Merge pull request #896 from jfy133/automated-linkml-linting #1

	---
	name: LinkML Linting GitHub Action
	on:
	push:
	paths:
	- "src/mixs/schema/mixs.yaml"
	jobs:
	linkml:
	permissions:
	pull-requests: write
	name: LinkML Linting
	runs-on: ubuntu-latest
	steps:
	- name: Check out repository
	uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'poetry'

	- name: Install Poetry
	run: pipx install poetry

	- name: Install dependencies
	run: poetry install --no-interaction --no-root

	- name: Run LinkML Linting
	run: \|
	## Results file header and basic formatting
	printf '# LinkML Linting Results \n\n' > linting-results.md
	printf "$(linkml --version) linting found the following issues. \n\n" >> linting-results.md
	printf "_For more information about the linting rule categories, see the [LinkML linter documentation](https://linkml.io/linkml/schemas/linter.html#rules)._\n" >> linting-results.md
	## Lint the schema, and further format
	poetry run linkml lint --config .linkml-lint-config.yml --ignore-warnings -f markdown src/mixs/schema/mixs.yaml >> linting-results.md
	- name: Reformat log
	run: \|
	sed -i -e 's/#### Errors/> [!CAUTION]/' -e 's/#### Warnings/> [!WARNING]/' -e 's/^/> /' -e '/###.yaml/ s/$/\n/' -e '/###.yaml/ s/^###/File:/' linting-results.md
	- name: Post PR comment
	uses: mshick/add-pr-comment@v2 # v2
	with:
	message-path: linting-results.md
	repo-token: ${{ secrets.GITHUB_TOKEN }}
	allow-repeats: true

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