Merge pull request #3678 from DimitriPapadopoulos/PIE

STY: Apply ruff/flake8-pie rules (PIE)

Author: effigies

nipype/algorithms/misc.py

@@ -714,7 +714,7 @@ def _run_interface(self, runtime):
                 mx = shape[0]
             else:
                 mx = 1
-            for idx in range(0, mx):
+            for idx in range(mx):
                 extrafieldlist.append(self.inputs.extra_field)
             iflogger.info(len(extrafieldlist))
             output[extraheading] = extrafieldlist

nipype/interfaces/ants/registration.py

@@ -1073,7 +1073,7 @@ def _format_metric(self, index):
         # from the non-list inputs.
         if isinstance(name_input, list):
             items = list(stage_inputs.items())
-            indexes = list(range(0, len(name_input)))
+            indexes = list(range(len(name_input)))
             specs = list()
             for i in indexes:
                 temp = {k: v[i] for k, v in items}

nipype/interfaces/cmtk/cmtk.py

@@ -72,7 +72,7 @@ def length(xyz, along=False):
 def get_rois_crossed(pointsmm, roiData, voxelSize):
     n_points = len(pointsmm)
     rois_crossed = []
-    for j in range(0, n_points):
+    for j in range(n_points):
         # store point
         x = int(pointsmm[j, 0] / float(voxelSize[0]))
         y = int(pointsmm[j, 1] / float(voxelSize[1]))
@@ -894,7 +894,7 @@ def _run_interface(self, runtime):
             iflogger.info("Number of labels in LUT: %s", numLUTLabels)
             LUTlabelDict = {}
             """ Create dictionary for input LUT table"""
-            for labels in range(0, numLUTLabels):
+            for labels in range(numLUTLabels):
                 LUTlabelDict[LUTlabelsRGBA[labels][0]] = [
                     LUTlabelsRGBA[labels][1],
                     LUTlabelsRGBA[labels][2],

nipype/interfaces/cmtk/nx.py

@@ -353,7 +353,7 @@ def add_edge_data(edge_array, ntwk, above=0, below=0):
     edge_ntwk = ntwk.copy()
     data = {}
     for x, row in enumerate(edge_array):
-        for y in range(0, np.max(np.shape(edge_array[x]))):
+        for y in range(np.max(np.shape(edge_array[x]))):
             if not edge_array[x, y] == 0:
                 data["value"] = edge_array[x, y]
                 if data["value"] <= below or data["value"] >= above:

nipype/interfaces/dcm2nii.py

@@ -471,20 +471,15 @@ def _parse_files(self, filenames):
         for filename in filenames:
             # search for relevant files, and sort accordingly
             for fl in search_files(filename, outtypes, self.inputs.crop):
-                if (
-                    fl.endswith(".nii")
-                    or fl.endswith(".gz")
-                    or fl.endswith(".nrrd")
-                    or fl.endswith(".nhdr")
-                ):
+                if fl.endswith((".nii", ".gz", ".nrrd", ".nhdr")):
                     outfiles.append(fl)
                 elif fl.endswith(".bval"):
                     bvals.append(fl)
                 elif fl.endswith(".bvec"):
                     bvecs.append(fl)
                 elif fl.endswith(".mvec"):
                     mvecs.append(fl)
-                elif fl.endswith(".json") or fl.endswith(".txt"):
+                elif fl.endswith((".json", ".txt")):
                     bids.append(fl)
 
         # in siemens mosaic conversion nipype misread dcm2niix output and generate a duplicate list of results

nipype/interfaces/dipy/reconstruction.py

@@ -136,7 +136,6 @@ def _run_interface(self, runtime):
             )
         except:
             bias = 0.0
-            pass
 
         sigma = mean_std * (1 + bias)
 

nipype/interfaces/dipy/simulate.py

@@ -344,7 +344,7 @@ def _generate_gradients(ndirs=64, values=[1000, 3000], nb0s=1):
         bvecs = np.vstack((bvecs, vertices))
         bvals = np.hstack((bvals, v * np.ones(vertices.shape[0])))
 
