fix. removed contributing.md from mkdocs

acmc/phen.py

@@ -54,7 +54,7 @@ CONFIG_SCHEMA = {
             "version": {
                 "type": "string",
                 "required": True,
-                "regex": r"^v\d+\.\d+\.\d+$"  # Enforces 'vN.N.N' format
+                "regex": r"^v\d+\.\d+\.\d+$",  # Enforces 'vN.N.N' format
             },
             "omop": {
                 "type": "dict",
@@ -65,9 +65,9 @@ CONFIG_SCHEMA = {
                     "vocabulary_reference": {
                         "type": "string",
                         "required": True,
-                        "regex": r"^https?://.*"  # Ensures it's a URL
+                        "regex": r"^https?://.*",  # Ensures it's a URL
+                    },
                 },
-                }
             },
             "concept_sets": {
                 "type": "list",
@@ -82,12 +82,12 @@ CONFIG_SCHEMA = {
                             "schema": {
                                 "path": {"type": "string", "required": True},
                                 "columns": {"type": "dict", "required": True},
-                                "category": {"type": "string"},  # Optional but must be string if present
+                                "category": {
+                                    "type": "string"
+                                },  # Optional but must be string if present
                                 "actions": {
                                     "type": "dict",
-                                    "schema": {
-                                        "divide_col": {"type": "string"}
-                                    },
+                                    "schema": {"divide_col": {"type": "string"}},
                                 },
                             },
                         },
@@ -99,6 +99,7 @@ CONFIG_SCHEMA = {
     }
 }
 
+
 class PhenValidationException(Exception):
     """Custom exception class raised when validation errors in phenotype configuration file"""
 
@@ -320,9 +321,7 @@ def validate(phen_dir):
                 logger.debug("YAML structure is valid.")
             else:
                 logger.error(f"YAML structure validation failed: {validator.errors}")
-                raise Exception(
-                    f"YAML structure validation failed: {validator.errors}"
-                )                
+                raise Exception(f"YAML structure validation failed: {validator.errors}")
         except yaml.YAMLError as e:
             logger.error(f"YAML syntax error: {e}")
             raise e
@@ -387,7 +386,6 @@ def validate(phen_dir):
                 if action not in COL_ACTIONS:
                     validation_errors.append(f"Action {action} is not supported")
 
-
     if len(validation_errors) > 0:
         logger.error(validation_errors)
         raise PhenValidationException(

docs/mkdocs.yml

-site_name: ACMC Documentation
-theme:
-  name: material
-  features:
-    - navigation.tabs
-    - navigation.expand
-    - content.code.copy  
-nav:
-  - Home: index.md
-  - Installation: installation.md
-  - Usage: usage.md
-  - Contributing: contributing.md
-  - API Reference: api.md
-  - Tutorials:
-    - Example 1 - Basic local phenotype: ./tutorials/example1.md
-    - Example 2 - More complex local phenotype: ./tutorials/example2.md
-    - Example 3 - Using a remote git repository: ./tutorials/example3.md
-  - Contributing: contributing.md
-  - Change Log: changelog.md
-  - Troubleshooting: troubleshooting.md
-repo_url: https://git.soton.ac.uk/meldb/concepts-processing/
-plugins:
-  - search
-  - mkdocstrings:
-      handlers:
-        python:
-          options:
-            show_source: false

mkdocs.yml

@@ -9,13 +9,11 @@ nav:
   - Home: index.md
   - Installation: installation.md
   - Usage: usage.md
-  - Contributing: contributing.md
   - API Reference: api.md
   - Tutorials:
     - Example 1 - Basic local phenotype: ./tutorials/example1.md
     - Example 2 - More complex local phenotype: ./tutorials/example2.md
     - Example 3 - Using a remote git repository: ./tutorials/example3.md
-  - Contributing: contributing.md
   - Change Log: changelog.md
   - Troubleshooting: troubleshooting.md
 repo_url: https://git.soton.ac.uk/meldb/concepts-processing/