Merge pull request #161 from yarikoptic/enh-codespell

Codespell: config, action, typos fixed
linkml · Jun 12, 2023 · 597f504 · 597f504
2 parents 28fc088 + 8a82e68
commit 597f504
Show file tree

Hide file tree

Showing 68 changed files with 186 additions and 153 deletions.
diff --git a/.github/workflows/codespell.yml b/.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
diff --git a/docs/03schemas/index.html b/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>

diff --git a/docs/04derived-schemas/index.html b/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

diff --git a/docs/ClassDefinition/index.html b/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

diff --git a/docs/Definition/index.html b/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

diff --git a/docs/EnumDefinition/index.html b/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

diff --git a/docs/Objectidentifier/index.html b/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>

diff --git a/docs/SchemaDefinition/index.html b/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:

diff --git a/docs/SlotDefinition/index.html b/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

diff --git a/docs/TypeDefinition/index.html b/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

diff --git a/docs/UnitOfMeasure/index.html b/docs/UnitOfMeasure/index.html
@@ -353,7 +353,7 @@ <h2 id="slots">Slots</h2>
 <tr>
 <td><a href="../has_quantity_kind/">has_quantity_kind</a></td>
 <td>0..1 <br/> <a href="../Uriorcurie/">Uriorcurie</a></td>
-<td>Concept in a vocabulary or ontology that denotes the kind of quanity being me...</td>
+<td>Concept in a vocabulary or ontology that denotes the kind of quantity being me...</td>
 <td>direct</td>
 </tr>
 <tr>
@@ -576,7 +576,7 @@ <h3 id="induced">Induced</h3>
     range: string
   has_quantity_kind:
     name: has_quantity_kind
-    description: Concept in a vocabulary or ontology that denotes the kind of quanity
+    description: Concept in a vocabulary or ontology that denotes the kind of quantity
       being measured, e.g. length
     comments:
     - Potential ontologies include but are not limited to PATO, NCIT, OBOE, qudt.quantityKind

diff --git a/docs/assets/javascripts/lunr/wordcut.js b/docs/assets/javascripts/lunr/wordcut.js
diff --git a/docs/base/index.html b/docs/base/index.html
@@ -643,7 +643,7 @@ <h2 id="properties">Properties</h2>
 <h2 id="comments">Comments</h2>
 <ul>
 <li>every root type must have a base</li>
-<li>the base is inherited by child types but may be overriden.  Base compatibility is not checked.</li>
+<li>the base is inherited by child types but may be overridden.  Base compatibility is not checked.</li>
 </ul>
 <h2 id="identifier-and-mapping-information">Identifier and Mapping Information</h2>
 <h3 id="schema-source">Schema Source</h3>
@@ -657,7 +657,7 @@ <h2 id="linkml-source">LinkML Source</h2>
 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 is
+- the base is inherited by child types but may be overridden.  Base compatibility is
   not checked.
 in_subset:
 - SpecificationSubset

diff --git a/docs/class_definition_mixins/index.html b/docs/class_definition_mixins/index.html
@@ -635,7 +635,7 @@ <h2 id="other-properties">Other properties</h2>
 <tr>
 <td><strong>Comments:</strong></td>
 <td></td>
-<td>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</td>
+<td>mixins act in the same way as parents (is_a). They allow a model to have a primary strict hierarchy, while keeping the benefits of multiple inheritance</td>
 </tr>
 <tr>
 <td><strong>In Subsets:</strong></td>

diff --git a/docs/has_quantity_kind/index.html b/docs/has_quantity_kind/index.html
@@ -617,7 +617,7 @@
 
 
 <h1 id="slot-has_quantity_kind">Slot: has_quantity_kind</h1>
-<p><em>Concept in a vocabulary or ontology that denotes the kind of quanity being measured, e.g. length</em></p>
+<p><em>Concept in a vocabulary or ontology that denotes the kind of quantity being measured, e.g. length</em></p>
 <p>URI: <a href="http://qudt.org/schema/qudt/hasQuantityKind">qudt:hasQuantityKind</a></p>
 <!-- no inheritance hierarchy -->
 
@@ -653,7 +653,7 @@ <h2 id="linkml-source">LinkML Source</h2>
 <details>
 
 <pre><code class="language-yaml">name: has_quantity_kind
-description: Concept in a vocabulary or ontology that denotes the kind of quanity
+description: Concept in a vocabulary or ontology that denotes the kind of quantity
   being measured, e.g. length
 comments:
 - Potential ontologies include but are not limited to PATO, NCIT, OBOE, qudt.quantityKind

diff --git a/docs/index.html b/docs/index.html
@@ -1667,7 +1667,7 @@ <h2 id="slots">Slots</h2>
 </tr>
 <tr>
 <td><a href="has_quantity_kind/">has_quantity_kind</a></td>
-<td>Concept in a vocabulary or ontology that denotes the kind of quanity being me...</td>
+<td>Concept in a vocabulary or ontology that denotes the kind of quantity being me...</td>
 </tr>
 <tr>
 <td><a href="iec61360code/">iec61360code</a></td>

