From eb1d4882187052af932fd847c0e0d084bb016999 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 12:33:33 +0200
Subject: [PATCH 1/8] STY: Apply ruff/flake8-simplify rule SIM101

SIM101 Multiple `isinstance` calls for expression, merge into a single call
---
 nipype/interfaces/base/specs.py              | 8 ++------
 nipype/interfaces/slicer/generate_classes.py | 4 ++--
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 2d7a6018b9..4255c555c4 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -177,7 +177,7 @@ def get_traitsfree(self, **kwargs):
 
     def _clean_container(self, objekt, undefinedval=None, skipundefined=False):
         """Convert a traited object into a pure python representation."""
-        if isinstance(objekt, TraitDictObject) or isinstance(objekt, dict):
+        if isinstance(objekt, (TraitDictObject, dict)):
             out = {}
             for key, val in list(objekt.items()):
                 if isdefined(val):
@@ -185,11 +185,7 @@ def _clean_container(self, objekt, undefinedval=None, skipundefined=False):
                 else:
                     if not skipundefined:
                         out[key] = undefinedval
-        elif (
-            isinstance(objekt, TraitListObject)
-            or isinstance(objekt, list)
-            or isinstance(objekt, tuple)
-        ):
+        elif isinstance(objekt, (TraitListObject, list, tuple)):
             out = []
             for val in objekt:
                 if isdefined(val):
diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
index 20ed8e9f21..8f20961086 100644
--- a/nipype/interfaces/slicer/generate_classes.py
+++ b/nipype/interfaces/slicer/generate_classes.py
@@ -54,7 +54,7 @@ def add_class_to_package(class_codes, class_names, module_name, package_dir):
 def crawl_code_struct(code_struct, package_dir):
     subpackages = []
     for k, v in code_struct.items():
-        if isinstance(v, str) or isinstance(v, (str, bytes)):
+        if isinstance(v, (str, bytes)):
             module_name = k.lower()
             class_name = k
             class_code = v
@@ -63,7 +63,7 @@ def crawl_code_struct(code_struct, package_dir):
             l1 = {}
             l2 = {}
             for key in list(v.keys()):
-                if isinstance(v[key], str) or isinstance(v[key], (str, bytes)):
+                if isinstance(v[key], (str, bytes)):
                     l1[key] = v[key]
                 else:
                     l2[key] = v[key]

From 01c3e76ff78012d5ff1f6e5a1f6b9ee78699a487 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 12:47:15 +0200
Subject: [PATCH 2/8] STY: Apply ruff/flake8-simplify rule SIM103

SIM103 Return the condition directly
---
 nipype/interfaces/afni/base.py       |  4 +---
 nipype/interfaces/freesurfer/base.py |  5 +----
 nipype/interfaces/fsl/base.py        |  5 +----
 nipype/interfaces/spm/base.py        | 10 ++--------
 nipype/pipeline/plugins/condor.py    |  4 +---
 nipype/pipeline/plugins/lsf.py       |  7 +++----
 nipype/utils/misc.py                 |  7 +------
 7 files changed, 10 insertions(+), 32 deletions(-)

diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py
index 5c36ed5f61..e883b22c6e 100644
--- a/nipype/interfaces/afni/base.py
+++ b/nipype/interfaces/afni/base.py
@@ -326,6 +326,4 @@ def _cmd_prefix(self):
 
 def no_afni():
     """Check whether AFNI is not available."""
-    if Info.version() is None:
-        return True
-    return False
+    return Info.version() is None
diff --git a/nipype/interfaces/freesurfer/base.py b/nipype/interfaces/freesurfer/base.py
index 0baedd4b82..c84fc78cd5 100644
--- a/nipype/interfaces/freesurfer/base.py
+++ b/nipype/interfaces/freesurfer/base.py
@@ -269,7 +269,4 @@ def no_freesurfer():
     used with skipif to skip tests that will
     fail if FreeSurfer is not installed"""
 
-    if Info.version() is None:
-        return True
-    else:
-        return False
+    return Info.version() is None
diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py
index cae9783362..7be822e4f2 100644
--- a/nipype/interfaces/fsl/base.py
+++ b/nipype/interfaces/fsl/base.py
@@ -262,10 +262,7 @@ def no_fsl():
     used with skipif to skip tests that will
     fail if FSL is not installed"""
 
-    if Info.version() is None:
-        return True
-    else:
-        return False
+    return Info.version() is None
 
 
 def no_fsl_course_data():
diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py
index 9c653bb266..ac20682696 100644
--- a/nipype/interfaces/spm/base.py
+++ b/nipype/interfaces/spm/base.py
@@ -52,10 +52,7 @@ def func_is_3d(in_file):
     else:
         img = load(in_file)
         shape = img.shape
-        if len(shape) == 3 or (len(shape) == 4 and shape[3] == 1):
-            return True
-        else:
-            return False
+        return len(shape) == 3 or len(shape) == 4 and shape[3] == 1
 
 
 def get_first_3dfile(in_files):
@@ -254,10 +251,7 @@ def no_spm():
     used with pytest.mark.skipif decorator to skip tests
     that will fail if spm is not installed"""
 
