fixed minor documentation issues

Author: keighrim

build-tools/docs.py

@@ -25,8 +25,6 @@ def build_docs_local(source_dir: Path):
     print("\n--- Step 1: Installing in editable mode ---")
     try:
         run_command([sys.executable, "-m", "pip", "install", "-e", "."], cwd=source_dir)
-        # Explicitly run schema generation to be sure
-        run_command([sys.executable, "setup.py", "generate_schema"], cwd=source_dir)
     except SystemExit:
         print("Warning: 'pip install -e .' failed. This might be due to an externally managed environment.")
         print("Attempting to proceed with documentation build assuming dependencies are met...")

clams/appmetadata/__init__.py

@@ -1,3 +1,4 @@
+import json
 import os
 import shutil
 import subprocess
@@ -523,4 +524,4 @@ def jsonify(self, pretty=False):
 
 
 if __name__ == '__main__':
-    print(AppMetadata.schema_json(indent=2))
+    print(json.dumps(AppMetadata.model_json_schema(), indent=2))

documentation/autodoc/clams.mmif_utils.rst

@@ -2,15 +2,3 @@ clams.mmif_utils package
 ========================
 
 Package providing utility functions for working with MMIF data.
-
-``rewind`` module
------------------
-
-.. automodule:: clams.mmif_utils.rewind
-   :members:
-
-``source`` module
------------------
-
-.. automodule:: clams.mmif_utils.source
-   :members:

documentation/conf.py

@@ -63,6 +63,8 @@
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 # dynamically generated files
 exclude_patterns.extend(['cli_help.rst', 'whatsnew.md'])
+# this is user manual, and not part of API docs, will be used in a remote site
+exclude_patterns.extend(['clamsapp.md'])
 
 
 # -- Options for HTML output -------------------------------------------------

documentation/tutorial.md

@@ -23,8 +23,7 @@ def tokenize(text):
 
 ```
 
-``` python
-$ python
+``` pycon
 >>> import tokenizer
 >>> tokenizer.tokenize('Fido barks.')
 [(0, 4), (5, 10)]