-    for i in range(0, nb0s):
+    for i in range(nb0s):
         bvals = bvals.tolist()
         bvals.insert(0, 0)
 

nipype/interfaces/freesurfer/preprocess.py

@@ -580,7 +580,7 @@ def _list_outputs(self):
                 stem = ".".join(outfile.split(".")[:-1])
                 ext = "." + outfile.split(".")[-1]
             outfile = []
-            for idx in range(0, tp):
+            for idx in range(tp):
                 outfile.append(stem + "%04d" % idx + ext)
         if isdefined(self.inputs.out_type):
             if self.inputs.out_type in ["spm", "analyze"]:

nipype/interfaces/freesurfer/utils.py

@@ -2836,7 +2836,7 @@ def _format_arg(self, name, spec, value):
             suffix = basename.split(".")[1]
             return spec.argstr % suffix
         elif name == "in_orig":
-            if value.endswith("lh.orig") or value.endswith("rh.orig"):
+            if value.endswith(("lh.orig", "rh.orig")):
                 # {lh,rh}.orig inputs are not specified on command line
                 return
             else:

nipype/interfaces/fsl/model.py

@@ -259,7 +259,7 @@ def _create_ev_files(
         # add ev orthogonalization
         for i in range(1, num_evs[0] + 1):
             initial = ev_ortho.substitute(c0=i, c1=0, orthogonal=1)
-            for j in range(0, num_evs[0] + 1):
+            for j in range(num_evs[0] + 1):
                 try:
                     orthogonal = int(orthogonalization[i][j])
                 except (KeyError, TypeError, ValueError, IndexError):

nipype/interfaces/mrtrix3/base.py

@@ -103,7 +103,6 @@ def _format_arg(self, name, trait_spec, value):
                 value = cpu_count()
             except:
                 iflogger.warning("Number of threads could not be computed")
-                pass
             return trait_spec.argstr % value
 
         if name == "in_bvec":

nipype/pipeline/engine/tests/test_engine.py

@@ -356,7 +356,7 @@ def func1(in1):
     # check that multiple json's don't trigger rerun
     with open(os.path.join(node.output_dir(), "test.json"), "w") as fp:
         fp.write("dummy file")
-    w1.config["execution"].update(**{"stop_on_first_rerun": True})
+    w1.config["execution"].update(stop_on_first_rerun=True)
 
     w1.run()
 

nipype/pipeline/plugins/sge.py

@@ -184,7 +184,6 @@ def _qacct_verified_complete(taskid):
             except:
                 sge_debug_print("NOTE: qacct call failed")
                 time.sleep(5)
-                pass
         return is_complete
 
     def _parse_qstat_job_list(self, xml_job_list):
@@ -259,7 +258,6 @@ def _parse_qstat_job_list(self, xml_job_list):
                             dictionary_job, self._task_dictionary[dictionary_job]
                         )
                     )
-                    pass
             if self._task_dictionary[dictionary_job].is_initializing():
                 is_completed = self._qacct_verified_complete(dictionary_job)
                 if is_completed:
@@ -271,7 +269,6 @@ def _parse_qstat_job_list(self, xml_job_list):
                             dictionary_job, self._task_dictionary[dictionary_job]
                         )
                     )
-                    pass
 
     def _run_qstat(self, reason_for_qstat, force_instant=True):
         """request all job information for the current user in xmlformat.
@@ -320,7 +317,6 @@ def _run_qstat(self, reason_for_qstat, force_instant=True):
                 )
                 sge_debug_print(exception_message)
                 time.sleep(5)
-                pass
 
     def print_dictionary(self):
         """For debugging"""

nipype/pipeline/plugins/tests/test_legacymultiproc_nondaemon.py

@@ -40,7 +40,7 @@ def dummyFunction(filename):
         This function writes the value 45 to the given filename.
         """
         j = 0
-        for i in range(0, 10):
+        for i in range(10):
             j += i
 
         # j is now 45 (0+1+2+3+4+5+6+7+8+9)

nipype/utils/draw_gantt_chart.py

@@ -20,7 +20,6 @@
         "Pandas not found; in order for full functionality of this module "
         "install the pandas package"
     )
-    pass
 
 
 def create_event_dict(start_time, nodes_list):

nipype/utils/filemanip.py

@@ -566,7 +566,7 @@ def load_json(filename):
 
 
 def loadcrash(infile, *args):
-    if infile.endswith("pkl") or infile.endswith("pklz"):
+    if infile.endswith(("pkl", "pklz")):
         return loadpkl(infile)
     else:
         raise ValueError("Only pickled crashfiles are supported")

nipype/utils/nipype2boutiques.py

@@ -288,7 +288,7 @@ def get_boutiques_input(
     if handler_type == "TraitCompound":
         input_list = []
         # Recursively create an input for each trait
-        for i in range(0, len(trait_handler.handlers)):
+        for i in range(len(trait_handler.handlers)):
             inp = get_boutiques_input(
                 inputs,
                 interface,