See linkml/linkml#2865 for details

See linkml/linkml#2865 for details

See linkml/linkml#2865 for details

See #2865 for details

* Fix YAML files

* Exclude invalid yaml test inputs

* Adding __future__type annotations to yaml_loader, loader_root.
generating URI to Path / str(Path) maps in __init__

* Typing additions and edits

* Fixing misc minor lint issues:
- create error messages before raise exceptions
- simplify some if/else cascades
- fix variable naming convention violations

* Move import-related functions to be closer together in the module for easier debugging

* Update linkml_runtime/utils/schemaview.py

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

* fix accidental commit II

* Use legacy type union notation for defining types

* Lint should ignore vendored linkml-model

* Exclude vendored linkml-model from coverage reporting

* tests(schemaview): optimize execution

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

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

* Fixes by Ruff

* added new variable: element_type that stores the type of element prior 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

* added description of element_type to yamlutils.as_json_object() docstring

* Convert trivial unitest cases to pytest

* Convert test walker utils to pytest

* Convert test schema as dict to pytest

* Convert test_inlined_as_list_forms to pytest

* Convert test_include_schema.py to pytest format

* Convet test_enum to pytest

* Convert distroutils to pytest

* fixed formatting in linkml_runtime/utils/yamlutils.py

Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>

* fixed formatting in linkml_runtime/dumpers/json_dumper.py

Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>

* fixed typ in json_dumper.py. return statement was appearing twice

* undid formatting change using black

* Convert dictutils to pytest

* Convert test_csv_tsv_loader_dumper.py to pytest format

- Remove unittest imports and TestCase class
- Convert 6 test methods to standalone functions
- Add pytest fixtures for schema_view, test_data, test_data2
- Use tmp_path fixture for temporary file handling

* Convert test_arrays.py to pytest format

- Convert setUp() method to pytest fixtures (normalizer, matrix_data)
- Convert test method to standalone function
- Convert assertEqual to assert statement

* Convert test introsepction to pytest

Apply review suggestion

* Convert test_object_index.py to pytest format

- Convert setUp() method to pytest fixtures (schema_view, container, object_index)
- Convert large test method to standalone function with detailed sections
- Convert assertRaises to pytest.raises
- Convert assertCountEqual to sorted comparison

Address review comment

* Convert test for inlined as dict forms to pytest

* Convert test poly dataclasses to pytest

* Fixes proposed by Ruff

* Convert test_loaders_dumpers.py from unittest to pytest

- Convert setUp method to module-scoped loader_dumper_setup pytest fixture
- Convert _check_objs from instance method to standalone helper function
- Convert all 3 test methods to standalone functions with fixture dependency

* Convert test dumpers to pytest

* Convert test ruleutils to pytest

* Improve disjunction rules test

* added unit test to check that @type is correctly set when JSONDumper.dumps() is called with a pydantic instance

* Convert test_rdflib_dumper.py from unittest to pytest

- Convert setUp methods to pytest fixtures (prefix_map, converter_prefix_map, issue_429_graph)
- Convert all 13 test methods from 2 classes to standalone functions
- Convert _check_objs from instance method to helper function

* Improve rdflib loader and dumper tests

* migrate to uv

* Migrate from Poetry to uv

- Replace Poetry with uv package manager
- Update all GitHub workflows to use uv
- Add uv.lock file and remove poetry.lock
- Update pyproject.toml to use modern dependency groups
- Remove obsolete tox.ini file

* add '&& uv add docker' for testing upstream

* Add requests-cache dependency to linkml installation in test-upstream workflow

This fixes ImportError for requests_cache module which is required by linkml-runtime tests.

* Fix upstream testing: use --all-extras instead of manually adding dependencies

This matches Poetry's '--all-extras' behavior which installs all optional dependencies
needed for the linkml tests, instead of manually adding individual packages.

* Install linkml-runtime with dev dependencies via dependency groups

Instead of manually adding individual packages, use uv's dependency groups
to properly install linkml-runtime with all its dev dependencies (docker,
requests-cache, etc.) that are needed for linkml tests.

* Add docker to dev dependencies

Docker is required by upstream linkml tests (imported in tests/conftest.py).
With Poetry this worked due to implicit dependency resolution, but uv
requires explicit declaration of dependencies.

* Explicitly add dev dependencies needed by linkml tests

The issue was that adding linkml-runtime to a dependency group doesn't
automatically install linkml-runtime's dev dependencies. We need to
explicitly add the packages that linkml tests require: docker and requests-cache.

* Add debug info and remaining missing dependencies for linkml tests

Added debug step to see what's installed and added the remaining dependencies
that linkml tests need: jsonpatch, testcontainers, and nbformat.

This should resolve all the ImportError issues we've been seeing.

* Properly declare upstream testing dependencies in pyproject.toml

Instead of manually adding dependencies in the workflow, properly declare
all dependencies needed for upstream linkml testing in linkml-runtime's
dev dependency group:

- docker (for container-based tests)
- jsonpatch (for dict comparison utilities)
- testcontainers (for PlantUML container tests)
- nbformat & nbconvert (for notebook testing)
- requests-cache (for caching test utilities)

This makes the dependency management much cleaner and more maintainable.

