Merge pull request #3680 from DimitriPapadopoulos/C4

 STY: Apply ruff/flake8-comprehensions rules (C4)

nipype/algorithms/modelgen.py

@@ -161,7 +161,7 @@ def bids_gen_info(
     for bids_event_file in bids_event_files:
         with open(bids_event_file) as f:
             f_events = csv.DictReader(f, skipinitialspace=True, delimiter="\t")
-            events = [{k: v for k, v in row.items()} for row in f_events]
+            events = list(f_events)
         if not condition_column:
             condition_column = "_trial_type"
             for i in events:

nipype/algorithms/tests/test_CompCor.py

@@ -287,9 +287,9 @@ def run_cc(
                 components_metadata = [
                     line.rstrip().split("\t") for line in metadata_file
                 ]
-                components_metadata = {
-                    i: j for i, j in zip(components_metadata[0], components_metadata[1])
-                }
+                components_metadata = dict(
+                    zip(components_metadata[0], components_metadata[1])
+                )
                 assert components_metadata == expected_metadata
 
         return ccresult

nipype/interfaces/ants/segmentation.py

@@ -194,7 +194,7 @@ def _format_arg(self, opt, spec, val):
                         priors_paths[0] % i for i in range(1, n_classes + 1)
                     ]
 
-                if not all([os.path.exists(p) for p in priors_paths]):
+                if not all(os.path.exists(p) for p in priors_paths):
                     raise FileNotFoundError(
                         "One or more prior images do not exist: "
                         "%s." % ", ".join(priors_paths)

nipype/interfaces/base/core.py

@@ -486,7 +486,7 @@ def load_inputs_from_json(self, json_file, overwrite=True):
         if not overwrite:
             def_inputs = list(self.inputs.get_traitsfree().keys())
 
-        new_inputs = list(set(list(inputs_dict.keys())) - set(def_inputs))
+        new_inputs = set(inputs_dict) - set(def_inputs)
         for key in new_inputs:
             if hasattr(self.inputs, key):
                 setattr(self.inputs, key, inputs_dict[key])

nipype/interfaces/cmtk/cmtk.py

@@ -248,7 +248,7 @@ def cmat(
                     axis=1,
                 )
             )
-            G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]])
+            G.nodes[int(u)]["dn_position"] = (xyz[0], xyz[2], -xyz[1])
 
     if intersections:
         iflogger.info("Filtering tractography from intersections")
@@ -1070,7 +1070,7 @@ def create_nodes(roi_file, resolution_network_file, out_filename):
                 np.where(np.flipud(roiData) == int(d["dn_correspondence_id"])), axis=1
             )
         )
-        G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]])
+        G.nodes[int(u)]["dn_position"] = (xyz[0], xyz[2], -xyz[1])
     with open(out_filename, 'wb') as f:
         pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
     return out_filename

nipype/interfaces/diffusion_toolkit/dti.py

@@ -97,7 +97,7 @@ class DTIRecon(CommandLine):
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = "gradient_matrix.txt"
         with open(bvals_file) as fbvals:
-            bvals = [val for val in re.split(r"\s+", fbvals.readline().strip())]
+            bvals = fbvals.readline().strip().split()
         with open(bvecs_file) as fbvecs:
             bvecs_x = fbvecs.readline().split()
             bvecs_y = fbvecs.readline().split()

nipype/interfaces/diffusion_toolkit/odf.py

@@ -98,12 +98,12 @@ class HARDIMat(CommandLine):
 
