Refresh linkml-model documentation pages with latest and greatest features (#226)

* upgrade linkml and other dependencies

* config changes to accommodate latest doc features

* remove redundant  in make gen-doc cmd

* Fix pydantic version mismatch in poetry.lock

Update pydantic from 1.10.7 to 2.12.5 to be compatible with linkml 1.9.6
which requires GetPydanticSchema from pydantic v2.9+.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Update uv.lock

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-authored-by: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>

Author: 3 people

Makefile

@@ -76,6 +76,8 @@ gen-doc:
 	cp -r $(PYMODEL) $(DOCDIR)/$(PYMODEL)
 	rm -rf $(DOCDIR)/$(PYMODEL)/model/docs
 	cp README.md $(DOCDIR)
+	mkdir -p $(DOCDIR)/javascripts
+	cp $(SRC)/utils/scripts/*.js $(DOCDIR)/javascripts/
 
 test: test-schema test-python test-validate-schema test-examples
 test-schema:

mkdocs.yml

@@ -21,16 +21,23 @@ theme:
       name: Switch to dark mode
 plugins:
   - search
-  - mermaid2
+  - mermaid2:
+      version: 10.9.0
   - mike:
       alias_type: symlink
       canonical_version: latest
 extra:
   version:
     provider: mike
-#markdown_extensions:
+markdown_extensions:
+  - admonition
+  - tables
+  - pymdownx.magiclink
 #  - toc:
 #      permalink: true
+extra_javascript:
+  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
+  - javascripts/tablesort.js
 docs_dir: docs/source
 site_dir: docs/build
 nav:

pyproject.toml

@@ -55,7 +55,7 @@ dev = [
 ]
 docs = [
     "mkdocs>=1.4.2",
-    "mkdocs-material>=8.2.8",
+    "mkdocs-material>=9.0.12",
     "mkdocs-mermaid2-plugin>=0.6.0",
     "mike>=2.0.0",
 ]

utils/scripts/tablesort.js

@@ -0,0 +1,6 @@
+document$.subscribe(function () {
+    var tables = document.querySelectorAll("article table:not([class])");
+    tables.forEach(function (table) {
+      new Tablesort(table);
+    });
+  });