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Change CI pytests to be more accurate #887

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merged 5 commits into from
Nov 22, 2024
+49 −26
Merged

Change CI pytests to be more accurate #887

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121c7dd
start [skip ci]
mattcieslak Nov 20, 2024
cd283f4
try it out
mattcieslak Nov 20, 2024
0c84e00
not
mattcieslak Nov 20, 2024
275f621
Merge branch 'master' into ci/more-coverage
tsalo Nov 21, 2024
f758f1d
Run ruff.
tsalo Nov 21, 2024
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75 changes: 49 additions & 26 deletions qsiprep/tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import os
import sys
from pathlib import Path
from unittest.mock import patch

import pytest
Expand All @@ -12,7 +13,7 @@
from qsiprep.cli.workflow import build_boilerplate, build_workflow
from qsiprep.reports.core import generate_reports
from qsiprep.tests.utils import check_generated_files, download_test_data, get_test_data_path
from qsiprep.utils.bids import write_derivative_description
from qsiprep.utils.bids import write_bidsignore, write_derivative_description

nipype_config.enable_debug_mode()

Expand Down Expand Up @@ -57,7 +58,7 @@ def test_dsdti_fmap(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -99,7 +100,7 @@ def test_dscsdsi_fmap(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -143,7 +144,7 @@ def test_cuda(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -189,7 +190,7 @@ def test_drbuddi_rpe(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -226,7 +227,7 @@ def test_drbuddi_shoreline_epi(data_dir, output_dir, working_dir):
'--shoreline-iters=1',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -263,7 +264,7 @@ def test_drbuddi_tensorline_epi(data_dir, output_dir, working_dir):
'--shoreline-iters=1',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -308,7 +309,7 @@ def test_dscsdsi(data_dir, output_dir, working_dir):
'--shoreline-iters=1',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -350,7 +351,7 @@ def test_dsdti_nofmap(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -392,7 +393,7 @@ def test_dsdti_synfmap(data_dir, output_dir, working_dir):
'--output-resolution=5',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -432,7 +433,7 @@ def test_intramodal_template(data_dir, output_dir, working_dir):
'--intramodal-template-iters=2',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -468,7 +469,7 @@ def test_multi_t1w(data_dir, output_dir, working_dir):
'--intramodal-template-iters=2',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -505,7 +506,7 @@ def test_maternal_brain_project(data_dir, output_dir, working_dir):
f'--bids-filter-file={bids_filter}',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


@pytest.mark.integration
Expand Down Expand Up @@ -541,7 +542,7 @@ def test_forrest_gump(data_dir, output_dir, working_dir):
f'--bids-filter-file={bids_filter}',
]

_run_and_generate(TEST_NAME, parameters, test_main=True)
_run_and_generate(TEST_NAME, parameters, test_main=False)


def _check_arg_specified(argname, arglist):
Expand All @@ -567,7 +568,7 @@ def _update_resources(parameters):
return parameters


def _run_and_generate(test_name, parameters, test_main=True):
def _run_and_generate(test_name, parameters, test_main=False):
from qsiprep import config

# TODO: Add --clean-workdir param to CLI
Expand All @@ -587,29 +588,51 @@ def _run_and_generate(test_name, parameters, test_main=True):

assert e.value.code == 0
else:
# XXX: This isn't working because config.execution.fs_license_file is None.
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={})
qsiprep_wf = retval['workflow']
qsiprep_wf.run()
write_derivative_description(config.execution.bids_dir, config.execution.output_dir)

build_boilerplate(str(config_file), qsiprep_wf)
session_list = (
config.execution.bids_filters.get('bold', {}).get('session')
if config.execution.bids_filters
else None
config.loggers.workflow.log(
15,
'\n'.join(['config:'] + [f'\t\t{s}' for s in config.dumps().splitlines()]),
)
generate_reports(
subject_list=config.execution.participant_label,

qsiprep_wf.run(**config.nipype.get_plugin())

boiler_file = config.execution.output_dir / 'logs' / 'CITATION.md'
if boiler_file.exists():
if config.environment.exec_env in (
'apptainer',
'singularity',
'docker',
):
boiler_file = Path('<OUTPUT_PATH>') / boiler_file.relative_to(
config.execution.output_dir
)
config.loggers.workflow.log(
25,
'Works derived from this QSIPrep execution should include the '
f'boilerplate text found in {boiler_file}.',
)

write_derivative_description(config.execution.bids_dir, config.execution.output_dir)
failed_reports = generate_reports(
processing_list=config.execution.processing_list,
output_level=config.workflow.subject_anatomical_reference,
output_dir=config.execution.output_dir,
run_uuid=config.execution.run_uuid,
session_list=session_list,
)
assert not failed_reports
write_derivative_description(
config.execution.bids_dir,
config.execution.output_dir,
# dataset_links=config.execution.dataset_links,
)
write_bidsignore(config.execution.output_dir)

output_list_file = os.path.join(get_test_data_path(), f'{test_name}_outputs.txt')
optional_outputs_list = os.path.join(get_test_data_path(), f'{test_name}_optional_outputs.txt')
Expand Down