(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:
```
Using CPython 3.8.18 interpreter at: /opt/hostedtoolcache/Python/3.8.18/x64/bin/python
× No solution found when resolving dependencies for split
│ (python_full_version == '3.9.*'):
╰─▶ Because only the following versions of rucio-clients{python_full_version >= '3.9'} are available:
rucio-clients{python_full_version >= '3.9'}<=33.6.1
rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
rucio-clients{python_full_version >= '3.9'}>=35.0.0
and all of:
rucio-clients{python_full_version >= '3.9'}>=33.6.0,<=33.6.1
rucio-clients{python_full_version >= '3.9'}>=34.0.0,<=34.6.0
rucio-clients{python_full_version >= '3.9'}>=35.0.0
require Python >=3.9, <4, we can conclude that all of:
rucio-clients{python_full_version >= '3.9'}>=33.6.0,<33.6.1
...
rucio-clients{python_full_version >= '3.9'}>35.4.1,<35.5.0
rucio-clients{python_full_version >= '3.9'}>35.5.0
are incompatible.
And because galaxy:dev depends on rucio-clients{python_full_version >=
'3.9'}>=33.6.0 and your project depends on galaxy:dev, we can conclude
that your project's requirements are unsatisfiable.
hint: The source distribution for rucio-clients{python_full_version >=
'3.9'}==35.5.0 does not include static metadata. Generating metadata for
this package requires Python >=3.9, <4, but Python 3.8.18 is installed.
```
See https://github.com/galaxyproject/galaxy/actions/runs/11684632042/job/32536277008
for lightning-fast Python dependency updates.
To update all dependencies (as done by the GitHub action):
$ make update-dependencies
To update only one package:
./lib/galaxy/dependencies/update.sh -p <PKG>
Drop galaxy_version and os from matrix and use galaxy_python_version.
Use actions/checkout instead of git clone.
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Nicola Soranzo