Fix some style issues.

aslprep/interfaces/cbf.py

@@ -237,7 +237,11 @@ def _run_interface(self, runtime):
             config.loggers.interface.info(
                 'Calculating deltaM from label-control pairs in ASL file.'
             )
-            assert len(label_volume_idx) == len(control_volume_idx)
+            if len(label_volume_idx) != len(control_volume_idx):
+                raise ValueError(
+                    f'Number of label volumes ({len(label_volume_idx)}) != '
+                    f'number of control volumes ({len(control_volume_idx)})'
+                )
             metadata_idx = control_volume_idx
             control_data = asl_data[:, :, :, control_volume_idx]
             label_data = asl_data[:, :, :, label_volume_idx]
@@ -435,7 +439,8 @@ def _run_interface(self, runtime):
         # NiftiMasker.transform, until 0.12.0, so the arrays will currently be 2D no matter what.
         masker = maskers.NiftiMasker(mask_img=mask_file)
         deltam_arr = masker.fit_transform(deltam_file).T  # Transpose to SxT
-        assert deltam_arr.ndim == 2, f'deltam is {deltam_arr.ndim}'
+        if deltam_arr.ndim != 2:
+            raise ValueError(f'deltam is {deltam_arr.ndim}')
 
         # Load the M0 map and average over time, in case there's more than one map in the file.
         m0data = masker.transform(m0_file)
@@ -551,21 +556,33 @@ def _run_interface(self, runtime):
             elif metadata['BolusCutOffTechnique'] == 'QUIPSS':
                 # PASL + QUIPSS
                 # Only one BolusCutOffDelayTime allowed.
-                assert isinstance(metadata['BolusCutOffDelayTime'], Number)
+                if not isinstance(metadata['BolusCutOffDelayTime'], Number):
+                    raise ValueError(
+                        f'Expected a single BolusCutOffDelayTime, but got '
+                        f'{metadata["BolusCutOffDelayTime"]}'
+                    )
                 denom_factor = plds - metadata['BolusCutOffDelayTime']  # delta_TI, per Wong 1998
 
             elif metadata['BolusCutOffTechnique'] == 'QUIPSSII':
                 # PASL + QUIPSSII
                 # Per SD, use PLD as TI for PASL, so we will just use 'plds' in the numerator when
                 # calculating the perfusion factor.
                 # Only one BolusCutOffDelayTime allowed.
-                assert isinstance(metadata['BolusCutOffDelayTime'], Number)
+                if not isinstance(metadata['BolusCutOffDelayTime'], Number):
+                    raise ValueError(
+                        f'Expected a single BolusCutOffDelayTime, but got '
+                        f'{metadata["BolusCutOffDelayTime"]}'
+                    )
                 denom_factor = metadata['BolusCutOffDelayTime']  # called TI1 in Alsop 2015
 
             elif metadata['BolusCutOffTechnique'] == 'Q2TIPS':
                 # PASL + Q2TIPS
                 # Q2TIPS should have two BolusCutOffDelayTimes.
-                assert len(metadata['BolusCutOffDelayTime']) == 2
+                if len(metadata['BolusCutOffDelayTime']) != 2:
+                    raise ValueError(
+                        f'Expected two BolusCutOffDelayTimes, but got '
+                        f'{metadata["BolusCutOffDelayTime"]}'
+                    )
                 denom_factor = metadata['BolusCutOffDelayTime'][0]  # called TI1 in Noguchi 2015
 
             else:

aslprep/interfaces/parcellation.py

@@ -141,7 +141,10 @@ def _run_interface(self, runtime):
 
         # Use nilearn to parcellate the file
         timeseries_arr = masker.fit_transform(self.inputs.in_file)
-        assert timeseries_arr.shape[1] == n_found_nodes
+        if timeseries_arr.shape[1] != n_found_nodes:
+            raise ValueError(
+                f'Expected {n_found_nodes} parcels, but found {timeseries_arr.shape[1]}.'
+            )
         masker_labels = masker.labels_[:]
         del masker
 

aslprep/interfaces/reference.py

@@ -54,7 +54,12 @@ class SelectHighestContrastVolumes(SimpleInterface):
     def _run_interface(self, runtime):
         asl_img = nb.load(self.inputs.asl_file)
         aslcontext_df = pd.read_table(self.inputs.aslcontext)
-        assert aslcontext_df.shape[0] == asl_img.shape[3]
+        if aslcontext_df.shape[0] != asl_img.shape[3]:
+            raise ValueError(
+                f'Number of volumes in {self.inputs.asl_file} ({asl_img.shape[3]}) '
+                f'does not match the number of rows in {self.inputs.aslcontext} '
+                f'({aslcontext_df.shape[0]})'
+            )
 
         if 'm0scan' in aslcontext_df['volume_type'].tolist() and self.inputs.prioritize_m0:
             target_type = 'm0scan'

