[med-svn] [Git][med-team/python-biopython][master] 4 commits: skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri Sep 6 06:27:03 BST 2024
Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
d6438407 by Étienne Mollier at 2024-09-04T21:17:22+02:00
skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
This patch is introduced to give some breath to Risc-V CI runners while
the core of the problem is investigated.
Closes: #1079439
- - - - -
1e20c051 by Étienne Mollier at 2024-09-04T21:29:26+02:00
d/rules: skip ncbi tools tests due to #1079439.
- - - - -
e65e38ea by Étienne Mollier at 2024-09-04T21:43:26+02:00
d/rules: update list of excluded tests due to missing packages.
- - - - -
d6aeea05 by Étienne Mollier at 2024-09-06T07:25:51+02:00
Ready for upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/patches/series
- + debian/patches/skip-scipy-in-codonalign.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+python-biopython (1.83+dfsg1-4) unstable; urgency=medium
+
+ * skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
+ This patch is introduced to give some breath to Risc-V CI runners while
+ the core of the problem is investigated. (Closes: #1079439)
+ * d/rules: skip ncbi tools tests due to #1079439.
+ * d/rules: update list of excluded tests due to missing packages.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 04 Sep 2024 21:44:05 +0200
+
python-biopython (1.83+dfsg1-3) unstable; urgency=medium
* Replace skip-xmlio-tests.patch by seqxml-parser.patch.
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ croak-on-muscle5.patch
muscle3.patch
#port_tutorial_to_muscle3.patch
seqxml-parser.patch
+skip-scipy-in-codonalign.patch
=====================================
debian/patches/skip-scipy-in-codonalign.patch
=====================================
@@ -0,0 +1,40 @@
+Description: skip scipy tests within test_Align_codonalign.
+ This patch is introduced to give some breath to Risc-V CI runners while
+ the core of the problem is investigated.
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1079439
+Forwarded: not-needed
+Last-Update: 2024-08-25
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Tests/test_Align_codonalign.py
++++ python-biopython/Tests/test_Align_codonalign.py
+@@ -8230,6 +8230,12 @@
+ self.assertAlmostEqual(dN, 0.0203, places=4)
+ self.assertAlmostEqual(dS, 0.0164, places=4)
+
++ import os
++ import sys
++ if os.uname().machine == 'riscv64':
++ print('note: tests involving scipy skipped, '
++ 'they hang on riscv64.', file=sys.stderr)
++ return
+ try:
+ import scipy
+ except ImportError:
+--- python-biopython.orig/Tests/test_codonalign.py
++++ python-biopython/Tests/test_codonalign.py
+@@ -307,6 +307,12 @@
+ self.assertAlmostEqual(dN, 0.0203, places=4)
+ self.assertAlmostEqual(dS, 0.0164, places=4)
+
++ import os
++ import sys
++ if os.uname().machine == 'riscv64':
++ print('note: tests involving scipy skipped, '
++ 'they hang on riscv64.', file=sys.stderr)
++ return
+ try:
+ import scipy
+ except ImportError:
=====================================
debian/rules
=====================================
@@ -23,25 +23,38 @@ EXCLUDEONLINE=
# This would not trigger a failure but bloats the build log with irrelevant noise
EXCLUDENONFREE=PAML_tools EmbossPhylipNew
-# avoid testing tools that are not packaged for Debian yet (or will never be packaged since they might be outdated)
-# This would not trigger a failure but bloats the build log with irrelevant noise
-EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth mmtf mmtf_online GraphicsBitmaps
+# avoid testing tools that are not packaged for Debian yet (or will
+# never be packaged since they might be outdated). This would not
+# trigger a failure but bloats the build log with irrelevant noise
+EXCLUDENOTPACKAGED=\
+ MSAProbs_tool \
+ PopGen_GenePop \
+ PopGen_GenePop_EasyController \
+ XXmotif_tool \
+ PDB_ResidueDepth \
+ mmtf \
+ mmtf_online \
+ GraphicsBitmaps
# avoid amd64 only tools on other architectures
-ifeq ($(BUILDARCH),amd64)
- EXCLUDEARCHamd64=
-else
- EXCLUDEARCHamd64=raxml_tool
+ifneq ($(BUILDARCH),amd64)
+ EXCLUDEARCH=raxml_tool
# The tutorial test reads through the documentation, and checks that the
# documented commands and output are working and matching. There is at
# least one output that assumes that the test runs on s390x, causing mostly
# undue regression, so skipping on that architecture, to avoid cluttering
# the documentation.
- EXCLUDEARCHamd64+=Tutorial
+ EXCLUDEARCH+=Tutorial
# FIXME: biopython > 1.83+dfsg1 will skip the faulty item with much finer
# grain, so this test will be restorable at that point.
endif
+ifeq ($(BUILDARCH),riscv64)
+ # FIXME: the below test is affected by #1080479, and can be
+ # restored once it is resolved.
+ EXCLUDEARCH+=NCBI_BLAST_tools
+endif
+
# avoid tests requiring data base connections if no server is running while we are doing the build
# This would not trigger a failure but bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
@@ -81,10 +94,17 @@ override_dh_auto_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
mkdir -p Tests_avoid
- for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
- ; do \
- mv Tests/test_$${avoid}.py Tests_avoid ; \
- done
+ set -e \
+ ; for avoid in \
+ $(EXCLUDEONLINE) \
+ $(EXCLUDENONFREE) \
+ $(EXCLUDENOTPACKAGED) \
+ $(EXCLUDEARCH) \
+ $(EXCLUDEDATABASE) \
+ $(EXCLUDEFAILINGTESTS) \
+ $(EXCLUDEPACKAGEINFLUX) \
+ ; do mv Tests/test_$${avoid}.py Tests_avoid \
+ ; done
# For the doc package we need a clean testsuite without all the remaining files. So keep a clean copy here
mkdir -p debian/tmp_tests
cp -a Tests debian/tmp_tests
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/005ea36db181df719278cd5a3868c0a6f3a83a53...d6aeea05e684eb76d338347f4598414d7c0e7c17
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/005ea36db181df719278cd5a3868c0a6f3a83a53...d6aeea05e684eb76d338347f4598414d7c0e7c17
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