Merge pull request #401 from mgxd/maint/update-parser

MAINT: Port over parser and tests from fmriprep

Author: mgxd

nibabies/cli/parser.py

@@ -102,19 +102,36 @@ def _drop_sub(value):
     def _drop_ses(value):
         return value[4:] if value.startswith('ses-') else value
 
-    def _filter_pybids_none_any(dct):
+    def _process_value(value):
         import bids
 
-        return {
-            k: bids.layout.Query.NONE if v is None else (bids.layout.Query.ANY if v == '*' else v)
-            for k, v in dct.items()
-        }
-
-    def _bids_filter(value):
-        from json import loads
+        if value is None:
+            return bids.layout.Query.NONE
+        elif value == '*':
+            return bids.layout.Query.ANY
+        else:
+            return value
 
-        if value and Path(value).exists():
-            return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)
+    def _filter_pybids_none_any(dct):
+        d = {}
+        for k, v in dct.items():
+            if isinstance(v, list):
+                d[k] = [_process_value(val) for val in v]
+            else:
+                d[k] = _process_value(v)
+        return d
+
+    def _bids_filter(value, parser):
+        from json import JSONDecodeError, loads
+
+        if value:
+            if Path(value).exists():
+                try:
+                    return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)
+                except JSONDecodeError as e:
+                    raise parser.error(f'JSON syntax error in: <{value}>.') from e
+            else:
+                raise parser.error(f'Path does not exist: <{value}>.')
 
     def _slice_time_ref(value, parser):
         if value == 'start':
@@ -142,6 +159,7 @@ def _slice_time_ref(value, parser):
     DirNotEmpty = partial(_dir_not_empty, 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)
 
     parser.description = f"""
@@ -214,7 +232,7 @@ def _slice_time_ref(value, parser):
         '--bids-filter-file',
         dest='bids_filters',
         action='store',
-        type=_bids_filter,
+        type=BIDSFilter,
         metavar='FILE',
         help='a JSON file describing custom BIDS input filters using PyBIDS. '
         'For further details, please check out '
@@ -546,9 +564,13 @@ def _slice_time_ref(value, parser):
     g_syn = parser.add_argument_group('Specific options for SyN distortion correction')
     g_syn.add_argument(
         '--use-syn-sdc',
-        action='store_true',
+        nargs='?',
+        choices=['warn', 'error'],
+        action='store',
+        const='error',
         default=False,
-        help='EXPERIMENTAL: Use fieldmap-free distortion correction',
+        help='Use fieldmap-less distortion correction based on anatomical image; '
+        'if unable, error (default) or warn based on optional argument.',
     )
     g_syn.add_argument(
         '--force-syn',

