🔀 Backmerge sgiavasis/C-PAC-1#2 to bids_ingress branch for sgiavasis/C-PAC-1#1

[shnizzedy]

Fixes

Resolves merge conflicts for sgiavasis#1 by merging 532322d (sgiavasis/C-PAC-1@develop after merging sgiavasis#2) onto 61d8b6d (latest commit to head branch for sgiavasis#1 as of now)

Description

This is a pretty big PR, just because sgiavasis#2 was a pretty big PR. sgiavasis/C-PAC-1@532322d...FCP-INDI:C-PAC:d5722da1840ad7a66a73ced25583590f9d251970#files_bucket is the diff between the head of this branch and the head of sgiavasis/C-PAC-1@develop (i.e., what the diff will be for sgiavasis#1 if this PR is merged).

Technical details

This PR is almost entirely just merging the changes from sgiavasis#2 and updating tests (see below).

changed logger.warning() + print() + sys.exit() → raise Exception()

Changed

C-PAC/CPAC/_entrypoints/run.py

Lines 789 to 792 in 494f0c7

	except Exception as e: # TODO: raise exception
	WFLOGGER.warning("Could not create bids table: %s", e)
	print("Could not create bids table: %s", e)
	sys.exit(1)

to

C-PAC/CPAC/_entrypoints/run.py

Lines 789 to 791 in 64a775b

	except Exception as e:
	msg = f"Could not create bids table: {e}"
	raise ValueError(msg) from e

Tests

Failing

The tests that are failing are because bids_ingress isn't done yet.

test_motion_filter_connections

I dropped some dummy inputs ("lateral-ventricles-mask", "TR", "scan", "subject") from this test initialization

C-PAC/CPAC/func_preproc/tests/test_preproc_connections.py

Lines 177 to 192 in d5722da

	before_this_test = create_dummy_node("created_before_this_test", pre_resources)
	rpool = ResourcePool(cfg=c)
	for resource in pre_resources:
	if resource.endswith("xfm"):
	rpool.set_data(
	resource,
	before_this_test,
	resource,
	{},
	"",
	f"created_before_this_test_{regtool}",
	)
	else:
	rpool.set_data(
	resource, before_this_test, resource, {}, "", "created_before_this_test"
	)

because they're (also) coming into the resource pool from ingress methods and the nuisance connections were forking across the permutations of these from the dummy node and the ingress nodes. I'm not sure how/why this was a problem here but not before this PR 🤷

test_plugin_param

Updated

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

Line 20 in 43a9b27

cfg = Configuration()

to

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

Lines 22 to 30 in 5bbc1e6

	cfg = Configuration(
	{
	"pipeline_setup": {
	"output_directory": {"path": str(tmp_path / "out")},
	"working_directory": {"path": str(tmp_path / "work")},
	"log_directory": {"path": str(tmp_path / "log")},
	}
	}
	)

to use pytest's tmp_path to ensure writeable testing output directories (again, not sure why this became a problem in this branch 🤷)

set_subject doctest

Updated

C-PAC/CPAC/utils/configuration/configuration.py

Lines 787 to 792 in 5bbc1e6

	>>> sub_dict = {'site_id': 'site1', 'subject_id': 'sub1',
	... 'unique_id': 'uid1'}
	>>> with TemporaryDirectory() as tmpdir:
	... subject_id, p_name, log_dir = set_subject(
	... sub_dict, Configuration({'pipeline_setup': {'log_directory':
	... {'path': tmpdir}}}))

to

C-PAC/CPAC/utils/configuration/configuration.py

Lines 788 to 792 in d5722da

	>>> sub_group = (('sub1', 'uid1', 'site1'), DataFrame([]))
	>>> with TemporaryDirectory() as tmpdir:
	... subject_id, p_name, log_dir = set_subject(
	... sub_group, Configuration({'pipeline_setup': {'log_directory':
	... {'path': tmpdir}}}))

to reflect changes in bids_ingress branch that were causing this doctest to fail

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the bids_ingress 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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