Updated the events summary and events quality

.github/workflows/ci.yaml

@@ -16,12 +16,12 @@ jobs:
         run: |
           if [[ "${{ github.event_name }}" == 'push' && "${{ github.ref }}" == 'refs/heads/master' ]]; then
             # Push to master branch
-            echo 'matrix=["3.8", "3.9", "3.10", "3.11"]' >> $GITHUB_OUTPUT
+            echo 'matrix=["3.9", "3.10", "3.11", "3.12", "3.13"]' >> $GITHUB_OUTPUT
           elif [[ "${{ github.event_name }}" == 'pull_request' && "${{ github.event.pull_request.base.ref }}" == 'master' ]]; then
             # PR to master branch
-            echo 'matrix=["3.8", "3.9", "3.10", "3.11"]' >> $GITHUB_OUTPUT
+            echo 'matrix=["3.9", "3.10", "3.11", "3.12", "3.13"]' >> $GITHUB_OUTPUT
           else
-            echo 'matrix=["3.9", "3.11"]' >> $GITHUB_OUTPUT
+            echo 'matrix=["3.9", "3.13"]' >> $GITHUB_OUTPUT
           fi
 
   build:
@@ -51,7 +51,7 @@ jobs:
       # Install dependencies
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade --upgrade-strategy eager pip
+          python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r docs/requirements.txt
 

.github/workflows/ci_cov.yaml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest]
-        python-version: [ "3.9" ]
+        python-version: [ "3.12" ]
 
     runs-on: ${{ matrix.platform }}
 
@@ -46,7 +46,7 @@ jobs:
       # Install dependencies
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade --upgrade-strategy eager pip
+          python -m pip install --upgrade pip
           pip install flake8 coverage -r requirements.txt -r docs/requirements.txt
 
       # Run flake8

.github/workflows/ci_windows.yaml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest]
-        python-version: ["3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13""]
 
     runs-on: ${{ matrix.platform }}
 
@@ -32,7 +32,7 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade --upgrade-strategy eager pip
+          python -m pip install --upgrade pip
           pip install -r requirements.txt
 
       - name: Test with unittest

.github/workflows/test_installer.yaml

@@ -1,44 +1,44 @@
-on:
-  push:
-    branches: ["develop"]
-  pull_request:
-    branches: ["develop"]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    strategy:
-      matrix:
-        python-version: ["3.8", "3.11"]
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Create work directory
-      run: |
-        mkdir workdir
-        echo "WORKDIR=$(pwd)/workdir" >> $GITHUB_OUTPUT
-
-    - name: Create and activate virtual environment
-      run: |
-        cd $WORKDIR
-        python -m venv .venv
-        source .venv/bin/activate
-
-    - name: Install package
-      run: |
-        cd $WORKDIR
-        source .venv/bin/activate
-        python -m pip install --upgrade pip
-        pip install $GITHUB_WORKSPACE
-
-    - name: Run post-installation test
-      run: |
-        cd $WORKDIR
-        source .venv/bin/activate
-        python -c "from hed.models.hed_string import HedString; print('Import test passed.')"
+on:
+  push:
+    branches: ["develop"]
+  pull_request:
+    branches: ["develop"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Create work directory
+      run: |
+        mkdir workdir
+        echo "WORKDIR=$(pwd)/workdir" >> $GITHUB_OUTPUT
+
+    - name: Create and activate virtual environment
+      run: |
+        cd $WORKDIR
+        python -m venv .venv
+        source .venv/bin/activate
+
+    - name: Install package
+      run: |
+        cd $WORKDIR
+        source .venv/bin/activate
+        python -m pip install --upgrade pip
+        pip install $GITHUB_WORKSPACE
+
+    - name: Run post-installation test
+      run: |
+        cd $WORKDIR
+        source .venv/bin/activate
+        python -c "from hed.models.hed_string import HedString; print('Import test passed.')"

docs/requirements.txt

@@ -1,12 +1,12 @@
 defusedxml>=0.7.1
-inflect>=6.0.5
-jsonschema>=4.17.3
-numpy>=1.21.6
-openpyxl>=3.1.0
-pandas>=1.3.5
-portalocker>=2.7.0
+inflect>=7.5.0
+jsonschema>=4.23.0
+numpy==2.0.2
+openpyxl>=3.1.5
+pandas>=2.2.3
+portalocker>=3.1.1
 semantic-version>=2.10.0
-myst-parser>=1.0.0
-Sphinx>=5.2.2
-sphinx_rtd_theme>=1.0.0
-wordcloud==1.9.4
+myst-parser==3.0.1
+Sphinx==7.4.7
+sphinx_rtd_theme>=3.0.2
+wordcloud>=1.9.4

hed/errors/error_messages.py

@@ -5,7 +5,18 @@
 
 from hed.errors.error_reporter import hed_error, hed_tag_error
 from hed.errors.error_types import (ValidationErrors, SidecarErrors, ErrorSeverity, DefinitionErrors,
-                                    TemporalErrors, ColumnErrors)
+                                    TemporalErrors, ColumnErrors, TagQualityErrors)
+
+def get_tag_list_str(tag_list):
+    """ Return a string representation of a list of tags.
+
+    Parameters:
+        tag_list (list): A list of tags to convert to a string.
+
+    Returns:
+        str: A string representation of the list of tags.
+    """
+    return "[" + ', '.join([str(tag) for tag in tag_list]) + "]"
 
 
 @hed_tag_error(ValidationErrors.UNITS_INVALID)
@@ -109,9 +120,9 @@ def val_error_duplicate_reserved_tag(tag, group):
 
 
 @hed_error(ValidationErrors.HED_RESERVED_TAG_GROUP_ERROR, actual_code=ValidationErrors.TAG_GROUP_ERROR)
-def val_error_group_for_reserved_tag(group, group_count):
+def val_error_group_for_reserved_tag(group, group_count, tag_list):
     return (f'The number of non-def-expand subgroups for group "{group}" is {group_count}, "'
-            f'which does not meet reserved tag requirements."')
+            f'which does not meet reserved tags {get_tag_list_str(tag_list)} requirements."')
 
