Separated coverage action from just tests

.github/workflows/ci.yaml

@@ -52,125 +52,21 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade --upgrade-strategy eager pip
-          pip install flake8
-          pip install coverage
           pip install -r requirements.txt
           pip install -r docs/requirements.txt
 
-
-      # Run flake8 only for Python 3.9
-      - name: Lint with flake8
-        if: matrix.python-version == '3.9'
-        run: |
-          pip install flake8
-          flake8 . --count --show-source --statistics --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 
-
-
-
-      # Run unittest with coverage for Python 3.9
-      - name: Test with unittest and coverage (v3.9)
+      # Run unittest without coverage
+      - name: Test with unittest
         env:
           HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: matrix.python-version == '3.9'
-        run: |  
-            pip install coverage
-            coverage run -m unittest discover tests
-            continue-on-error: true
-      
-
-
-      # Run unittest without coverage for non Python 3.9
-      - name: Test with unittest (non-3.9)
-        env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: matrix.python-version != '3.9'
         run: |
           python -m unittest discover tests
           continue-on-error: true
 
-
-
-      # Run spec tests with coverage for Python 3.9
-      - name: Run spec_test coverage
-        env:
-          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: matrix.python-version == '3.9'
-        run: |  
-           coverage run --append -m unittest discover tests/spec_tests
-           ls -a
-           continue-on-error: true
-
-
       # Run spec tests without coverage for non Python 3.9
       - name: Run spec_test
         env:
           HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        if: matrix.python-version != '3.9'
         run: |  
            python -m unittest discover tests/spec_tests
            continue-on-error: true
-
-      # Archive code coverage results for Python 3.9
-      - name: Archive code coverage results for Python 3.9
-        if: ${{matrix.python-version == '3.9'}}
-        uses: actions/upload-artifact@v4
-        with:
-          name: code-coverage-report
-          path: .coverage
-          if-no-files-found: error
-
-  check-secret:
-    runs-on: ubuntu-latest
-    outputs:
-      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
-    steps:
-      - name: Check for Secret availability
-        id: check-for-secrets
-        # perform secret check & put boolean result as an output
-        shell: bash
-        run: |
-          if [ "${{ secrets.CC_TEST_REPORTER_ID }}" != '' ]; then
-            echo "defined=true" >> $GITHUB_OUTPUT;
-          else
-            echo "defined=false" >> $GITHUB_OUTPUT;
-          fi
-
-  coverage:
-    name: Publish coverage
-    needs: [build, check-secret]
-    runs-on: ubuntu-latest
-    if: needs.check-secret.outputs.secrets-exist == 'true'
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-
-      - uses: actions/cache@v4
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade --upgrade-strategy eager pip
-          pip install flake8
-          pip install coverage
-          pip install -r requirements.txt
-          pip install -r docs/requirements.txt
-
-      - name: Download a single artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: code-coverage-report
-
-      - name: publish-coverages
-        with:
-          coverageCommand: coverage xml
-          debug: true
-        uses: paambaati/[email protected]
-        env:
-          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
-

.github/workflows/ci_cov.yaml

@@ -0,0 +1,89 @@
+name: CI
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+jobs:
+
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-exist: ${{ steps.check-for-secrets.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: check-for-secrets
+        # perform secret check & put boolean result as an output
+        shell: bash
+        run: |
+          if [ "${{ secrets.CC_TEST_REPORTER_ID }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
+  build:
+    needs: check-secret
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [ "3.9" ]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade --upgrade-strategy eager pip
+          pip install flake8
+          pip install coverage
+          pip install -r requirements.txt
+          pip install -r docs/requirements.txt
+
+      # Run flake8 only for Python 3.9
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          flake8 . --count --show-source --statistics --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 
+
+      # Run unittest with coverage
+      - name: Test with unittest and coverage
+        env:
+          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |  
+            coverage run -m unittest discover tests
+            continue-on-error: true  
+
+      # Run spec tests with coverage
+      - name: Run spec_test coverage
+        env:
+          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |  
+           coverage run --append -m unittest discover tests/spec_tests
+           continue-on-error: true
+
+      - name: publish-coverages
+        with:
+          coverageCommand: coverage xml
+          debug: true
+        uses: paambaati/[email protected]
+        env:
+          CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
+

hed/errors/error_messages.py

@@ -51,16 +51,19 @@ def val_error_element_deprecatedr(tag):
 def val_error_invalid_tag_character(tag, problem_tag):
     return f"Invalid character '{problem_tag}' in tag '{tag}'"
 
+
 @hed_tag_error(ValidationErrors.INVALID_VALUE_CLASS_CHARACTER, has_sub_tag=True,
                actual_code=ValidationErrors.CHARACTER_INVALID)
 def val_error_INVALID_VALUE_CLASS_CHARACTER(tag, problem_tag, value_class):
     return f"Invalid character '{problem_tag}' in tag '{tag}' for value class '{value_class}'"
 