-    if "NIPYPE_NO_MATLAB" in os.environ or Info.version() is None:
-        return True
-    else:
-        return False
+    return "NIPYPE_NO_MATLAB" in os.environ or Info.version() is None
 
 
 class SPMCommandInputSpec(BaseInterfaceInputSpec):
diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py
index 6ebd080e61..0fff477377 100644
--- a/nipype/pipeline/plugins/condor.py
+++ b/nipype/pipeline/plugins/condor.py
@@ -55,9 +55,7 @@ def _is_pending(self, taskid):
         iflogger.setLevel(logging.getLevelName("CRITICAL"))
         result = cmd.run(ignore_exception=True)
         iflogger.setLevel(oldlevel)
-        if result.runtime.stdout.count("\n%d" % taskid):
-            return True
-        return False
+        return bool(result.runtime.stdout.count("\n%d" % taskid))
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py
index d2753a264c..cf334be051 100644
--- a/nipype/pipeline/plugins/lsf.py
+++ b/nipype/pipeline/plugins/lsf.py
@@ -54,10 +54,9 @@ def _is_pending(self, taskid):
         result = cmd.run(ignore_exception=True)
         iflogger.setLevel(oldlevel)
         # logger.debug(result.runtime.stdout)
-        if "DONE" in result.runtime.stdout or "EXIT" in result.runtime.stdout:
-            return False
-        else:
-            return True
+        return (
+            "DONE" not in result.runtime.stdout and "EXIT" not in result.runtime.stdout
+        )
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(
diff --git a/nipype/utils/misc.py b/nipype/utils/misc.py
index 95f4b408c2..dc76a433bc 100644
--- a/nipype/utils/misc.py
+++ b/nipype/utils/misc.py
@@ -87,12 +87,7 @@ def is_container(item):
         True if container
         False if not (eg string)
     """
-    if isinstance(item, str):
-        return False
-    elif hasattr(item, "__iter__"):
-        return True
-    else:
-        return False
+    return not isinstance(item, str) and hasattr(item, "__iter__")
 
 
 def container_to_string(cont):

From 4b88c39cfa9a2d3ece03e1121b612ca35b917cce Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 12:49:32 +0200
Subject: [PATCH 3/8] STY: Apply ruff/flake8-simplify rule SIM113

SIM113 Use `enumerate()` for index variable in `for` loop
---
 nipype/pipeline/engine/utils.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/nipype/pipeline/engine/utils.py b/nipype/pipeline/engine/utils.py
index 3601290cd9..9c53938cb5 100644
--- a/nipype/pipeline/engine/utils.py
+++ b/nipype/pipeline/engine/utils.py
@@ -1709,13 +1709,11 @@ def topological_sort(graph, depth_first=False):
     logger.debug("Performing depth first search")
     nodes = []
     groups = []
-    group = 0
     G = nx.Graph()
     G.add_nodes_from(graph.nodes())
     G.add_edges_from(graph.edges())
     components = nx.connected_components(G)
-    for desc in components:
-        group += 1
+    for group, desc in enumerate(components, start=1):
         indices = [nodesort.index(node) for node in desc]
         nodes.extend(
             np.array(nodesort)[np.array(indices)[np.argsort(indices)]].tolist()

From d294476c7b43deed1dbf0cdd089eb89d54283117 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 13:08:22 +0200
Subject: [PATCH 4/8] STY: Apply ruff/flake8-simplify rule SIM115

SIM115 Use a context manager for opening files
---
 nipype/interfaces/fsl/model.py               | 33 ++++++-------
 nipype/interfaces/nitime/analysis.py         | 23 ++++-----
 nipype/interfaces/slicer/generate_classes.py | 50 ++++++++++----------
 tools/checkspecs.py                          |  6 +--
 4 files changed, 50 insertions(+), 62 deletions(-)

diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
index 70ce3d7439..da2a979992 100644
--- a/nipype/interfaces/fsl/model.py
+++ b/nipype/interfaces/fsl/model.py
@@ -142,13 +142,12 @@ class Level1Design(BaseInterface):
     output_spec = Level1DesignOutputSpec
 
     def _create_ev_file(self, evfname, evinfo):
-        f = open(evfname, "w")
-        for i in evinfo:
-            if len(i) == 3:
-                f.write(f"{i[0]:f} {i[1]:f} {i[2]:f}\n")
-            else:
-                f.write("%f\n" % i[0])
-        f.close()
+        with open(evfname, "w") as f:
+            for i in evinfo:
+                if len(i) == 3:
+                    f.write(f"{i[0]:f} {i[1]:f} {i[2]:f}\n")
+                else:
+                    f.write("%f\n" % i[0])
 
     def _create_ev_files(
         self,
@@ -403,9 +402,8 @@ def _run_interface(self, runtime):
             fsf_txt += cond_txt
             fsf_txt += fsf_postscript.substitute(overwrite=1)
 
