Merge pull request populse#342 from DimitriPapadopoulos/codespell

Fix typos found by codespell

capsul/__main__.py

@@ -157,8 +157,8 @@ def set_executable_cmd_args(executable, args):
     from soma.qt_gui.qt_backend import Qt
     from capsul.qt_gui.widgets import PipelineDeveloperView
 
-    # WARNING: QApplication should always be instanciated before aims PluginLoader
-    # has been called otherwise another QCoreApplication is instanciated
+    # WARNING: QApplication should always be instantiated before aims PluginLoader
+    # has been called otherwise another QCoreApplication is instantiated
     # that can conflict with the QApplication created.
     Qt.QApplication.setAttribute(Qt.Qt.AA_ShareOpenGLContexts, True)
     app = Qt.QApplication(sys.argv)

capsul/dataset.py

@@ -711,7 +711,7 @@ def __getitem__(self, key):
             super().__setattr__("_item", key)
         else:
             raise Exception(
-                "invalid metdata modification, attribute too deep: "
+                "invalid metadata modification, attribute too deep: "
                 f"{self._parameter}, {self._item}, {key}"
             )
         return self
@@ -733,23 +733,23 @@ def value(self):
     def __setitem__(self, key, value):
         if isinstance(value, MetadataModification):
             if self._item:
-                raise Exception(f"invalid metdata copy, unexpected item: {self._item}")
+                raise Exception(f"invalid metadata copy, unexpected item: {self._item}")
             if not self._parameter:
                 if not value._parameter:
-                    raise Exception("invalid metdata copy, no source parameter")
+                    raise Exception("invalid metadata copy, no source parameter")
                 if value._item:
                     raise Exception(
-                        "invalid metdata copy, source item {value._item} cannot be copied to a whole parameter"
+                        "invalid metadata copy, source item {value._item} cannot be copied to a whole parameter"
                     )
                 self._copy_all(
                     dest_parameters=key,
                     source_parameters=value._parameter,
                 )
             else:
                 if not value._parameter:
-                    raise Exception("invalid metdata copy, no source parameter")
+                    raise Exception("invalid metadata copy, no source parameter")
                 if not value._item:
-                    raise Exception("invalid metdata copy, no source item")
+                    raise Exception("invalid metadata copy, no source item")
                 self._copy_item(
                     parameters=self._parameter,
                     items=key,
@@ -758,10 +758,10 @@ def __setitem__(self, key, value):
                 )
         else:
             if not self._parameter:
-                raise Exception("invalid metdata modification, no parameter")
+                raise Exception("invalid metadata modification, no parameter")
             if self._item:
                 raise Exception(
-                    f"invalid metdata modification, unexpected item: {self._item}"
+                    f"invalid metadata modification, unexpected item: {self._item}"
                 )
             self._set(
                 parameters=self._parameter,
@@ -834,9 +834,9 @@ def _items(self, items):
 
     def unused(self, value=True):
         if not self._parameter:
-            raise Exception("invalid metdata modification, no parameter")
+            raise Exception("invalid metadata modification, no parameter")
         if not self._item:
-            raise Exception("invalid metdata modification, no item")
+            raise Exception("invalid metadata modification, no item")
         if self.executable.activated:
             for parameter in self._parameters(self._parameter):
                 for item in self._items(self._item):
@@ -849,9 +849,9 @@ def used(self, value=True):
 
     def append(self, value, sep="_"):
         if not self._parameter:
-            raise Exception("invalid metdata modification, no parameter")
+            raise Exception("invalid metadata modification, no parameter")
         if not self._item:
-            raise Exception("invalid metdata modification, no item")
+            raise Exception("invalid metadata modification, no item")
         if self.executable.activated:
             if isinstance(value, MetadataModification):
                 value = value.value()
@@ -871,9 +871,9 @@ def append(self, value, sep="_"):
 
     def prepend(self, value, sep="_"):
         if not self._parameter:
-            raise Exception("invalid metdata modification, no parameter")
+            raise Exception("invalid metadata modification, no parameter")
         if not self._item:
-            raise Exception("invalid metdata modification, no item")
+            raise Exception("invalid metadata modification, no item")
         if isinstance(value, MetadataModification):
             value = value.value()
         if self.executable.activated:
@@ -1337,7 +1337,7 @@ def path_for_parameters(self, executable, parameters=None):
             # print("!-" * 40)
             parameters_equivalence = find_parameters_equivalence(executable)
             for parameter in parameters:
-                # Ignore path generation for parameters that are equivelent to another one
+                # Ignore path generation for parameters that are equivalent to another one
                 equivalent = parameters_equivalence.get(executable, {}).get(parameter)
                 if equivalent and equivalent != parameter:
                     # print(f"!skip! {parameter} => {equivalent}")

