Draft testing code.

src/fmripost_aroma/tests/run_local_tests.py

@@ -12,7 +12,9 @@ def _get_parser():
     -------
     parser.parse_args() : argparse dict
     """
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
     parser.add_argument(
         '-k',
         dest='test_regex',

src/fmripost_aroma/tests/test_cli.py

@@ -0,0 +1,147 @@
+"""Command-line interface tests."""
+
+import os
+import sys
+from unittest.mock import patch
+
+import pytest
+from fmripost_aroma.cli import run
+from fmripost_aroma.cli.parser import parse_args
+from fmripost_aroma.cli.workflow import build_boilerplate, build_workflow
+from fmripost_aroma.reports.core import generate_reports
+from fmripost_aroma.tests.utils import (
+    check_generated_files,
+    download_test_data,
+    get_test_data_path,
+)
+from fmripost_aroma.utils.bids import write_derivative_description
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_deriv_only()
+def test_ds005115_deriv_only(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 fMRIPrep derivatives with MNI152NLin6Asym-space data."""
+    test_name = 'test_ds005115_deriv_only'
+
+    fmriprep_dir = download_test_data('ds005115_deriv_mni6', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        fmriprep_dir,
+        out_dir,
+        'participant',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_deriv_and_raw()
+def test_ds005115_deriv_and_raw(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 raw BIDS + fMRIPrep derivatives w/o MNI152NLin6Asym data."""
+    test_name = 'test_ds005115_deriv_and_raw'
+
+    raw_dir = download_test_data('ds005115_raw', data_dir)
+    fmriprep_dir = download_test_data('ds005115_deriv_no_mni6', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        raw_dir,
+        out_dir,
+        'participant',
+        '--derivatives',
+        f'fmriprep={fmriprep_dir}',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+@pytest.mark.integration()
+@pytest.mark.ds005115_resampling_and_raw()
+def test_ds005115_resampling_and_raw(data_dir, output_dir, working_dir):
+    """Run fMRIPost-AROMA on ds005115 raw BIDS + resampling-level fMRIPrep derivatives."""
+    test_name = 'test_ds005115_resampling_and_raw'
+
+    raw_dir = download_test_data('ds005115_raw', data_dir)
+    fmriprep_dir = download_test_data('ds005115_resampling', data_dir)
+    out_dir = os.path.join(output_dir, test_name)
+
+    parameters = [
+        raw_dir,
+        out_dir,
+        'participant',
+        '--derivatives',
+        f'fmriprep={fmriprep_dir}',
+        '--work-dir',
+        working_dir,
+        '--denoising-method',
+        'aggr',
+        'nonaggr',
+        'orthaggr',
+    ]
+    _run_and_generate(
+        test_name=test_name,
+        parameters=parameters,
+    )
+
+
+def _run_and_generate(test_name, parameters, test_main=False):
+    from fmripost_aroma import config
+
+    parameters.append('--clean-workdir')
+    parameters.append('--stop-on-first-crash')
+    parameters.append('--notrack')
+    parameters.append('-v')
+
+    if test_main:
+        # This runs, but for some reason doesn't count toward coverage.
+        argv = ['fmripost_aroma'] + parameters
+        with patch.object(sys, 'argv', argv):
+            with pytest.raises(SystemExit) as e:
+                run.main()
+
+            assert e.value.code == 0
+    else:
+        # XXX: I want to drop this option and use the main function,
+        # but the main function doesn't track coverage correctly.
+        parse_args(parameters)
+        config_file = config.execution.work_dir / f'config-{config.execution.run_uuid}.toml'
+        config.loggers.cli.warning(f'Saving config file to {config_file}')
+        config.to_filename(config_file)
+
+        retval = build_workflow(config_file, retval={})
+        xcpd_wf = retval['workflow']
+        xcpd_wf.run()
+        write_derivative_description(config.execution.bids_dir, config.execution.output_dir)
+
+        build_boilerplate(str(config_file), xcpd_wf)
+        session_list = (
+            config.execution.bids_filters.get('bold', {}).get('session')
+            if config.execution.bids_filters
+            else None
+        )
+        generate_reports(
+            subject_list=config.execution.participant_label,
+            output_dir=config.execution.output_dir,
+            run_uuid=config.execution.run_uuid,
+            session_list=session_list,
+        )
+
+    output_list_file = os.path.join(get_test_data_path(), f'{test_name}_outputs.txt')
+    check_generated_files(config.execution.output_dir, output_list_file)