sty: automatic changes by ruff

mriqc/__init__.py

@@ -27,6 +27,6 @@
 """
 from mriqc._version import __version__
 
-__copyright__ = "Copyright 2022, The NiPreps Developers"
-__download__ = f"https://github.com/nipreps/mriqc/archive/{__version__}.tar.gz"
-__all__ = ["__version__", "__copyright__", "__download__"]
+__copyright__ = 'Copyright 2022, The NiPreps Developers'
+__download__ = f'https://github.com/nipreps/mriqc/archive/{__version__}.tar.gz'
+__all__ = ['__version__', '__copyright__', '__download__']

mriqc/__main__.py

@@ -22,11 +22,12 @@
 #
 from .cli.run import main
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     import sys
+
     from . import __name__ as module
 
     # `python -m <module>` typically displays the command as __main__.py
-    if "__main__.py" in sys.argv[0]:
-        sys.argv[0] = f"{sys.executable} -m {module}"
+    if '__main__.py' in sys.argv[0]:
+        sys.argv[0] = f'{sys.executable} -m {module}'
     main()

mriqc/_warnings.py

@@ -24,17 +24,17 @@
 import logging
 import warnings
 
-_wlog = logging.getLogger("py.warnings")
+_wlog = logging.getLogger('py.warnings')
 _wlog.addHandler(logging.NullHandler())
 
 
 def _warn(message, category=None, stacklevel=1, source=None):
     """Redefine the warning function."""
     if category is not None:
         category = type(category).__name__
-        category = category.replace("type", "WARNING")
+        category = category.replace('type', 'WARNING')
 
-    logging.getLogger("py.warnings").warning(f"{category or 'WARNING'}: {message}")
+    logging.getLogger('py.warnings').warning(f"{category or 'WARNING'}: {message}")
 
 
 def _showwarning(message, category, filename, lineno, file=None, line=None):

mriqc/bin/abide2bids.py

@@ -34,42 +34,43 @@
 from xml.etree import ElementTree as et
 
 import numpy as np
+
 from mriqc.bin import messages
 
 
 def main():
     """Entry point."""
     parser = ArgumentParser(
-        description="ABIDE2BIDS downloader.",
+        description='ABIDE2BIDS downloader.',
         formatter_class=RawTextHelpFormatter,
     )
-    g_input = parser.add_argument_group("Inputs")
-    g_input.add_argument("-i", "--input-abide-catalog", action="store", required=True)
+    g_input = parser.add_argument_group('Inputs')
+    g_input.add_argument('-i', '--input-abide-catalog', action='store', required=True)
     g_input.add_argument(
-        "-n", "--dataset-name", action="store", default="ABIDE Dataset"
+        '-n', '--dataset-name', action='store', default='ABIDE Dataset'
     )
     g_input.add_argument(
-        "-u", "--nitrc-user", action="store", default=os.getenv("NITRC_USER")
+        '-u', '--nitrc-user', action='store', default=os.getenv('NITRC_USER')
     )
     g_input.add_argument(
-        "-p",
-        "--nitrc-password",
-        action="store",
-        default=os.getenv("NITRC_PASSWORD"),
+        '-p',
+        '--nitrc-password',
+        action='store',
+        default=os.getenv('NITRC_PASSWORD'),
     )
 
-    g_outputs = parser.add_argument_group("Outputs")
-    g_outputs.add_argument("-o", "--output-dir", action="store", default="ABIDE-BIDS")
+    g_outputs = parser.add_argument_group('Outputs')
+    g_outputs.add_argument('-o', '--output-dir', action='store', default='ABIDE-BIDS')
 
     opts = parser.parse_args()
 
     if opts.nitrc_user is None or opts.nitrc_password is None:
-        raise RuntimeError("NITRC user and password are required")
+        raise RuntimeError('NITRC user and password are required')
 
     dataset_desc = {
-        "BIDSVersion": "1.0.0rc3",
-        "License": "CC Attribution-NonCommercial-ShareAlike 3.0 Unported",
-        "Name": opts.dataset_name,
+        'BIDSVersion': '1.0.0rc3',
+        'License': 'CC Attribution-NonCommercial-ShareAlike 3.0 Unported',
+        'Name': opts.dataset_name,
     }
 
     out_dir = op.abspath(opts.output_dir)
@@ -79,22 +80,22 @@ def main():
         if exc.errno != errno.EEXIST:
             raise exc
 
