[med-svn] r16448 - in trunk/packages/python-biopython/trunk/debian: . patches tests
Philipp Benner
philipp at moszumanska.debian.org
Sat Mar 15 20:36:41 UTC 2014
Author: philipp
Date: 2014-03-15 20:36:41 +0000 (Sat, 15 Mar 2014)
New Revision: 16448
Added:
trunk/packages/python-biopython/trunk/debian/tests/
trunk/packages/python-biopython/trunk/debian/tests/control
trunk/packages/python-biopython/trunk/debian/tests/upstream
Removed:
trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
Modified:
trunk/packages/python-biopython/trunk/debian/control
trunk/packages/python-biopython/trunk/debian/patches/series
trunk/packages/python-biopython/trunk/debian/rules
Log:
a very first autopkgtest
Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control 2014-03-15 12:07:13 UTC (rev 16447)
+++ trunk/packages/python-biopython/trunk/debian/control 2014-03-15 20:36:41 UTC (rev 16448)
@@ -9,45 +9,16 @@
dpkg-dev (>= 1.16.1~),
python-all-dev,
python3-all-dev,
- flex,
- python-reportlab,
- python-numpy,
- python3-reportlab,
- python3-numpy,
- bwa [any-amd64],
- clustalo,
- clustalw,
- dialign,
- dssp,
- emboss,
- fasttree,
- mafft,
- muscle,
- ncbi-blast+,
- phyml,
- prank,
- 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,
- t-coffee,
- wise
+ python-numpy,
+ python3-numpy,
+ flex
Standards-Version: 3.9.5
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
@@ -57,14 +28,36 @@
python-reportlab
Recommends: python-biopython-doc (= ${source:Version})
Suggests: python-tk,
- wise,
- muscle,
+ python-numpy,
+ python3-numpy,
+ bwa [any-amd64],
+ clustalo,
clustalw,
+ dialign,
+ dssp,
+ emboss,
+ fasttree,
mafft,
- emboss,
- blast2,
+ muscle,
+ ncbi-blast+,
+ phyml,
+ prank,
+ probcons,
+ python-mysqldb,
+ python-matplotlib,
+ python3-matplotlib,
+ python-numpy,
+ python3-numpy,
+ python-pil,
+ python3-pil,
+ python-rdflib,
+ python-renderpm,
+ python3-renderpm,
python-psycopg2,
- probcons
+ python3-psycopg2,
+ raxml,
+ t-coffee,
+ wise
Description: Python library for bioinformatics (implemented in Python 2)
The Biopython Project is an international association
of developers of freely available Python tools for
@@ -89,14 +82,37 @@
python3-reportlab
Recommends: python-biopython-doc (= ${source:Version})
Suggests: python3-tk,
- wise,
- muscle,
+ python-reportlab,
+ python-numpy,
+ python3-numpy,
+ bwa [any-amd64],
+ clustalo,
clustalw,
+ dialign,
+ dssp,
+ emboss,
+ fasttree,
mafft,
- emboss,
- blast2,
+ muscle,
+ ncbi-blast+,
+ phyml,
+ prank,
+ 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,
- probcons
+ raxml,
+ t-coffee,
+ wise
Description: Python library for bioinformatics (implemented in Python 3)
The Biopython Project is an international association
of developers of freely available Python tools for
Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch 2014-03-15 12:07:13 UTC (rev 16447)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_dssp.patch 2014-03-15 20:36:41 UTC (rev 16448)
@@ -1,39 +0,0 @@
-Index: python-biopython-1.63/Bio/PDB/DSSP.py
-===================================================================
---- python-biopython-1.63.orig/Bio/PDB/DSSP.py 2014-03-12 17:58:51.000000000 +0000
-+++ python-biopython-1.63/Bio/PDB/DSSP.py 2014-03-12 18:00:02.000000000 +0000
-@@ -80,7 +80,7 @@
- assert 0
-
-
--def dssp_dict_from_pdb_file(in_file, DSSP="dssp"):
-+def dssp_dict_from_pdb_file(in_file, DSSP="mkdssp"):
- """
- Create a DSSP dictionary from a PDB file.
-
-@@ -199,7 +199,7 @@
- -42.399999999999999)
- """
-
-- def __init__(self, model, pdb_file, dssp="dssp"):
-+ def __init__(self, model, pdb_file, dssp="mkdssp"):
- """
- @param model: the first model of the structure
- @type model: L{Model}
-Index: python-biopython-1.63/Tests/test_DSSP_tool.py
-===================================================================
---- python-biopython-1.63.orig/Tests/test_DSSP_tool.py 2014-03-12 17:59:10.000000000 +0000
-+++ python-biopython-1.63/Tests/test_DSSP_tool.py 2014-03-12 17:59:33.000000000 +0000
-@@ -22,10 +22,10 @@
- try:
- try:
- # Newer versions of DSSP
-- subprocess.check_call(["dssp", "--version"], **quiet_kwargs)
-+ subprocess.check_call(["mkdssp", "--version"], **quiet_kwargs)
- except subprocess.CalledProcessError:
- # Older versions of DSSP
-- subprocess.check_call(["dssp", "-h"], **quiet_kwargs)
-+ subprocess.check_call(["mkdssp", "-h"], **quiet_kwargs)
- except OSError:
- raise MissingExternalDependencyError(
- "Install dssp if you want to use it from Biopython.")
Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series 2014-03-15 12:07:13 UTC (rev 16447)
+++ trunk/packages/python-biopython/trunk/debian/patches/series 2014-03-15 20:36:41 UTC (rev 16448)
@@ -1,2 +1 @@
fix_test_emboss.patch
-fix_dssp.patch
Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules 2014-03-15 12:07:13 UTC (rev 16447)
+++ trunk/packages/python-biopython/trunk/debian/rules 2014-03-15 20:36:41 UTC (rev 16448)
@@ -7,13 +7,6 @@
#export PYBUILD_DESTDIR_python2=debian/python-biopython/
#export PYBUILD_DESTDIR_python3=debian/python3-biopython/
-BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-ifeq ($(BUILDARCH),amd64)
- EXCLUDEBWA=
-else
- EXCLUDEBWA=BWA_tool
-endif
-
%:
dh $@ --with python2,python3 --buildsystem=pybuild
@@ -23,28 +16,6 @@
dh_numpy3 -ppython3-biopython
override_dh_auto_test:
- # 1. avoid some tests which need online access
- # 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL)
- # 3. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
- # 4. avoid testing tools that are not packaged for Debian yet
- # 5. avoid amd64 only tools on other architectures
- # While 2. and 3. do not create errors there is no point in bloating
- # the build log and this kind of documentation makes things more transparent
- mkdir -p Tests_avoid
- for avoid in \
- Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS \
- BioSQL_MySQLdb BioSQL_psycopg2 \
- PAML_tools EmbossPhylipNew \
- MSAProbs_tool NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool \
- $(EXCLUDEBWA) \
- ; do \
- mv Tests/test_$${avoid}.py Tests_avoid ; \
- done
- # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir
- # to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
- dh_auto_test -- --test --system=custom --test-args='env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} {interpreter} setup.py test'
- mv Tests_avoid/* Tests
- rmdir Tests_avoid
override_dh_installdocs:
dh_installdocs
Added: trunk/packages/python-biopython/trunk/debian/tests/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/tests/control (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/tests/control 2014-03-15 20:36:41 UTC (rev 16448)
@@ -0,0 +1,36 @@
+Tests: upstream
+Depends: python-all-dev,
+ python3-all-dev,
+ flex,
+ python-reportlab,
+ python-numpy,
+ python3-reportlab,
+ python3-numpy,
+ bwa [any-amd64],
+ clustalo,
+ clustalw,
+ dialign,
+ dssp,
+ emboss,
+ fasttree,
+ mafft,
+ muscle,
+ ncbi-blast+,
+ phyml,
+ prank,
+ 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,
+ t-coffee,
+ wise
Added: trunk/packages/python-biopython/trunk/debian/tests/upstream
===================================================================
--- trunk/packages/python-biopython/trunk/debian/tests/upstream (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/tests/upstream 2014-03-15 20:36:41 UTC (rev 16448)
@@ -0,0 +1,64 @@
+#! /bin/sh
+
+################################################################################
+# 1. avoid some tests which need online access
+# 2. avoid tests needing a ready setup database server (MySQL and PostgreSQL)
+# 3. avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip are non-free
+# 4. avoid testing tools that are not packaged for Debian yet
+# 5. avoid amd64 only tools on other architectures
+#
+# While 2. and 3. do not create errors there is no point in bloating
+# the build log and this kind of documentation makes things more transparent
+################################################################################
+
+# definitions
+################################################################################
+
+BUILDARCH=$(dpkg-architecture -qDEB_BUILD_ARCH)
+
+EXCLUDE="Entrez_online"
+EXCLUDE="$EXCLUDE:HotRand"
+EXCLUDE="$EXCLUDE:NCBI_qblast"
+EXCLUDE="$EXCLUDE:SCOP_online"
+EXCLUDE="$EXCLUDE:SeqIO_online"
+EXCLUDE="$EXCLUDE:TogoWS"
+EXCLUDE="$EXCLUDE:BioSQL_MySQLdb"
+EXCLUDE="$EXCLUDE:BioSQL_psycopg2"
+EXCLUDE="$EXCLUDE:PAML_tools"
+EXCLUDE="$EXCLUDE:EmbossPhylipNew"
+EXCLUDE="$EXCLUDE:MSAProbs_tool"
+EXCLUDE="$EXCLUDE:NACCESS_tool"
+EXCLUDE="$EXCLUDE:PopGen_DFDist"
+EXCLUDE="$EXCLUDE:PopGen_FDist"
+EXCLUDE="$EXCLUDE:PopGen_GenePop"
+EXCLUDE="$EXCLUDE:PopGen_GenePop_EasyController"
+EXCLUDE="$EXCLUDE:PopGen_SimCoal"
+EXCLUDE="$EXCLUDE:XXmotif_tool"
+
+if [ "x$BUILDARCH" = "xamd64" ]; then
+ EXCLUDE="$EXCLUDE:BWA_tool"
+fi
+
+# move excluded tests
+################################################################################
+
+mkdir -p Tests_avoid
+for i in $(echo $EXCLUDE | tr ':' '\n'); do \
+ mv Tests/test_${i}.py Tests_avoid ; \
+done
+
+# execute tests
+################################################################################
+# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the
+# test is verifying this dir to run the EMBOSS test
+# test_Emboss also requires to have the environment variable EMBOSS_ROOT set
+
+for python in $(pyversions -i) $(py3versions -i); do
+ DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} python setup.py test
+done
+
+# restore test directory
+################################################################################
+
+mv Tests_avoid/* Tests
+rmdir Tests_avoid
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