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = "gradient_matrix.txt"
-        bvals = [val for val in re.split(r"\s+", open(bvals_file).readline().strip())]
-        bvecs_f = open(bvecs_file)
-        bvecs_x = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
-        bvecs_y = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
-        bvecs_z = [val for val in re.split(r"\s+", bvecs_f.readline().strip())]
-        bvecs_f.close()
+        with open(bvals_file) as bvals_f:
+            bvals = bvals_f.readline().strip().split()
+        with open(bvecs_file) as bvecs_f:
+            bvecs_x = bvecs_f.readline().strip().split()
+            bvecs_y = bvecs_f.readline().strip().split()
+            bvecs_z = bvecs_f.readline().strip().split()
         gradient_matrix_f = open(_gradient_matrix_file, "w")
         for i in range(len(bvals)):
             if int(bvals[i]) == 0:

nipype/interfaces/freesurfer/preprocess.py

@@ -692,11 +692,11 @@ def _get_runs(self):
             if self.inputs.seq_list:
                 if self.inputs.ignore_single_slice:
                     if (int(s[8]) > 1) and any(
-                        [s[12].startswith(sn) for sn in self.inputs.seq_list]
+                        s[12].startswith(sn) for sn in self.inputs.seq_list
                     ):
                         runs.append(int(s[2]))
                 else:
-                    if any([s[12].startswith(sn) for sn in self.inputs.seq_list]):
+                    if any(s[12].startswith(sn) for sn in self.inputs.seq_list):
                         runs.append(int(s[2]))
             else:
                 runs.append(int(s[2]))

nipype/interfaces/fsl/model.py

@@ -1503,8 +1503,8 @@ def _run_interface(self, runtime):
         regs = sorted(self.inputs.regressors.keys())
         nwaves = len(regs)
         npoints = len(self.inputs.regressors[regs[0]])
-        ntcons = sum([1 for con in self.inputs.contrasts if con[1] == "T"])
-        nfcons = sum([1 for con in self.inputs.contrasts if con[1] == "F"])
+        ntcons = sum(1 for con in self.inputs.contrasts if con[1] == "T")
+        nfcons = sum(1 for con in self.inputs.contrasts if con[1] == "F")
         # write mat file
         mat_txt = ["/NumWaves       %d" % nwaves, "/NumPoints      %d" % npoints]
         ppheights = []
@@ -1591,7 +1591,7 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        nfcons = sum([1 for con in self.inputs.contrasts if con[1] == "F"])
+        nfcons = sum(1 for con in self.inputs.contrasts if con[1] == "F")
         for field in list(outputs.keys()):
             if ("fts" in field) and (nfcons == 0):
                 continue

nipype/interfaces/io.py

@@ -942,7 +942,7 @@ def _list_outputs(self):
         # get list of all files in s3 bucket
         conn = boto.connect_s3(anon=self.inputs.anon)
         bkt = conn.get_bucket(self.inputs.bucket)
-        bkt_files = list(k.key for k in bkt.list(prefix=self.inputs.bucket_path))
+        bkt_files = [k.key for k in bkt.list(prefix=self.inputs.bucket_path)]
 
         # keys are outfields, args are template args for the outfield
         for key, args in list(self.inputs.template_args.items()):
@@ -1022,7 +1022,7 @@ def _list_outputs(self):
                         if self.inputs.sort_filelist:
                             outfiles = human_order_sorted(outfiles)
                         outputs[key].append(simplify_list(outfiles))
-            if any([val is None for val in outputs[key]]):
+            if None in outputs[key]:
                 outputs[key] = []
             if len(outputs[key]) == 0:
                 outputs[key] = None
@@ -1297,7 +1297,7 @@ def _list_outputs(self):
             if self.inputs.drop_blank_outputs:
                 outputs[key] = [x for x in outputs[key] if x is not None]
             else:
-                if any([val is None for val in outputs[key]]):
+                if None in outputs[key]:
                     outputs[key] = []
             if len(outputs[key]) == 0:
                 outputs[key] = None
@@ -2302,7 +2302,7 @@ def __init__(self, input_names, **inputs):
         super().__init__(**inputs)
 
         self._input_names = ensure_list(input_names)
-        add_traits(self.inputs, [name for name in self._input_names])
+        add_traits(self.inputs, self._input_names)
 
     def _list_outputs(self):
         """Execute this module."""
@@ -2364,7 +2364,7 @@ def __init__(self, input_names, **inputs):
         super().__init__(**inputs)
 
         self._input_names = ensure_list(input_names)
-        add_traits(self.inputs, [name for name in self._input_names])
+        add_traits(self.inputs, self._input_names)
 
     def _list_outputs(self):
         """Execute this module."""
@@ -2642,7 +2642,7 @@ def _list_outputs(self):
                     outputs[key].append(self._get_files_over_ssh(filledtemplate))
 
