[24.0] Backport fix for test_singularity_container_test test
#19349
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(which started failing since ubuntu-latest was moved to 24.04) by upgrading apptainer to >=1.3.3 to include apptainer/apptainer#2262 . Fix: ``` > assert "samtools:1.0--1" in results["passed"], results E AssertionError: E {'failed': [{'commands': ['python -c "import pyBigWig; assert(pyBigWig.numpy ' E '== 1); assert(pyBigWig.remote == 1)"'], E 'container': 'pybigwig:0.3.22--py36h54a71a5_0', E 'errors': [{'command': 'python -c "import pyBigWig; ' E 'assert(pyBigWig.numpy == 1); ' E 'assert(pyBigWig.remote == 1)"', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}, E {'import': 'pyBigWig', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}], E 'import_lang': 'python -c', E 'imports': ['pyBigWig']}, E {'commands': ['samtools view --help 2>&1 | grep Notes > /dev/null'], E 'container': 'samtools:1.0--1', E 'errors': [{'command': 'samtools view --help 2>&1 | grep Notes > ' E '/dev/null', E 'output': '\x1b[91mERROR : Could not write info to ' E 'setgroups: Permission denied\n' E '\x1b[0m\x1b[91mERROR : Error while ' E 'waiting event for user namespace mappings: ' E 'no event received\n' E '\x1b[0m'}], E 'import_lang': 'python -c'}], E 'notest': ['yasm:1.3.0--0'], E 'passed': []} E assert 'samtools:1.0--1' in [] ``` Also: - Improve assertion messages to facilitate debugging
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test_singularity_container_test testtest_singularity_container_test test
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Dec 18, 2024
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