STY: Apply ruff/flake8-quotes rule Q000

DimitriPapadopoulos · DimitriPapadopoulos · commit 6fe841cb010c · 2024-10-09T10:41:53.000+02:00
Q000 Single quotes found but double quotes preferred
diff --git a/doc/devel/matlab_example1.py b/doc/devel/matlab_example1.py
@@ -11,7 +11,7 @@
 
 class ConmapTxt2MatInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True)
-    out_file = File('cmatrix.mat', usedefault=True)
+    out_file = File("cmatrix.mat", usedefault=True)
 
 
 class ConmapTxt2MatOutputSpec(TraitedSpec):
@@ -48,5 +48,5 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs
diff --git a/doc/devel/matlab_example2.py b/doc/devel/matlab_example2.py
@@ -4,7 +4,7 @@
 
 
 class HelloWorldInputSpec(MatlabInputSpec):
-    name = traits.Str(mandatory=True, desc='Name of person to say hello to')
+    name = traits.Str(mandatory=True, desc="Name of person to say hello to")
 
 
 class HelloWorldOutputSpec(TraitedSpec):
diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
@@ -225,7 +225,7 @@ def cmat(
     # Add node information from specified parcellation scheme
     path, name, ext = split_filename(resolution_network_file)
     if ext == ".pck":
-        with open(resolution_network_file, 'rb') as f:
+        with open(resolution_network_file, "rb") as f:
             gp = pickle.load(f)
     elif ext == ".graphml":
         gp = nx.read_graphml(resolution_network_file)
@@ -380,7 +380,7 @@ def cmat(
                 fibdev.add_edge(u, v, weight=di["fiber_length_std"])
 
     iflogger.info("Writing network as %s", matrix_name)
-    with open(op.abspath(matrix_name), 'wb') as f:
+    with open(op.abspath(matrix_name), "wb") as f:
         pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
 
     numfib_mlab = nx.to_numpy_array(numfib, dtype=int)
@@ -396,7 +396,7 @@ def cmat(
         path, name, ext = split_filename(matrix_name)
         intersection_matrix_name = op.abspath(name + "_intersections") + ext
         iflogger.info("Writing intersection network as %s", intersection_matrix_name)
-        with open(intersection_matrix_name, 'wb') as f:
+        with open(intersection_matrix_name, "wb") as f:
             pickle.dump(I, f, pickle.HIGHEST_PROTOCOL)
 
     path, name, ext = split_filename(matrix_mat_name)
@@ -1071,7 +1071,7 @@ def create_nodes(roi_file, resolution_network_file, out_filename):
             )
         )
         G.nodes[int(u)]["dn_position"] = (xyz[0], xyz[2], -xyz[1])
-    with open(out_filename, 'wb') as f:
+    with open(out_filename, "wb") as f:
         pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
     return out_filename
 
diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py
@@ -18,7 +18,7 @@
 def _read_pickle(fname):
     import pickle
 
-    with open(fname, 'rb') as f:
+    with open(fname, "rb") as f:
         return pickle.load(f)
 
 
@@ -193,17 +193,17 @@ def _run_interface(self, runtime):
             for data in self.inputs.data_files:
                 _, data_name, _ = split_filename(data)
                 cda = cf.CData(name=data_name, src=data, fileformat="NumPy")
-                if 'lengths' in data_name:
+                if "lengths" in data_name:
                     cda.dtype = "FinalFiberLengthArray"
-                if 'endpoints' in data_name:
+                if "endpoints" in data_name:
                     cda.dtype = "FiberEndpoints"
-                if 'labels' in data_name:
+                if "labels" in data_name:
                     cda.dtype = "FinalFiberLabels"
                 a.add_connectome_data(cda)
 
         a.print_summary()
         _, name, ext = split_filename(self.inputs.out_file)
-        if ext != '.cff':
+        if ext != ".cff":
             ext = ".cff"
         cf.save_to_cff(a, op.abspath(name + ext))
 
@@ -212,7 +212,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if ext != '.cff':
+        if ext != ".cff":
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs
@@ -280,7 +280,7 @@ def _run_interface(self, runtime):
         metadata.set_email("My Email")
 
         _, name, ext = split_filename(self.inputs.out_file)
-        if ext != '.cff':
+        if ext != ".cff":
             ext = ".cff"
         cf.save_to_cff(newcon, op.abspath(name + ext))
 