aslprep/interfaces/utility.py

@@ -187,7 +187,8 @@ def _run_interface(self, runtime):
             # run rmsdiff
             rmsdiff = RMSDiff(matrixfile1=file1, matrixfile2=file2, ref_vol=self.inputs.ref_file)
             res = rmsdiff.run()
-            assert isinstance(res.outputs.rmsd, float)
+            if not isinstance(res.outputs.rmsd, float):
+                raise ValueError(f'Expected a float, got {res.outputs.rmsd}')
             rmsd.append(str(res.outputs.rmsd))
 
         self._results['out_file'] = fname_presuffix(
@@ -225,8 +226,14 @@ def _run_interface(self, runtime):
         out_par = [None] * aslcontext.shape[0]
         out_mat_files = [None] * aslcontext.shape[0]
 
-        assert len(self.inputs.volume_types) == len(self.inputs.mat_files)
-        assert len(self.inputs.volume_types) == len(self.inputs.par_files)
+        if len(self.inputs.volume_types) != len(self.inputs.mat_files):
+            raise ValueError(
+                'Number of volume types and number of mat files must be the same.'
+            )
+        if len(self.inputs.volume_types) != len(self.inputs.par_files):
+            raise ValueError(
+                'Number of volume types and number of par files must be the same.'
+            )
 
         for i_type, volume_type in enumerate(self.inputs.volume_types):
             type_mat_files = self.inputs.mat_files[i_type]

aslprep/utils/asl.py

@@ -47,8 +47,8 @@ def select_processing_target(aslcontext):
 
     try:
         aslcontext_df = pd.read_table(aslcontext)
-    except:
-        raise FileNotFoundError(aslcontext)
+    except Exception:
+        raise FileNotFoundError(aslcontext) from None
 
     voltypes = aslcontext_df['volume_type'].tolist()
 

aslprep/utils/cbf.py

@@ -555,10 +555,12 @@ def estimate_att_pcasl(deltam_arr, plds, lds, t1blood, t1tissue):
     .. footbibliography::
     """
     n_voxels, n_plds = plds.shape
-    assert deltam_arr.shape == plds.shape, f'{deltam_arr.shape} != {plds.shape}'
+    if deltam_arr.shape != plds.shape:
+        raise ValueError(f'{deltam_arr.shape} != {plds.shape}')
 
     # Beginning of auxil_asl_gen_wsum
-    assert lds.size == n_plds, f'{lds.size} != {n_plds}'
+    if lds.size != n_plds:
+        raise ValueError(f'{lds.size} != {n_plds}')
 
     att_arr = np.empty(n_voxels)
     for i_voxel in range(n_voxels):
@@ -694,7 +696,9 @@ def estimate_cbf_pcasl_multipld(
     """
     n_voxels, n_volumes = deltam_arr.shape
     n_voxels_pld, n_plds = plds.shape
-    assert n_voxels_pld == n_voxels
+    if n_voxels_pld != n_voxels:
+        raise ValueError(f'{n_voxels_pld} != {n_voxels}')
+
     first_voxel_plds = plds[0, :]
 
     if n_plds != n_volumes:

aslprep/utils/plotting.py

@@ -206,8 +206,8 @@ def plot(self, figure=None):
                 confoundplot(
                     tseries, grid[grid_id], tr=self.tr, color=palette[i], name=name, **kwargs
                 )
-            except:
-                raise ValueError(name)
+            except Exception:
+                raise ValueError(name) from None
             grid_id += 1
 
         plt_carpet(

aslprep/workflows/asl/base.py

@@ -31,7 +31,7 @@
 def init_asl_wf(
     *,
     asl_file: str,
-    precomputed: dict = {},
+    precomputed: dict = None,
     fieldmap_id: str | None = None,
 ):
     """Perform the functional preprocessing stages of ASLPrep.

aslprep/workflows/asl/fit.py

@@ -88,7 +88,7 @@ def init_asl_fit_wf(
     asl_file: str,
     m0scan: str | None,
     use_ge: bool,
-    precomputed: dict = {},
+    precomputed: dict = None,
     fieldmap_id: str | None = None,
     omp_nthreads: int = 1,
     name: str = 'asl_fit_wf',

docs/conf.py

@@ -22,7 +22,6 @@
 
 import os
 import sys
-from datetime import datetime
 
 from packaging import version as pver
 from sphinx import __version__ as sphinxversion
@@ -133,7 +132,7 @@
 # General information about the project.
 project = 'aslprep'
 author = 'ASLPrep developers'
-copyright = f'2020-{datetime.now().year}, {author}'
+copyright = f'2020-, {author}'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/sphinxext/github_link.py

@@ -44,7 +44,7 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
         return
 
     class_name = info['fullname'].split('.')[0]
-    if type(class_name) != str:
+    if not isinstance(class_name, str):
         # Python 2 only
         class_name = class_name.encode('utf-8')
     module = __import__(info['module'], fromlist=[class_name])