Fix some style issues.

src/fmripost_aroma/interfaces/nilearn.py

@@ -17,25 +17,25 @@ class _MeanImageInputSpec(BaseInterfaceInputSpec):
     bold_file = File(
         exists=True,
         mandatory=True,
-        desc="A 4D BOLD file to process.",
+        desc='A 4D BOLD file to process.',
     )
     mask_file = File(
         exists=True,
         mandatory=True,
-        desc="A binary brain mask.",
+        desc='A binary brain mask.',
     )
     out_file = File(
-        "mean.nii.gz",
+        'mean.nii.gz',
         usedefault=True,
         exists=False,
-        desc="The name of the mean file to write out. mean.nii.gz by default.",
+        desc='The name of the mean file to write out. mean.nii.gz by default.',
     )
 
 
 class _MeanImageOutputSpec(TraitedSpec):
     out_file = File(
         exists=True,
-        desc="Mean output file.",
+        desc='Mean output file.',
     )
 
 
@@ -51,8 +51,8 @@ def _run_interface(self, runtime):
         data = apply_mask(self.inputs.bold_file, self.inputs.mask_file)
         mean_data = data.mean(axis=0)
         mean_img = unmask(mean_data, self.inputs.mask_file)
-        self._results["out_file"] = os.path.join(runtime.cwd, self.inputs.out_file)
-        mean_img.to_filename(self._results["out_file"])
+        self._results['out_file'] = os.path.join(runtime.cwd, self.inputs.out_file)
+        mean_img.to_filename(self._results['out_file'])
 
         return runtime
 
@@ -61,12 +61,12 @@ class _MedianValueInputSpec(BaseInterfaceInputSpec):
     bold_file = File(
         exists=True,
         mandatory=True,
-        desc="A 4D BOLD file to process.",
+        desc='A 4D BOLD file to process.',
     )
     mask_file = File(
         exists=True,
         mandatory=True,
-        desc="A binary brain mask.",
+        desc='A binary brain mask.',
     )
 
 
@@ -84,6 +84,6 @@ def _run_interface(self, runtime):
         from nilearn.masking import apply_mask
 
         data = apply_mask(self.inputs.bold_file, self.inputs.mask_file)
-        self._results["median_value"] = np.median(data)
+        self._results['median_value'] = np.median(data)
 
         return runtime

src/fmripost_aroma/tests/conftest.py

@@ -9,76 +9,76 @@
 def pytest_addoption(parser):
     """Collect pytest parameters for running tests."""
     parser.addoption(
-        "--working_dir",
-        action="store",
+        '--working_dir',
+        action='store',
         default=(
-            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
-            "tests/data/test_data/run_pytests/work"
+            '/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/'
+            'tests/data/test_data/run_pytests/work'
         ),
     )
     parser.addoption(
-        "--data_dir",
-        action="store",
+        '--data_dir',
+        action='store',
         default=(
-            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
-            "tests/data/test_data"
+            '/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/'
+            'tests/data/test_data'
         ),
     )
     parser.addoption(
-        "--output_dir",
-        action="store",
+        '--output_dir',
+        action='store',
         default=(
-            "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/"
-            "tests/data/test_data/run_pytests/out"
+            '/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma/fmripost_aroma/'
+            'tests/data/test_data/run_pytests/out'
         ),
     )
 
 
 # Set up the commandline options as fixtures
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def data_dir(request):
     """Grab data directory."""
-    return request.config.getoption("--data_dir")
+    return request.config.getoption('--data_dir')
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def working_dir(request):
     """Grab working directory."""
-    workdir = request.config.getoption("--working_dir")
+    workdir = request.config.getoption('--working_dir')
     os.makedirs(workdir, exist_ok=True)
     return workdir
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def output_dir(request):
     """Grab output directory."""
-    outdir = request.config.getoption("--output_dir")
+    outdir = request.config.getoption('--output_dir')
     os.makedirs(outdir, exist_ok=True)
     return outdir
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(scope='session', autouse=True)
 def fslicense(working_dir):
     """Set the FreeSurfer license as an environment variable."""
-    FS_LICENSE = os.path.join(working_dir, "license.txt")
-    os.environ["FS_LICENSE"] = FS_LICENSE
+    FS_LICENSE = os.path.join(working_dir, 'license.txt')
+    os.environ['FS_LICENSE'] = FS_LICENSE
     LICENSE_CODE = (
-        "bWF0dGhldy5jaWVzbGFrQHBzeWNoLnVjc2IuZWR1CjIwNzA2CipDZmVWZEg1VVQ4clkKRlNCWVouVWtlVElDdwo="
+        'bWF0dGhldy5jaWVzbGFrQHBzeWNoLnVjc2IuZWR1CjIwNzA2CipDZmVWZEg1VVQ4clkKRlNCWVouVWtlVElDdwo='
     )
-    with open(FS_LICENSE, "w") as f:
+    with open(FS_LICENSE, 'w') as f:
         f.write(base64.b64decode(LICENSE_CODE).decode())
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def base_config():
     from fmripost_aroma.tests.tests import mock_config
 