-            f = open(os.path.join(cwd, "run%d.fsf" % i), "w")
-            f.write(fsf_txt)
-            f.close()
+            with open(os.path.join(cwd, "run%d.fsf" % i), "w") as f:
+                f.write(fsf_txt)
 
         return runtime
 
@@ -946,9 +944,8 @@ def _run_interface(self, runtime):
         for i, rundir in enumerate(ensure_list(self.inputs.feat_dirs)):
             fsf_txt += fsf_dirs.substitute(runno=i + 1, rundir=os.path.abspath(rundir))
         fsf_txt += fsf_footer.substitute()
-        f = open(os.path.join(os.getcwd(), "register.fsf"), "w")
-        f.write(fsf_txt)
-        f.close()
+        with open(os.path.join(os.getcwd(), "register.fsf"), "w") as f:
+            f.write(fsf_txt)
 
         return runtime
 
@@ -1414,9 +1411,8 @@ def _run_interface(self, runtime):
 
         # write design files
         for i, name in enumerate(["design.mat", "design.con", "design.grp"]):
-            f = open(os.path.join(cwd, name), "w")
-            f.write(txt[name])
-            f.close()
+            with open(os.path.join(cwd, name), "w") as f:
+                f.write(txt[name])
 
         return runtime
 
@@ -1583,9 +1579,8 @@ def _run_interface(self, runtime):
             if ("fts" in key) and (nfcons == 0):
                 continue
             filename = key.replace("_", ".")
-            f = open(os.path.join(cwd, filename), "w")
-            f.write(val)
-            f.close()
+            with open(os.path.join(cwd, filename), "w") as f:
+                f.write(val)
 
         return runtime
 
diff --git a/nipype/interfaces/nitime/analysis.py b/nipype/interfaces/nitime/analysis.py
index 351b981077..7c936e4b03 100644
--- a/nipype/interfaces/nitime/analysis.py
+++ b/nipype/interfaces/nitime/analysis.py
@@ -142,15 +142,13 @@ def _read_csv(self):
 
         """
         # Check that input conforms to expectations:
-        first_row = open(self.inputs.in_file).readline()
+        with open(self.inputs.in_file) as f:
+            first_row = f.readline()
         if not first_row[1].isalpha():
             raise ValueError(
                 "First row of in_file should contain ROI names as strings of characters"
             )
-
-        roi_names = (
-            open(self.inputs.in_file).readline().replace('"', "").strip("\n").split(",")
-        )
+        roi_names = first_row.replace('"', "").strip("\n").split(",")
         # Transpose, so that the time is the last dimension:
         data = np.loadtxt(self.inputs.in_file, skiprows=1, delimiter=",").T
 
@@ -255,16 +253,15 @@ def _make_output_files(self):
             tmp_f = tempfile.mkstemp()[1]
             np.savetxt(tmp_f, this[0], delimiter=",")
 
-            fid = open(
+            with open(
                 fname_presuffix(self.inputs.output_csv_file, suffix="_%s" % this[1]),
                 "w+",
-            )
-            # this writes ROIs as header line
-            fid.write("," + ",".join(self.ROIs) + "\n")
-            # this writes ROI and data to a line
-            for r, line in zip(self.ROIs, open(tmp_f)):
-                fid.write(f"{r},{line}")
-            fid.close()
+            ) as fid:
+                # this writes ROIs as header line
+                fid.write("," + ",".join(self.ROIs) + "\n")
+                # this writes ROI and data to a line
+                for r, line in zip(self.ROIs, open(tmp_f)):
+                    fid.write(f"{r},{line}")
 
     def _make_output_figures(self):
         """
diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
index 8f20961086..b5a68d27a6 100644
--- a/nipype/interfaces/slicer/generate_classes.py
+++ b/nipype/interfaces/slicer/generate_classes.py
@@ -33,22 +33,22 @@ def force_to_valid_python_variable_name(old_name):
 
 def add_class_to_package(class_codes, class_names, module_name, package_dir):
     module_python_filename = os.path.join(package_dir, "%s.py" % module_name)
-    f_m = open(module_python_filename, "w")
-    f_i = open(os.path.join(package_dir, "__init__.py"), "a+")
-    f_m.write(
-        """# -*- coding: utf-8 -*-
+    with (
+        open(module_python_filename, "w") as f_m,
+        open(os.path.join(package_dir, "__init__.py"), "a+") as f_i,
+    ):
+        f_m.write(
+            """# -*- coding: utf-8 -*-
 \"\"\"Autogenerated file - DO NOT EDIT
 If you spot a bug, please report it on the mailing list and/or change the generator.\"\"\"\n\n"""
-    )
-    imports = """\
+        )
+        imports = """\
 from ..base import (CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec,
                     File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath)
 import os\n\n\n"""
-    f_m.write(imports)
-    f_m.write("\n\n".join(class_codes))
-    f_i.write("from {} import {}\n".format(module_name, ", ".join(class_names)))
-    f_m.close()
-    f_i.close()
+        f_m.write(imports)
+        f_m.write("\n\n".join(class_codes))
+        f_i.write("from {} import {}\n".format(module_name, ", ".join(class_names)))
 