nibabies/cli/tests/__init__.py

@@ -0,0 +1,272 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Test parser."""
+
+from argparse import ArgumentError
+from contextlib import nullcontext
+
+import pytest
+from packaging.version import Version
+
+from nibabies import config
+from nibabies.cli import version as _version
+from nibabies.cli.parser import _build_parser, parse_args
+from nibabies.tests.test_config import _reset_config
+
+MIN_ARGS = ['data/', 'out/', 'participant']
+
+
+@pytest.mark.parametrize(
+    ('args', 'code'),
+    [
+        ([], 2),
+        (MIN_ARGS, 2),  # bids_dir does not exist
+        (MIN_ARGS + ['--fs-license-file'], 2),
+        (MIN_ARGS + ['--fs-license-file', 'fslicense.txt'], 2),
+    ],
+)
+def test_parser_errors(args, code):
+    """Check behavior of the parser."""
+    with pytest.raises(SystemExit) as error:
+        _build_parser().parse_args(args)
+
+    assert error.value.code == code
+
+
+@pytest.mark.parametrize('args', [MIN_ARGS, MIN_ARGS + ['--fs-license-file']])
+def test_parser_valid(tmp_path, args):
+    """Check valid arguments."""
+    datapath = tmp_path / 'data'
+    datapath.mkdir(exist_ok=True)
+    args[0] = str(datapath)
+
+    if '--fs-license-file' in args:
+        _fs_file = tmp_path / 'license.txt'
+        _fs_file.write_text('')
+        args.insert(args.index('--fs-license-file') + 1, str(_fs_file.absolute()))
+
+    opts = _build_parser().parse_args(args)
+
+    assert opts.bids_dir == datapath
+
+
+@pytest.mark.parametrize(
+    ('argval', 'gb'),
+    [
+        ('1G', 1),
+        ('1GB', 1),
+        ('1000', 1),  # Default units are MB
+        ('32000', 32),  # Default units are MB
+        ('4000', 4),  # Default units are MB
+        ('1000M', 1),
+        ('1000MB', 1),
+        ('1T', 1000),
+        ('1TB', 1000),
+        ('%dK' % 1e6, 1),
+        ('%dKB' % 1e6, 1),
+        ('%dB' % 1e9, 1),
+    ],
+)
+def test_memory_arg(tmp_path, argval, gb):
+    """Check the correct parsing of the memory argument."""
+    datapath = tmp_path / 'data'
+    datapath.mkdir(exist_ok=True)
+    _fs_file = tmp_path / 'license.txt'
+    _fs_file.write_text('')
+
+    args = [str(datapath)] + MIN_ARGS[1:] + ['--fs-license-file', str(_fs_file), '--mem', argval]
+    opts = _build_parser().parse_args(args)
+
+    assert opts.memory_gb == gb
+
+
+@pytest.mark.parametrize(('current', 'latest'), [('1.0.0', '1.3.2'), ('1.3.2', '1.3.2')])
+def test_get_parser_update(monkeypatch, capsys, current, latest):
+    """Make sure the out-of-date banner is shown."""
+    expectation = Version(current) < Version(latest)
+
+    def _mock_check_latest(*args, **kwargs):
+        return Version(latest)
+
+    monkeypatch.setattr(config.environment, 'version', current)
+    monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    msg = f"""\
+You are using NiBabies-{current}, and a newer version of NiBabies is available: {latest}.
+Please check out our documentation about how and when to upgrade:
+https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading"""
+
+    assert (msg in captured) is expectation
+
+
+@pytest.mark.parametrize('flagged', [(True, None), (True, 'random reason'), (False, None)])
+def test_get_parser_blacklist(monkeypatch, capsys, flagged):
+    """Make sure the blacklisting banner is shown."""
+
+    def _mock_is_bl(*args, **kwargs):
+        return flagged
+
+    monkeypatch.setattr(_version, 'is_flagged', _mock_is_bl)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    assert ('FLAGGED' in captured) is flagged[0]
+    if flagged[0]:
+        assert (flagged[1] or 'reason: unknown') in captured
+
+
+def test_parse_args(tmp_path, minimal_bids):
+    """Basic smoke test showing that our parse_args() function
+    implements the BIDS App protocol"""
+    out_dir = tmp_path / 'out'
+    work_dir = tmp_path / 'work'
+
+    parse_args(
+        args=[
+            str(minimal_bids),
+            str(out_dir),
+            'participant',  # BIDS App
+            '-w',
+            str(work_dir),  # Don't pollute CWD
