Merge pull request #3671 from DimitriPapadopoulos/B

STY: Apply ruff/flake8-bugbear rules (B)

nipype/algorithms/tests/test_modelgen.py

@@ -122,7 +122,7 @@ def test_modelgen_spm_concat(tmpdir):
     s = SpecifySPMModel()
     s.inputs.input_units = "secs"
     s.inputs.concatenate_runs = True
-    setattr(s.inputs, "output_units", "secs")
+    s.inputs.output_units = "secs"
     assert s.inputs.output_units == "secs"
     s.inputs.functional_runs = [filename1, filename2]
     s.inputs.time_repetition = 6
@@ -147,7 +147,7 @@ def test_modelgen_spm_concat(tmpdir):
     )
 
     # Test case of scans as output units instead of seconds
-    setattr(s.inputs, "output_units", "scans")
+    s.inputs.output_units = "scans"
     assert s.inputs.output_units == "scans"
     s.inputs.subject_info = deepcopy(info)
     res = s.run()

nipype/interfaces/afni/utils.py

@@ -3244,11 +3244,11 @@ def _run_interface(self, runtime):
             for line in runtime.stdout.split("\n")
             if line.strip().startswith("GCOR = ")
         ][-1]
-        setattr(self, "_gcor", float(gcor_line[len("GCOR = ") :]))
+        self._gcor = float(gcor_line[len("GCOR = ") :])
         return runtime
 
     def _list_outputs(self):
-        return {"out": getattr(self, "_gcor")}
+        return {"out": self._gcor}
 
 
 class AxializeInputSpec(AFNICommandInputSpec):

nipype/interfaces/ants/utils.py

@@ -536,7 +536,7 @@ def _format_arg(self, opt, spec, val):
         return super()._format_arg(opt, spec, val)
 
     def _list_outputs(self):
-        return getattr(self, "_output")
+        return self._output
 
 
 class AverageAffineTransformInputSpec(ANTSCommandInputSpec):

nipype/interfaces/base/support.py

@@ -99,7 +99,7 @@ def __exit__(self, exc_type, exc_value, exc_tb):
                 traceback.format_exception(exc_type, exc_value, exc_tb)
             )
             # Gather up the exception arguments and append nipype info.
-            exc_args = exc_value.args if getattr(exc_value, "args") else tuple()
+            exc_args = exc_value.args or ()
             exc_args += (
                 f"An exception of type {exc_type.__name__} occurred while "
                 f"running interface {self._runtime.interface}.",

nipype/interfaces/elastix/utils.py

@@ -164,18 +164,18 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs["output_file"] = getattr(self, "_out_file")
+        outputs["output_file"] = self._out_file
         return outputs
 
     def _get_outfile(self):
-        val = getattr(self, "_out_file")
+        val = self._out_file
         if val is not None and val != "":
             return val
 
         if isdefined(self.inputs.output_file):
-            setattr(self, "_out_file", self.inputs.output_file)
+            self._out_file = self.inputs.output_file
             return self.inputs.output_file
 
         out_file = op.abspath(op.basename(self.inputs.transform_file))
-        setattr(self, "_out_file", out_file)
+        self._out_file = out_file
         return out_file

nipype/interfaces/fsl/utils.py

@@ -929,7 +929,7 @@ def _run_interface(self, runtime):
                 float(r) for r in out["translations"].strip().split(" ")
             ]
 
-        setattr(self, "_results", outputs)
+        self._results = outputs
         return runtime
 
     def _list_outputs(self):
@@ -2513,8 +2513,8 @@ def _format_arg(self, name, trait_spec, value):
 
     def _parse_inputs(self, skip=None):
         fname, ext = op.splitext(self.inputs.in_coords)
-        setattr(self, "_in_file", fname)
-        setattr(self, "_outformat", ext[1:])
+        self._in_file = fname
+        self._outformat = ext[1:]
         first_args = super()._parse_inputs(skip=["in_coords", "out_file"])
 