             # disclude where there was any invalid matches
-            if any([val is None for val in outputs[key]]):
+            if None in outputs[key]:
                 outputs[key] = []
 
             # no outputs is None, not empty list

nipype/interfaces/spm/model.py

@@ -159,7 +159,7 @@ def _parse_inputs(self):
         """validate spm realign options if set to None ignore"""
         einputs = super()._parse_inputs(skip=("mask_threshold", "flags"))
         if isdefined(self.inputs.flags):
-            einputs[0].update({flag: val for (flag, val) in self.inputs.flags.items()})
+            einputs[0].update(self.inputs.flags)
         for sessinfo in einputs[0]["sess"]:
             sessinfo["scans"] = scans_for_fnames(
                 ensure_list(sessinfo["scans"]), keep4d=False
@@ -309,7 +309,7 @@ def _parse_inputs(self):
         """validate spm realign options if set to None ignore"""
         einputs = super()._parse_inputs(skip=("flags"))
         if isdefined(self.inputs.flags):
-            einputs[0].update({flag: val for (flag, val) in self.inputs.flags.items()})
+            einputs[0].update(self.inputs.flags)
         return einputs
 
     def _list_outputs(self):

nipype/interfaces/utility/wrappers.py

@@ -95,11 +95,9 @@ def __init__(
         self.inputs.on_trait_change(self._set_function_string, "function_str")
         self._input_names = ensure_list(input_names)
         self._output_names = ensure_list(output_names)
-        add_traits(self.inputs, [name for name in self._input_names])
+        add_traits(self.inputs, self._input_names)
         self.imports = imports
-        self._out = {}
-        for name in self._output_names:
-            self._out[name] = None
+        self._out = {name: None for name in self._output_names}
 
     def _set_function_string(self, obj, name, old, new):
         if name == "function_str":

nipype/pipeline/engine/nodes.py

@@ -240,7 +240,7 @@ def needed_outputs(self):
     @needed_outputs.setter
     def needed_outputs(self, new_outputs):
         """Needed outputs changes the hash, refresh if changed"""
-        new_outputs = sorted(list(set(new_outputs or [])))
+        new_outputs = sorted(set(new_outputs or []))
         if new_outputs != self._needed_outputs:
             # Reset hash
             self._hashvalue = None
@@ -1283,7 +1283,7 @@ def _collate_results(self, nodes):
                     )
                 setattr(finalresult.outputs, key, values)
 
-        if returncode and any([code is not None for code in returncode]):
+        if returncode and any(code is not None for code in returncode):
             msg = []
             for i, code in enumerate(returncode):
                 if code is not None:

nipype/pipeline/engine/utils.py

@@ -1046,7 +1046,7 @@ def make_field_func(*pair):
         logger.debug("node: %s iterables: %s", inode, iterables)
 
         # collect the subnodes to expand
-        subnodes = [s for s in dfs_preorder(graph_in, inode)]
+        subnodes = list(dfs_preorder(graph_in, inode))
         prior_prefix = [re.findall(r"\.(.)I", s._id) for s in subnodes if s._id]
         prior_prefix = sorted([l for item in prior_prefix for l in item])
         if not prior_prefix:
@@ -1482,11 +1482,8 @@ def clean_working_directory(
     files2remove = []
     if str2bool(config["execution"]["remove_unnecessary_outputs"]):
         for f in walk_files(cwd):
-            if f not in needed_files:
-                if not needed_dirs:
-                    files2remove.append(f)
-                elif not any([f.startswith(dname) for dname in needed_dirs]):
-                    files2remove.append(f)
+            if f not in needed_files and not f.startswith(tuple(needed_dirs)):
+                files2remove.append(f)
     else:
         if not str2bool(config["execution"]["keep_inputs"]):
             input_files = {

