misc spelling fixes

Author: mr-c

.github/workflows/ci-tests.yml

@@ -1,4 +1,4 @@
-name: Continous integration tests
+name: Continuous integration tests
 
 on:
   push:

Makefile

@@ -102,7 +102,7 @@ diff_pydocstyle_report: pydocstyle_report.txt
 
 ## codespell              : check for common misspellings
 codespell:
-	codespell -w $(shell git ls-files | grep -v mypy-stubs | grep -v gitignore | grep -v EDAM.owl | grep -v pre.yml)
+	codespell -w $(shell git ls-files | grep -v mypy-stubs | grep -v gitignore | grep -v EDAM.owl | grep -v pre.yml | grep -v test_schema)
 
 ## format                 : check/fix all code indentation and formatting (runs black)
 format:
@@ -189,7 +189,7 @@ pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: FORCE
-	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
+	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
 	./release-test.sh
 
 release:

schema_salad/codegen.py

@@ -1,4 +1,4 @@
-"""Generate langauge specific loaders for a particular SALAD schema."""
+"""Generate language specific loaders for a particular SALAD schema."""
 import sys
 from io import TextIOWrapper
 from typing import (

schema_salad/dotnet/util/Utilities.cs

@@ -3,7 +3,7 @@
 public static class Utilities
 {
     /**
-     * Compute the shortname of a fully qualified identifer.
+     * Compute the shortname of a fully qualified identifier.
      * See https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names. 
      *
      */

schema_salad/metaschema.py

@@ -720,7 +720,7 @@ def save_relative_uri(
 
 def shortname(inputid: str) -> str:
     """
-    Compute the shortname of a fully qualified identifer.
+    Compute the shortname of a fully qualified identifier.
 
     See https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names.
     """

schema_salad/metaschema/metaschema.yml

@@ -154,7 +154,7 @@ $graph:
         then finally `#foo`.  The first valid URI in the search order shall be
         used as the fully resolved value of the identifier.  The value of the
         refScope field is the specified number of levels from the containing
-        identifer scope before starting the search, so if `refScope: 2` then
+        identifier scope before starting the search, so if `refScope: 2` then
         "baz" and "bar" must be stripped to get the base `#foo` and search
         `#foo/foo` and the `#foo`.  The last scope searched must be the top
         level scope before determining if the identifier cannot be resolved.

schema_salad/python_codegen.py

@@ -135,8 +135,8 @@ def prologue(self) -> None:
 """
         )
 
-        for primative in prims.values():
-            self.declare_type(primative)
+        for primitive in prims.values():
+            self.declare_type(primitive)
 
     def begin_class(
         self,  # pylint: disable=too-many-arguments

schema_salad/python_codegen_support.py

@@ -717,7 +717,7 @@ def save_relative_uri(
 
 def shortname(inputid: str) -> str:
     """
-    Compute the shortname of a fully qualified identifer.
+    Compute the shortname of a fully qualified identifier.
 
     See https://w3id.org/cwl/v1.2/SchemaSalad.html#Short_names.
     """

