Merge pull request #600 from hed-standard/develop

Added manual link checker and corrected links

.github/workflows/links.yaml

@@ -0,0 +1,24 @@
+---
+name: Lychee link checker
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Lychee link checker
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1
+        with:
+          # Check all markdown, html and reStructuredText files in repo (default)
+          args: --base . --verbose --no-progress './**/*.md' './**/*.html' './**/*.rst'

.lycheeignore

@@ -0,0 +1,5 @@
+<!-- This file lists all links/regex to be ignored by lychee in the link checker -->
+https://www.sciencedirect.com/science/article/pii/S1053811921010387
+https://www.sciencedirect.com/science/article/pii/S0010945221001106
+(_anchor|-anchor)
+

CHANGELOG.md

@@ -30,7 +30,8 @@ error messages in the validators could use the error code as a link into the spe
 for more information about the cause of errors.
 * [**Improvement**] A standardized set of validation test data keyed to the error codes 
 was added to the specification repository in the 
-[**error_tests**](https://github.com/hed-standard/hed-specification/tree/master/docs/source/_static/data/error_tests) directory. This test data will be validated by both the Python 
+[**tests**](https://github.com/hed-standard/hed-specification/tree/master/tests) directory. 
+This test data will be validated by both the Python 
 and JavaScript validators in addition to their internal tests as part of the GitHub actions.
 * [**Clarification**] All chapters of the specification were edited for clarity and correctness.
 

README.md

@@ -10,7 +10,7 @@ as well as rules for how tools should treat HED-annotated data.
 
 If you want to annotate your data, please visit the [**HED resources**](https://www.hed-resources.org/en/latest/index.html) documentation website. 
 If you are a developer of a new HED vocabulary (schema) please see the
-[Schema development guide](https://www.hed-resources.org/en/latest/HedSchemaDevelopmentGuide.html).
+[Schema developer's guide](https://www.hed-resources.org/en/latest/HedSchemaDevelopersGuide.html).
 
 The latest version of the HED specification is available at the
 [**HED specification**](https://hed-specification.readthedocs.io/en/latest/index.html).

docs/source/08_HED_ontology.md

@@ -60,7 +60,11 @@ This HED information space is illustrated schematically in the following diagram
 
 The embedding is anchored by the `hedId` schema attribute introduced with HED standard schema 8.3.0.
 The `hedId` values are of the form `HED_xxxxxxx` and resolve to IRIs (International Resource Identifiers) 
-of the form *https://purl.org/hed/HED_xxxxxxx*.
+in the [**https://purl.org/hed/hed.owl**](https://purl.org/hed/hed.owl) file.
+This file is currently hosted on GitHub and does not have a mechanism to address individual IDs defined within the file.
+The ontology files are versioned by release date.
+Releases are located in the [**releases**](https://github.com/hed-standard/hed-ontology/tree/main/releases)
+subdirectory of the [**hed-ontology**](https://github.com/hed-standard/hed-ontology) repository on GitHub.
 
 The extended information space is completely represented by the HED ontology in OWL format.
 In this document we use OWL Manchester format (`.omn`) for readability.  
@@ -679,4 +683,4 @@ using the range assignments described in the following table.
 ### 8.3.3. HED IRIs
 
 HED IRIs [(**International Resource Identifiers**)](https://datatracker.ietf.org/doc/html/rfc3987) are mapped
-to [**https://purl.org/hed**](https://purl.org/hed).
+to [**https://purl.org/hed/hed.owl**](https://purl.org/hed/hed.owl).

docs/source/Appendix_A.md

@@ -901,7 +901,7 @@ The `HED` node is the root node of the XML schema.
 
 The file name corresponding to this example is `HED8.0.0.xml`.
 The file is found in the [**standard_schema/hedxml**](https://github.com/hed-standard/hed-schemas/tree/main/standard_schema/hedxml)
-directory of the [**hed-schemas**](https://github.com/hed-standard/hedschemas) GitHub repository.
+directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas) GitHub repository.
 
 Library schemas must include the `library` attribute with the library name
 in their header line as shown in the following example.
@@ -915,7 +915,7 @@ in their header line as shown in the following example.
 
 The `library` and `version` values are used to form the official xml file name `HED_testlib_1.0.2.xml`.
 The file is found in [**library_schemas/testlib/hedxml**](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/testlib/hedxml)
-directory of the [**hed-schemas**](https://github.com/hed-standard/hedschemas) GitHub repository.
+directory of the [**hed-schemas**](https://github.com/hed-standard/hed-schemas) GitHub repository.
 
 Unknown header attributes are translated as attributes of the `HED` root node of the 
 `.xml` version, but a warning is issued when the `.mediawiki` file is validated.

docs/source/_template/layout.html

@@ -7,14 +7,14 @@
     </p>
     <ul>
       <li class="toctree-li">
-        <a href="https://hedtags.org">Project homepage</a></li>
+        <a href="https://www.hedtags.org">Project homepage</a></li>
       <li class="toctree-li">
         <a href="https://www.youtube.com/channel/UCYu8B1eFb-gRemamXod-exQ">HED YouTube channel</a></li>
       <li class="toctree-li">
-        <a href="https://hed-examples.readthedocs.io/en/latest/DocumentationSummary.html">Documentation summary</a></li>
+        <a href="https://www.hed-resources.org/en/latest/DocumentationSummary.html">Documentation summary</a></li>
       <li class="toctree-li">
         <a href="https://hed-specification.readthedocs.io/en/latest/index.html">Specification</a></li>
-      <li class="toctree-li"><a href="https://hedtools.ucsd.edu/hed">Online tools</a></li>
+      <li class="toctree-li"><a href="https://hedtools.org/hed">Online tools</a></li>
       <li class="toctree-li"><a href="https://hed-python.readthedocs.io/en/latest/">HEDTools API</a></li>
       <li class="toctree-li"><a href="https://hed-web.readthedocs.io/en/latest/">Web deployment</a></li>
     </ul>