[med-svn] r20872 - in trunk/packages/python-cogent/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Dec 23 14:22:10 UTC 2015
Author: tille
Date: 2015-12-23 14:22:09 +0000 (Wed, 23 Dec 2015)
New Revision: 20872
Modified:
trunk/packages/python-cogent/trunk/debian/changelog
trunk/packages/python-cogent/trunk/debian/control
trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
trunk/packages/python-cogent/trunk/debian/rules
Log:
* Build-Depends: bwa [any-amd64] and exclude bwa tests for other
architectures
Closes: #808799
* Really activate tests but only those that are known to pass. All
failed tests excluded for the moment - more detailed investigation
is needed
* Drop debug package in favour of automatically generated one
Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog 2015-12-23 09:58:22 UTC (rev 20871)
+++ trunk/packages/python-cogent/trunk/debian/changelog 2015-12-23 14:22:09 UTC (rev 20872)
@@ -1,3 +1,15 @@
+python-cogent (1.5.3-4) UNRELEASED; urgency=medium
+
+ * Build-Depends: bwa [any-amd64] and exclude bwa tests for other
+ architectures
+ Closes: #808799
+ * Really activate tests but only those that are known to pass. All
+ failed tests excluded for the moment - more detailed investigation
+ is needed
+ * Drop debug package in favour of automatically generated one
+
+ -- Andreas Tille <tille at debian.org> Wed, 23 Dec 2015 14:23:42 +0100
+
python-cogent (1.5.3-3) unstable; urgency=medium
* cme fix dpkg-control
Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control 2015-12-23 09:58:22 UTC (rev 20871)
+++ trunk/packages/python-cogent/trunk/debian/control 2015-12-23 14:22:09 UTC (rev 20872)
@@ -12,7 +12,7 @@
python-sphinx,
cython,
blast2,
- bwa,
+ bwa [any-amd64],
cd-hit,
clearcut,
clustalw,
@@ -34,9 +34,21 @@
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends}
+Recommends: blast2,
+ bwa [any-amd64],
+ cd-hit,
+ clearcut,
+ dialign,
+ muscle
Suggests: python-cogent-doc,
+ clustalw,
+ infernal,
+ mafft,
cd-hit,
- parsinsert
+ mothur,
+ parsinsert,
+ raxml,
+ rtax
Description: framework for genomic biology
PyCogent is a software library for genomic biology. It is a fully
integrated and thoroughly tested framework for:
@@ -49,22 +61,6 @@
alignment) and the frequent addition of entirely new methods for the analysis
of genomic data.
-Package: python-cogent-dbg
-Architecture: any
-Section: debug
-Priority: extra
-Depends: python-cogent (= ${binary:Version}),
- ${misc:Depends}
-Description: debug information for pycogent
- PyCogent is a software library for genomic biology.
- .
- It is distinguished by many unique built-in capabilities (such as true codon
- alignment) and the frequent addition of entirely new methods for the analysis
- of genomic data.
- .
- This package is needed to improve significantly the bug reports
- that users may feel inclined to send.
-
Package: python-cogent-doc
Architecture: all
Section: doc
Modified: trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch 2015-12-23 09:58:22 UTC (rev 20871)
+++ trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch 2015-12-23 14:22:09 UTC (rev 20872)
@@ -20,6 +20,36 @@
_parameters.update({\
--- a/tests/test_app/test_cd_hit.py
+++ b/tests/test_app/test_cd_hit.py
+@@ -22,24 +22,24 @@ class CD_HIT_Tests(TestCase):
+ """CD_HIT BaseCommand should return the correct BaseCommand"""
+ c = CD_HIT()
+ self.assertEqual(c.BaseCommand,\
+- ''.join(['cd "',getcwd(),'/"; ','cd-hit']))
++ ''.join(['cd "',getcwd(),'/"; ','cdhit']))
+ c.Parameters['-i'].on('seq.txt')
+ self.assertEqual(c.BaseCommand,\
+- ''.join(['cd "',getcwd(),'/"; ','cd-hit -i "seq.txt"']))
++ ''.join(['cd "',getcwd(),'/"; ','cdhit -i "seq.txt"']))
+ c.Parameters['-c'].on(0.8)
+ self.assertEqual(c.BaseCommand,\
+- ''.join(['cd "',getcwd(),'/"; ','cd-hit -c 0.8' +
++ ''.join(['cd "',getcwd(),'/"; ','cdhit -c 0.8' +
+ ' -i "seq.txt"']))
+
+ def test_changing_working_dir(self):
+ """CD_HIT BaseCommand should change according to WorkingDir"""
+ c = CD_HIT(WorkingDir='/tmp/cdhit_test')
+ self.assertEqual(c.BaseCommand,\
+- ''.join(['cd "','/tmp/cdhit_test','/"; ','cd-hit']))
++ ''.join(['cd "','/tmp/cdhit_test','/"; ','cdhit']))
+ c = CD_HIT()
+ c.WorkingDir = '/tmp/cdhit_test2'
+ self.assertEqual(c.BaseCommand,\
+- ''.join(['cd "','/tmp/cdhit_test2','/"; ','cd-hit']))
++ ''.join(['cd "','/tmp/cdhit_test2','/"; ','cdhit']))
+
+ #removing the dirs is proof that they were created at the same time
+ #if the dirs are not there, an OSError will be raised
@@ -58,24 +58,24 @@ class CD_HIT_EST_Tests(TestCase):
"""CD_HIT_EST BaseCommand should return the correct BaseCommand"""
c = CD_HIT_EST()
Modified: trunk/packages/python-cogent/trunk/debian/rules
===================================================================
--- trunk/packages/python-cogent/trunk/debian/rules 2015-12-23 09:58:22 UTC (rev 20871)
+++ trunk/packages/python-cogent/trunk/debian/rules 2015-12-23 14:22:09 UTC (rev 20872)
@@ -4,6 +4,20 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
+
+FAILED_TESTS := test_infernal \
+ test_mothur \
+ test_parsinsert \
+ test_raxml_v730 \
+ test_rtax \
+ test_clustalw \
+ test_mafft \
+ test_unifrac \
+ test_seqsim.test_usage
+
+ONLYAMD64_TESTS := test_bwa
+
export PYBUILD_NAME=cogent
PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
@@ -40,11 +54,19 @@
dh_installdocs
rm -rf debian/$(PKG)/usr/share/doc/$(PKG)/html/_sources
-override_dh_strip:
- dh_strip --dbg-package=python-cogent-dbg
-
override_dh_auto_test:
- # BLASTMAT=/usr/share/ncbi/data/ $(CURDIR)/run_tests # --debug
+ cp -a tests/alltests.py tests/alltests.py~
+ # exclude tests known to fail
+ for tst in $(FAILED_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
+# avoid amd64 only tools on other architectures
+ifeq ($(BUILDARCH),amd64)
+ echo "bwa can be tested on amd64 arch"
+else
+ for tst in $(ONLYAMD64_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
+endif
+ BLASTMAT=/usr/share/ncbi/data/ $(CURDIR)/run_tests # --debug
+ # restore original tests file
+ mv tests/alltests.py~ tests/alltests.py
get-orig-source:
mkdir -p ../tarballs
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