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FIX: --slice-time-ref option parsing #2573

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merged 4 commits into from
Oct 5, 2021
Merged

FIX: --slice-time-ref option parsing #2573

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ede646f
ENH: Allow _build_parser() to pass kwargs to ArgumentParser
effigies Oct 5, 2021
031bc75
TEST: Add test for parsing slice_time_reference options
effigies Oct 5, 2021
c2d5e99
FIX: Make partially applied "type" for --slice-time-ref
effigies Oct 5, 2021
56893d1
DOC: Explain kwargs in _build_parser
effigies Oct 5, 2021
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6 changes: 4 additions & 2 deletions fmriprep/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
from .. import config


def _build_parser():
def _build_parser(**kwargs):
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Maybe add a docstring line stating kwargs are intended for argparse.ArgumentParser?

"""Build parser object."""
from functools import partial
from pathlib import Path
Expand Down Expand Up @@ -92,11 +92,13 @@ def _slice_time_ref(value, parser):
config.environment.version
),
formatter_class=ArgumentDefaultsHelpFormatter,
**kwargs,
)
PathExists = partial(_path_exists, parser=parser)
IsFile = partial(_is_file, parser=parser)
PositiveInt = partial(_min_one, parser=parser)
BIDSFilter = partial(_bids_filter, parser=parser)
SliceTimeRef = partial(_slice_time_ref, parser=parser)

# Arguments as specified by BIDS-Apps
# required, positional arguments
Expand Down Expand Up @@ -335,7 +337,7 @@ def _slice_time_ref(value, parser):
required=False,
action="store",
default=None,
type=_slice_time_ref,
type=SliceTimeRef,
help="The time of the reference slice to correct BOLD values to, as a fraction "
"acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end "
"of acquisition. The alias `start` corresponds to 0, and `middle` to 0.5. "
Expand Down
17 changes: 17 additions & 0 deletions fmriprep/cli/tests/test_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
from ..parser import _build_parser
from .. import version as _version
from ... import config
from ...tests.test_config import _reset_config

MIN_ARGS = ["data/", "out/", "participant"]

Expand Down Expand Up @@ -139,3 +140,19 @@ def test_bids_filter_file(tmp_path, capsys):

err = capsys.readouterr().err
assert "JSON syntax error in:" in err
_reset_config()


@pytest.mark.parametrize("st_ref", (None, "0", "1", "0.5", "start", "middle"))
def test_slice_time_ref(tmp_path, st_ref):
bids_path = tmp_path / "data"
out_path = tmp_path / "out"
args = [str(bids_path), str(out_path), "participant"]
if st_ref:
args.extend(["--slice-time-ref", st_ref])
bids_path.mkdir()

parser = _build_parser()

parser.parse_args(args)
_reset_config()