Used uvx in some actions

Author: VisLab

.github/workflows/black.yaml

@@ -22,13 +22,5 @@ jobs:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Create virtual environment
-        run: |
-          uv venv --clear .venv
-          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
-
-      - name: Install Black
-        run: uv pip install "black>=24.0.0"
-
-      - name: Check code formatting with Black
-        run: black --check --diff --workers 1 .
+      - name: Run Black formatter (check only)
+        run: uvx black --check --diff .

.github/workflows/codespell.yaml

@@ -22,17 +22,8 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v5
         with:
-          python-version: '3.10'
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Create virtual environment
-        run: |
-          uv venv --clear .venv
-          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: uv pip install codespell tomli
-
       - name: Run Codespell
-        run: codespell .
+        run: uvx --with tomli codespell .

.github/workflows/mdformat.yaml

@@ -26,15 +26,6 @@ jobs:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Create virtual environment
-        run: |
-          uv venv --clear .venv
-          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
-
-      - name: Install dependencies
-        run: uv pip install "mdformat>=0.7.0" "mdformat-myst>=0.1.5"
-
       - name: Run mdformat (check only)
         run: |
-          mdformat --check --wrap no --number docs/
-          mdformat --check --wrap no --number *.md
+          run: uvx --with "mdformat-myst>=0.1.5" mdformat --check --wrap no --number docs/ *.md

.github/workflows/ruff.yaml

@@ -24,13 +24,5 @@ jobs:
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
 
-      - name: Create virtual environment
-        run: |
-          uv venv --clear .venv
-          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
-
-      - name: Install Ruff
-        run: uv pip install "ruff>=0.8.0"
-
-      - name: Run Ruff linter
-        run: ruff check .
+      - name: Run Ruff linter and formatter check
+        run: uvx ruff check . && uvx ruff format --check .

hed/schema/schema_attribute_validators.py

@@ -43,11 +43,11 @@ class SchemaComparer:
         MISC_SECTION: "Misc Metadata",
         HED_ID_SECTION: "Modified Hed Ids",
         EXTRAS_SECTION: "Extras",
+        SOURCES: "Sources",
+        PREFIXES: "Prefixes",
+        ANNOTATION_PROPERTY_EXTERNAL: "AnnotationPropertyExternal",
     }
 
-    # TODO: Check that the cases of these are correct.
-    DF_EXTRAS = {SOURCES, PREFIXES, ANNOTATION_PROPERTY_EXTERNAL}
-
     def __init__(self, schema1, schema2):
         """Initialize the SchemaComparer with two schemas.
 
@@ -305,8 +305,6 @@ def _add_unequal_entries(self, change_dict, unequal_entries):
         for section_key, changes in unequal_entries.items():
             if section_key == self.MISC_SECTION:
                 self._add_misc_section_changes(change_dict, section_key, changes)
-            elif section_key in self.DF_EXTRAS:
-                self._add_extras_section_changes(change_dict, section_key, changes)
             else:
                 for tag, (entry1, entry2) in changes.items():
                     if section_key == HedSectionKey.UnitClasses:
@@ -339,35 +337,6 @@ def _add_misc_section_changes(change_dict, section_key, changes):
             )
             change_dict[section_key].append({"change_type": change_type, "change": change_desc, "tag": misc_section})
 
-    def _add_extras_section_changes(self, change_dict, section_key, changes):
-        """Add changes for extras sections (dataframes) to the change dictionary.
-
-        Handles changes to dataframe-based extras like Sources, Prefixes, and AnnotationPropertyExternal.
-        Note: Extras sections are actually handled by _add_extras_changes which directly compares
-        the dataframes from schema.extras. This method handles any extras-related entries that
-        might appear in the unequal_entries from compare_schemas.
-
-        Parameters:
-            change_dict (defaultdict): Change dictionary to append to.
-            section_key (str): The section identifier (e.g., SOURCES, PREFIXES).
-            changes (dict): Dictionary mapping entry names to (entry1, entry2) tuples.
-        """
-        # Extras sections (Sources, Prefixes, AnnotationPropertyExternal) are stored as dataframes
-        # in schema.extras rather than as schema entries, so they're handled separately
-        # by _add_extras_changes. If we somehow get extras entries here, treat them generically.
-        for name, (entry1, entry2) in changes.items():
-            # Compare the entries as generic schema entries
-            if hasattr(entry1, "attributes") and hasattr(entry2, "attributes"):
-                if entry1.attributes != entry2.attributes:
-                    change_dict[section_key].append(
-                        {"change_type": "Patch", "change": f"{name} attributes modified", "tag": name}
-                    )
-            if hasattr(entry1, "description") and hasattr(entry2, "description"):
-                if entry1.description != entry2.description:
-                    change_dict[section_key].append(
-                        {"change_type": "Patch", "change": f"{name} description modified", "tag": name}
-                    )
-
     @staticmethod
     def _add_unit_classes_changes(change_dict, section_key, entry1, entry2):
         """Add changes in unit class definitions to the change dictionary.
@@ -546,7 +515,7 @@ def _add_extras_changes(self, change_dict):
         Parameters:
             change_dict (defaultdict): Change dictionary to append to.
         """
-        from hed.schema.schema_io.df_constants import UNIQUE_EXTRAS_KEYS
+        from hed.schema.schema_io.df_constants import UNIQUE_EXTRAS_KEYS, in_library as _in_library
 
         extras1 = getattr(self.schema1, "extras", {}) or {}
         extras2 = getattr(self.schema2, "extras", {}) or {}
@@ -575,9 +544,9 @@ def _add_extras_changes(self, change_dict):
 
             key_cols = UNIQUE_EXTRAS_KEYS.get(key)
             if not key_cols:
-                key_cols = list(set(df1.columns) & set(df2.columns))
+                key_cols = [c for c in set(df1.columns) & set(df2.columns) if c != _in_library]
 
-            compare_cols = list(set(df1.columns) & set(df2.columns))
+            compare_cols = [c for c in set(df1.columns) & set(df2.columns) if c != _in_library]
             if not compare_cols:
                 continue
 

hed/schema/schema_comparer.py

@@ -33,9 +33,9 @@ def _is_prerelease_partner(base_schema) -> bool:
 
 
 def validate_schema_object(base_schema, schema_name):
-    """Validate a schema object by checking compliance and roundtrip conversion.
+    """Validate a schema object by checking non-warning compliance and roundtrip conversion.
 
-    Tests the schema for compliance issues and validates that it can be successfully
+    Tests the schema for non-warningcompliance issues and validates that it can be successfully
     converted to and reloaded from all four formats (MEDIAWIKI, XML, JSON, TSV).
 
     Parameters: