Fix SQLFluff test and derived tables copying #100

	name: SQLFluff

	on:
	- pull_request

	jobs:
	lint-mimic-iv:
	runs-on: ubuntu-latest
	steps:
	- name: checkout
	uses: actions/checkout@v4
	- name: Install Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"
	- name: install sqlfluff
	run: "pip install sqlfluff==3.5.0"
	- name: Get changed files
	id: get_file_changes
	uses: trilom/[email protected]
	with:
	output: ' '
	- name: Get changed .sql files in mimic-iv concepts folder
	id: get_files_to_lint
	shell: bash
	run: \|
	# Compose list of changed SQL files under mimic-iv/concepts and export to step output
	raw="${{ steps.get_file_changes.outputs.files_modified }} ${{ steps.get_file_changes.outputs.files_added }}"
	# Check for mimic-iv SQL files which may have changed
	filtered="$(printf '%s' "$raw" \| tr -s ' ' '\n' \| grep -E '^mimic-iv/concepts/.*[.]sql$' \|\| true)"
	# Turn this into a space separated list for the next step
	files="$(printf '%s' "$filtered" \| tr -s '\n' ' ')"
	echo "lintees=${files}" >> "$GITHUB_OUTPUT"

	- name: Lint SQL files
	id: sqlfluff_json
	if: steps.get_files_to_lint.outputs.lintees != ''
	shell: bash
	run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
	- name: Annotate
	uses: yuzutech/[email protected]
	with:
	repo-token: "${{ secrets.GITHUB_TOKEN }}"
	title: "SQLFluff Lint"
	input: "./annotations.json"

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