Fixed script tests

Author: VisLab

docs/user_guide.md

@@ -288,7 +288,6 @@ HEDTools provides a unified command-line interface (CLI) using a **git-style com
 | `hedpy schema validate`        | Validate HED schema files                                   |
 | `hedpy schema convert`         | Convert schemas between formats (XML, MEDIAWIKI, TSV, JSON) |
 | `hedpy schema add-ids`         | Add unique HED IDs to schema terms                          |
-| `hedpy schema create-ontology` | Generate OWL ontology files from HED schemas                |
 
 ### Installation and basic usage
 
@@ -517,23 +516,6 @@ hedpy schema add-ids /path/to/hed-schemas score 2.2.0
 - Modifies all schema formats (XML, MEDIAWIKI, TSV, JSON) in-place
 - Should be run after all schema content changes are finalized
 
-#### Create ontology
-
-Generate OWL (Web Ontology Language) ontology files from HED schemas for semantic web applications and ontology-based tools.
-
-```bash
-# Create ontology for a standard schema
-hedpy schema create-ontology /path/to/hed-schemas standard 8.4.0
-
-# Create ontology for a library schema with custom output location
-hedpy schema create-ontology /path/to/hed-schemas score 2.1.0 \
-  --dest /path/to/output
-
-# Create ontology with all outputs in specific directory
-hedpy schema create-ontology /path/to/hed-schemas lang 1.1.0 \
-  --dest ./ontologies
-```
-
 **Best practices:**
 
 1. Validate schema thoroughly before adding IDs
@@ -614,11 +596,8 @@ hedpy schema validate my_schema.xml --add-all-extensions
 #### Workflow 4: Preparing for schema release
 
 ```bash
-# Step 1: Add HED IDs
+# Add HED IDs
 hedpy schema add-ids /path/to/hed-schemas my_library 1.0.0
-
-# Step 2: Generate ontology
-hedpy schema create-ontology /path/to/hed-schemas my_library 1.0.0
 ```
 
 ______________________________________________________________________

tests/test_cli_parameter_parity.py

@@ -244,25 +244,6 @@ def test_schema_add_ids_parameters(self):
         self.assertEqual(cli_opts["positional"][1], "schema_name", "Second positional should be schema_name")
         self.assertEqual(cli_opts["positional"][2], "schema_version", "Third positional should be schema_version")
 
-    def test_schema_create_ontology_parameters(self):
-        """Test schema create-ontology uses positional arguments."""
-        schema_group = cli.commands.get("schema")
-        ontology_command = schema_group.commands.get("create-ontology")
-        self.assertIsNotNone(ontology_command, "create-ontology command not found")
-
-        cli_opts = self._get_click_options(ontology_command)
-
-        # Should have 3 positional arguments
-        self.assertEqual(
-            len(cli_opts["positional"]), 3, f"Should have 3 positional arguments, got {len(cli_opts['positional'])}"
-        )
-        self.assertEqual(cli_opts["positional"][0], "repo_path", "First positional should be repo_path")
-        self.assertEqual(cli_opts["positional"][1], "schema_name", "Second positional should be schema_name")
-        self.assertEqual(cli_opts["positional"][2], "schema_version", "Third positional should be schema_version")
-
-        # Check --dest option exists
-        self.assertIn("dest", cli_opts["optional"], "--dest option not found")
-
     def test_all_legacy_commands_have_cli_equivalents(self):
         """Test that all legacy script entry points have CLI equivalents."""
         # Legacy commands from pyproject.toml
@@ -272,7 +253,6 @@ def test_all_legacy_commands_have_cli_equivalents(self):
             "hed_validate_schemas": "schema validate",
             "hed_update_schemas": "schema convert",
             "hed_add_ids": "schema add-ids",
-            "hed_create_ontology": "schema create-ontology",
         }
 
         for legacy, cli_path in legacy_to_cli.items():