         second_args = fname + ".txt"
@@ -2580,11 +2580,11 @@ def _coords_to_trk(self, points, out_file):
 
     def _overload_extension(self, value, name):
         if name == "out_file":
-            return "{}.{}".format(value, getattr(self, "_outformat"))
+            return "{}.{}".format(value, self._outformat)
 
     def _run_interface(self, runtime):
-        fname = getattr(self, "_in_file")
-        outformat = getattr(self, "_outformat")
+        fname = self._in_file
+        outformat = self._outformat
         tmpfile = None
 
         if outformat == "vtk":

nipype/interfaces/spm/model.py

@@ -849,30 +849,22 @@ def _make_matlab_command(self, _):
 
     def aggregate_outputs(self, runtime=None):
         outputs = self._outputs()
-        setattr(outputs, "thresholded_map", self._gen_thresholded_map_filename())
-        setattr(outputs, "pre_topo_fdr_map", self._gen_pre_topo_map_filename())
+        outputs.thresholded_map = self._gen_thresholded_map_filename()
+        outputs.pre_topo_fdr_map = self._gen_pre_topo_map_filename()
         for line in runtime.stdout.split("\n"):
             if line.startswith("activation_forced = "):
-                setattr(
-                    outputs,
-                    "activation_forced",
-                    line[len("activation_forced = ") :].strip() == "1",
+                outputs.activation_forced = (
+                    line[len("activation_forced = ") :].strip() == "1"
                 )
             elif line.startswith("n_clusters = "):
-                setattr(
-                    outputs, "n_clusters", int(line[len("n_clusters = ") :].strip())
-                )
+                outputs.n_clusters = int(line[len("n_clusters = ") :].strip())
             elif line.startswith("pre_topo_n_clusters = "):
-                setattr(
-                    outputs,
-                    "pre_topo_n_clusters",
-                    int(line[len("pre_topo_n_clusters = ") :].strip()),
+                outputs.pre_topo_n_clusters = int(
+                    line[len("pre_topo_n_clusters = ") :].strip()
                 )
             elif line.startswith("cluster_forming_thr = "):
-                setattr(
-                    outputs,
-                    "cluster_forming_thr",
-                    float(line[len("cluster_forming_thr = ") :].strip()),
+                outputs.cluster_forming_thr = float(
+                    line[len("cluster_forming_thr = ") :].strip()
                 )
         return outputs
 

nipype/interfaces/tests/test_io.py

@@ -517,7 +517,7 @@ def test_datasink_copydir_2(_temp_analyze_files, tmpdir):
         base_directory=tmpdir.mkdir("basedir").strpath, parameterization=False
     )
     ds.inputs.remove_dest_dir = True
-    setattr(ds.inputs, "outdir", pth)
+    ds.inputs.outdir = pth
     ds.run()
     sep = os.path.sep
     assert not tmpdir.join("basedir", pth.split(sep)[-1], fname).check()

nipype/interfaces/utility/wrappers.py

@@ -72,7 +72,7 @@ def __init__(
 
         super().__init__(**inputs)
         if function:
-            if hasattr(function, "__call__"):
+            if callable(function):
                 try:
                     self.inputs.function_str = getsource(function)
                 except OSError:
@@ -101,7 +101,7 @@ def __init__(
 
     def _set_function_string(self, obj, name, old, new):
         if name == "function_str":
-            if hasattr(new, "__call__"):
+            if callable(new):
                 function_source = getsource(new)
                 fninfo = new.__code__
             elif isinstance(new, (str, bytes)):