@@ -289,7 +289,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if ext != '.cff':
+        if ext != ".cff":
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs
diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py
@@ -23,7 +23,7 @@
 
 
 def _read_pickle(fname):
-    with open(fname, 'rb') as f:
+    with open(fname, "rb") as f:
         return pickle.load(f)
 
 
@@ -174,13 +174,13 @@ def _run_interface(self, runtime):
 
         path = op.abspath("NBS_Result_" + details)
         iflogger.info(path)
-        with open(path, 'wb') as f:
+        with open(path, "wb") as f:
             pickle.dump(nbsgraph, f, pickle.HIGHEST_PROTOCOL)
         iflogger.info("Saving output NBS edge network as %s", path)
 
         pval_path = op.abspath("NBS_P_vals_" + details)
         iflogger.info(pval_path)
-        with open(pval_path, 'wb') as f:
+        with open(pval_path, "wb") as f:
             pickle.dump(nbs_pval_graph, f, pickle.HIGHEST_PROTOCOL)
         iflogger.info("Saving output p-value network as %s", pval_path)
         return runtime
diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
@@ -23,7 +23,7 @@
 
 
 def _read_pickle(fname):
-    with open(fname, 'rb') as f:
+    with open(fname, "rb") as f:
         return pickle.load(f)
 
 
@@ -203,7 +203,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
 
     # Writes the networks and returns the name
     network_name = group_id + "_average.pck"
-    with open(op.abspath(network_name), 'wb') as f:
+    with open(op.abspath(network_name), "wb") as f:
         pickle.dump(avg_ntwk, f, pickle.HIGHEST_PROTOCOL)
     iflogger.info("Saving average network as %s", op.abspath(network_name))
     avg_ntwk = fix_keys_for_gexf(avg_ntwk)
@@ -487,7 +487,7 @@ def _run_interface(self, runtime):
         for key in list(node_measures.keys()):
             newntwk = add_node_data(node_measures[key], ntwk)
             out_file = op.abspath(self._gen_outfilename(key, "pck"))
-            with open(out_file, 'wb') as f:
+            with open(out_file, "wb") as f:
                 pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL)
             nodentwks.append(out_file)
         if isdefined(self.inputs.out_node_metrics_matlab):
@@ -502,7 +502,7 @@ def _run_interface(self, runtime):
         for key in list(edge_measures.keys()):
             newntwk = add_edge_data(edge_measures[key], ntwk)
             out_file = op.abspath(self._gen_outfilename(key, "pck"))
-            with open(out_file, 'wb') as f:
+            with open(out_file, "wb") as f:
                 pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL)
             edgentwks.append(out_file)
         if isdefined(self.inputs.out_edge_metrics_matlab):
@@ -527,7 +527,7 @@ def _run_interface(self, runtime):
                 out_file = op.abspath(
                     self._gen_outfilename(self.inputs.out_k_crust, "pck")
                 )
-            with open(out_file, 'wb') as f:
+            with open(out_file, "wb") as f:
                 pickle.dump(ntwk_measures[key], f, pickle.HIGHEST_PROTOCOL)
             kntwks.append(out_file)
         gpickled.extend(kntwks)
diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py
@@ -21,7 +21,7 @@ def creating_graphs(tmpdir):
         G = nx.from_numpy_array(graph)
         out_file = tmpdir.strpath + graphnames[idx] + ".pck"
         # Save as pck file
-        with open(out_file, 'wb') as f:
+        with open(out_file, "wb") as f:
             pickle.dump(G, f, pickle.HIGHEST_PROTOCOL)
         graphlist.append(out_file)
     return graphlist
diff --git a/nipype/interfaces/dipy/tests/test_base.py b/nipype/interfaces/dipy/tests/test_base.py
@@ -124,19 +124,19 @@ def test_get_default_args():
     def test(dummy=11, x=3):
         return dummy, x
 
-    @deprecated_params('x', None, '0.3', '0.5', alternative='test2.y')
+    @deprecated_params("x", None, "0.3", "0.5", alternative="test2.y")
     def test2(dummy=11, x=3):
         return dummy, x
 
-    @deprecated_params(['dummy', 'x'], None, '0.3', alternative='test2.y')
+    @deprecated_params(["dummy", "x"], None, "0.3", alternative="test2.y")
     def test3(dummy=11, x=3):
         return dummy, x
 
