sty(black): revise style of all files (except for workflows) [skip ci]

nipreps · Apr 5, 2020 · d8925a2 · d8925a2
1 parent be1da38
commit d8925a2
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diff --git a/mriqc/__about__.py b/mriqc/__about__.py
@@ -3,18 +3,13 @@
 """MRIQC."""
 
 from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
 
-__copyright__ = ('Copyright 2009, Center for Reproducible Neuroscience, '
-                 'Stanford University')
-__credits__ = 'Oscar Esteban'
-__download__ = ('https://github.com/poldracklab/mriqc/archive/'
-                '{}.tar.gz'.format(__version__))
+__version__ = get_versions()["version"]
+del get_versions
 
-__all__ = [
-    '__version__',
-    '__copyright__',
-    '__credits__',
-    '__download__'
-]
+__copyright__ = (
+    "Copyright 2020, Center for Reproducible Neuroscience, Stanford University"
+)
+__credits__ = "Oscar Esteban"
+__download__ = f"https://github.com/poldracklab/mriqc/archive/{__version__}.tar.gz"
+__all__ = ["__version__", "__copyright__", "__credits__", "__download__"]
diff --git a/mriqc/__init__.py b/mriqc/__init__.py
@@ -14,7 +14,7 @@
 
 
 __all__ = [
-    '__copyright__',
-    '__credits__',
-    '__version__',
+    "__copyright__",
+    "__credits__",
+    "__version__",
 ]
diff --git a/mriqc/_warnings.py b/mriqc/_warnings.py
@@ -12,9 +12,7 @@ def _warn(message, category=None, stacklevel=1, source=None):
         category = type(category).__name__
         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):

diff --git a/mriqc/bin/abide2bids.py b/mriqc/bin/abide2bids.py
@@ -25,30 +25,34 @@
 
 def main():
     """Entry point"""
-    parser = ArgumentParser(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.add_argument('-n', '--dataset-name', action='store',
-                         default='ABIDE Dataset')
-    g_input.add_argument('-u', '--nitrc-user', action='store',
-                         default=os.getenv('NITRC_USER'))
-    g_input.add_argument('-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')
+    parser = ArgumentParser(
+        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.add_argument(
+        "-n", "--dataset-name", action="store", default="ABIDE Dataset"
+    )
+    g_input.add_argument(
+        "-u", "--nitrc-user", action="store", default=os.getenv("NITRC_USER")
+    )
+    g_input.add_argument(
+        "-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")
 
     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}
+    dataset_desc = {
+        "BIDSVersion": "1.0.0rc3",
+        "License": "CC Attribution-NonCommercial-ShareAlike 3.0 Unported",
+        "Name": opts.dataset_name,
+    }
 
     out_dir = op.abspath(opts.output_dir)
     try:
@@ -57,19 +61,18 @@ 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]
+    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)
-    np.savetxt(op.join(out_dir, 'participants.tsv'), tsv_data, fmt='%s', delimiter='\t')
+    tsv_data = np.array([("subject_id", "site_name")] + res)
+    np.savetxt(op.join(out_dir, "participants.tsv"), tsv_data, fmt="%s", delimiter="\t")
 
 
 def fetch(args):
@@ -86,55 +89,57 @@ def fetch(args):
     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', '%s:%s' % (user, password), '-o', sub_file, url]
+    cmd = ["curl", "-s", "-u", "%s:%s" % (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]))
 
-    site_name, sub_str = files[0][len(abide_root) + 1:].split('/')[0].split('_')
-    subject_id = 'sub-' + sub_str
+    site_name, sub_str = files[0][len(abide_root) + 1:].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)
 