+
 @hed_tag_error(ValidationErrors.INVALID_VALUE_CLASS_VALUE, has_sub_tag=True,
                actual_code=ValidationErrors.VALUE_INVALID)
 def val_error_INVALID_VALUE_CLASS_VALUE(tag, problem_tag, value_class):
     return f"'{tag}' has an invalid value portion for value class '{value_class}'"
 
+
 @hed_error(ValidationErrors.TILDES_UNSUPPORTED)
 def val_error_tildes_not_supported(source_string, char_index):
     character = source_string[char_index]

hed/errors/schema_error_messages.py

@@ -33,19 +33,22 @@ def schema_error_SCHEMA_INVALID_CHILD(tag, child_tag_list):
 
 @hed_error(SchemaAttributeErrors.SCHEMA_ATTRIBUTE_INVALID)
 def schema_error_unknown_attribute(attribute_name, source_tag):
-    return f"Attribute '{attribute_name}' used by '{source_tag}' was not defined in the schema, or was used outside of it's defined class."
+    return f"Attribute '{attribute_name}' used by '{source_tag}' "
+    f"was not defined in the schema, or was used outside of it's defined class."
 
 
 @hed_error(SchemaWarnings.SCHEMA_PRERELEASE_VERSION_USED, default_severity=ErrorSeverity.WARNING)
 def schema_error_SCHEMA_PRERELEASE_VERSION_USED(current_version, known_versions):
-    return f"Schema version {current_version} used, which is prerelease or unofficial.  Known versions are: {', '.join(known_versions)}"
+    return f"Schema version {current_version} used, which is prerelease or unofficial. "
+    f"Known versions are: {', '.join(known_versions)}"
 
 
 @hed_error(SchemaWarnings.SCHEMA_PROLOGUE_CHARACTER_INVALID, default_severity=ErrorSeverity.WARNING,
            actual_code=SchemaWarnings.SCHEMA_CHARACTER_INVALID)
 def schema_error_invalid_character_prologue(char_index, source_string, section_name):
     invalid_char = source_string[char_index]
-    return f"'{section_name}' has invalid character '{invalid_char}' at position {char_index} of string: {source_string}"
+    return f"'{section_name}' has invalid character '{invalid_char}' at "
+    f"position {char_index} of string: {source_string}"
 
 
 @hed_error(SchemaWarnings.SCHEMA_INVALID_CHARACTERS_IN_DESC, default_severity=ErrorSeverity.WARNING,

hed/models/definition_dict.py

@@ -209,7 +209,7 @@ def _find_group(self, definition_tag, group, error_handler):
         # initial validation
         groups = group.groups()
         issues = []
-        tags = group.tags()
+        # tags = group.tags()
         # if len(tags) != 1:
         #     issues += \
         #         ErrorHandler.format_error_with_context(error_handler,

hed/schema/hed_schema_df_constants.py

@@ -26,7 +26,7 @@
 
 
 DF_EXTRA_SUFFIXES = {PREFIXES_KEY, EXTERNAL_ANNOTATION_KEY}
-DF_SUFFIXES_OMN = { *DF_SUFFIXES, *DF_EXTRA_SUFFIXES}
+DF_SUFFIXES_OMN = {*DF_SUFFIXES, *DF_EXTRA_SUFFIXES}
 
 
 section_mapping_hed_id = {

hed/schema/schema_io/df2schema.py

@@ -104,7 +104,7 @@ def _read_schema(self, dataframe):
             dataframe (pd.DataFrame): The dataframe for the main tags section
         """
         self._schema._initialize_attributes(HedSectionKey.Tags)
-        known_parent_tags =  {"HedTag": []}
+        known_parent_tags = {"HedTag": []}
         iterations = 0
         # Handle this over multiple iterations in case tags have parent tags listed later in the file.
         # A properly formatted .tsv file will never have parents after the child.
@@ -179,7 +179,7 @@ def _create_tag_entry(self, parent_tags, row_number, row):
                 long_tag_name = tag_name
             return self._create_entry(row_number, row, HedSectionKey.Tags, long_tag_name)
 
-        self._add_fatal_error(row_number, row, f"No tag name found in row.",
+        self._add_fatal_error(row_number, row, "No tag name found in row.",
                               error_code=HedExceptions.GENERIC_ERROR)
 
     def _read_section(self, df, section_key):
@@ -276,5 +276,3 @@ def load_dataframes_from_strings(schema_data):
     return {key: value if isinstance(value, pd.DataFrame) else pd.read_csv(io.StringIO(value), sep="\t",
                                                                            dtype=str, na_filter=False)
             for key, value in schema_data.items()}
-
-