 
 def crawl_code_struct(code_struct, package_dir):
@@ -70,9 +70,8 @@ def crawl_code_struct(code_struct, package_dir):
             if l2:
                 v = l2
                 subpackages.append(k.lower())
-                f_i = open(os.path.join(package_dir, "__init__.py"), "a+")
-                f_i.write("from %s import *\n" % k.lower())
-                f_i.close()
+                with open(os.path.join(package_dir, "__init__.py"), "a+") as f_i:
+                    f_i.write("from %s import *\n" % k.lower())
                 new_pkg_dir = os.path.join(package_dir, k.lower())
                 if os.path.exists(new_pkg_dir):
                     rmtree(new_pkg_dir)
@@ -88,9 +87,9 @@ def crawl_code_struct(code_struct, package_dir):
                     list(v.values()), list(v.keys()), module_name, package_dir
                 )
         if subpackages:
-            f = open(os.path.join(package_dir, "setup.py"), "w")
-            f.write(
-                """# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+            with open(os.path.join(package_dir, "setup.py"), "w") as f:
+                f.write(
+                    """# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 def configuration(parent_package='',top_path=None):
     from numpy.distutils.misc_util import Configuration
@@ -105,16 +104,15 @@ def configuration(parent_package='',top_path=None):
     from numpy.distutils.core import setup
     setup(**configuration(top_path='').todict())
 """.format(
-                    pkg_name=package_dir.split("/")[-1],
-                    sub_pks="\n    ".join(
-                        [
-                            "config.add_data_dir('%s')" % sub_pkg
-                            for sub_pkg in subpackages
-                        ]
-                    ),
+                        pkg_name=package_dir.split("/")[-1],
+                        sub_pks="\n    ".join(
+                            [
+                                "config.add_data_dir('%s')" % sub_pkg
+                                for sub_pkg in subpackages
+                            ]
+                        ),
+                    )
                 )
-            )
-            f.close()
 
 
 def generate_all_classes(
diff --git a/tools/checkspecs.py b/tools/checkspecs.py
index ea3d877484..42e6d03f88 100644
--- a/tools/checkspecs.py
+++ b/tools/checkspecs.py
@@ -124,10 +124,8 @@ def _parse_module(self, uri):
         if filename is None:
             # nothing that we could handle here.
             return ([], [])
-        f = open(filename)
-        functions, classes = self._parse_lines(f, uri)
-        f.close()
-        return functions, classes
+        with open(filename) as f:
+            return self._parse_lines(f, uri)
 
     def _parse_lines(self, linesource, module):
         """Parse lines of text for functions and classes"""

From 697297b178b60d2ee58937b7287e057347535137 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 13:10:51 +0200
Subject: [PATCH 5/8] STY: Apply ruff/flake8-simplify rule SIM118

SIM118 Use `key in dict` instead of `key in dict.keys()`
---
 nipype/interfaces/afni/model.py           |  4 ++--
 nipype/interfaces/afni/utils.py           |  2 +-
 nipype/interfaces/base/specs.py           |  2 +-
 nipype/interfaces/dipy/tests/test_base.py | 16 ++++++++--------
 nipype/interfaces/fsl/model.py            |  2 +-
 nipype/interfaces/fsl/tests/test_base.py  |  2 +-
 nipype/interfaces/spm/model.py            |  6 +++---
 nipype/utils/draw_gantt_chart.py          |  4 ++--
 8 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/nipype/interfaces/afni/model.py b/nipype/interfaces/afni/model.py
index 88c4ba716c..a227e90867 100644
--- a/nipype/interfaces/afni/model.py
+++ b/nipype/interfaces/afni/model.py
@@ -636,7 +636,7 @@ def _parse_inputs(self, skip=None):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 
@@ -722,7 +722,7 @@ class Synthesize(AFNICommand):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 
diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
index ab528f3bae..2426010ffb 100644
--- a/nipype/interfaces/afni/utils.py
+++ b/nipype/interfaces/afni/utils.py
@@ -234,7 +234,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
             m = re.search(pattern, line)
             if m:
                 d = m.groupdict()
-                outputs.trait_set(**{k: int(d[k]) for k in d.keys()})
+                outputs.trait_set(**{k: int(d[k]) for k in d})
         return outputs
 
