Try to fix current Codespell errors in Continuous Integration

capsul/engine/__init__.py

@@ -540,7 +540,7 @@ def capsul_engine(database_location=None, require=None):
     Configuration is read from a dictionary stored in two database entries.
     The first entry has the key 'global_config' (i.e.
     database.json_value('global_config')), it contains the configuration
-    values that are shared by all processings engines. The secon entry is 
+    values that are shared by all processing engines. The second entry is
     computing_config`. It contains a dictionary with one item per computing
     resource where the key is the resource name and the value is configuration 
     values that are specific to this computing resource.

capsul/engine/settings.py

@@ -413,7 +413,7 @@ def new_config(self, module, environment, values):
     def remove_config(self, module, environment, config_id):
         '''
         Removes a configuration (document in the database) for a given module /
-        environment, idenfified by its `Settings.config_id_field` value.
+        environment, identified by its `Settings.config_id_field` value.
         '''
         collection = self.collection_name(module)
         id = '%s-%s' % (config_id, environment)
@@ -450,7 +450,7 @@ def configs(self, module, environment, selection=None):
 
     def config(self, module, environment, selection=None, any=True):
         '''
-        Selects configurations (like in :meth:`congigs`) and ensures at most
+        Selects configurations (like in :meth:`configs`) and ensures at most
         one one is selected
 
         Parameters

capsul/in_context/fsl.py

@@ -12,7 +12,7 @@
    with ce:
        fsl_check_call(['bet', '/somewhere/myimage.nii'])
 
-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/in_context/spm.py

@@ -12,7 +12,7 @@
    with ce:
       spm_check_call(spm_batch_filename)
 
-For calling SPM command with this module, the first arguent of
+For calling SPM command with this module, the first argument of
 command line must be the SPM batch file to execute with Matlab.
 '''
 

capsul/pipeline/pipeline.py

@@ -166,7 +166,7 @@ def pipeline_definition(self):
         a dictionary containing the pipeline nodes and where the pipeline node
         name is ''
     workflow_list: list
-        a list of odered nodes that can be executed
+        a list of ordered nodes that can be executed
     workflow_repr: str
         a string representation of the workflow list <node_i>-><node_i+1>
 

capsul/pipeline/pipeline_tools.py

@@ -363,7 +363,7 @@ def _link_color(plug, link):
                     edge = (id, dest)
                     old_edge = edges.get(edge)
                     if old_edge is not None:
-                        # use stongest color/style
+                        # use strongest color/style
                         if not old_edge[2]:
                             weak = False
                             style = old_edge[0]['style']

capsul/qt_apps/main_window.py

@@ -232,7 +232,7 @@ def onSearchClicked(self):
     def onTreeSelectionChanged(self):
         """ Event to refresh the pipeline load button status.
         """
-        # Get the cuurent item
+        # Get the current item
         item = self.ui.menu_treectrl.currentItem()
         if item is None:
             return

capsul/qt_apps/utils/find_pipelines.py

@@ -127,7 +127,7 @@ def find_pipeline_and_process(module_name):
         sub_module_path = os.path.join(
             module_path, *sub_module.split(".")[shift:])
 
-        # List all the mdule in sub module path
+        # List all the module in submodule path
         sub_sub_module_names = [
             sub_module + "." + x[:-3] for x in os.listdir(sub_module_path)
             if (x.endswith(".py") and not x.startswith("_"))]
@@ -169,8 +169,8 @@ def find_pipeline_and_process(module_name):
 
 
 def lists2dict(list_of_pipeline_description, url, d):
-    """ Convert a list of split module names to a hierachic dictionary with
-    list leafs that contain the url to the module docuementation.
+    """ Convert a list of split module names to a hierarchic dictionary with
+    list leafs that contain the url to the module documentation.
 
