Fix incorrect YAML encoding, ignore intentionally corrupted files

Fixup Monarch Schemaview notebook

generating URI to Path / str(Path) maps in __init__

- create error messages before raise exceptions
- simplify some if/else cascades
- fix variable naming convention violations

… easier debugging

Co-authored-by: Silvano Cirujano Cuesta <silvano.cirujano-cuesta@siemens.com>

SchemaView: linter fixes, minor code reorganisation

Adding __future__type annotations to yaml_loader, loader_root.

Avoid opening the same schema 9 times for very similar tests.

Signed-off-by: Silvano Cirujano Cuesta <silvano.cirujano-cuesta@siemens.com>

tests(schemaview): optimize execution

…rage

Exclude vendored linkml-model from coverage reporting

Simple fixes by Ruff

…r to it being converted to a dictionary. This will allow @type to be asssigned to the true type of element in yamlutils.as_json_object(), rather than the being assigned to 'dict' which is the type returned from element.model_dump(). This change only effects cases when element is of type:pydantic.BaseModel

…ring

Resolved directory rename conflicts by moving new files from main to the new package structure:
- dependency_sorter.py
- transforms/collection_dict_loader.py
- transforms/simple_dict_loader.py

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Co-Authored-By: Claude <noreply@anthropic.com>

…update actions and paths

… in the runtime repo

- Fix YAML indentation error in array.yaml:14 (contributors field)
- Add ClassE to codespell ignore-words-list in both root and runtime pyproject.toml
- Configure pre-commit codespell hook to read pyproject.toml config and exclude .toml files
- Apply pre-commit auto-fixes: end-of-file-fixer, trailing-whitespace, ruff-format

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Co-Authored-By: Claude <noreply@anthropic.com>

Change from parents[2] to parents[3] to correctly locate the examples
folder at the repository root. This fixes path errors after the monorepo
restructuring.

Fixes 3 test functions:
- test_rustgen_personschema_maturin
- test_rustgen_personschema_stubgen
- test_rustgen_file_mode_generation

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Co-Authored-By: Claude <noreply@anthropic.com>

Reverted trailing whitespace removal from schema YAML files to preserve
exact formatting required by snapshot tests. Added exclusion pattern to
pre-commit config to prevent future modifications.

Files reverted:
- types.yaml
- meta.yaml
- datasets.yaml
- units.yaml
- validation.yaml

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Co-Authored-By: Claude <noreply@anthropic.com>

Apply ruff-format to fix line length violation in _diff_text call.

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Co-Authored-By: Claude <noreply@anthropic.com>

1. Fix .gitattributes paths after test refactoring
   - Updated snapshot paths from tests/test_scripts/ to tests/linkml/test_scripts/
   - Added .yuml files to eol=lf enforcement
   - Fixes Windows line ending mismatches in snapshot comparisons

2. Remove linkml_runtime slow tests from workflow
   - No tests in linkml_runtime are marked with @pytest.mark.slow
   - Removed step that was causing exit code 5 (no tests collected)
   - Removed corresponding codecov upload

Both issues introduced during monorepo merge/refactoring.

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Co-Authored-By: Claude <noreply@anthropic.com>