diff --git a/docs/mixins/index.html b/docs/mixins/index.html
@@ -673,7 +673,7 @@ <h2 id="aliases">Aliases</h2>
 </ul>
 <h2 id="comments">Comments</h2>
 <ul>
-<li>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</li>
+<li>mixins act in the same way as parents (is_a). They allow a model to have a primary strict hierarchy, while keeping the benefits of multiple inheritance</li>
 </ul>
 <h2 id="see-also">See Also</h2>
 <ul>
@@ -692,7 +692,7 @@ <h2 id="linkml-source">LinkML Source</h2>
   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

diff --git a/docs/path_rule/index.html b/docs/path_rule/index.html
@@ -610,7 +610,7 @@
 
 
 <h1 id="slot-path_rule">Slot: path_rule</h1>
-<p><em>a rule for inferring a slot assignment based on evaluating a path through a sequence of slot assignemnts</em></p>
+<p><em>a rule for inferring a slot assignment based on evaluating a path through a sequence of slot assignments</em></p>
 <p>URI: <a href="https://w3id.org/linkml/path_rule">linkml:path_rule</a></p>
 <!-- no inheritance hierarchy -->
 
@@ -643,7 +643,7 @@ <h2 id="linkml-source">LinkML Source</h2>
 
 <pre><code class="language-yaml">name: path_rule
 description: a rule for inferring a slot assignment based on evaluating a path through
-  a sequence of slot assignemnts
+  a sequence of slot assignments
 from_schema: https://w3id.org/linkml/meta
 rank: 1000
 domain: slot_definition

diff --git a/docs/permissible_value_mixins/index.html b/docs/permissible_value_mixins/index.html
@@ -635,7 +635,7 @@ <h2 id="other-properties">Other properties</h2>
 <tr>
 <td><strong>Comments:</strong></td>
 <td></td>
-<td>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</td>
+<td>mixins act in the same way as parents (is_a). They allow a model to have a primary strict hierarchy, while keeping the benefits of multiple inheritance</td>
 </tr>
 <tr>
 <td><strong>In Subsets:</strong></td>

diff --git a/docs/search/search_index.json b/docs/search/search_index.json
diff --git a/docs/slot_definition_mixins/index.html b/docs/slot_definition_mixins/index.html
@@ -635,7 +635,7 @@ <h2 id="other-properties">Other properties</h2>
 <tr>
 <td><strong>Comments:</strong></td>
 <td></td>
-<td>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</td>
+<td>mixins act in the same way as parents (is_a). They allow a model to have a primary strict hierarchy, while keeping the benefits of multiple inheritance</td>
 </tr>
 <tr>
 <td><strong>In Subsets:</strong></td>

diff --git a/docs/source_file/index.html b/docs/source_file/index.html
@@ -648,7 +648,7 @@ <h2 id="linkml-source">LinkML Source</h2>
 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
 domain_of:
 - schema_definition

diff --git a/docs/specification/01introduction/index.html b/docs/specification/01introduction/index.html
@@ -814,7 +814,7 @@ <h3 id="part-1-introduction">Part 1: Introduction</h3>
 <p>This section. Background information and preliminary definitions.</p>
 <h3 id="part-2-structure-and-syntax-of-instances">Part 2: Structure and Syntax of Instances</h3>
 <p>Part 2 provides a <em>structural specification</em> of LinkML <strong>instances</strong>. The structural specification is provided as a normative abstract functional-style syntax. UML diagrams are provided for informative purposes.</p>
-<p>This syntax is not intended as an actual exchange syntax for LinkML data. For that, existing syntaxes such as JSON, YAML, or RDF syntaxes should be used (see Part 6). The abstract syntax allows for a seperation of the essential features of the language from issues related to any particular syntax.</p>
+<p>This syntax is not intended as an actual exchange syntax for LinkML data. For that, existing syntaxes such as JSON, YAML, or RDF syntaxes should be used (see Part 6). The abstract syntax allows for a separation of the essential features of the language from issues related to any particular syntax.</p>
 <p>Part 2 also introduces a <strong>path accessor</strong> syntax for specifying how to traverse LinkML instances.</p>
 <p>The abstract syntax and path accessor syntax are used in the remainder of the specification.</p>
 <h3 id="part-3-structure-of-schemas">Part 3: Structure of Schemas</h3>

diff --git a/docs/specification/03schemas/index.html b/docs/specification/03schemas/index.html
@@ -1351,7 +1351,7 @@ <h3 id="slotdefinition-normative-subset-metaslots">SlotDefinition: Normative sub
 <tr>
 <td><a href="all_members.md">all_members</a></td>
 <td>0..* <br/> <a href="SlotDefinition.md">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.md">abstract</a></td>