Preliminary merge of develop to adjust doc links

.github/workflows/ci.yaml

@@ -39,11 +39,11 @@ jobs:
           submodules: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
@@ -69,10 +69,11 @@ jobs:
 
       - name: Run spec_test coverage
         run: HED_GITHUB_TOKEN=${{ secrets.HED_GITHUB_TOKEN }} coverage run --append -m unittest spec_tests/test_errors.py
+        continue-on-error: true
 
       - name: Archive code coverage results
         if: ${{matrix.python-version == '3.9'}}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: code-coverage-report
           path: .coverage
@@ -102,11 +103,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
@@ -120,7 +121,7 @@ jobs:
           pip install -r docs/requirements.txt
 
       - name: Download a single artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: code-coverage-report
 

.github/workflows/spec_tests.yaml

@@ -22,7 +22,7 @@ jobs:
           submodules: true
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -31,13 +31,30 @@ jobs:
           python -m pip install --upgrade --upgrade-strategy eager pip
           pip install -r requirements.txt
 
-      - name: Test with unittest
+      - name: Spec Error Tests
+        id: spec_error_tests
+        continue-on-error: true
         run: |
-           python -m unittest spec_tests/test_errors.py > test_results.txt
+           python -m unittest spec_tests/test_errors.py > error_results.txt
 
-      - name: Upload spec test results
-        uses: actions/upload-artifact@v3
+      - name: Bids Validation Test
+        id: bids_validation_test
+        continue-on-error: true
+        run: |
+           python -m unittest spec_tests/validate_bids.py > validate_bids_results.txt
+
+      - name: Upload error test results
+        uses: actions/upload-artifact@v4
+        with:
+          name: error-test-results
+          path: error_results.txt
+
+      - name: Upload bids test results
+        uses: actions/upload-artifact@v4
         with:
-          name: spec-test-results
-          path: test_results.txt
+          name: bids-test-results
+          path: validate_bids_results.txt
 
+      - name: Fail if Tests Failed
+        if: steps.spec_error_tests.outcome == 'failure' || steps.bids_validation_test.outcome == 'failure'
+        run: exit 1

.github/workflows/test_installer.yaml

@@ -0,0 +1,31 @@
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.10"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel
+    - name: Install package
+      run: |
+        pip install .
+    - name: Run post-installation test
+      run: |
+        python -c "import hed"

.gitmodules

@@ -2,3 +2,8 @@
 	path = spec_tests/hed-specification
 	url = https://github.com/hed-standard/hed-specification/
 	branch = develop
+
+[submodule "spec_tests/hed-examples"]
+	path = spec_tests/hed-examples
+	url = https://github.com/hed-standard/hed-examples/
+	branch = develop

docs/requirements.txt

@@ -1,5 +1,6 @@
 defusedxml>=0.7.1
 inflect>=6.0.5
+jsonschema>=4.17.3
 numpy>=1.21.6
 openpyxl>=3.1.0
 pandas>=1.3.5
@@ -8,4 +9,5 @@ semantic_version>=2.10.0
 myst-parser>=1.0.0
 Sphinx>=5.2.2
 sphinx_rtd_theme>=1.0.0
-wordcloud==1.9.2
+wordcloud==1.9.3
+rdflib>=6

docs/source/_static/customize_icon.css

@@ -0,0 +1,13 @@
+.icon-home:before {
+  content: '';
+  /* Other styles to adjust size, positioning, etc. */
+  display: inline-block;
+  width: 24px;
+  height: 24px;
+  background: url('images/croppedWideLogo.png') no-repeat center center;
+  background-size: contain;
+}
+
+.icon-home {
+  font-family: inherit;
+}

docs/source/_templates/custom-class-template.rst

@@ -8,34 +8,24 @@
 .. rubric:: {{ _('Methods') }}
 
 .. autosummary::
-{% for item in methods %}
-   {{ module }}.{{ objname }}.{{ item }}
+{%- for item in methods %}
+   {{ objname }}.{{ item }}
 {%- endfor %}
 
 .. rubric:: {{ _('Attributes') }}
 
 .. autosummary::
-{% for item in attributes %}
-   {{ module }}.{{ objname }}.{{ item }}
+{%- for item in attributes %}
+   {{ objname }}.{{ item }}
 {%- endfor %}
 
-.. toctree::
-   :hidden:
-
-{% for item in methods %}
-   {{ fullname }}#method-{{ item }}
-{%- endfor %}
-{% for item in attributes %}
-   {{ fullname }}#attribute-{{ item }}
-{%- endfor %}
-
-{% for item in methods %}
+{%- for item in methods %}
 .. _method-{{ item }}:
 
