(which started failing since ubuntu-latest was moved to 24.04)
by upgrading apptainer to >=1.3.3 to include
https://github.com/apptainer/apptainer/pull/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
Fix the following warning in unit tests:
```
.venv/lib/python3.7/site-packages/pytest_asyncio/plugin.py:191
/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/pytest_asyncio/plugin.py:191: DeprecationWarning: The 'asyncio_mode' default value will change to 'strict' in future, please explicitly use 'asyncio_mode=strict' or 'asyncio_mode=auto' in pytest configuration file.
config.issue_config_time_warning(LEGACY_MODE, stacklevel=2)
```
1) Download conformance tests to `test/functional/tools/cwl_tools` where
they can be used also by framework and unit tests in the future.
2) Add populators to enable executing CWL conformance tests
3) Generate CWL conformance API tests only when needed for tests
Nicola Soranzo