-    print('Successfully processed subject %s from site %s' % (subject_id[4:], site_name))
+    print(
+        "Successfully processed subject %s from site %s" % (subject_id[4:], site_name)
+    )
     return subject_id[4:], site_name
 
 
 def _myerror(msg):
-    print('WARNING: Error deleting temporal files: %s' % msg)
+    print("WARNING: Error deleting temporal files: %s" % msg)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/mriqc/bin/dfcheck.py b/mriqc/bin/dfcheck.py
@@ -20,15 +20,34 @@
 def main():
     """Entry point"""
     from ..classifier.data import read_iqms
-    parser = ArgumentParser(description='compare two pandas dataframes',
-                            formatter_class=RawTextHelpFormatter)
-    g_input = parser.add_argument_group('Inputs')
-    g_input.add_argument('-i', '--input-csv', action='store', type=Path,
-                         required=True, help='input data frame')
-    g_input.add_argument('-r', '--reference-csv', action='store', type=Path,
-                         required=True, help='reference dataframe')
-    g_input.add_argument('--tolerance', type=float, default=1.e-5,
-                         help='relative tolerance for comparison')
+
+    parser = ArgumentParser(
+        description="compare two pandas dataframes",
+        formatter_class=RawTextHelpFormatter,
+    )
+    g_input = parser.add_argument_group("Inputs")
+    g_input.add_argument(
+        "-i",
+        "--input-csv",
+        action="store",
+        type=Path,
+        required=True,
+        help="input data frame",
+    )
+    g_input.add_argument(
+        "-r",
+        "--reference-csv",
+        action="store",
+        type=Path,
+        required=True,
+        help="reference dataframe",
+    )
+    g_input.add_argument(
+        "--tolerance",
+        type=float,
+        default=1.0e-5,
+        help="relative tolerance for comparison",
+    )
 
     opts = parser.parse_args()
 
@@ -39,17 +58,19 @@ def main():
     tst_df.set_index(tst_bids)
 
     if sorted(ref_bids) != sorted(tst_bids):
-        sys.exit('Dataset has different BIDS bits w.r.t. reference')
+        sys.exit("Dataset has different BIDS bits w.r.t. reference")
 
     if sorted(ref_names) != sorted(tst_names):
-        sys.exit('Output CSV file changed number of columns')
+        sys.exit("Output CSV file changed number of columns")
 
     ref_df = ref_df.sort_values(by=ref_bids)
     tst_df = tst_df.sort_values(by=tst_bids)
 
     if len(ref_df) != len(tst_df):
-        print('Input datases have different lengths (input %d, reference %d).' % (
-            len(ref_df), len(tst_df)))
+        print(
+            "Input datases have different lengths (input %d, reference %d)."
+            % (len(ref_df), len(tst_df))
+        )
         tst_rows = tst_df[tst_bids]
         ref_rows = ref_df[ref_bids]
 
@@ -58,7 +79,9 @@ def main():
         tst_keep = np.sum(tst_rows.isin(ref_rows).values.ravel().tolist())
         print(tst_keep)
 
-    diff = ~np.isclose(ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance)
+    diff = ~np.isclose(
+        ref_df[ref_names].values, tst_df[tst_names].values, rtol=opts.tolerance
+    )
     if np.any(diff):
         # ne_stacked = pd.DataFrame(data=diff, columns=ref_names).stack()
         # ne_stacked = np.isclose(ref_df[ref_names], tst_df[ref_names]).stack()
@@ -69,26 +92,32 @@ 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'] = [float(np.corrcoef(ref_df[[var]].values.ravel(),
-                                        tst_df[[var]].values.ravel(),
-                                        rowvar=False)[0, 1])
-                      for var in ref_names]
+        corr["iqms"] = ref_names
+        corr["cc"] = [
+            float(
+                np.corrcoef(
+                    ref_df[[var]].values.ravel(),
+                    tst_df[[var]].values.ravel(),
+                    rowvar=False,
+                )[0, 1]
+            )
+            for var in ref_names
+        ]
 
         if np.any(corr.cc < 0.95):
-            print('IQMs with Pearson correlation < 0.95:')
+            print("IQMs with Pearson correlation < 0.95:")
             print(corr[corr.cc < 0.95])
-            sys.exit('Output CSV file changed one or more values')
+            sys.exit("Output CSV file changed one or more values")
         else:
-            print('All IQMs show a Pearson correlation >= 0.95')
+            print("All IQMs show a Pearson correlation >= 0.95")
 
     sys.exit(0)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()