-    @deprecated_params(['dummy', 'x'], None, '0.3', '0.5', alternative='test2.y')
+    @deprecated_params(["dummy", "x"], None, "0.3", "0.5", alternative="test2.y")
     def test4(dummy=11, x=3):
         return dummy, x
 
-    expected_res = {'dummy': 11, 'x': 3}
+    expected_res = {"dummy": 11, "x": 3}
     for func in [test, test2, test3, test4]:
         assert get_default_args(func) == expected_res
 
diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
@@ -451,9 +451,9 @@ class GLMFitInputSpec(FSTraitedSpec):
     sim_done_file = File(
         argstr="--sim-done %s", desc="create file when simulation finished"
     )
-    _ext_xor = ['nii', 'nii_gz']
-    nii = traits.Bool(argstr='--nii', desc='save outputs as nii', xor=_ext_xor)
-    nii_gz = traits.Bool(argstr='--nii.gz', desc='save outputs as nii.gz', xor=_ext_xor)
+    _ext_xor = ["nii", "nii_gz"]
+    nii = traits.Bool(argstr="--nii", desc="save outputs as nii", xor=_ext_xor)
+    nii_gz = traits.Bool(argstr="--nii.gz", desc="save outputs as nii.gz", xor=_ext_xor)
 
 
 class GLMFitOutputSpec(TraitedSpec):
@@ -511,11 +511,11 @@ def _list_outputs(self):
         outputs["glm_dir"] = glmdir
 
         if isdefined(self.inputs.nii_gz):
-            ext = 'nii.gz'
+            ext = "nii.gz"
         elif isdefined(self.inputs.nii):
-            ext = 'nii'
+            ext = "nii"
         else:
-            ext = 'mgh'
+            ext = "mgh"
 
         # Assign the output files that always get created
         outputs["beta_file"] = os.path.join(glmdir, f"beta.{ext}")
diff --git a/nipype/interfaces/freesurfer/petsurfer.py b/nipype/interfaces/freesurfer/petsurfer.py
@@ -125,10 +125,10 @@ class GTMSeg(FSCommand):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['out_file'] = os.path.join(
+        outputs["out_file"] = os.path.join(
             self.inputs.subjects_dir,
             self.inputs.subject_id,
-            'mri',
+            "mri",
             self.inputs.out_file,
         )
         return outputs
@@ -516,7 +516,7 @@ class GTMPVC(FSCommand):
     def _format_arg(self, name, spec, val):
         # Values taken from
         # https://github.com/freesurfer/freesurfer/blob/fs-7.2/mri_gtmpvc/mri_gtmpvc.cpp#L115-L122
-        if name == 'optimization_schema':
+        if name == "optimization_schema":
             return (
                 spec.argstr
                 % {
@@ -530,8 +530,8 @@ def _format_arg(self, name, spec, val):
                     "MB3": 8,
                 }[val]
             )
-        if name == 'mg':
-            return spec.argstr % (val[0], ' '.join(val[1]))
+        if name == "mg":
+            return spec.argstr % (val[0], " ".join(val[1]))
         return super()._format_arg(name, spec, val)
 
     def _list_outputs(self):
diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
@@ -1967,7 +1967,7 @@ def _format_arg(self, name, spec, value):
         if name == "lta_in" and self.inputs.invert_lta_in:
             spec = "--lta-inv %s"
         if name in ("fsl_out", "lta_out") and value is True:
-            value = self._list_outputs()[f'{name[:3]}_file']
+            value = self._list_outputs()[f"{name[:3]}_file"]
         return super()._format_arg(name, spec, value)
 
     def _list_outputs(self):
diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
@@ -820,9 +820,9 @@ class FILMGLS(FSLCommand):
     def __init__(self, **inputs):
         super(FILMGLS, self).__init__(**inputs)
         if Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.6"):
-            if 'output_type' not in inputs:
-                if isdefined(self.inputs.mode) and self.inputs.mode == 'surface':
-                    self.inputs.output_type = 'GIFTI'
+            if "output_type" not in inputs:
+                if isdefined(self.inputs.mode) and self.inputs.mode == "surface":
+                    self.inputs.output_type = "GIFTI"
 
