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https://github.com/galaxyproject/galaxy.git
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Nicola Soranzo
94427e5dea
Fix ``test_singularity_container_test`` unit test, which failed with:
```
test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py:48:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py:62: in singularity_container_test
check_output(exec_command.extend(["bash", "-c", test_command]), stderr=subprocess.STDOUT)
/usr/lib/python3.8/subprocess.py:415: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
/usr/lib/python3.8/subprocess.py:493: in run
with Popen(*popenargs, **kwargs) as process:
/usr/lib/python3.8/subprocess.py:858: in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
> args = list(args)
E TypeError: 'NoneType' object is not iterable
/usr/lib/python3.8/subprocess.py:1569: TypeError
```
Broken in commit 1dc1e5f219 .
Also:
- Use `tmp_path` pytest fixture.
- Add type annotations.
- Code refactorings.
- Install singularity in the mulled GitHub workflow so that the 2 singularity
unit tests are not skipped any more.