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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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)