* Go nuclear: explicitly install all dependencies needed for linkml tests

The dependency group approach isn't working - uv isn't installing
linkml-runtime's dev dependencies into linkml's environment.

Fall back to explicitly installing every dependency that linkml tests need:
docker, requests-cache, jsonpatch, testcontainers, nbformat, nbconvert.

Sometimes you just have to be explicit with dependency management.

* fetch #2779 for updated pandera for upstream test

* update default upstream repo/branch for testing during migration

* update test-upstream.yaml and pyproject.toml as fork iquxle/linkml-runtime#400

* remove manual docker add - should be included via testcontainers dependency

* revert test-upstream defaults to linkml/linkml:main after migration completion

* Bump actions/download-artifact from 4.3.0 to 5.0.0

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 4.3.0 to 5.0.0.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v4.3.0...v5.0.0)

---
updated-dependencies:
- dependency-name: actions/download-artifact
  dependency-version: 5.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump checkout action to v5

See #2865 for details

* Use full versions specs for all github actions

* Convert test_loaders_pydantic.py to pytest format

- Extract loader_test helper function from base class
- Convert 4 test methods to standalone functions
- Test both YAML and JSON loaders with different models

* Inline and simplify loader test

Explicitly add input files for test cases do not read test inputs from output directory

* Whitespace fix

* Convert test_loaders.py to pytest format

- Convert setUpClass to pytest module-scoped fixture
- Convert 6 test methods to standalone functions
- Convert unittest.skipIf to pytest.mark.skip
- Convert unittest.SkipTest to pytest.skip
- Reuse loader_test helper function from test_loaders_pydantic
- Preserve RDF loader functionality and context server setup

* Spelling fixes

* Minor tidying and enfixtureification of tests and test data in test_schemaview.py

* Add comprehensive tests for range determination

* Add in tests for slot_applicable_range_elements

* Misc tidying, documentation clarification

* Improve some tests and more general test tidying

* module_name parameter for compile_python

* Bump actions/setup-python from 5.6.0 to 6.0.0

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.6.0 to 6.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v5.6.0...v6.0.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: 6.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.12.4 to 1.13.0.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.12.4...v1.13.0)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-version: 1.13.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump astral-sh/setup-uv from 6.6.1 to 6.8.0

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 6.6.1 to 6.8.0.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](astral-sh/setup-uv@v6.6.1...v6.8.0)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: 6.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump codecov/codecov-action from 5.4.3 to 5.5.1

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5.4.3 to 5.5.1.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v5.4.3...v5.5.1)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: 5.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Misc edits: add in tests for get_element, edit typing, rename some variables for clarity

* clarifying documentation, removing dupe line

* Add tests for get_identifier_slot and get_key_slot

* Split out long test method into many tests

* Break up long `test_imports` test into separate pieces

* Rearrange tests and remove duplicate lines

* Reordering functions relating to calculating relationships (ancestors/descendants, etc)

* Add kwargs input args to all the functions that use _closure(); edit the _closure function to remove some redundancy

* Add comprehensive tests for class relationships

* Edit permissible_value methods to throw an error if the enum-permissible value pairing is incorrect.

* Add a type_roots function to find all base types in a schema

* Adding function to detect cycles within a graph and hooking it up to the _closure function

* Adding comments

* Clarify function docs

* Add comprehensive tests for range determination

* Add in tests for slot_applicable_range_elements

* Misc tidying, documentation clarification

* Adding `induced_slot_range` function for generating a non-redundant set of possible ranges for a slot

* Fix format issues, adjust tox config

* Adding tests for namespaces and get_elements_applicable_by_prefix function

* Minor documentation fixes

* Edit namespaces function so that it does not retrieve curi_maps unnecessarily

* typo

* Adding tests for test_get_elements_applicable_by_identifier

* Skip issue in csv tests due to upstream for now.

* Adding tests for SchemaView's modification functions: adding or deleting elements in a schema.

* Add tests for the schemaview equality checks

* A couple of bonus tests, just for fun!

* update pydantic minimum version to 2.0.0

* move compile_python test; fix docstrings

* Allow detect_cycles to receive a list of nodes instead of just a single node

* Moving some functions and test data around in schemaview and test_schemaview

* Adding function get_string_type to retrieve the appropriate type for strings in the schema

* Deprecate `permissible_value_parent` and replace it with `permissible_value_parents`.

* Fix docs for permissible_value_parents/children

* make function private

* Add in checks to ensure that the slot is populated correctly when calling various slot range functions'

* Implementing suggestions made in PR comments

* Bump coverage from 7.9.1 to 7.10.7

Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.9.1 to 7.10.7.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.9.1...7.10.7)

---
updated-dependencies:
- dependency-name: coverage
  dependency-version: 7.10.7
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump the dependencies group with 2 updates

Bumps the dependencies group with 2 updates: [pyyaml](https://github.com/yaml/pyyaml) and [requests](https://github.com/psf/requests).