 .. automethod:: {{ module }}.{{ objname }}.{{ item }}
 {%- endfor %}
 
-{% for item in attributes %}
+{%- for item in attributes %}
 .. _attribute-{{ item }}:
 
 .. autoattribute:: {{ module }}.{{ objname }}.{{ item }}

docs/source/_templates/custom-module-template.rst

@@ -38,7 +38,7 @@
    .. rubric:: {{ _('Classes') }}
 
    .. autosummary::
-      :toctree:
+      :toctree: _generated_classes
       :template: custom-class-template.rst
    {% for item in classes %}
       {{ item }}

docs/source/conf.py

@@ -39,7 +39,7 @@
     "myst_parser",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
-    "sphinx.ext.autosectionlabel",
+    # "sphinx.ext.autosectionlabel",
     "sphinx.ext.intersphinx",
     "sphinx.ext.coverage",
     "sphinx.ext.mathjax",
@@ -97,3 +97,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+
+html_css_files = [
+    'customize_icon.css',
+]

docs/source/introduction.rst

@@ -42,10 +42,6 @@ Finding help
 
     The `HED online tools <https://hedtools.org>`_ provide an easy-to-use interface that requires no programming. 
 
-:Mailing lists and forums:
-
-    * Don't hesitate to ask questions about the python hedtools on `NeuroStars
-      <https://neurostars.org/tags/hedtools>`_.
 
 :Issues and problems:
     * If you notice a bug in the python hedtools code or encounter other problems using the tools, please `open an issue`_ in the

hed/errors/error_messages.py

@@ -25,6 +25,12 @@ def val_error_empty_group(tag):
     return f"HED tags cannot be empty.  Extra delimiters found: '{tag}'"
 
 
+@hed_tag_error(OnsetErrors.HED_ONSET_WITH_NO_COLUMN, actual_code=ValidationErrors.ONSET_OFFSET_INSET_ERROR)
+def val_error_hed_onset_with_no_column(tag):
+    return f"Cannot have Temporal tags without an 'Onset' column.  Found tag: '{tag}'"
+
+
+
 @hed_tag_error(ValidationErrors.TAG_EXTENDED, has_sub_tag=True, default_severity=ErrorSeverity.WARNING)
 def val_error_tag_extended(tag, problem_tag):
     return f"Hed tag is extended. '{problem_tag}' in {tag}"
@@ -39,7 +45,7 @@ def val_error_invalid_char(source_string, char_index):
 @hed_tag_error(ValidationErrors.INVALID_TAG_CHARACTER, has_sub_tag=True,
                actual_code=ValidationErrors.CHARACTER_INVALID)
 def val_error_invalid_tag_character(tag, problem_tag):
-    return f"Invalid character '{problem_tag}' in {tag}"
+    return f"Invalid character '{problem_tag}' in tag '{tag}'"
 
 
 @hed_error(ValidationErrors.TILDES_UNSUPPORTED)
@@ -48,6 +54,12 @@ def val_error_tildes_not_supported(source_string, char_index):
     return f"Tildes not supported.  Replace (a ~ b ~ c) with (a, (b, c)).  '{character}' at index {char_index}'"
 
 
+@hed_tag_error(ValidationErrors.CURLY_BRACE_UNSUPPORTED_HERE, has_sub_tag=True,
+               actual_code=SidecarErrors.SIDECAR_BRACES_INVALID)
+def val_error_CURLY_BRACE_UNSUPPORTED_HERE(tag, problem_tag):
+    return (f"Curly braces are only permitted in sidecars, fully wrapping text in place of a tag.  "
+            f"Invalid character '{problem_tag}' in tag '{tag}'")
+
 @hed_error(ValidationErrors.COMMA_MISSING)
 def val_error_comma_missing(tag):
     return f"Comma missing after - '{tag}'"
@@ -227,7 +239,6 @@ def val_warning_capitalization(tag):
 
 @hed_tag_error(ValidationErrors.UNITS_MISSING, default_severity=ErrorSeverity.WARNING)
 def val_warning_default_units_used(tag, default_unit):
-    # todo: add a test case for no default unit.
     if default_unit is None:
         return f"No unit specified on - '{tag}'.  No default unit is specified for type."
     return f"No unit specified. Using '{default_unit}' as the default - '{tag}'"
@@ -383,7 +394,7 @@ def onset_wrong_placeholder(tag, has_placeholder):
 
 @hed_error(ColumnErrors.INVALID_COLUMN_REF, actual_code=SidecarErrors.SIDECAR_BRACES_INVALID)
 def invalid_column_ref(bad_ref):
-    return f"The column '{bad_ref}' is unknown.'"
+    return f"The column '{bad_ref}' is unknown or does not have HED annotations.'"
 
