We are always running them via minikube since commit 992edaa8b4 .
Also:
- Update PostgreSQL image version to 17 in minikube test setup to
sync it with the other CI workflows.
Now that we've fixed most TypeScript errors, switch to failing on any
vue-tsc errors instead of comparing against baseline. This simplifies
the workflow and ensures we maintain zero TypeScript errors going
forward.
Fix the following traceback:
```
galaxy/selenium/context.py:25: error: Cannot override writeable attribute with
read-only property [override]
def driver(self):
^
```
This error didn't happen during the normal `tox -e mypy` because
the `selenium` package was not installed into the tox virtual environment.
To prevent this issue and improve the code type checking, this commit
defines a new `test` dependency group and corresponding
`lib/galaxy/dependencies/pinned-test-requirements.txt` requirements
file to be used by mypy and other tests that don't need packages
used purely for developing (like black, isort, Sphinx...).
Fix the 6 new mypy errors resulting from installing the test
dependencies into the tox virtual environment.
(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
(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
Nicola Soranzo