Updates `pyyaml` from 6.0.2 to 6.0.3
- [Release notes](https://github.com/yaml/pyyaml/releases)
- [Changelog](https://github.com/yaml/pyyaml/blob/6.0.3/CHANGES)
- [Commits](yaml/pyyaml@6.0.2...6.0.3)

Updates `requests` from 2.32.4 to 2.32.5
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.32.4...v2.32.5)

---
updated-dependencies:
- dependency-name: pyyaml
  dependency-version: 6.0.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: dependencies
- dependency-name: requests
  dependency-version: 2.32.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jsonschema from 4.24.0 to 4.25.1

Bumps [jsonschema](https://github.com/python-jsonschema/jsonschema) from 4.24.0 to 4.25.1.
- [Release notes](https://github.com/python-jsonschema/jsonschema/releases)
- [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst)
- [Commits](python-jsonschema/jsonschema@v4.24.0...v4.25.1)

---
updated-dependencies:
- dependency-name: jsonschema
  dependency-version: 4.25.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump curies from 0.10.19 to 0.10.23

Bumps [curies](https://github.com/biopragmatics/curies) from 0.10.19 to 0.10.23.
- [Release notes](https://github.com/biopragmatics/curies/releases)
- [Commits](biopragmatics/curies@v0.10.19...v0.10.23)

---
updated-dependencies:
- dependency-name: curies
  dependency-version: 0.10.23
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* pyproject.toml in need of repairs, but committing to share the challenge

* Temporarily ignore cleanup-script

* Move linkml source code to packages/linkml/src/linkml

This is part of the monorepo migration to uv-workspace structure.
Moves the main linkml package source code to its proper location.

* Move linkml tests to packages/linkml/tests

Moves all linkml-specific tests to the new monorepo structure.
Runtime tests remain in tests/linkml_runtime/ for next step.

* Move linkml_runtime tests to packages/linkml_runtime/tests

Moves runtime tests from tests/linkml_runtime/ to the package-specific
tests directory. Removes the now-empty root tests directory.

* Restructure linkml_runtime source to src/linkml/runtime

Moves runtime source code from packages/linkml_runtime/* to
packages/linkml_runtime/src/linkml/runtime/* following the
proper package structure for the monorepo.

* Fix linkml_runtime package structure

Move from src/linkml/runtime to src/linkml_runtime to maintain
the linkml_runtime import path and avoid breaking changes.

* Complete monorepo workspace configuration

- Update monorepo-cleanup.sh to use correct src/linkml_runtime path
- Add packages/linkml/pyproject.toml with workspace configuration
- Add packages/linkml/README.md
- Configure hatchling build targets for both packages
- Workspace now supports 'uv sync' and individual package builds

* Fix notebooks path for monorepo structure

Updated test_notebooks.py to use correct relative path to notebooks
directory from the new monorepo location (packages/linkml/tests).

* refactor tests, moving out of packages and into test/<package>, plus update actions and paths

* update linking expectations on runtime tests to match what we had set in the runtime repo

* move merged files to the right spot, fix imports

* turn off more lint checks for runtime tests

* update path to ignored E501 (long line) list

* one more to ignore for runtime tests

* fix ruff import ignore for notebooks

* fix import sorting in tests/linkml

* lint fix up at the top

* Fix quality checks: YAML syntax, codespell config, and formatting

- 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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* Fix rustgen test path calculation for examples folder

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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* Fix _diff_text() call for pytest 8.4.2 compatibility

pytest 8.4.2 changed the signature of _diff_text() to require a
'highlighter' parameter. Added a no-op highlighter function
(lambda x, **kwargs: x) to maintain compatibility.

This fixes TypeError when running tests with snapshot comparisons.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* Revert trailing whitespace changes to linkml_runtime model schemas

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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* Fix ruff formatting in conftest.py

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

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* Fix Windows test failures and slow test collection issues

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.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

* update uv build command in main action to build all packages

* also uv build all packages in the Dockerfile

---------

Signed-off-by: Silvano Cirujano Cuesta <silvano.cirujano-cuesta@siemens.com>
Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Vlad Korolev <vlad@v-lad.org>
Co-authored-by: i alarmed alien <ialarmedalien@users.noreply.github.com>
Co-authored-by: ialarmedalien <ialarmedalien@gmail.com>
Co-authored-by: Silvano Cirujano Cuesta <silvano.cirujano-cuesta@siemens.com>
Co-authored-by: Sierra Moxon <sierra.taylor@gmail.com>
Co-authored-by: Kevin Schaper <kevinschaper@gmail.com>
Co-authored-by: Puja Trivedi <xspuja@gmail.com>
Co-authored-by: puja-trivedi <44144244+puja-trivedi@users.noreply.github.com>
Co-authored-by: iQuxLE <ckroll95@gmail.com>
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Co-authored-by: Tim Fliss <t.fliss@gmail.com>
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Co-authored-by: Sujay Patil <sujaysanjeev.patil@gmail.com>
Co-authored-by: David Linke <david.linke@catalysis.de>
Co-authored-by: Claude <noreply@anthropic.com>