     def _get_pe_files(self, cwd):
         files = None
diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py
@@ -152,7 +152,7 @@ def _process_inputs(self):
         if self.inputs.include_global:
             global_label_data = label_data.dataobj.sum(axis=3)  # sum across all regions
             global_label_data = (
-                np.rint(global_label_data).clip(0, 1).astype('u1')
+                np.rint(global_label_data).clip(0, 1).astype("u1")
             )  # binarize
             global_label_data = self._4d(global_label_data, label_data.affine)
             global_masker = nl.NiftiLabelsMasker(
diff --git a/nipype/interfaces/robex/preprocess.py b/nipype/interfaces/robex/preprocess.py
@@ -16,7 +16,7 @@ class RobexInputSpec(CommandLineInputSpec):
         position=1,
         argstr="%s",
         hash_files=False,
-        name_template='%s_brain',
+        name_template="%s_brain",
         name_source=["in_file"],
         keep_extension=True,
     )
@@ -25,7 +25,7 @@ class RobexInputSpec(CommandLineInputSpec):
         position=2,
         argstr="%s",
         hash_files=False,
-        name_template='%s_brainmask',
+        name_template="%s_brainmask",
         name_source=["in_file"],
         keep_extension=True,
     )
@@ -61,4 +61,4 @@ class RobexSegment(CommandLine):
 
     input_spec = RobexInputSpec
     output_spec = RobexOutputSpec
-    _cmd = 'runROBEX.sh'
+    _cmd = "runROBEX.sh"
diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
@@ -350,17 +350,17 @@ def _list_outputs(self):
 
             if contrast:
                 outputs["con_images"] = [
-                    os.path.join(pth, cont) for cont in contrast if 'con' in cont
+                    os.path.join(pth, cont) for cont in contrast if "con" in cont
                 ]
                 outputs["ess_images"] = [
-                    os.path.join(pth, cont) for cont in contrast if 'ess' in cont
+                    os.path.join(pth, cont) for cont in contrast if "ess" in cont
                 ]
             if contrast_spm:
                 outputs["spmT_images"] = [
-                    os.path.join(pth, cont) for cont in contrast_spm if 'spmT' in cont
+                    os.path.join(pth, cont) for cont in contrast_spm if "spmT" in cont
                 ]
                 outputs["spmF_images"] = [
-                    os.path.join(pth, cont) for cont in contrast_spm if 'spmF' in cont
+                    os.path.join(pth, cont) for cont in contrast_spm if "spmF" in cont
                 ]
 
         outputs["mask_image"] = os.path.join(pth, f"mask.{outtype}")
diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
@@ -334,11 +334,11 @@ class ApplyVDM(SPMCommand):
     def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for spm"""
 
-        if opt == 'in_files':
+        if opt == "in_files":
             return scans_for_fnames(
                 ensure_list(val), keep4d=False, separate_sessions=False
             )
-        if opt == 'vdmfile':
+        if opt == "vdmfile":
             return scans_for_fname(ensure_list(val))
         return super()._format_arg(opt, spec, val)
 
diff --git a/nipype/interfaces/tests/test_io.py b/nipype/interfaces/tests/test_io.py
@@ -707,7 +707,7 @@ def _mock_get_ssh_client(self):
 
 def test_ExportFile(tmp_path):
     test_in = tmp_path / "in.txt"
-    test_in.write_text("test string", encoding='utf-8')
+    test_in.write_text("test string", encoding="utf-8")
     i = nio.ExportFile()
     i.inputs.in_file = str(test_in)
     i.inputs.out_file = str(tmp_path / "out.tsv")
diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py
@@ -755,10 +755,10 @@ def _tab(text):
 
                 if not text:
                     return ""
-                return indent(text, '\t')
+                return indent(text, "\t")
 
             msg = f"Exception raised while executing Node {self.name}.\n\n"
-            if hasattr(runtime, 'cmdline'):
+            if hasattr(runtime, "cmdline"):
                 msg += (
                     f"Cmdline:\n{_tab(runtime.cmdline)}\n"
                     f"Stdout:\n{_tab(runtime.stdout)}\n"
diff --git a/nipype/pipeline/engine/tests/test_nodes.py b/nipype/pipeline/engine/tests/test_nodes.py
diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
diff --git a/nipype/utils/subprocess.py b/nipype/utils/subprocess.py
diff --git a/tools/update_requirements.py b/tools/update_requirements.py
diff --git a/tools/update_zenodo.py b/tools/update_zenodo.py