capsul/engine/__init__.py

@@ -413,21 +413,21 @@ def run(self, executable, timeout=None, print_report=False, debug=False, **kwarg
     def prepare_pipeline_for_retry(self, pipeline, execution_id):
         """Modify a pipeline given a previous execution to select only the nodes that
         weren't successful. Running the pipeline after this step will retry the
-        execution of faile jobs. This method adds (or modify if it exists) an unselectd
-        pipeline step called "succesfully_executed" containing all nodes that were
-        succesfully executed.
-        """ ""
+        execution of failed jobs. This method adds (or modifies if it exists) an
+        unselected pipeline step called "successfully_executed" containing all nodes
+        that were successfully executed.
+        """
         successful_nodes = []
         for path in self.database.successful_node_paths(self.engine_id, execution_id):
             successful_nodes.append(pipeline.node_from_path(path).name)
         step_field = None
         if pipeline.field("pipeline_steps"):
-            step_field = pipeline.pipeline_steps.fields("succesfully_executed")
+            step_field = pipeline.pipeline_steps.fields("successfully_executed")
         if step_field is None:
-            pipeline.add_pipeline_step("succesfully_executed", successful_nodes, False)
+            pipeline.add_pipeline_step("successfully_executed", successful_nodes, False)
         else:
             step_field.nodes = successful_nodes
-            setattr(pipeline.pipeline_steps, "succesfully_executed", False)
+            setattr(pipeline.pipeline_steps, "successfully_executed", False)
 
 
 class Workers(Controller):

capsul/format.py

@@ -50,7 +50,7 @@ def __init__(self):
 
     def __setitem__(self, label, value):
         """
-        Adds a new fromat. Label is the format name that is displayed to
+        Adds a new format. Label is the format name that is displayed to
         the user. It must be unique among all format labels independently
         of character case. value is a list of extensions or a format object.
         """
@@ -72,7 +72,7 @@ def __setitem__(self, label, value):
     def __getitem__(self, label_or_key):
         """
         Return a Format instance from its label. Research is case independent.
-        A KeyError is raised if the fomat is not found.
+        A KeyError is raised if the format is not found.
         """
         return self._formats[label_or_key.lower()]
 
@@ -537,11 +537,11 @@ def global_formats():
                         "gz compressed SPM image",
                         "SPM image",
                     ],
-                    "aims partialy writable volume formats": [
+                    "aims partially writable volume formats": [
                         "GIS image",
                         "NIFTI-1 image",
                     ],
-                    "aims partialy readable volume formats": [
+                    "aims partially readable volume formats": [
                         "GIS image",
                         "NIFTI-1 image",
                         "TIFF image",

capsul/in_context/__init__.py

@@ -2,7 +2,7 @@
 """
 The ``in_context`` module provides functions to call some external software from Capsul processes (SPM, FSL, etc.). The main functions perform calls to the software in a similar way as ``subprocess`` functions (:class:`~subprocess.Popen`, :func:`~subprocess.call`, :func:`~subprocess.check_call` and :func:`subprocess.check_output`).
 The notable difference is that they use an :class:`~capsul.execution_context.ExecutionContext` object instance to get configuration from.
-These functions are only run from within the :meth:`~capsul.process.Process.execute` method of a Process, which gets the context as a paremeter::
+These functions are only run from within the :meth:`~capsul.process.Process.execute` method of a Process, which gets the context as a parameter::
 
     from capsul.api import Process
     from capsul.in_context.fsl import fsl_check_call

capsul/in_context/fsl.py

@@ -16,7 +16,7 @@
         def execute(self, execution_context):
             fsl_check_call(['bet', '-h'], execution_context=execution_context)
 
-For calling FSL command with this module, the first arguent of
+For calling FSL command with this module, the first argument of
 command line must be the FSL executable without any path nor prefix.
 Prefix are used in Neurodebian install. For instance on Ubuntu 16.04
 Neurodebian FSL commands are prefixed with "fsl5.0-".

capsul/run.py

@@ -116,7 +116,7 @@ def execute_job(database, engine_id, execution_id, job_uuid, debug=False):
 if __name__ == "__main__":
     if len(sys.argv) != 4:
         print(
-            "Wrong number of paramaters, 3 expected:" f"command={sys.argv}",
+            "Wrong number of parameters, 3 expected:" f"command={sys.argv}",
             file=sys.stderr,
         )
         sys.exit(1)