Make PyBIDS database generation optional in `PipelineRunner`

[michellewang]

We can add a user-specified field under PipelineStepConfig (by default turned off), which would give more flexibility since even fMRIPrep/MRIQC don't strictly need the PyBIDS database to be generated in advance

[michellewang]

@jacobsanz97

[michellewang]

@jacobsanz97

• PipelineRunner in https://github.com/nipoppy/nipoppy/blob/main/nipoppy/workflows/runner.py contains the function call that makes a PyBIDS database
• Add a field (e.g. GENERATE_PYBIDS_DATABASE) in ProcPipelineConfigStep (https://github.com/nipoppy/nipoppy/blob/main/nipoppy/config/pipeline_step.py#L73C7-L73C29)
  • Then this field can be accessed in a PipelineRunner object through self.pipeline_config.get_step_config(self.pipeline_step).GENERATE_PYBIDS_DATABASE
    • Once [ENH] Make TRACKER_CONFIG_FILE part of pipeline step config instead of pipeline config #352 gets merged then this should be self.pipeline_step_config.GENERATE_PYBIDS_DATABASE instead

[michellewang]

@jacobsanz97

See this test for checking if a function calls another function (needs import pytest_mock)

nipoppy/tests/test_workflow_pipeline.py

Lines 618 to 629 in 756fb35

	def test_run_main_analysis_level(
	workflow: PipelineWorkflow,
	mocker: pytest_mock.MockFixture,
	):
	mocked = mocker.patch("nipoppy.workflows.pipeline.apply_analysis_level")
	participants_and_sessions = {"01": ["1", "2", "3"], "02": ["1"]}
	manifest = prepare_dataset(
	participants_and_sessions_manifest=participants_and_sessions
	)
	manifest.save_with_backup(workflow.layout.fpath_manifest)
	workflow.run_main()
	assert mocked.call_count == 1