Fix misspellings

capsul/application.py

@@ -55,7 +55,7 @@ def _is_nipype_interface_subclass(obj):
 class Capsul:
     """User entry point to Capsul features.
     This objects reads Capsul configuration in site and user environments.
-    It allows configuration customization and instanciation of a
+    It allows configuration customization and instantiation of a
     CapsulEngine instance to reach an execution environment.
 
     If database_path is given, it replaces
@@ -255,13 +255,13 @@ def executable(definition, **kwargs):
         except ImportError as e:
             raise TypeError(
                 f"Class {definition} cannot be used to create a Process "
-                "beacause its module cannot be imported : {e}"
+                "because its module cannot be imported : {e}"
             )
         cls = getattr(module, object_name, None)
         if cls is not definition:
             raise TypeError(
                 f"Class {definition} cannot be used to create a Process "
-                f"beacause variable {object_name} of module {module_name} "
+                f"because variable {object_name} of module {module_name} "
                 f"contains {cls}"
             )
         result = definition(definition=f"{module_name}.{object_name}")

capsul/config/configuration.py

@@ -168,7 +168,7 @@ class EngineConfiguration(Controller):
     )
 
     def add_module(self, module_name, allow_existing=False):
-        """Loads a modle and adds it in the engine configuration.
+        """Loads a module and adds it in the engine configuration.
 
         This operation is performed automatically, thus should not need to be
         called manually.

capsul/database/__init__.py

@@ -499,7 +499,7 @@ def worker_ended(self, engine_id, worker_id):
 
     def persistent(self, engine_id):
         """
-        Return wether an engine is persistent or not.
+        Return whether an engine is persistent or not.
         """
         raise NotImplementedError
 
@@ -512,7 +512,7 @@ def set_persistent(self, engine_id, persistent):
     def dispose_engine(self, engine_id):
         """
         Tell Capsul that this engine will not be used anymore by any client.
-        The ressource it uses must be freed as soon as possible. If no
+        The resource it uses must be freed as soon as possible. If no
         execution is running, engine is destroyed. Otherwise, workers will
         process ongoing executions and cleanup when done.
         """

capsul/database/redis.py

@@ -559,7 +559,7 @@ def dispose_engine(self, engine_id):
                 # Removes association between label and engine_id
                 self.redis.hdel("capsul:engine", label)
                 self.redis.hdel(f"capsul:{engine_id}", "label")
-                # Check if some executions had been submited or are ongoing
+                # Check if some executions had been submitted or are ongoing
                 # An empty list modified with Redis Lua scripts may be encoded as empty dict
                 executions = json.loads(
                     self.redis.hget(f"capsul:{engine_id}", "executions")

capsul/database/sqlite.py

@@ -471,7 +471,7 @@ def job_finished_json(
 
             sql = "SELECT ready, ongoing, failed, waiting, done FROM capsul_execution WHERE engine_id=? AND execution_id=?"
             row = sqlite.execute(sql, [engine_id, execution_id]).fetchone()
-            ready, ongoing, failed, waiting, done = [json.loads(i) for i in row]
+            ready, ongoing, failed, waiting, done = (json.loads(i) for i in row)
             ongoing.remove(job_id)
             if return_code != 0:
                 failed.append(job_id)

capsul/dataset.py

@@ -29,7 +29,7 @@ class Dataset(Controller):
     Dataset representation.
     You don't need to define or instantiate this class yourself, it will be done automatically and internally in the path generation system.
 
-    Instead, users need to define datsets in the Capsul config. See :func:`generate_paths`.
+    Instead, users need to define datasets in the Capsul config. See :func:`generate_paths`.
     """
 
     path: Directory
@@ -676,7 +676,7 @@ def apply(self, metadata, process, parameter, initial_meta):
                         continue
                     if callable(v):
                         if debug:
-                            print("call modifier funciton for", k)
+                            print("call modifier function for", k)
                             print(
                                 ":",
                                 v(
@@ -700,7 +700,7 @@ def apply(self, metadata, process, parameter, initial_meta):
                         setattr(metadata, k, v)
             else:
                 if debug:
-                    print("call modifier funciton")
+                    print("call modifier function")
                 modifier(metadata, process, parameter, initial_meta=initial_meta)
 
 

capsul/engine/__init__.py

@@ -19,7 +19,7 @@ def execution_context(engine_label, engine_config, executable):
     # {'spm': {'spm12-standalone': {...}, 'spm8': {...}}
     # whereas EXecutionContext expects an execution-side single, filtered
     # config: {'spm': {...}}
-    # Thie filtering is done here in this function, but later after the context
+    # This filtering is done here in this function, but later after the context
     # is built.
     # So for now, give it only the dataset and config_modules part, removing
     # all modules config.

capsul/info.py

@@ -1,4 +1,3 @@
-from __future__ import absolute_import
 import os.path
 import sys
 