-    with open(op.join(out_dir, "dataset_description.json"), "w") as dfile:
+    with open(op.join(out_dir, 'dataset_description.json'), 'w') as dfile:
         json.dump(dataset_desc, dfile)
 
     catalog = et.parse(opts.input_abide_catalog).getroot()
-    urls = [el.get("URI") for el in catalog.iter() if el.get("URI") is not None]
+    urls = [el.get('URI') for el in catalog.iter() if el.get('URI') is not None]
 
     pool = Pool()
     args_list = [(url, opts.nitrc_user, opts.nitrc_password, out_dir) for url in urls]
     res = pool.map(fetch, args_list)
 
-    tsv_data = np.array([("subject_id", "site_name")] + res)
+    tsv_data = np.array([('subject_id', 'site_name')] + res)
     np.savetxt(
-        op.join(out_dir, "participants.tsv"),
+        op.join(out_dir, 'participants.tsv'),
         tsv_data,
-        fmt="%s",
-        delimiter="\t",
+        fmt='%s',
+        delimiter='\t',
     )
 
 
@@ -124,46 +125,46 @@ def fetch(args: Tuple[str, str, str, str]) -> Tuple[str, str]:
     else:
         out_dir = op.abspath(out_dir)
 
-    pkg_id = [u[9:] for u in url.split("/") if u.startswith("NITRC_IR_")][0]
-    sub_file = op.join(tmpdir, "%s.zip" % pkg_id)
+    pkg_id = [u[9:] for u in url.split('/') if u.startswith('NITRC_IR_')][0]
+    sub_file = op.join(tmpdir, '%s.zip' % pkg_id)
 
-    cmd = ["curl", "-s", "-u", f"{user}:{password}", "-o", sub_file, url]
+    cmd = ['curl', '-s', '-u', f'{user}:{password}', '-o', sub_file, url]
     sp.check_call(cmd)
-    sp.check_call(["unzip", "-qq", "-d", tmpdir, "-u", sub_file])
+    sp.check_call(['unzip', '-qq', '-d', tmpdir, '-u', sub_file])
 
-    abide_root = op.join(tmpdir, "ABIDE")
+    abide_root = op.join(tmpdir, 'ABIDE')
     files = []
     for root, path, fname in os.walk(abide_root):
-        if fname and (fname[0].endswith("nii") or fname[0].endswith("nii.gz")):
+        if fname and (fname[0].endswith('nii') or fname[0].endswith('nii.gz')):
             if path:
                 root = op.join(root, path[0])
             files.append(op.join(root, fname[0]))
 
     index = len(abide_root) + 1
-    site_name, sub_str = files[0][index:].split("/")[0].split("_")
-    subject_id = "sub-" + sub_str
+    site_name, sub_str = files[0][index:].split('/')[0].split('_')
+    subject_id = 'sub-' + sub_str
 
     for i in files:
-        ext = ".nii.gz"
-        if i.endswith(".nii"):
-            ext = ".nii"
-        if "mprage" in i:
-            bids_dir = op.join(out_dir, subject_id, "anat")
+        ext = '.nii.gz'
+        if i.endswith('.nii'):
+            ext = '.nii'
+        if 'mprage' in i:
+            bids_dir = op.join(out_dir, subject_id, 'anat')
             try:
                 os.makedirs(bids_dir)
             except OSError as exc:
                 if exc.errno != errno.EEXIST:
                     raise exc
-            shutil.copy(i, op.join(bids_dir, subject_id + "_T1w" + ext))
+            shutil.copy(i, op.join(bids_dir, subject_id + '_T1w' + ext))
 
-        if "rest" in i:
-            bids_dir = op.join(out_dir, subject_id, "func")
+        if 'rest' in i:
+            bids_dir = op.join(out_dir, subject_id, 'func')
             try:
                 os.makedirs(bids_dir)
             except OSError as exc:
                 if exc.errno != errno.EEXIST:
                     raise exc
-            shutil.copy(i, op.join(bids_dir, subject_id + "_rest_bold" + ext))
+            shutil.copy(i, op.join(bids_dir, subject_id + '_rest_bold' + ext))
 
     shutil.rmtree(tmpdir, ignore_errors=True, onerror=_myerror)
 
@@ -187,5 +188,5 @@ def _myerror(message: str):
     print(warning)
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     main()

mriqc/bin/dfcheck.py

@@ -29,6 +29,7 @@
 
 import numpy as np
 import pandas as pd
+
 from mriqc.bin import messages
 from mriqc.utils.misc import BIDS_COMP
 
