Applied codespell

LanderOtto · LanderOtto · commit ad502793b246 · 2025-12-19T16:03:20.000+01:00
diff --git a/cwl_utils/parser/cwl_v1_0.py b/cwl_utils/parser/cwl_v1_0.py
@@ -4035,7 +4035,7 @@ class Directory(Saveable):
     the same Directory.
 
     When executing a CommandLineTool, Directories must be recursively staged
-    first and have local values of `path` assigend.
+    first and have local values of `path` assigned.
 
     Directory objects in CommandLineTool output must provide either a
     `location` URI or a `path` property in the context of the tool execution
@@ -16266,7 +16266,7 @@ class ShellCommandRequirement(ProcessRequirement):
     Modify the behavior of CommandLineTool to generate a single string
     containing a shell command line.  Each item in the argument list must be
     joined into a string separated by single spaces and quoted to prevent
-    intepretation by the shell, unless `CommandLineBinding` for that argument
+    interpretation by the shell, unless `CommandLineBinding` for that argument
     contains `shellQuote: false`.  If `shellQuote: false` is specified, the
     argument is joined into the command string without quoting, which allows
     the use of shell metacharacters such as `|` for pipes.
@@ -20275,7 +20275,7 @@ class Workflow(Process):
     The `source` field expresses the dependency of one parameter on another
     such that when a value is associated with the parameter specified by
     `source`, that value is propagated to the destination parameter.  When all
-    data links inbound to a given step are fufilled, the step is ready to
+    data links inbound to a given step are fulfilled, the step is ready to
     execute.
 
     ## Workflow success and failure
diff --git a/cwl_utils/parser/cwl_v1_1.py b/cwl_utils/parser/cwl_v1_1.py
@@ -4035,7 +4035,7 @@ class Directory(Saveable):
     the same Directory.
 
     When executing a CommandLineTool, Directories must be recursively staged
-    first and have local values of `path` assigend.
+    first and have local values of `path` assigned.
 
     Directory objects in CommandLineTool output must provide either a
     `location` URI or a `path` property in the context of the tool execution
@@ -17590,7 +17590,7 @@ class ShellCommandRequirement(ProcessRequirement):
     Modify the behavior of CommandLineTool to generate a single string
     containing a shell command line.  Each item in the argument list must be
     joined into a string separated by single spaces and quoted to prevent
-    intepretation by the shell, unless `CommandLineBinding` for that argument
+    interpretation by the shell, unless `CommandLineBinding` for that argument
     contains `shellQuote: false`.  If `shellQuote: false` is specified, the
     argument is joined into the command string without quoting, which allows
     the use of shell metacharacters such as `|` for pipes.
@@ -18331,7 +18331,7 @@ class WorkReuse(ProcessRequirement):
     For implementations that support reusing output from past work (on
     the assumption that same code and same input produce same
     results), control whether to enable or disable the reuse behavior
-    for a particular tool or step (to accomodate situations where that
+    for a particular tool or step (to accommodate situations where that
     assumption is incorrect).  A reused step is not executed but
     instead returns the same output as the original execution.
 
@@ -18529,7 +18529,7 @@ class NetworkAccess(ProcessRequirement):
     may apply their own security policies to restrict what is
     accessible by the tool.
 
-    Enabling network access does not imply a publically routable IP
+    Enabling network access does not imply a publicly routable IP
     address or the ability to accept inbound connections.
 
     """
@@ -18727,7 +18727,7 @@ class InplaceUpdateRequirement(ProcessRequirement):
     read-only in every step.
 
     Workflow steps which modify a file must produce the modified file
-    as output.  Downstream steps which futher process the file must
+    as output.  Downstream steps which further process the file must
     use the output of previous steps, and not refer to a common input
     (this is necessary for both ordering and correctness).
 
@@ -21672,7 +21672,7 @@ class WorkflowStepInput(IdentifierRequired, Sink, LoadContents, Labeled):
     workflow inputs, or the outputs of other workflows steps) with the input
     parameters of the process specified by the `run` field. Only input parameters
     declared by the target process will be passed through at runtime to the process
-    though additonal parameters may be specified (for use within `valueFrom`
+    though additional parameters may be specified (for use within `valueFrom`
     expressions for instance) - unconnected or unused parameters do not represent an
     error condition.
 
