Add weekly LinkML toolkit compatibility check

[matentzn]

Adds a GitHub Actions workflow that runs every Monday to verify the linkml-model metamodel remains compatible with the latest linkml toolkit.

What it does

1. Checks out linkml/linkml at HEAD and runs gen-project against meta.yaml
2. Verifies that key outputs were generated (Python, JSON Schema, OWL, ShEx, GraphQL)
3. On failure, automatically files a GitHub issue (or comments on an existing one) with the last 100 lines of output

The workflow runs on schedule (Mondays at 10:00 UTC, 1 hour after linkml's own metamodel check) and can be triggered manually via workflow_dispatch.

It intentionally tests against the latest linkml main rather than a pinned version — the goal is early detection of incompatibilities before they reach a release.

[Copilot]

Pull request overview

Adds an automated GitHub Actions workflow to continuously validate that linkml-model’s metamodel can still be processed by the latest linkml toolkit, with scheduled weekly runs and failure-to-issue reporting.

Changes:

• Introduces a scheduled + manual workflow that checks out linkml/linkml and runs gen-project against linkml_model/model/schema/meta.yaml.
• Adds a post-run verification step for expected generated artifacts (Python, JSON Schema, OWL, ShEx, GraphQL).
• On failure, attempts to create/update a GitHub issue with the last 100 lines of captured output.

---

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[Copilot]

The output checks hard-code output/meta.py, but in this repo the documented generation flow produces Python files via separate gen-python calls (see Makefile), and gen_project_config.yaml explicitly excludes the python generator. As written, this check can either (a) fail even when gen-project succeeded (if using the repo config), or (b) pass while diverging from the repo’s actual build artifacts. Adjust the verification list to match the outputs that are actually expected from the chosen generation command(s).

[Copilot]

The failure handler always does tail -n 100 genproject_output.txt, but that file is only created by the gen-project step. If the workflow fails earlier (e.g., checkout/uv sync/Graphviz), this tail will fail and prevent the issue from being created/updated. Consider guarding for a missing log file (fallback message), or narrowing the if: condition so this step runs only when the gen-project step actually executed.

Suggested change

	LOG_OUTPUT=$(tail -n 100 genproject_output.txt)
	if [ -f genproject_output.txt ]; then
	LOG_OUTPUT=$(tail -n 100 genproject_output.txt)
	else
	LOG_OUTPUT="genproject_output.txt was not created. The workflow likely failed before the gen-project step ran."
	fi

[Copilot]

This job uses gh issue ... / gh label ... to create and update issues/labels, but the workflow doesn't declare any permissions:. In repositories with restricted default GITHUB_TOKEN permissions, these steps will fail (especially label creation and issue commenting). Consider explicitly setting job permissions (e.g., contents: read and issues: write) so scheduled/manual runs can reliably file/update the tracking issue.

Suggested change

	runs-on: ubuntu-latest
	runs-on: ubuntu-latest
	permissions:
	contents: read
	issues: write

[Copilot]

This workflow pins older action versions (actions/checkout@v4.2.2, actions/setup-python@v5.6.0, astral-sh/setup-uv@v7.2.0) while the rest of the repo’s workflows use newer pins (e.g., .github/workflows/main.yaml uses actions/checkout@v6.0.2, actions/setup-python@v6.2.0, setup-uv@v7.3.0). To keep maintenance and security updates consistent across CI, align these action versions with the versions already used elsewhere in this repository (or explain why this workflow must differ).

Suggested change

	uses: actions/checkout@v4.2.2
	- name: Check out linkml toolkit
	uses: actions/checkout@v4.2.2
	with:
	repository: linkml/linkml
	path: linkml-toolkit
	- name: Install uv
	uses: astral-sh/setup-uv@v7.2.0
	with:
	version: ${{ env.UV_VERSION }}
	enable-cache: true
	- name: Set up Python
	uses: actions/setup-python@v5.6.0
	uses: actions/checkout@v6.0.2
	- name: Check out linkml toolkit
	uses: actions/checkout@v6.0.2
	with:
	repository: linkml/linkml
	path: linkml-toolkit
	- name: Install uv
	uses: astral-sh/setup-uv@v7.3.0
	with:
	version: ${{ env.UV_VERSION }}
	enable-cache: true
	- name: Set up Python
	uses: actions/setup-python@v6.2.0

[Copilot]

gen-project is invoked without the repo’s gen_project_config.yaml, but this repository’s Makefile consistently runs gen-project with that config (which also excludes some generators like python and markdown). Running without the config may introduce failures unrelated to compatibility (extra generators, different output layout) and makes the output verification brittle. Consider using the same config file as the repo’s normal generation path, and if you want to validate Python output too, run the repo’s gen-python --genmeta step separately rather than assuming gen-project will emit meta.py.

Suggested change

	uv run gen-project ../linkml_model/model/schema/meta.yaml -d ../output 2>&1 | tee ../genproject_output.txt
	- name: Verify key outputs were generated
	id: verify_outputs
	run: |
	MISSING=""
	# Python files go in root, others in subdirectories (per GEN_MAP in projectgen.py)
	uv run gen-project --config-file ../gen_project_config.yaml ../linkml_model/model/schema/meta.yaml -d ../output 2>&1 | tee ../genproject_output.txt
	- name: Run gen-python --genmeta against metamodel
	id: run_genpython
	working-directory: linkml-toolkit
	run: |
	uv run gen-python --genmeta ../linkml_model/model/schema/meta.yaml > ../output/meta.py
	- name: Verify key outputs were generated
	id: verify_outputs
	run: |
	MISSING=""
	# meta.py is generated separately via gen-python --genmeta; the remaining files come from gen-project.