     return mock_config
 
 
-@pytest.fixture(scope="session")
+@pytest.fixture(scope='session')
 def base_parser():
     from argparse import ArgumentParser
 
-    parser = ArgumentParser(description="Test parser")
+    parser = ArgumentParser(description='Test parser')
     return parser

src/fmripost_aroma/tests/run_local_tests.py

@@ -14,20 +14,20 @@ def _get_parser():
     """
     parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument(
-        "-k",
-        dest="test_regex",
-        metavar="PATTERN",
+        '-k',
+        dest='test_regex',
+        metavar='PATTERN',
         type=str,
-        help="Test pattern.",
+        help='Test pattern.',
         required=False,
         default=None,
     )
     parser.add_argument(
-        "-m",
-        dest="test_mark",
-        metavar="LABEL",
+        '-m',
+        dest='test_mark',
+        metavar='LABEL',
         type=str,
-        help="Test mark label.",
+        help='Test mark label.',
         required=False,
         default=None,
     )
@@ -52,35 +52,35 @@ def run_command(command, env=None):
     )
     while True:
         line = process.stdout.readline()
-        line = str(line, "utf-8")[:-1]
+        line = str(line, 'utf-8')[:-1]
         print(line)
-        if line == "" and process.poll() is not None:
+        if line == '' and process.poll() is not None:
             break
 
     if process.returncode != 0:
         raise RuntimeError(
-            f"Non zero return code: {process.returncode}\n" f"{command}\n\n{process.stdout.read()}"
+            f'Non zero return code: {process.returncode}\n' f'{command}\n\n{process.stdout.read()}'
         )
 
 
 def run_tests(test_regex, test_mark):
     """Run the tests."""
     local_patch = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
-    mounted_code = "/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma"
-    run_str = "docker run --rm -ti "
-    run_str += f"-v {local_patch}:{mounted_code} "
-    run_str += "--entrypoint pytest "
-    run_str += "nipreps/fmripost_aroma:unstable "
+    mounted_code = '/usr/local/miniconda/lib/python3.11/site-packages/fmripost_aroma'
+    run_str = 'docker run --rm -ti '
+    run_str += f'-v {local_patch}:{mounted_code} '
+    run_str += '--entrypoint pytest '
+    run_str += 'nipreps/fmripost_aroma:unstable '
     run_str += (
-        f"{mounted_code}/fmripost_aroma "
-        f"--data_dir={mounted_code}/fmripost_aroma/tests/test_data "
-        f"--output_dir={mounted_code}/fmripost_aroma/tests/pytests/out "
-        f"--working_dir={mounted_code}/fmripost_aroma/tests/pytests/work "
+        f'{mounted_code}/fmripost_aroma '
+        f'--data_dir={mounted_code}/fmripost_aroma/tests/test_data '
+        f'--output_dir={mounted_code}/fmripost_aroma/tests/pytests/out '
+        f'--working_dir={mounted_code}/fmripost_aroma/tests/pytests/work '
     )
     if test_regex:
-        run_str += f"-k {test_regex} "
+        run_str += f'-k {test_regex} '
     elif test_mark:
-        run_str += f"-rP -o log_cli=true -m {test_mark} "
+        run_str += f'-rP -o log_cli=true -m {test_mark} '
 
     run_command(run_str)
 
@@ -92,5 +92,5 @@ def _main(argv=None):
     run_tests(**kwargs)
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     _main()

src/fmripost_aroma/tests/tests.py

@@ -28,9 +28,8 @@
 from pathlib import Path
 from tempfile import mkdtemp
 
-from toml import loads
-
 from fmripost_aroma.data import load as load_data
+from toml import loads
 
 
 @contextmanager