+            '--skip-bids-validation',  # Empty files make BIDS sad
+        ]
+    )
+    assert config.execution.layout.root == str(minimal_bids)
+    _reset_config()
+
+
+def test_bids_filter_file(tmp_path, capsys):
+    bids_path = tmp_path / 'data'
+    out_path = tmp_path / 'out'
+    bff = tmp_path / 'filter.json'
+    args = [str(bids_path), str(out_path), 'participant', '--bids-filter-file', str(bff)]
+    bids_path.mkdir()
+
+    parser = _build_parser()
+
+    with pytest.raises(SystemExit):
+        parser.parse_args(args)
+
+    err = capsys.readouterr().err
+    assert 'Path does not exist:' in err
+
+    bff.write_text('{"invalid json": }')
+
+    with pytest.raises(SystemExit):
+        parser.parse_args(args)
+
+    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'))  # noqa: PT007
+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()
+
+
+@pytest.mark.parametrize(
+    ('args', 'expectation'),
+    [
+        ([], False),
+        (['--use-syn-sdc'], 'error'),
+        (['--use-syn-sdc', 'error'], 'error'),
+        (['--use-syn-sdc', 'warn'], 'warn'),
+        (['--use-syn-sdc', 'other'], (SystemExit, ArgumentError)),
+    ],
+)
+def test_use_syn_sdc(tmp_path, args, expectation):
+    bids_path = tmp_path / 'data'
+    out_path = tmp_path / 'out'
+    args = [str(bids_path), str(out_path), 'participant'] + args
+    bids_path.mkdir()
+
+    parser = _build_parser()
+
+    cm = nullcontext()
+    if isinstance(expectation, tuple):
+        cm = pytest.raises(expectation)
+
+    with cm:
+        opts = parser.parse_args(args)
+
+    if not isinstance(expectation, tuple):
+        assert opts.use_syn_sdc == expectation
+
+    _reset_config()
+
+
+def test_derivatives(tmp_path):
+    """Check the correct parsing of the derivatives argument."""
+    bids_path = tmp_path / 'data'
+    out_path = tmp_path / 'out'
+    args = [str(bids_path), str(out_path), 'participant']
+    bids_path.mkdir()
+
+    parser = _build_parser()
+
+    # Providing --derivatives without a path should raise an error
+    temp_args = args + ['--derivatives']
+    with pytest.raises((SystemExit, ArgumentError)):
+        parser.parse_args(temp_args)
+    _reset_config()
+
+    # Providing --derivatives without names should automatically label them
+    temp_args = args + ['--derivatives', str(bids_path / 'derivatives/smriprep')]
+    opts = parser.parse_args(temp_args)
+    assert opts.derivatives == {'smriprep': bids_path / 'derivatives/smriprep'}
+    _reset_config()
+
+    # Providing --derivatives with names should use them
+    temp_args = args + [
+        '--derivatives',
+        f'anat={str(bids_path / "derivatives/smriprep")}',
+    ]
+    opts = parser.parse_args(temp_args)
+    assert opts.derivatives == {'anat': bids_path / 'derivatives/smriprep'}
+    _reset_config()
+
+    # Providing multiple unlabeled derivatives with the same name should raise an error
+    temp_args = args + [
+        '--derivatives',
+        str(bids_path / 'derivatives_01/smriprep'),
+        str(bids_path / 'derivatives_02/smriprep'),
+    ]
+    with pytest.raises(ValueError, match='Received duplicate derivative name'):
+        parser.parse_args(temp_args)
+
+    _reset_config()

nibabies/cli/tests/test_parser.py

@@ -1,8 +1,11 @@
 """py.test configuration"""
 
+import json
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
+import nibabel as nb
+import numpy as np
 import pytest
 
 from nibabies.data import load as load_data
@@ -37,3 +40,16 @@ def _populate_namespace(doctest_namespace, data_dir):
     doctest_namespace['data_dir'] = data_dir
     doctest_namespace['test_data'] = load_data.cached('../tests/data')
     doctest_namespace['Path'] = Path
+
+
+@pytest.fixture
+def minimal_bids(tmp_path):
+    bids = tmp_path / 'bids'
+    bids.mkdir()
+    Path.write_text(
+        bids / 'dataset_description.json', json.dumps({'Name': 'Test DS', 'BIDSVersion': '1.8.0'})
+    )
+    T1w = bids / 'sub-01' / 'anat' / 'sub-01_T1w.nii.gz'
+    T1w.parent.mkdir(parents=True)
+    nb.Nifti1Image(np.zeros((5, 5, 5)), np.eye(4)).to_filename(T1w)
+    return bids