 
 @hed_error(ColumnErrors.SELF_COLUMN_REF, actual_code=SidecarErrors.SIDECAR_BRACES_INVALID)

hed/errors/error_reporter.py

@@ -298,10 +298,9 @@ def format_error_from_context(error_type, error_context, *args, actual_error=Non
         if not error_func:
             error_object = ErrorHandler.val_error_unknown(*args, **kwargs)
             error_object['code'] = error_type
-            ErrorHandler._add_context_to_errors(error_object, error_context)
-            return [error_object]
+        else:
+            error_object = error_func(*args, **kwargs)
 
-        error_object = error_func(*args, **kwargs)
         if actual_error:
             error_object['code'] = actual_error
 
@@ -321,8 +320,6 @@ def _add_context_to_errors(error_object, error_context_to_add):
             list: A list of dict with needed context strings added at the beginning of the list.
 
         """
-        if error_object is None:
-            error_object = {}
         for (context_type, context) in error_context_to_add:
             error_object[context_type] = context
 
@@ -345,11 +342,7 @@ def _get_tag_span_to_error_object(error_object):
         if ErrorContext.HED_STRING not in error_object:
             return None, None
 
-        if 'char_index' in error_object:
-            char_index = error_object['char_index']
-            char_index_end = error_object.get('char_index_end', char_index + 1)
-            return char_index, char_index_end
-        elif 'source_tag' in error_object:
+        if 'source_tag' in error_object:
             source_tag = error_object['source_tag']
             if isinstance(source_tag, int):
                 return None, None
@@ -364,7 +357,9 @@ def _get_tag_span_to_error_object(error_object):
     def _update_error_with_char_pos(error_object):
         # This part is optional as you can always generate these as needed.
         start, end = ErrorHandler._get_tag_span_to_error_object(error_object)
-        if start is not None and end is not None:
+        if start is not None:
+            # silence warning in pycharm
+            start = int(start)
             source_tag = error_object.get('source_tag', None)
             # Todo: Move this functionality somewhere more centralized.
             # If the tag has been modified from the original, don't try to use sub indexing.

hed/errors/error_types.py

@@ -90,6 +90,8 @@ class ValidationErrors:
 
     INVALID_TAG_CHARACTER = 'invalidTagCharacter'
 
+    CURLY_BRACE_UNSUPPORTED_HERE = "CURLY_BRACE_UNSUPPORTED_HERE"
+
 
 
 class SidecarErrors:
@@ -164,7 +166,7 @@ class OnsetErrors:
     ONSET_TAG_OUTSIDE_OF_GROUP = "ONSET_TAG_OUTSIDE_OF_GROUP"
     INSET_BEFORE_ONSET = "INSET_BEFORE_ONSET"
     ONSET_SAME_DEFS_ONE_ROW = "ONSET_SAME_DEFS_ONE_ROW"
-
+    HED_ONSET_WITH_NO_COLUMN = 'HED_ONSET_WITH_NO_COLUMN'
 
 class ColumnErrors:
     INVALID_COLUMN_REF = "INVALID_COLUMN_REF"

hed/errors/exceptions.py

@@ -4,6 +4,7 @@
 class HedExceptions:
     GENERIC_ERROR = 'GENERIC_ERROR'
     # A list of all exceptions that can be generated by the hedtools.
+    URL_ERROR = "URL_ERROR"
     FILE_NOT_FOUND = 'fileNotFound'
     BAD_PARAMETERS = 'badParameters'
     CANNOT_PARSE_XML = 'cannotParseXML'
@@ -40,8 +41,13 @@ class HedExceptions:
     HED_SCHEMA_NODE_NAME_INVALID = 'HED_SCHEMA_NODE_NAME_INVALID'
 
     SCHEMA_DUPLICATE_PREFIX = 'schemaDuplicatePrefix'
+    SCHEMA_DUPLICATE_LIBRARY = "SCHEMA_LIBRARY_INVALID"
     BAD_COLUMN_NAMES = 'BAD_COLUMN_NAMES'
 
+    SCHEMA_DUPLICATE_NAMES = "SCHEMA_DUPLICATE_NAMES"
+
+    CANNOT_PARSE_RDF = "CANNOT_PARSE_RDF"
+
 
 class HedFileError(Exception):
     """Exception raised when a file cannot be parsed due to being malformed, file IO, etc."""
@@ -51,8 +57,4 @@ def __init__(self, code, message, filename, issues=None):
         self.filename = filename
         self.issues = issues
         if self.issues is None:
-            self.issues = [
-                {'message': message,
-                 ErrorContext.FILE_NAME: filename,
-                 'code': code}
-            ]
+            self.issues = []