schema_salad/ref_resolver.py

@@ -734,21 +734,21 @@ def _resolve_identifier(
         self, document: CommentedMap, loader: "Loader", base_url: str
     ) -> str:
         # Expand identifier field (usually 'id') to resolve scope
-        for identifer in loader.identifiers:
-            if identifer in document:
-                if isinstance(document[identifer], str):
-                    document[identifer] = loader.expand_url(
-                        document[identifer], base_url, scoped_id=True
+        for identifier in loader.identifiers:
+            if identifier in document:
+                if isinstance(document[identifier], str):
+                    document[identifier] = loader.expand_url(
+                        document[identifier], base_url, scoped_id=True
                     )
-                    if document[identifer] not in loader.idx or isinstance(
-                        loader.idx[document[identifer]], str
+                    if document[identifier] not in loader.idx or isinstance(
+                        loader.idx[document[identifier]], str
                     ):
-                        loader.idx[document[identifer]] = document
-                    base_url = document[identifer]
+                        loader.idx[document[identifier]] = document
+                    base_url = document[identifier]
                 else:
                     raise ValidationException(
                         "identifier field '{}' must be a string".format(
-                            document[identifer]
+                            document[identifier]
                         )
                     )
         return base_url
@@ -761,17 +761,17 @@ def _resolve_identity(
     ) -> None:
         # Resolve scope for identity fields (fields where the value is the
         # identity of a standalone node, such as enum symbols)
-        for identifer in loader.identity_links:
-            if identifer in document and isinstance(
-                document[identifer], MutableSequence
+        for identifier in loader.identity_links:
+            if identifier in document and isinstance(
+                document[identifier], MutableSequence
             ):
-                for n, v in enumerate(document[identifer]):
+                for n, v in enumerate(document[identifier]):
                     if isinstance(v, str):
-                        document[identifer][n] = loader.expand_url(  # type: ignore
+                        document[identifier][n] = loader.expand_url(  # type: ignore
                             v, base_url, scoped_id=True
                         )
-                        if document[identifer][n] not in loader.idx:
-                            loader.idx[cast(str, document[identifer][n])] = v
+                        if document[identifier][n] not in loader.idx:
+                            loader.idx[cast(str, document[identifier][n])] = v
 
     def _normalize_fields(self, document: CommentedMap, loader: "Loader") -> None:
         # Normalize fields which are prefixed or full URIn to vocabulary terms
@@ -877,13 +877,13 @@ def resolve_all(
             if newctx is not None:
                 loader = newctx
 
-            for identifer in loader.identity_links:
-                if identifer in document:
-                    if isinstance(document[identifer], str):
-                        document[identifer] = loader.expand_url(
-                            document[identifer], base_url, scoped_id=True
+            for identifier in loader.identity_links:
+                if identifier in document:
+                    if isinstance(document[identifier], str):
+                        document[identifier] = loader.expand_url(
+                            document[identifier], base_url, scoped_id=True
                         )
-                        loader.idx[document[identifer]] = document
+                        loader.idx[document[identifier]] = document
 
             metadata = document
             if "$graph" in document:

schema_salad/tests/metaschema-pre.yml

@@ -359,7 +359,7 @@
                     "null",
                     "int"
                 ],
-                "doc": "If the field contains a relative reference, it must be resolved by\nsearching for valid document references in each successive parent scope\nin the document fragment.  For example, a reference of `foo` in the\ncontext `#foo/bar/baz` will first check for the existence of\n`#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and\nthen finally `#foo`.  The first valid URI in the search order shall be\nused as the fully resolved value of the identifier.  The value of the\nrefScope field is the specified number of levels from the containing\nidentifer scope before starting the search, so if `refScope: 2` then\n\"baz\" and \"bar\" must be stripped to get the base `#foo` and search\n`#foo/foo` and the `#foo`.  The last scope searched must be the top\nlevel scope before determining if the identifier cannot be resolved.\n"
+                "doc": "If the field contains a relative reference, it must be resolved by\nsearching for valid document references in each successive parent scope\nin the document fragment.  For example, a reference of `foo` in the\ncontext `#foo/bar/baz` will first check for the existence of\n`#foo/bar/baz/foo`, followed by `#foo/bar/foo`, then `#foo/foo` and\nthen finally `#foo`.  The first valid URI in the search order shall be\nused as the fully resolved value of the identifier.  The value of the\nrefScope field is the specified number of levels from the containing\nidentifier scope before starting the search, so if `refScope: 2` then\n\"baz\" and \"bar\" must be stripped to get the base `#foo` and search\n`#foo/foo` and the `#foo`.  The last scope searched must be the top\nlevel scope before determining if the identifier cannot be resolved.\n"
             },
             {
                 "name": "https://w3id.org/cwl/salad#JsonldPredicate/typeDSL",