 
diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 4255c555c4..a7f61e6889 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -383,7 +383,7 @@ def __deepcopy__(self, memo):
         dup_dict = deepcopy(self.trait_get(), memo)
         # access all keys
         for key in self.copyable_trait_names():
-            if key in self.__dict__.keys():
+            if key in self.__dict__:
                 _ = getattr(self, key)
         # clone once
         dup = self.clone_traits(memo=memo)
diff --git a/nipype/interfaces/dipy/tests/test_base.py b/nipype/interfaces/dipy/tests/test_base.py
index 896d477ed6..d2d81ec005 100644
--- a/nipype/interfaces/dipy/tests/test_base.py
+++ b/nipype/interfaces/dipy/tests/test_base.py
@@ -109,10 +109,10 @@ def test_create_interface_specs():
     assert new_interface.__name__ == "MyInterface"
     current_params = new_interface().get()
     assert len(current_params) == 4
-    assert "params1" in current_params.keys()
-    assert "params2_files" in current_params.keys()
-    assert "params3" in current_params.keys()
-    assert "out_params" in current_params.keys()
+    assert "params1" in current_params
+    assert "params2_files" in current_params
+    assert "params3" in current_params
+    assert "out_params" in current_params
 
 
 @pytest.mark.skipif(
@@ -184,10 +184,10 @@ def run(self, in_files, param1=1, out_dir="", out_ref="out1.txt"):
     params_in = new_specs().inputs.get()
     params_out = new_specs()._outputs().get()
     assert len(params_in) == 4
-    assert "in_files" in params_in.keys()
-    assert "param1" in params_in.keys()
-    assert "out_dir" in params_out.keys()
-    assert "out_ref" in params_out.keys()
+    assert "in_files" in params_in
+    assert "param1" in params_in
+    assert "out_dir" in params_out
+    assert "out_ref" in params_out
 
     with pytest.raises(ValueError):
         new_specs().run()
diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py
index da2a979992..82601f1d72 100644
--- a/nipype/interfaces/fsl/model.py
+++ b/nipype/interfaces/fsl/model.py
@@ -318,7 +318,7 @@ def _create_ev_files(
 
                     for fconidx in ftest_idx:
                         fval = 0
-                        if con[0] in con_map.keys() and fconidx in con_map[con[0]]:
+                        if con[0] in con_map and fconidx in con_map[con[0]]:
                             fval = 1
                         ev_txt += contrast_ftest_element.substitute(
                             cnum=ftest_idx.index(fconidx) + 1,
diff --git a/nipype/interfaces/fsl/tests/test_base.py b/nipype/interfaces/fsl/tests/test_base.py
index c1cc56fc36..d87bc73d70 100644
--- a/nipype/interfaces/fsl/tests/test_base.py
+++ b/nipype/interfaces/fsl/tests/test_base.py
@@ -79,7 +79,7 @@ def test_gen_fname(args, desired_name):
     cmd = fsl.FSLCommand(command="junk", output_type="NIFTI_GZ")
     pth = os.getcwd()
     fname = cmd._gen_fname("foo.nii.gz", **args)
-    if "dir" in desired_name.keys():
+    if "dir" in desired_name:
         desired = os.path.join(desired_name["dir"], desired_name["file"])
     else:
         desired = os.path.join(pth, desired_name["file"])
diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py
index 62bf4447ea..8bc38a1f02 100644
--- a/nipype/interfaces/spm/model.py
+++ b/nipype/interfaces/spm/model.py
@@ -322,8 +322,8 @@ def _list_outputs(self):
 
         betas = [vbeta.fname[0] for vbeta in spm["SPM"][0, 0].Vbeta[0]]
         if (
-            "Bayesian" in self.inputs.estimation_method.keys()
-            or "Bayesian2" in self.inputs.estimation_method.keys()
+            "Bayesian" in self.inputs.estimation_method
+            or "Bayesian2" in self.inputs.estimation_method
         ):
             outputs["labels"] = os.path.join(pth, f"labels.{outtype}")
             outputs["SDerror"] = glob(os.path.join(pth, "Sess*_SDerror*"))
@@ -332,7 +332,7 @@ def _list_outputs(self):
                 outputs["Cbetas"] = [os.path.join(pth, f"C{beta}") for beta in betas]
                 outputs["SDbetas"] = [os.path.join(pth, f"SD{beta}") for beta in betas]
 
-        if "Classical" in self.inputs.estimation_method.keys():
+        if "Classical" in self.inputs.estimation_method:
             outputs["residual_image"] = os.path.join(pth, f"ResMS.{outtype}")
             outputs["RPVimage"] = os.path.join(pth, f"RPV.{outtype}")
             if self.inputs.write_residuals:
diff --git a/nipype/utils/draw_gantt_chart.py b/nipype/utils/draw_gantt_chart.py
index 79af8262ac..ef4ec58ec2 100644
--- a/nipype/utils/draw_gantt_chart.py
+++ b/nipype/utils/draw_gantt_chart.py
@@ -114,9 +114,9 @@ def _convert_string_to_datetime(datestring):
 
     date_object_node_list: list = list()
     for n in nodes_list:
-        if "start" in n.keys():
+        if "start" in n:
             n["start"] = _convert_string_to_datetime(n["start"])
-        if "finish" in n.keys():
+        if "finish" in n:
             n["finish"] = _convert_string_to_datetime(n["finish"])
         date_object_node_list.append(n)
 