@@ -19,7 +18,7 @@
 _version_extra = version_extra
 
 # Expected by setup.py: string of form "X.Y.Z"
-__version__ = "{0}.{1}.{2}".format(version_major, version_minor, version_micro)
+__version__ = "{}.{}.{}".format(version_major, version_minor, version_micro)
 
 brainvisa_dependencies = [
     "soma-base",
@@ -84,25 +83,25 @@
 PROVIDES = ["capsul"]
 REQUIRES = [
     "redis <4.5.0",
-    "pydantic >={0}".format(PYDANTIC_MIN_VERSION),
-    "soma-base >={0}".format(SOMA_MIN_VERSION),
-    "soma-workflow >={0}".format(SOMA_WORKFLOW_MIN_VERSION),
-    "populse-db >={0}".format(POPULSE_DB_MIN_VERSION),
+    "pydantic >={}".format(PYDANTIC_MIN_VERSION),
+    "soma-base >={}".format(SOMA_MIN_VERSION),
+    "soma-workflow >={}".format(SOMA_WORKFLOW_MIN_VERSION),
+    "populse-db >={}".format(POPULSE_DB_MIN_VERSION),
     "PyYAML",
 ]
 EXTRA_REQUIRES = {
     "test": ["pytest", "jupyter"],
     "doc": [
         "sphinx >=1.0",
-        "numpy >={0}".format(NUMPY_MIN_VERSION),
+        "numpy >={}".format(NUMPY_MIN_VERSION),
     ],
     "nipype": [
         "traits >={}".format(TRAITS_MIN_VERSION),
-        "numpy >={0}".format(NUMPY_MIN_VERSION),
-        "scipy >={0}".format(SCIPY_MIN_VERSION),
-        "nibabel >={0}".format(NIBABEL_MIN_VERSION),
-        "networkx >={0}".format(NETWORKX_MIN_VERSION),
-        "nipype =={0}".format(NIPYPE_VERSION),
+        "numpy >={}".format(NUMPY_MIN_VERSION),
+        "scipy >={}".format(SCIPY_MIN_VERSION),
+        "nibabel >={}".format(NIBABEL_MIN_VERSION),
+        "networkx >={}".format(NETWORKX_MIN_VERSION),
+        "nipype =={}".format(NIPYPE_VERSION),
     ],
 }
 

capsul/pipeline/custom_nodes/cv_node.py

@@ -26,7 +26,7 @@ def __init__(self, pipeline, name, input_type=None):
             in_fields.append({"name": tr, "optional": True})
         for tr in out_fieldsl:
             out_fields.append({"name": tr, "optional": True})
-        super(CrossValidationFoldNode, self).__init__(
+        super().__init__(
             None, pipeline, name, in_fields, out_fields
         )
         if input_type:

capsul/pipeline/custom_nodes/loo_node.py

@@ -4,7 +4,6 @@
 """
 
 
-from __future__ import absolute_import
 from capsul.process.node import Node
 from soma.controller import Controller, Any, type_from_str
 
@@ -47,7 +46,7 @@ def __init__(
             in_fields.append({"name": tr, "optional": True})
         for tr in out_fieldsl:
             out_fields.append({"name": tr, "optional": True})
-        super(LeaveOneOutNode, self).__init__(
+        super().__init__(
             None, pipeline, name, in_fields, out_fields
         )
         if input_type:

capsul/pipeline/custom_nodes/map_node.py

@@ -4,7 +4,6 @@
 """
 
 
-from __future__ import absolute_import
 from capsul.process.node import Node, Plug
 from soma.controller import Controller, File, undefined, field, type_from_str
 
@@ -54,7 +53,7 @@ def __init__(
 
         for tr in input_names:
             in_fields.append({"name": tr, "optional": False})
-        super(MapNode, self).__init__(None, pipeline, name, in_fields, out_fields)
+        super().__init__(None, pipeline, name, in_fields, out_fields)
 
         for tr, ptype in zip(input_names, ptypes):
             self.add_field(tr, list[ptype], output=False, default_factory=list)

capsul/pipeline/custom_nodes/reduce_node.py

@@ -51,7 +51,7 @@ def __init__(
 
         for tr in output_names:
             out_fields.append({"name": tr, "optional": False})
-        super(ReduceNode, self).__init__(None, pipeline, name, in_fields, out_fields)
+        super().__init__(None, pipeline, name, in_fields, out_fields)
 
         for tr, ptype in zip(output_names, ptypes):
             self.add_field(

capsul/pipeline/custom_nodes/strcat_node.py

@@ -3,7 +3,6 @@
 -------------------
 """
 
-from __future__ import absolute_import
 from capsul.process.node import Node
 from soma.controller import Controller, Any, type_from_str
 
@@ -62,7 +61,7 @@ def __init__(
             node_inputs.append(
                 {"name": concat_plug, "optional": concat_plug in make_optional}
             )
-        super(StrCatNode, self).__init__(
+        super().__init__(
             None, pipeline, name, node_inputs, node_outputs
         )
         self._concat_sequence = params

capsul/pipeline/custom_nodes/strconv.py

@@ -24,7 +24,7 @@ def __init__(self, pipeline, name, input_type=None):
             in_fields.append({"name": tr, "optional": True})
         for tr in out_fieldsl:
             out_fields.append({"name": tr, "optional": True})
-        super(StrConvNode, self).__init__(None, pipeline, name, in_fields, out_fields)
+        super().__init__(None, pipeline, name, in_fields, out_fields)
         if input_type:
             ptype = input_type
         else: