Bug#1108997: unblock: mdanalysis/2.9.0-9
Package: release.debian.org
Followup-For: Bug #1108997
Control: retitle 1108997 unblock: mdanalysis/2.9.0-12
Control: tags 1108997 - moreinfo
Santiago clarified that skipping tests on 1 or 2 cpu won't actually
help. Tests still randomly timeout on more than 2 cpu.
mdanalysis/2.9.0-12 deactivates all tests altogether, both build-time
and run-time. Can this one be unblocked? debdiff attached.
unblock mdanalysis/2.9.0-12
diff -Nru mdanalysis-2.9.0/debian/changelog mdanalysis-2.9.0/debian/changelog
--- mdanalysis-2.9.0/debian/changelog 2025-05-11 23:44:46.000000000 +0200
+++ mdanalysis-2.9.0/debian/changelog 2025-07-10 11:07:57.000000000 +0200
@@ -1,3 +1,38 @@
+mdanalysis (2.9.0-12) unstable; urgency=medium
+
+ * skip all tests, both build-time and run-time. See Bug#1108309.
+
+ -- Drew Parsons <dparsons@debian.org> Thu, 10 Jul 2025 11:07:57 +0200
+
+mdanalysis (2.9.0-11) unstable; urgency=medium
+
+ * fix order of conditional control of build-time tests
+
+ -- Drew Parsons <dparsons@debian.org> Wed, 09 Jul 2025 19:16:36 +0200
+
+mdanalysis (2.9.0-10) unstable; urgency=medium
+
+ * apply suggestion from Bug#1108309 to skip tests (build and
+ runtime) if less than 2 CPUs are available
+ * do not run build-time tests on hurd-i386
+ or when nocheck is set in DEB_BUILD_OPTIONS
+
+ -- Drew Parsons <dparsons@debian.org> Wed, 09 Jul 2025 15:12:21 +0200
+
+mdanalysis (2.9.0-9) unstable; urgency=medium
+
+ * debian/tests/control: mark mdanalysis with Restrictions: flaky.
+ mdanalysis tests are generally unreliable and fail often and
+ randomly. Closes: #1108309
+ * debian/tests: skip tests observed failing in debci
+ migration-reference runs:
+ test_dihedral_attr_warning test_AnalysisFromFunction
+ test_villin_unfolded test_rmsd_frames test_file_guess_hydrogens
+ test_gnm_run_step test_all_backends_give_correct_results
+ test_startframe test_hbond_analysis
+
+ -- Drew Parsons <dparsons@debian.org> Fri, 04 Jul 2025 10:23:27 +0200
+
mdanalysis (2.9.0-8) unstable; urgency=medium
* skip test_distances, since NSGrid is flaky and causes distance
diff -Nru mdanalysis-2.9.0/debian/rules mdanalysis-2.9.0/debian/rules
--- mdanalysis-2.9.0/debian/rules 2025-05-11 23:44:46.000000000 +0200
+++ mdanalysis-2.9.0/debian/rules 2025-07-10 11:07:57.000000000 +0200
@@ -6,6 +6,23 @@
export PYBUILD_NAME=mdanalysis
export PYBUILD_DIR=package
+# skip tests on these arches
+ARCH_NO_TEST_LIST = hurd-i386
+
+empty :=
+space := $(empty)$(empty)
+
+# run tests, or not
+#RUNTEST=yes
+# always skip all tests for now, see Bug#1108309
+RUNTEST=no
+ifneq (,$(findstring $(space)$(DEB_HOST_ARCH)$(space), $(space)$(ARCH_NO_TEST_LIST)$(space)))
+ RUNTEST=no
+endif
+ifeq (nocheck,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
+ RUNTEST=no
+endif
+
# parallel and openmp tests are unstable, often timing out
SKIP_TEST_LIST += parallel multiprocess openmp
@@ -103,14 +120,16 @@
rm -rf testsuite/.pytest_cache
override_dh_auto_test:
+ifeq (yes,$(findstring yes,$(RUNTEST)))
set -e; \
- for py in $(shell py3versions -rv); do \
+ if [ $(shell nproc) -gt 2 ]; then for py in $(shell py3versions -rv); do \
echo "=== testing with python$$py ==="; \
pydir=`pybuild -p $$py --system=distutils --print {build_dir}`; \
MPLBACKEND=agg PYTHONPATH=$$pydir python$$py -mpytest -v -k "$(SKIP_TESTS)" --disable-pytest-warnings testsuite; \
rm -rf $$pydir/MDAnalysis/.hypothesis; \
rm -rf $$pydir/MDAnalysis/.duecredit.p; \
- done
+ done; fi
+endif
execute_after_dh_python3:
dh_numpy3
diff -Nru mdanalysis-2.9.0/debian/tests/control mdanalysis-2.9.0/debian/tests/control
--- mdanalysis-2.9.0/debian/tests/control 2025-05-11 23:44:46.000000000 +0200
+++ mdanalysis-2.9.0/debian/tests/control 2025-07-10 11:07:57.000000000 +0200
@@ -4,4 +4,4 @@
python3-pytest,
python3-sklearn,
python3-all
-Restrictions: allow-stderr
+Restrictions: allow-stderr, flaky
diff -Nru mdanalysis-2.9.0/debian/tests/test-mdanalysis mdanalysis-2.9.0/debian/tests/test-mdanalysis
--- mdanalysis-2.9.0/debian/tests/test-mdanalysis 2025-05-11 23:44:46.000000000 +0200
+++ mdanalysis-2.9.0/debian/tests/test-mdanalysis 2025-07-10 11:07:57.000000000 +0200
@@ -1,6 +1,14 @@
#!/bin/bash
set -efu
+# mdanalysis tests are generally flakey, often timing out randomly
+# see Bug#1108309 and https://github.com/MDAnalysis/mdanalysis/issues/5078
+# so skip all tests for now
+echo "mdanalysis tests are not stable, see Bug#1108309 and https://github.com/MDAnalysis/mdanalysis/issues/5078";
+echo "hence skipping tests"
+exit 2
+
+
arch=$(dpkg-architecture -qDEB_HOST_ARCH)
EXTRA_TEST_FLAGS=-v
@@ -9,6 +17,12 @@
# so list tests to skip in array variable SKIP_TEST_LIST
declare -a SKIP_TEST_LIST
+# mdanalysis tests are generally flakey, and fail often and randomly
+# skip observed failures to reduce the failure cross-section
+SKIP_TEST_LIST=("${SKIP_TEST_LIST[@]}" test_dihedral_attr_warning test_AnalysisFromFunction \
+ test_villin_unfolded test_rmsd_frames test_file_guess_hydrogens test_gnm_run_step \
+ test_all_backends_give_correct_results test_startframe test_hbond_analysis)
+
# parallel and openmp tests are unstable, often timing out
SKIP_TEST_LIST=("${SKIP_TEST_LIST[@]}" parallel multiprocess openmp)
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