Merge pull request #161 from yarikoptic/enh-codespell

Codespell: config, action, typos fixed

Author: cmungall

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

docs/03schemas/index.html

@@ -1135,7 +1135,7 @@ <h3 id="slotdefinition-normative-subset-metaslots">SlotDefinition: Normative sub
 <tr>
 <td><a href="../all_members/">all_members</a></td>
 <td>0..* <br/> <a href="../SlotDefinition/">SlotDefinition</a></td>
-<td>the value of the multiavlued slot is a list where all elements conform to the...</td>
+<td>the value of the multivalued slot is a list where all elements conform to the...</td>
 </tr>
 <tr>
 <td><a href="../abstract/">abstract</a></td>

docs/04derived-schemas/index.html

@@ -507,9 +507,9 @@ <h2 id="rule-generation-of-patterns-from-structured-patterns">Rule: Generation o
 <p>If <code>p.interpolated</code> is True, then the value of <code>s.syntax</code> is <em>interpolated</em>, by replacing all occurrences of braced text <code>{VAR}</code>
 with the value of <code>VAR</code>. The value of <code>VAR</code> is obtained using <code>m.settings[VAR]</code>, where <code>m</code> is the schema in which <code>p</code> is introduced.</p>
 <p>If <code>p.interpolated</code> is not True, then the value of <code>s.syntax</code> is used directly.</p>
-<p>If <code>p.partial_match</code> is not True, then <code>s.pattern</code> has a '^' character inserted at the begining and a '$' character inserted as the end.</p>
+<p>If <code>p.partial_match</code> is not True, then <code>s.pattern</code> has a '^' character inserted at the beginning and a '$' character inserted as the end.</p>
 <h3 id="rule-generation-of-classdefinitionreferences">Rule: Generation of ClassDefinitionReferences</h3>
-<p>For every <strong>ClassDefinition</strong> <code>c</code>, if there exists a slot <code>s</code> such that <code>s.identifer=True</code>,
+<p>For every <strong>ClassDefinition</strong> <code>c</code>, if there exists a slot <code>s</code> such that <code>s.identifier=True</code>,
 then a corresponding <strong>ClassDefinitionReference</strong> <code>r</code> is generated.</p>
 <p><code>r.name</code> is assigned to be the concatenation of <code>c.name</code> and <code>s.name</code></p>
 <p><code>r</code> functionally serves as a <em>foreign key</em> to instances of <code>r</code>, and allows for non-inlined

docs/ClassDefinition/index.html

@@ -1577,7 +1577,7 @@ <h3 id="induced">Induced</h3>
       is the identifier of an entire value set.  Additionally, this is different than
       an enumeration in that in an enumeration, the values of the enumeration are
       listed directly in the model itself. Setting this property on a slot does not
-      guarantee an expansion of the ontological hiearchy into an enumerated list of
+      guarantee an expansion of the ontological hierarchy into an enumerated list of
       possible values in every serialization of the model.'
     from_schema: https://w3id.org/linkml/meta
     rank: 1000

docs/Definition/index.html

@@ -1187,7 +1187,7 @@ <h3 id="induced">Induced</h3>
       metaslots are propagated from.
     comments:
     - mixins act in the same way as parents (is_a). They allow a model to have a primary
-      strict hierachy, while keeping the benefits of multiple inheritance
+      strict hierarchy, while keeping the benefits of multiple inheritance
     in_subset:
     - SpecificationSubset
     - BasicSubset
@@ -1231,7 +1231,7 @@ <h3 id="induced">Induced</h3>
       is the identifier of an entire value set.  Additionally, this is different than
       an enumeration in that in an enumeration, the values of the enumeration are
       listed directly in the model itself. Setting this property on a slot does not
-      guarantee an expansion of the ontological hiearchy into an enumerated list of
+      guarantee an expansion of the ontological hierarchy into an enumerated list of
       possible values in every serialization of the model.'
     from_schema: https://w3id.org/linkml/meta
     rank: 1000

docs/EnumDefinition/index.html

@@ -1135,7 +1135,7 @@ <h3 id="induced">Induced</h3>
       metaslots are propagated from.
     comments:
     - mixins act in the same way as parents (is_a). They allow a model to have a primary
-      strict hierachy, while keeping the benefits of multiple inheritance
+      strict hierarchy, while keeping the benefits of multiple inheritance
     in_subset:
     - SpecificationSubset
     - BasicSubset
@@ -1179,7 +1179,7 @@ <h3 id="induced">Induced</h3>
       is the identifier of an entire value set.  Additionally, this is different than
       an enumeration in that in an enumeration, the values of the enumeration are
       listed directly in the model itself. Setting this property on a slot does not
-      guarantee an expansion of the ontological hiearchy into an enumerated list of
+      guarantee an expansion of the ontological hierarchy into an enumerated list of
       possible values in every serialization of the model.'
     from_schema: https://w3id.org/linkml/meta
     rank: 1000

docs/Objectidentifier/index.html

@@ -611,7 +611,7 @@ <h1 id="type-objectidentifier">Type: Objectidentifier</h1>
 </ul>
 <h2 id="comments">Comments</h2>
 <ul>
-<li>Used for inheritence and type checking</li>
+<li>Used for inheritance and type checking</li>
 </ul>
 <h2 id="identifier-and-mapping-information">Identifier and Mapping Information</h2>
 <h3 id="schema-source">Schema Source</h3>

docs/SchemaDefinition/index.html

@@ -1246,7 +1246,7 @@ <h3 id="induced">Induced</h3>
     from_schema: https://w3id.org/linkml/meta
     rank: 1000
     domain: schema_definition
-    readonly: suppplied by the schema loader
+    readonly: supplied by the schema loader
     alias: source_file
     owner: schema_definition
     domain_of:

docs/SlotDefinition/index.html

@@ -2102,7 +2102,7 @@ <h3 id="induced">Induced</h3>
   subproperty_of:
     name: subproperty_of
     description: 'Ontology property which this slot is a subproperty of.  Note: setting
-      this property on a slot does not guarantee an expansion of the ontological hiearchy
+      this property on a slot does not guarantee an expansion of the ontological hierarchy
       into an enumerated list of possible values in every serialization of the model.'
     examples:
     - value: RO:HOM0000001
@@ -2383,7 +2383,7 @@ <h3 id="induced">Induced</h3>
   path_rule:
     name: path_rule
     description: a rule for inferring a slot assignment based on evaluating a path
-      through a sequence of slot assignemnts
+      through a sequence of slot assignments
     from_schema: https://w3id.org/linkml/meta
     rank: 1000
     domain: slot_definition
@@ -2997,7 +2997,7 @@ <h3 id="induced">Induced</h3>
       is the identifier of an entire value set.  Additionally, this is different than
       an enumeration in that in an enumeration, the values of the enumeration are
       listed directly in the model itself. Setting this property on a slot does not
-      guarantee an expansion of the ontological hiearchy into an enumerated list of
+      guarantee an expansion of the ontological hierarchy into an enumerated list of
       possible values in every serialization of the model.'
     from_schema: https://w3id.org/linkml/meta
     rank: 1000

docs/TypeDefinition/index.html

@@ -858,7 +858,7 @@ <h3 id="induced">Induced</h3>
     description: python base type that implements this type definition
     comments:
     - every root type must have a base
-    - the base is inherited by child types but may be overriden.  Base compatibility
+    - the base is inherited by child types but may be overridden.  Base compatibility
       is not checked.
     in_subset:
     - SpecificationSubset