Add LinkML behavior tests for required: False -> True slot_usage refinement#408
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Add LinkML behavior tests for required: False -> True slot_usage refinement#408candleindark wants to merge 8 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## linkml-conversion #408 +/- ##
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+ Coverage 96.67% 97.83% +1.16%
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Files 20 19 -1
Lines 2436 2407 -29
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Hits 2355 2355
+ Misses 81 52 -29
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…finement Adds a detached hatch env (`linkml-behavior-test`) and a new test tree (`tests/linkml_behavior/`) asserting that `linkml-validate` honors a `slot_usage` entry that tightens an inherited slot's `required` from `False` to `True` while preserving the slot's other inherited constraints (here, `range`). This is the LinkML behavior the LinkML version of `dandischema` relies on; see issue #405. The env is detached (no dandischema install) with only `linkml` and `pytest` as dependencies, and it does not pin a LinkML version so the tests run against the latest release and surface upstream regressions early. The new directory carries its own `pytest.toml` so pytest's config-file discovery stops there and does not inherit the repo-root `tox.ini` `[pytest]` section, which is tailored to the `dandischema` package test suite. A follow-up will add a GitHub Actions workflow that invokes the hatch env so the same checks run in CI. Co-Authored-By: Claude Code 2.1.139 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
Extends the `required_refinement` behavior tests to also assert that the JSON Schema produced by running `gen-json-schema --title-from title` against `schema.yaml` (matching the invocation in `pyproject.toml`'s `linkml-auto-converted:2json` script) honors the `required: False -> True` `slot_usage` refinement while preserving the inherited `range` constraint. Validation is performed via the `check-jsonschema` CLI, which has JSON Schema `format` keyword validation enabled by default. Adds a `conftest.py` with two session-scoped fixtures: - `json_schemas` — per-target-class JSON schemas generated once from `schema.yaml`. - `json_instances` — the YAML data instances converted once to JSON. The detached `linkml-behavior-test` hatch env now also depends on `check-jsonschema` and `PyYAML`. Co-Authored-By: Claude Code 2.1.139 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
The `test_validate.py` and `test_json_schema_validate.py` files exercise the same six `(target_class, instance)` cases against different validators. Move the case lists into a shared `_cases.py` so adding or adjusting a case updates both test files at once. Co-Authored-By: Claude Code 2.1.141 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
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Add `test_pydantic_validate.py`, mirroring `test_validate.py` and `test_json_schema_validate.py`. A new session-scoped `pydantic_module` fixture runs `gen-pydantic --black --template-dir <...>` (matching the invocation in the `linkml-auto-converted:2pydantic` script) and loads the generated module dynamically; the new `instance_data` fixture provides YAML instances parsed into Python dicts for `model_validate`. The dynamically-loaded module is registered in `sys.modules` under a topic-folder-suffixed name so future sibling fixtures don't collide. Also add `black` and `pydantic` to the `linkml-behavior-test` env so `--black` formatting works and `pydantic.ValidationError` is importable. Co-Authored-By: Claude Code 2.1.141 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
Set version environment to 3.10. The lowest currently supported Python
Runs the `tests/linkml_behavior/` suite under the `linkml-behavior-test` hatch env on push/PR to `master`, on a daily 06:00 UTC schedule, and on manual dispatch. The env doesn't pin a LinkML version, so the daily schedule surfaces upstream LinkML regressions early. Co-Authored-By: Claude Code 2.1.141 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
The env provides `hatch run linkml-behavior-typing:check`, which runs `mypy --install-types --non-interactive` over `tests/linkml_behavior/`. It is kept distinct from `linkml-behavior-test` and from the tox `typing` env (which targets `dandischema`). Co-Authored-By: Claude Code 2.1.141 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
Runs `hatch run linkml-behavior-typing:check` on push/PR to `master`. No cron — typing breakages from upstream stub or library releases are rare and typically don't cause runtime errors. Co-Authored-By: Claude Code 2.1.141 / Claude Opus 4.7 claude-opus-4-7 <noreply@anthropic.com>
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Summary
Adds a detached
linkml-behavior-testhatch env and a newtests/linkml_behavior/tree, which together assert LinkML behavior that the LinkML version ofdandischemarelies on. This PR covers therequired: False -> Trueslot_usagerefinement; the tests live undertests/linkml_behavior/required_refinement/.The env is detached (no
dandischemainstall) and does not pin a LinkML version, so the tests run against the latest LinkML release and surface upstream regressions early.Closes #405.
Checklist
tests/linkml_behavior/required_refinement/against the LinkML schema, usinglinkml-validate.gen-json-schema --title-from title(matching the invocation inpyproject.toml'slinkml-auto-converted:2jsonscript), usingcheck-jsonschema(JSON Schemaformat-keyword checks enabled by default).gen-pydantic --black --template-dir tools/linkml_conversion_tools/pydantic_templates(matching the invocation inpyproject.toml'slinkml-auto-converted:2pydanticscript).master, PR tomaster, manual dispatch, and a daily schedule.tests/linkml_behavior/—linkml-behavior-typing— distinct fromlinkml-behavior-testand from the existing toxtypingenv (which targetsdandischema), plus a GitHub Actions workflow that runs the type-check on push tomasterand PR tomaster.Test plan
hatch run linkml-behavior-test:test— 18 passed locally (Python 3.10,linkml1.11.0).hatch run linkml-behavior-typing:check— no issues found locally.