From d557f71d3de73650f3eecdfd67a6ebbc7d401a6d Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 13:13:07 +0200
Subject: [PATCH 6/8] STY: Apply ruff/flake8-simplify rule SIM201

SIM201 Use `... != ...` instead of `not ... == ...`
---
 nipype/algorithms/misc.py           |  8 ++++----
 nipype/interfaces/cmtk/cmtk.py      | 12 ++++++------
 nipype/interfaces/cmtk/convert.py   | 14 +++++++-------
 nipype/interfaces/cmtk/nx.py        |  8 ++++----
 nipype/interfaces/dcmstack.py       |  2 +-
 nipype/interfaces/io.py             |  4 ++--
 nipype/interfaces/mne/base.py       |  2 +-
 nipype/interfaces/mrtrix/convert.py |  2 +-
 8 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py
index b7bbd3ce21..8d2e406793 100644
--- a/nipype/algorithms/misc.py
+++ b/nipype/algorithms/misc.py
@@ -684,7 +684,7 @@ def _run_interface(self, runtime):
 
         output_array = merge_csvs(self.inputs.in_files)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
 
         out_file = op.abspath(name + ext)
@@ -725,7 +725,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file
@@ -771,7 +771,7 @@ class AddCSVColumn(BaseInterface):
     def _run_interface(self, runtime):
         in_file = open(self.inputs.in_file)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
 
@@ -791,7 +791,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file
diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py
index baf1bccaae..c620941c3d 100644
--- a/nipype/interfaces/cmtk/cmtk.py
+++ b/nipype/interfaces/cmtk/cmtk.py
@@ -77,7 +77,7 @@ def get_rois_crossed(pointsmm, roiData, voxelSize):
         x = int(pointsmm[j, 0] / float(voxelSize[0]))
         y = int(pointsmm[j, 1] / float(voxelSize[1]))
         z = int(pointsmm[j, 2] / float(voxelSize[2]))
-        if not roiData[x, y, z] == 0:
+        if roiData[x, y, z] != 0:
             rois_crossed.append(roiData[x, y, z])
     rois_crossed = list(
         dict.fromkeys(rois_crossed).keys()
@@ -91,7 +91,7 @@ def get_connectivity_matrix(n_rois, list_of_roi_crossed_lists):
         for idx_i, roi_i in enumerate(rois_crossed):
             for idx_j, roi_j in enumerate(rois_crossed):
                 if idx_i > idx_j:
-                    if not roi_i == roi_j:
+                    if roi_i != roi_j:
                         connectivity_matrix[roi_i - 1, roi_j - 1] += 1
     connectivity_matrix = connectivity_matrix + connectivity_matrix.T
     return connectivity_matrix
@@ -371,7 +371,7 @@ def cmat(
             di["fiber_length_mean"] = 0
             di["fiber_length_median"] = 0
             di["fiber_length_std"] = 0
-        if not u == v:  # Fix for self loop problem
+        if u != v:  # Fix for self loop problem
             G.add_edge(u, v, **di)
             if "fiblist" in d:
                 numfib.add_edge(u, v, weight=di["number_of_fibers"])
@@ -400,7 +400,7 @@ def cmat(
             pickle.dump(I, f, pickle.HIGHEST_PROTOCOL)
 
     path, name, ext = split_filename(matrix_mat_name)
-    if not ext == ".mat":
+    if ext != ".mat":
         ext = ".mat"
         matrix_mat_name = matrix_mat_name + ext
 
@@ -608,7 +608,7 @@ def _run_interface(self, runtime):
 
         matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file)
         path, name, ext = split_filename(matrix_mat_file)
-        if not ext == ".mat":
+        if ext != ".mat":
             ext = ".mat"
             matrix_mat_file = matrix_mat_file + ext
 
@@ -673,7 +673,7 @@ def _list_outputs(self):
 
         matrix_mat_file = op.abspath(self.inputs.out_matrix_mat_file)
         path, name, ext = split_filename(matrix_mat_file)
-        if not ext == ".mat":
+        if ext != ".mat":
             ext = ".mat"
             matrix_mat_file = matrix_mat_file + ext
 
diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py
index 72d105b715..4f55242a94 100644
--- a/nipype/interfaces/cmtk/convert.py
+++ b/nipype/interfaces/cmtk/convert.py
@@ -194,17 +194,17 @@ 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 not string.find(data_name, "lengths") == -1:
+                if string.find(data_name, 'lengths') != -1:
                     cda.dtype = "FinalFiberLengthArray"
-                if not string.find(data_name, "endpoints") == -1:
+                if string.find(data_name, 'endpoints') != -1:
                     cda.dtype = "FiberEndpoints"
-                if not string.find(data_name, "labels") == -1:
+                if string.find(data_name, 'labels') != -1:
                     cda.dtype = "FinalFiberLabels"
                 a.add_connectome_data(cda)
 
         a.print_summary()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         cf.save_to_cff(a, op.abspath(name + ext))
 