 
 @hed_error(ValidationErrors.PARENTHESES_MISMATCH)
@@ -211,8 +222,8 @@ def val_error_extra_slashes_spaces(tag, problem_tag):
 
 
 @hed_error(ValidationErrors.SIDECAR_KEY_MISSING, default_severity=ErrorSeverity.WARNING)
-def val_error_sidecar_key_missing(invalid_keys, category_keys):
-    return f"Category keys '{invalid_keys}' do not exist in column.  Valid keys are: {category_keys}"
+def val_error_sidecar_key_missing(invalid_keys, category_keys, column_name):
+    return f"Category keys {invalid_keys} do not exist in sidecar for column '{column_name}'.  Valid keys are: {category_keys}"
 
 
 @hed_error(ValidationErrors.TSV_COLUMN_MISSING, actual_code=ValidationErrors.SIDECAR_KEY_MISSING,
@@ -338,8 +349,7 @@ def def_error_no_group_tags(def_name):
 
 @hed_error(DefinitionErrors.WRONG_NUMBER_GROUPS, actual_code=ValidationErrors.DEFINITION_INVALID)
 def def_error_wrong_number_groups(def_name, tag_list):
-    tag_list_strings = [str(tag) for tag in tag_list]
-    return f"Too many group tags found in definition for {def_name}.  Expected 1, found: {tag_list_strings}"
+    return f"Too many group tags found in definition for {def_name}.  Expected 1, found: {get_tag_list_str(tag_list)}"
 
 
 @hed_error(DefinitionErrors.WRONG_NUMBER_TAGS, actual_code=ValidationErrors.DEFINITION_INVALID)
@@ -350,9 +360,8 @@ def def_error_wrong_number_tags(def_name, tag_list):
 
 @hed_error(DefinitionErrors.WRONG_NUMBER_PLACEHOLDER_TAGS, actual_code=ValidationErrors.DEFINITION_INVALID)
 def def_error_wrong_placeholder_count(def_name, expected_count, tag_list):
-    tag_list_strings = [str(tag) for tag in tag_list]
     return f"Incorrect number placeholders or placeholder tags found in definition for {def_name}.  " + \
-           f"Expected {expected_count}, found: {tag_list_strings}"
+           f"Expected {expected_count}, found:  {get_tag_list_str(tag_list)}"
 
 
 @hed_error(DefinitionErrors.DUPLICATE_DEFINITION, actual_code=ValidationErrors.DEFINITION_INVALID)
@@ -462,3 +471,42 @@ def nested_column_ref(column_name, ref_column):
 @hed_error(ColumnErrors.MALFORMED_COLUMN_REF, actual_code=SidecarErrors.SIDECAR_BRACES_INVALID)
 def malformed_column_ref(column_name, index, symbol):
     return f"Column {column_name} has a malformed column reference.  Improper symbol {symbol} found at index {index}."
+
+
+@hed_error(TagQualityErrors.MISSING_EVENT_TYPE, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.MISSING_EVENT_TYPE)
+def missing_event_type(string, line):
+    return f"The HED string '{string}' at line {line} has no Event type."
+
+
+@hed_error(TagQualityErrors.IMPROPER_EVENT_GROUPS, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.IMPROPER_EVENT_GROUPS)
+def improper_event_groups(event_types, string, line):
+    return f"The HED string '{string}' at line {line} has multiple events [{event_types}] but is improperly " + \
+    f"parenthesized so the other tags cannot be uniquely associated with an event."
+
+
+@hed_error(TagQualityErrors.MISSING_TASK_ROLE, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.MISSING_TASK_ROLE)
+def missing_task_role(event_type, string, line):
+    return f"The HED string '{string}' at line {line} with event {event_type} has no Task-event-role type tag."
+
+
+@hed_error(TagQualityErrors.AMBIGUOUS_TAG_GROUPING, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.AMBIGUOUS_TAG_GROUPING)
+def ambiguous_tag_grouping(tag_list, string, line):
+    return f"The HED string '{string}' at line {line} has ambiguously grouped tags {get_tag_list_str(tag_list)}and needs parentheses."
+
+
+@hed_error(TagQualityErrors.MISSING_SENSORY_PRESENTATION, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.MISSING_SENSORY_PRESENTATION)
+def missing_sensory_presentation(string, line):
+    return f"The HED string '{string}' at line {line} is a Sensory-event but does not have a sensory presentation " + \
+    f"modality tag such as Visual-presentation or Auditory-presentation."
+
+
+@hed_error(TagQualityErrors.MISSING_ACTION_TAG, default_severity=ErrorSeverity.WARNING,
+           actual_code=TagQualityErrors.MISSING_ACTION_TAG)
+def missing_action_tag(string, line):
+    return f"The HED string '{string}' at line {line} is an Agent-action event but does not any Action tags " + \
+    f"such as Move or Perform."