Upgrade documentation: mkdocstrings, jupyter notebooks, and theme fix

setup_docs.py

@@ -0,0 +1,46 @@
+import os
+import shutil
+
+# Create directories
+os.makedirs("docs/reference", exist_ok=True)
+os.makedirs("docs/cookbook", exist_ok=True)
+
+# Modules to generate docs for
+modules = {
+    "core": "semantica.core",
+    "ingest": "semantica.ingest",
+    "parse": "semantica.parse",
+    "normalize": "semantica.normalize",
+    "semantic_extract": "semantica.semantic_extract",
+    "kg": "semantica.kg",
+    "embeddings": "semantica.embeddings",
+    "vector_store": "semantica.vector_store",
+    "triple_store": "semantica.triple_store",
+    "ontology": "semantica.ontology",
+    "reasoning": "semantica.reasoning",
+    "pipeline": "semantica.pipeline",
+    "export": "semantica.export",
+    "visualization": "semantica.visualization",
+    "utils": "semantica.utils"
+}
+
+# Generate reference markdown files
+for name, package in modules.items():
+    content = f"# {name.replace('_', ' ').title()}\n\n::: {package}\n"
+    with open(f"docs/reference/{name}.md", "w") as f:
+        f.write(content)
+    print(f"Created docs/reference/{name}.md")
+
+# Copy cookbook directory
+if os.path.exists("cookbook"):
+    if os.path.exists("docs/cookbook"):
+        shutil.rmtree("docs/cookbook")
+    shutil.copytree("cookbook", "docs/cookbook")
+    print("Copied cookbook to docs/cookbook")
+
+# Remove old files
+files_to_remove = ["docs/MODULES_DOCUMENTATION.md", "docs/cookbook.md", "docs/api.md"]
+for f in files_to_remove:
+    if os.path.exists(f):
+        os.remove(f)
+        print(f"Removed {f}")