@@ -213,7 +213,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs
@@ -281,7 +281,7 @@ def _run_interface(self, runtime):
         metadata.set_email("My Email")
 
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         cf.save_to_cff(newcon, op.abspath(name + ext))
 
@@ -290,7 +290,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self._outputs().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".cff":
+        if ext != '.cff':
             ext = ".cff"
         outputs["connectome_file"] = op.abspath(name + ext)
         return outputs
diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
index 7a9e2f9d8a..164009541e 100644
--- a/nipype/interfaces/cmtk/nx.py
+++ b/nipype/interfaces/cmtk/nx.py
@@ -167,7 +167,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
             data = ntwk.edge[edge[0]][edge[1]]
             if ntwk.edge[edge[0]][edge[1]]["count"] >= count_to_keep_edge:
                 for key in list(data.keys()):
-                    if not key == "count":
+                    if key != "count":
                         data[key] = data[key] / len(in_files)
                 ntwk.edge[edge[0]][edge[1]] = data
                 avg_ntwk.add_edge(edge[0], edge[1], **data)
@@ -184,7 +184,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
         for edge in avg_edges:
             data = avg_ntwk.edge[edge[0]][edge[1]]
             for key in list(data.keys()):
-                if not key == "count":
+                if key != "count":
                     edge_dict[key] = np.zeros(
                         (avg_ntwk.number_of_nodes(), avg_ntwk.number_of_nodes())
                     )
@@ -342,7 +342,7 @@ def add_node_data(node_array, ntwk):
     node_ntwk = nx.Graph()
     newdata = {}
     for idx, data in ntwk.nodes(data=True):
-        if not int(idx) == 0:
+        if int(idx) != 0:
             newdata["value"] = node_array[int(idx) - 1]
             data.update(newdata)
             node_ntwk.add_node(int(idx), **data)
@@ -354,7 +354,7 @@ def add_edge_data(edge_array, ntwk, above=0, below=0):
     data = {}
     for x, row in enumerate(edge_array):
         for y in range(np.max(np.shape(edge_array[x]))):
-            if not edge_array[x, y] == 0:
+            if edge_array[x, y] != 0:
                 data["value"] = edge_array[x, y]
                 if data["value"] <= below or data["value"] >= above:
                     if edge_ntwk.has_edge(x + 1, y + 1):
diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py
index b76255ab84..8e9b8feb42 100644
--- a/nipype/interfaces/dcmstack.py
+++ b/nipype/interfaces/dcmstack.py
@@ -152,7 +152,7 @@ def _run_interface(self, runtime):
         meta_filter = dcmstack.make_key_regex_filter(exclude_regexes, include_regexes)
         stack = dcmstack.DicomStack(meta_filter=meta_filter)
         for src_path in src_paths:
-            if not imghdr.what(src_path) == "gif":
+            if imghdr.what(src_path) != "gif":
                 src_dcm = pydicom.dcmread(src_path, force=self.inputs.force_read)
                 stack.add_dcm(src_dcm)
         nii = stack.to_nifti(embed_meta=True)
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index 34dbc1b461..606122021e 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -1053,9 +1053,9 @@ def s3tolocal(self, s3path, bkt):
         local_directory = str(self.inputs.local_directory)
         bucket_path = str(self.inputs.bucket_path)
         template = str(self.inputs.template)
-        if not os.path.basename(local_directory) == "":
+        if os.path.basename(local_directory) != "":
             local_directory += "/"
-        if not os.path.basename(bucket_path) == "":
+        if os.path.basename(bucket_path) != "":
             bucket_path += "/"
         if template[0] == "/":
             template = template[1:]
diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py
index 6e9b766305..c8b1f6012d 100644
--- a/nipype/interfaces/mne/base.py
+++ b/nipype/interfaces/mne/base.py
@@ -138,7 +138,7 @@ def _list_outputs(self):
                     else:
                         raise TypeError
                     outputs[k] = out_files
-                    if not k.rfind("surface") == -1:
+                    if k.rfind("surface") != -1:
                         mesh_paths.append(out_files)
         outputs["mesh_files"] = mesh_paths
         return outputs
diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py
index 8a0e14d3eb..f47bc0eff2 100644
--- a/nipype/interfaces/mrtrix/convert.py
+++ b/nipype/interfaces/mrtrix/convert.py
@@ -116,7 +116,7 @@ def track_gen(track_points):
             pts_str = fileobj.read(n_pts * bytesize)
             nan_str = fileobj.read(bytesize)
             if len(pts_str) < (n_pts * bytesize):
-                if not n_streams == stream_count:
+                if n_streams != stream_count:
                     raise nb.trackvis.HeaderError(
                         f"Expecting {stream_count} points, found only {n_streams}"
                     )

