14 @@
+python-biopython (1.64+dfsg-5) unstable; urgency=medium
+
+ * Exclude samtools test from unit testing for the moment since this
+ package is in flux and it is not clear what architectures will be
+ supported finally
+ * Do not suggest python3 packages in python-biopython and no
+ python package sin python3-biopython
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Sep 2014 10:08:12 +0200
+
python-biopython (1.64+dfsg-4) unstable; urgency=medium
* debian/patches/fix_test_problem_on_powerpc.patch: Patch provided by
Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control 2014-09-24 11:56:51 UTC (rev 18115)
+++ trunk/packages/python-biopython/trunk/debian/control 2014-09-24 12:18:43 UTC (rev 18116)
@@ -4,13 +4,14 @@
Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
Section: python
+Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
dpkg-dev (>= 1.16.1~),
python-all-dev,
python3-all-dev,
- python-numpy,
- python3-numpy,
+ python-numpy,
+ python3-numpy,
flex,
python-reportlab,
python3-reportlab,
@@ -30,28 +31,23 @@
python-mysqldb,
python-matplotlib,
python3-matplotlib,
- python-numpy,
- python3-numpy,
python-pil,
python3-pil,
python-rdflib,
+ python3-rdflib,
python-renderpm,
python3-renderpm,
python-psycopg2,
python3-psycopg2,
raxml [any-amd64],
- samtools,
t-coffee,
wise (>= 2.4.1-16)
-# python-rdflib (>= 4) # only in experimental
-# python3-rdflib (>= 4) # only in experimental
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biopython/trunk/
Homepage: http://biopython.org
X-Python-Version: >= 2.5
X-Python3-Version: >= 3.3
-XS-Testsuite: autopkgtest
Package: python-biopython
Architecture: any
@@ -62,8 +58,6 @@
Recommends: python-biopython-doc (= ${source:Version}),
ncbi-blast+
Suggests: python-tk,
- python-numpy,
- python3-numpy,
bwa [any-amd64],
clustalo,
clustalw,
@@ -78,21 +72,15 @@
probcons,
python-mysqldb,
python-matplotlib,
- python3-matplotlib,
python-numpy,
- python3-numpy,
python-pil,
- python3-pil,
python-rdflib,
python-renderpm,
- python3-renderpm,
python-psycopg2,
- python3-psycopg2,
raxml,
samtools,
t-coffee,
wise (>= 2.4.1-16)
-# python-rdflib (>= 4) # only in experimental
Description: Python library for bioinformatics (implemented in Python 2)
The Biopython Project is an international association
of developers of freely available Python tools for
@@ -119,8 +107,6 @@
ncbi-blast+
Suggests: python3-tk,
python-reportlab,
- python-numpy,
- python3-numpy,
bwa [any-amd64],
clustalo,
clustalw,
@@ -134,22 +120,16 @@
prank,
probcons,
python-mysqldb,
- python-matplotlib,
python3-matplotlib,
- python-numpy,
python3-numpy,
- python-pil,
python3-pil,
- python-rdflib,
- python-renderpm,
+ python3-rdflib,
python3-renderpm,
- python-psycopg2,
python3-psycopg2,
raxml,
samtools,
t-coffee,
wise (>= 2.4.1-16)
-# python3-rdflib (>= 4) # only in experimental
Description: Python library for bioinformatics (implemented in Python 3)
The Biopython Project is an international association
of developers of freely available Python tools for
Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules 2014-09-24 11:56:51 UTC (rev 18115)
+++ trunk/packages/python-biopython/trunk/debian/rules 2014-09-24 12:18:43 UTC (rev 18116)
@@ -34,7 +34,7 @@
# This would not trigger a failure but bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
-# The following test works only with python-rdflib (>= 4) which is in experimental
+# The following test works only with python-rdflib (>= 4)
# If python-rdflib (>= 4) then do not exclude it - otherwise we exclude this test
EXCLUDERDFLIB=$(shell if dpkg --compare-versions `dpkg -l python-rdflib | grep ^ii | sed 's/ii *python-rdflib *\([-.0-9]\+\) *.*/\1/'` gt 4 ; then echo ""; else echo "Phylo_CDAO" ; fi)
@@ -44,6 +44,11 @@
# Regarding the Tutorial test it depends from a fix for python-reportlab (see #745985)
EXCLUDEFAILINGTESTS=GenomeDiagram Fasttree_tool Mafft_tool Tutorial ColorSpiral trie
+# FIXME: Currently it is not sure for what architecture samtools will be available
+# to anable a smooth migration to testing the build-dependency will be dropped
+# for the moment
+EXCLUDEPACKAGEINFLUX=samtools_tool
+
%:
dh $@ --with python2,python3 --buildsystem=pybuild
@@ -65,7 +70,7 @@
else
mkdir -p Tests_avoid
if [ "$(EXCLUDERDFLIB)" != "" ] ; then echo "You might like to install python-rdflib from experimental to run Phylo_CDAO test" ; else echo "Phylo_CDAO will be done"; fi
- for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDERDFLIB) $(EXCLUDEFAILINGTESTS) \
+ for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDERDFLIB) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
; do \
mv Tests/test_$${avoid}.py Tests_avoid ; \
done
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