nipype/pipeline/engine/workflows.py

@@ -191,10 +191,8 @@ def connect(self, *args, **kwargs):
                     and (
                         ".io" in str(destnode._interface.__class__)
                         or any(
-                            [
-                                ".io" in str(val)
-                                for val in destnode._interface.__class__.__bases__
-                            ]
+                            ".io" in str(val)
+                            for val in destnode._interface.__class__.__bases__
                         )
                     )
                 ):
@@ -205,10 +203,8 @@ def connect(self, *args, **kwargs):
                     and (
                         ".io" in str(srcnode._interface.__class__)
                         or any(
-                            [
-                                ".io" in str(val)
-                                for val in srcnode._interface.__class__.__bases__
-                            ]
+                            ".io" in str(val)
+                            for val in srcnode._interface.__class__.__bases__
                         )
                     )
                 ):

nipype/pipeline/plugins/base.py

@@ -455,7 +455,7 @@ def _remove_node_deps(self, jobid, crashfile, graph):
             dfs_preorder = nx.dfs_preorder
         except AttributeError:
             dfs_preorder = nx.dfs_preorder_nodes
-        subnodes = [s for s in dfs_preorder(graph, self.procs[jobid])]
+        subnodes = list(dfs_preorder(graph, self.procs[jobid]))
         for node in subnodes:
             idx = self.procs.index(node)
             self.proc_done[idx] = True

nipype/pipeline/plugins/linear.py

@@ -50,7 +50,7 @@ def run(self, graph, config, updatehash=False):
                 # node might fail
                 crashfile = report_crash(node)
                 # remove dependencies from queue
-                subnodes = [s for s in dfs_preorder(graph, node)]
+                subnodes = list(dfs_preorder(graph, node))
                 notrun.append(
                     {"node": node, "dependents": subnodes, "crashfile": crashfile}
                 )

nipype/scripts/instance.py

@@ -39,7 +39,7 @@ def list_interfaces(module):
     the given module.
     """
     iface_names = []
-    for k, v in sorted(list(module.__dict__.items())):
+    for k, v in sorted(module.__dict__.items()):
         if inspect.isclass(v) and issubclass(v, Interface):
             iface_names.append(k)
     return iface_names

nipype/utils/docparse.py

@@ -283,7 +283,7 @@ def _parse_doc(doc, style=["--"]):
         flag = [
             item
             for i, item in enumerate(linelist)
-            if i < 2 and any([item.startswith(s) for s in style]) and len(item) > 1
+            if i < 2 and item.startswith(tuple(style)) and len(item) > 1
         ]
         if flag:
             if len(flag) == 1:

nipype/utils/filemanip.py

@@ -499,7 +499,7 @@ def ensure_list(filename):
     elif isinstance(filename, list):
         return filename
     elif is_container(filename):
-        return [x for x in filename]
+        return list(filename)
     else:
         return None
 

nipype/utils/misc.py

@@ -53,7 +53,7 @@ def trim(docstring, marker=None):
             if (
                 marker is not None
                 and stripped
-                and all([s == stripped[0] for s in stripped])
+                and all(s == stripped[0] for s in stripped)
                 and stripped[0] not in [":"]
             ):
                 line = line.replace(stripped[0], marker)

nipype/utils/nipype_cmd.py

@@ -13,7 +13,7 @@ def listClasses(module=None):
         __import__(module)
         pkg = sys.modules[module]
         print("Available Interfaces:")
-        for k, v in sorted(list(pkg.__dict__.items())):
+        for k, v in sorted(pkg.__dict__.items()):
             if inspect.isclass(v) and issubclass(v, Interface):
                 print("\t%s" % k)