     Parameters
     ----------

capsul/qt_gui/widgets/pipeline_developer_view.py

@@ -2092,7 +2092,7 @@ def link_tooltip_text(self, source_dest):
 
         Parameters
         ----------
-        source_dest: tupe (2 tuples of 2 strings)
+        source_dest: tuple (2 tuples of 2 strings)
             link description:
             ((source_node, source_param), (dest_node, dest_param))
         '''
@@ -3538,7 +3538,7 @@ def enable_step(self, step_name, state):
         setattr(self.scene.pipeline.pipeline_steps, step_name, state)
 
     def disable_preceding_steps(self, step_name, dummy):
-        # don't know why we get this additionall dummy parameter (False)
+        # don't know why we get this additional dummy parameter (False)
         steps = self.scene.pipeline.pipeline_steps
         for step in steps.user_traits():
             if step == step_name:

capsul/sphinxext/__init__.py

@@ -2,7 +2,7 @@
 '''
 Extension to sphinx to document Capsul processes
 
-This moduls allows to make sphinx source to automatically document Capsul processes and pipelines. The module can be used as a commandline:
+This module allows to make sphinx source to automatically document Capsul processes and pipelines. The module can be used as a commandline:
 
 .. code-block:: bash
 

capsul/sphinxext/capsul_pipeline_rst.py

@@ -64,7 +64,7 @@
 from capsul.sphinxext.pipelinedocgen import PipelineHelpWriter
 
 ###############################################################################
-# Generate shemas first
+# Generate schemas first
 ###############################################################################
 
 if schema and shutil.which('dot'):

capsul/study_config/memory.py

@@ -684,15 +684,15 @@ def has_attribute(trait, attribute_name, attribute_value=None,
     return count > 0
 
 
-def file_fingerprint(afile):
+def file_fingerprint(a_file):
     """ Computes the file fingerprint.
 
     Do not consider the file content, just the fingerprint (ie. the mtime,
     the size and the file location).
 
     Parameters
     ----------
-    afile: string
+    a_file: string
         the file to process.
 
     Returns
@@ -701,12 +701,12 @@ def file_fingerprint(afile):
         the file location, mtime and size.
     """
     fingerprint = {
-        "name": afile,
+        "name": a_file,
         "mtime": None,
         "size": None
     }
-    if os.path.isfile(afile):
-        stat = os.stat(afile)
+    if os.path.isfile(a_file):
+        stat = os.stat(a_file)
         fingerprint["size"] = str(stat.st_size)
         fingerprint["mtime"] = str(stat.st_mtime)
     return fingerprint

capsul/subprocess/fsl.py

@@ -9,7 +9,7 @@
   environment variable is set (fsl.sh can be sourced or not)
 - FSL was installed from Neurodebian packages
 
-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 areused  in Neurodebian install. For instance on Ubuntu 16.04 
 Neurodebian FSL commands are prefixed with "fsl5.0-".

doc/source/status.rst

@@ -19,7 +19,7 @@ Pipeline execution:
     * sequential execution:                                             |OK|
     * via Soma-Workflow:                                                |OK|
 Switch nodes:                                                           |OK|
-Iteraton nodes:                                                         |OK|
+Iteration nodes:                                                         |OK|
 StudyConfig:                                                            |OK|
 Workflow transformation:                                                |OK|
 Attributes and parameters completion:                                   |OK|

doc/source/user_guide_tree/xml_spec.rst

@@ -357,7 +357,7 @@ Attributes:
 -  **name**: node name in the pipeline (as in process elements)
 -  **switch\_value** (optional): value of the "switch" parameter: name
    of the active input
--  **enabed** (optional): as in process elements
+-  **enabled** (optional): as in process elements
 
 Children:
 
@@ -392,7 +392,7 @@ temporary values inside the pipeline if they are left undefined.
 Attributes:
 
 -  **name**: node name in the pipeline (as in process elements)
--  **enabed** (optional): as in process elements
+-  **enabled** (optional): as in process elements
 
 Children: