🐛 Fix -S parameter

[shnizzedy]

Related to

Related to #2150 (comment) by @nimzodisaster

Description

Replaces

C-PAC/CPAC/pipeline/cpac_runner.py

Line 105 in 96db8b0

shell = subprocess.getoutput('echo $SHELL')

C-PAC/CPAC/pipeline/cpac_runner.py

Line 134 in 96db8b0

'shell': shell,

with

C-PAC/CPAC/pipeline/utils.py

Lines 30 to 41 in 68baf2e

	def get_shell() -> str:
	"""Return the path to default shell."""
	shell: Optional[str] = subprocess.getoutput(
	f"which $(ps -p {os.getppid()} -o comm=)"
	)
	if not shell:
	try:
	shell = os.environ["_SHELL"]
	except KeyError:
	msg = "Shell command not found."
	raise EnvironmentError(msg)
	return shell

C-PAC/CPAC/pipeline/cpac_runner.py

Line 176 in 68baf2e

"shell": get_shell(),

Technical details

This PR should resolve the identified empty -S parameter, but I the batch scripts C-PAC generates look like they're intended for uncontainerized runs, which we no longer support, so I think they'll need more of an update to get them working again.

This PR is just makes this small fix, functionalizes it and adds a unit test for the function. I thought it'd be easier to just make the small PR than to keep track of my notes from investigating the issue.

Tests

C-PAC/CPAC/pipeline/test/test_cpac_runner.py

Lines 13 to 18 in 964cb4b

	def test_shell() -> None:
	"""Test that ``get_shell`` returns a path to an executable BASH."""
	shell: str = get_shell()
	assert shell.lower().endswith("bash"), "Default shell isn't BASH?"
	assert Path(shell).exists(), "No default shell found."
	assert os.access(shell, os.X_OK), "Default shell not executable."

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[sgiavasis]

So basically it checks the actual shell used by the parent process instead of relying on the environmental variable. Nice, thanks!