nipype/pipeline/engine/tests/test_engine.py

@@ -25,7 +25,7 @@
 def test_1mod(iterables, expected):
     pipe = pe.Workflow(name="pipe")
     mod1 = pe.Node(interface=EngineTestInterface(), name="mod1")
-    setattr(mod1, "iterables", iterables["1"])
+    mod1.iterables = iterables["1"]
     pipe.add_nodes([mod1])
     pipe._flatgraph = pipe._create_flat_graph()
     pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph))
@@ -49,7 +49,7 @@ def test_2mods(iterables, expected):
     mod1 = pe.Node(interface=EngineTestInterface(), name="mod1")
     mod2 = pe.Node(interface=EngineTestInterface(), name="mod2")
     for nr in ["1", "2"]:
-        setattr(eval("mod" + nr), "iterables", iterables[nr])
+        eval("mod" + nr).iterables = iterables[nr]
     pipe.connect([(mod1, mod2, [("output1", "input2")])])
     pipe._flatgraph = pipe._create_flat_graph()
     pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph))
@@ -87,7 +87,7 @@ def test_3mods(iterables, expected, connect):
     mod2 = pe.Node(interface=EngineTestInterface(), name="mod2")
     mod3 = pe.Node(interface=EngineTestInterface(), name="mod3")
     for nr in ["1", "2", "3"]:
-        setattr(eval("mod" + nr), "iterables", iterables[nr])
+        eval("mod" + nr).iterables = iterables[nr]
     if connect == ("1-2", "2-3"):
         pipe.connect(
             [

nipype/pipeline/engine/utils.py

@@ -852,7 +852,7 @@ def _identity_nodes(graph, include_iterables):
         node
         for node in nx.topological_sort(graph)
         if isinstance(node.interface, IdentityInterface)
-        and (include_iterables or getattr(node, "iterables") is None)
+        and (include_iterables or node.iterables is None)
     ]
 
 

nipype/pipeline/plugins/debug.py

@@ -15,7 +15,7 @@ def __init__(self, plugin_args=None):
         if (
             plugin_args
             and "callable" in plugin_args
-            and hasattr(plugin_args["callable"], "__call__")
+            and callable(plugin_args["callable"])
         ):
             self._callable = plugin_args["callable"]
         else:

nipype/utils/config.py

@@ -353,7 +353,7 @@ def _mock():
 
             # Older versions of xvfbwrapper used vdisplay_num
             if not hasattr(self._display, "new_display"):
-                setattr(self._display, "new_display", self._display.vdisplay_num)
+                self._display.new_display = self._display.vdisplay_num
             return self.get_display()
 
     def stop_display(self):

nipype/utils/profiler.py

@@ -174,9 +174,9 @@ def log_nodes_cb(node, status):
     status_dict = {
         "name": node.name,
         "id": node._id,
-        "start": getattr(node.result.runtime, "startTime"),
-        "finish": getattr(node.result.runtime, "endTime"),
-        "duration": getattr(node.result.runtime, "duration"),
+        "start": node.result.runtime.startTime,
+        "finish": node.result.runtime.endTime,
+        "duration": node.result.runtime.duration,
         "runtime_threads": getattr(node.result.runtime, "cpu_percent", "N/A"),
         "runtime_memory_gb": getattr(node.result.runtime, "mem_peak_gb", "N/A"),
         "estimated_memory_gb": node.mem_gb,

nipype/utils/provenance.py

@@ -300,7 +300,7 @@ def write_provenance(results, filename="provenance", format="all"):
         import traceback
 
         err_msg = traceback.format_exc()
-        if getattr(e, "args"):
+        if e.args:
             err_msg += "\n\nException arguments:\n" + ", ".join(
                 ['"%s"' % arg for arg in e.args]
             )

tools/checkspecs.py

@@ -287,7 +287,7 @@ def test_specs(self, uri):
                         continue
                     parent_metadata = []
                     if "parent" in trait.__dict__:
-                        parent_metadata = list(getattr(trait, "parent").__dict__.keys())
+                        parent_metadata = list(trait.parent.__dict__)
                     if (
                         key
                         not in allowed_keys
@@ -375,7 +375,7 @@ def test_specs(self, uri):
                         continue
                     parent_metadata = []
                     if "parent" in trait.__dict__:
-                        parent_metadata = list(getattr(trait, "parent").__dict__.keys())
+                        parent_metadata = list(trait.parent.__dict__)
                     if (
                         key
                         not in allowed_keys