@@ -23210,7 +23210,7 @@ class Workflow(Process):
     The `source` field expresses the dependency of one parameter on another
     such that when a value is associated with the parameter specified by
     `source`, that value is propagated to the destination parameter.  When all
-    data links inbound to a given step are fufilled, the step is ready to
+    data links inbound to a given step are fulfilled, the step is ready to
     execute.
 
     ## Workflow success and failure
diff --git a/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md b/cwl_utils/templates/WorkflowInputJsonSchemaTemplate.md
@@ -717,7 +717,7 @@ def add_cwl_metadata_to_schema(schema_dict: Dict) -> Dict:
     # Always do a deepcopy on the input
     schema_dict = deepcopy(schema_dict)
 
-    # Assert defintions
+    # Assert definitions
     assert_definitions_key(schema_dict)
 
     # Add in the CWL metadata to the definitions
@@ -1059,7 +1059,7 @@ def fix_hints(schema_dict, definition_key):
 
 def add_file_and_directory_to_schema(schema_dict: Dict) -> Dict:
     """
-    Add file and directory defintions to schema
+    Add file and directory definitions to schema
     :param schema_dict:
     :return:
     """
diff --git a/cwl_utils/testdata/EDAM_subset.owl b/cwl_utils/testdata/EDAM_subset.owl
@@ -39,7 +39,7 @@
         <oboInOwl:hasSubset>data &quot;EDAM types of data&quot;</oboInOwl:hasSubset>
         <oboInOwl:hasSubset>relations &quot;EDAM relations&quot;</oboInOwl:hasSubset>
         <oboInOwl:hasSubset>edam &quot;EDAM&quot;</oboInOwl:hasSubset>
-        <oboOther:remark>EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.</oboOther:remark>
+        <oboOther:remark>EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contributions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence.</oboOther:remark>
         <oboInOwl:hasSubset>operations &quot;EDAM operations&quot;</oboInOwl:hasSubset>
         <oboOther:idspace>EDAM http://edamontology.org/ &quot;EDAM relations and concept properties&quot;</oboOther:idspace>
         <dc:format>application/rdf+xml</dc:format>
@@ -97,7 +97,7 @@
 
     <owl:AnnotationProperty rdf:about="http://edamontology.org/example">
         <rdfs:label>Example</rdfs:label>
-        <oboInOwl:hasDefinition>&apos;Example&apos; concept property (&apos;example&apos; metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
+        <oboInOwl:hasDefinition>&apos;Example&apos; concept property (&apos;example&apos; metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too.</oboInOwl:hasDefinition>
         <oboOther:is_metadata_tag>true</oboOther:is_metadata_tag>
         <oboInOwl:inSubset>concept_properties</oboInOwl:inSubset>
     </owl:AnnotationProperty>
diff --git a/cwl_utils/testdata/revsort-run-1-packed.cwl b/cwl_utils/testdata/revsort-run-1-packed.cwl
@@ -24,7 +24,7 @@
                 {
                     "type": "boolean",
                     "default": true,
-                    "doc": "If true, reverse (decending) sort",
+                    "doc": "If true, reverse (descending) sort",
                     "id": "#main/reverse_sort"
                 }
             ],
diff --git a/lint-requirements.txt b/lint-requirements.txt
@@ -1,4 +1,5 @@
-flake8-bugbear < 25.12
+auto-walrus == 0.3.4
 black == 25.*
-codespell
+codespell == 2.4.1
+flake8-bugbear < 25.12
 isort >= 5
diff --git a/pyproject.toml b/pyproject.toml
@@ -142,3 +142,6 @@ ignore = [
 
 [tool.bandit]
 exclude_dirs = ["cwl_utils/tests"]
+
+[tool.codespell]
+ignore-words-list = "afile"

Original file line number	Diff line number	Diff line change
`@@ -24,7 +24,7 @@`
`24`	`24`	`{`
`25`	`25`	`"type": "boolean",`
`26`	`26`	`"default": true,`
`27`		`- "doc": "If true, reverse (decending) sort",`
	`27`	`+ "doc": "If true, reverse (descending) sort",`
`28`	`28`	`"id": "#main/reverse_sort"`
`29`	`29`	`}`
`30`	`30`	`],`