@@ -37,7 +38,7 @@ def read_iqms(feat_file):
     """Read in a features table."""
     feat_file = Path(feat_file)
 
-    if feat_file.suffix == ".csv":
+    if feat_file.suffix == '.csv':
         x_df = pd.read_csv(
             feat_file, index_col=False, dtype={col: str for col in BIDS_COMP}
         )
@@ -46,7 +47,7 @@ def read_iqms(feat_file):
         bids_comps_present = [bit for bit in BIDS_COMP if bit in bids_comps_present]
         x_df = x_df.sort_values(by=bids_comps_present)
         # Remove sub- prefix in subject_id
-        x_df.subject_id = x_df.subject_id.str.lstrip("sub-")
+        x_df.subject_id = x_df.subject_id.str.lstrip('sub-')
 
         # Remove columns that are not IQMs
         feat_names = list(x_df._get_numeric_data().columns.ravel())
@@ -56,18 +57,18 @@ def read_iqms(feat_file):
             except ValueError:
                 pass
     else:
-        bids_comps_present = ["subject_id"]
+        bids_comps_present = ['subject_id']
         x_df = pd.read_csv(
-            feat_file, index_col=False, sep="\t", dtype={"bids_name": str}
+            feat_file, index_col=False, sep='\t', dtype={'bids_name': str}
         )
-        x_df = x_df.sort_values(by=["bids_name"])
-        x_df["subject_id"] = x_df.bids_name.str.lstrip("sub-")
-        x_df = x_df.drop(columns=["bids_name"])
-        x_df.subject_id = ["_".join(v.split("_")[:-1]) for v in x_df.subject_id.ravel()]
+        x_df = x_df.sort_values(by=['bids_name'])
+        x_df['subject_id'] = x_df.bids_name.str.lstrip('sub-')
+        x_df = x_df.drop(columns=['bids_name'])
+        x_df.subject_id = ['_'.join(v.split('_')[:-1]) for v in x_df.subject_id.ravel()]
         feat_names = list(x_df._get_numeric_data().columns.ravel())
 
     for col in feat_names:
-        if col.startswith(("size_", "spacing_", "Unnamed")):
+        if col.startswith(('size_', 'spacing_', 'Unnamed')):
             feat_names.remove(col)
 
     return x_df, feat_names, bids_comps_present
@@ -76,31 +77,31 @@ def read_iqms(feat_file):
 def main():
     """Entry point."""
     parser = ArgumentParser(
-        description="Compare two pandas dataframes.",
+        description='Compare two pandas dataframes.',
         formatter_class=RawTextHelpFormatter,
     )
-    g_input = parser.add_argument_group("Inputs")
+    g_input = parser.add_argument_group('Inputs')
     g_input.add_argument(
-        "-i",
-        "--input-csv",
-        action="store",
+        '-i',
+        '--input-csv',
+        action='store',
         type=Path,
         required=True,
-        help="input data frame",
+        help='input data frame',
     )
     g_input.add_argument(
-        "-r",
-        "--reference-csv",
-        action="store",
+        '-r',
+        '--reference-csv',
+        action='store',
         type=Path,
         required=True,
-        help="reference dataframe",
+        help='reference dataframe',
     )
     g_input.add_argument(
-        "--tolerance",
+        '--tolerance',
         type=float,
         default=1.0e-5,
-        help="relative tolerance for comparison",
+        help='relative tolerance for comparison',
     )
 
     opts = parser.parse_args()
@@ -146,13 +147,13 @@ def main():
         changed_to = tst_df[ref_names].values[difference_locations]
         cols = [ref_names[v] for v in difference_locations[1]]
         bids_df = ref_df.loc[difference_locations[0], ref_bids].reset_index()
-        chng_df = pd.DataFrame({"iqm": cols, "from": changed_from, "to": changed_to})
+        chng_df = pd.DataFrame({'iqm': cols, 'from': changed_from, 'to': changed_to})
         table = pd.concat([bids_df, chng_df], axis=1)
-        print(table[ref_bids + ["iqm", "from", "to"]].to_string(index=False))
+        print(table[ref_bids + ['iqm', 'from', 'to']].to_string(index=False))
 
         corr = pd.DataFrame()
-        corr["iqms"] = ref_names
-        corr["cc"] = [
+        corr['iqms'] = ref_names
+        corr['cc'] = [
             float(
                 np.corrcoef(
                     ref_df[[var]].values.ravel(),
@@ -174,5 +175,5 @@ def main():
     sys.exit(0)
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     main()