From 5f200ce21080dd8af9edab0d03e8be80b1a4c3ea Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 22 Sep 2024 13:14:28 +0200
Subject: [PATCH 7/8] STY: Apply ruff/flake8-simplify rule SIM401

SIM401 Use `.get()` instead of an `if` block
---
 nipype/interfaces/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index 606122021e..1c424825db 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -2938,7 +2938,7 @@ def __init__(self, infields=None, **kwargs):
         undefined_traits = {}
         for key in self._infields:
             self.inputs.add_trait(key, traits.Any)
-            undefined_traits[key] = kwargs[key] if key in kwargs else Undefined
+            undefined_traits[key] = kwargs.get(key, Undefined)
 
         self.inputs.trait_set(trait_change_notify=False, **undefined_traits)
 

From d040d844c279db0abb9d63c4ab771c8252d3f2f2 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos Orfanos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 6 Oct 2024 16:24:31 +0200
Subject: [PATCH 8/8] STY: Further simplification

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/afni/utils.py              | 2 +-
 nipype/interfaces/cmtk/convert.py            | 6 +++---
 nipype/interfaces/cmtk/nx.py                 | 4 ++--
 nipype/interfaces/slicer/generate_classes.py | 6 ++----
 4 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py
index 2426010ffb..95d7985d68 100644
--- a/nipype/interfaces/afni/utils.py
+++ b/nipype/interfaces/afni/utils.py
@@ -234,7 +234,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
             m = re.search(pattern, line)
             if m:
                 d = m.groupdict()
-                outputs.trait_set(**{k: int(d[k]) for k in d})
+                outputs.trait_set(**{k: int(v) for k, v in d.items()})
         return outputs
 
 
diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py
index 4f55242a94..b2e21c3bb9 100644
--- a/nipype/interfaces/cmtk/convert.py
+++ b/nipype/interfaces/cmtk/convert.py
@@ -194,11 +194,11 @@ 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 string.find(data_name, 'lengths') != -1:
+                if 'lengths' in data_name:
                     cda.dtype = "FinalFiberLengthArray"
-                if string.find(data_name, 'endpoints') != -1:
+                if 'endpoints' in data_name:
                     cda.dtype = "FiberEndpoints"
-                if string.find(data_name, 'labels') != -1:
+                if 'labels' in data_name:
                     cda.dtype = "FinalFiberLabels"
                 a.add_connectome_data(cda)
 
diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py
index 164009541e..53706389aa 100644
--- a/nipype/interfaces/cmtk/nx.py
+++ b/nipype/interfaces/cmtk/nx.py
@@ -166,7 +166,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
         for edge in edges:
             data = ntwk.edge[edge[0]][edge[1]]
             if ntwk.edge[edge[0]][edge[1]]["count"] >= count_to_keep_edge:
-                for key in list(data.keys()):
+                for key in data:
                     if key != "count":
                         data[key] = data[key] / len(in_files)
                 ntwk.edge[edge[0]][edge[1]] = data
@@ -183,7 +183,7 @@ def average_networks(in_files, ntwk_res_file, group_id):
         avg_edges = avg_ntwk.edges()
         for edge in avg_edges:
             data = avg_ntwk.edge[edge[0]][edge[1]]
-            for key in list(data.keys()):
+            for key in data:
                 if key != "count":
                     edge_dict[key] = np.zeros(
                         (avg_ntwk.number_of_nodes(), avg_ntwk.number_of_nodes())
diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py
index b5a68d27a6..a36dd6b55a 100644
--- a/nipype/interfaces/slicer/generate_classes.py
+++ b/nipype/interfaces/slicer/generate_classes.py
@@ -33,10 +33,7 @@ def force_to_valid_python_variable_name(old_name):
 
 def add_class_to_package(class_codes, class_names, module_name, package_dir):
     module_python_filename = os.path.join(package_dir, "%s.py" % module_name)
-    with (
-        open(module_python_filename, "w") as f_m,
-        open(os.path.join(package_dir, "__init__.py"), "a+") as f_i,
-    ):
+    with open(module_python_filename, "w") as f_m:
         f_m.write(
             """# -*- coding: utf-8 -*-
 \"\"\"Autogenerated file - DO NOT EDIT
@@ -48,6 +45,7 @@ def add_class_to_package(class_codes, class_names, module_name, package_dir):
 import os\n\n\n"""
         f_m.write(imports)
         f_m.write("\n\n".join(class_codes))
+    with open(os.path.join(package_dir, "__init__.py"), "a+") as f_i:
         f_i.write("from {} import {}\n".format(module_name, ", ".join(class_names)))