update-defining-mutations #27

	# Download defining mutations from Cornelius and merge with hand-curated defining mutations from Emma
	name: update-defining-mutations

	on:
	schedule:
	- cron: "0 0 1,15 * *"

	workflow_dispatch:

	concurrency:
	group: web-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number \|\| github.ref \|\| github.run_id }}
	cancel-in-progress: true

	defaults:
	run:
	shell: bash -euxo pipefail {0}

	env:
	GITHUB_REPOSITORY_URL: ${{ github.server_url }}/${{ github.repository }}

	jobs:
	update-defining-mutations:
	name: "update-defining-mutations"
	runs-on: ubuntu-22.04

	steps:
	- name: "checkout repo"
	uses: actions/checkout@v4

	- name: "install python"
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'

	- name: "install python dependencies"
	run: \|
	pip install -r requirements.txt

	- name: "run tests"
	run: \|
	mkdir tests/data/defining_mutations/output
	pytest

	- name: "download defining mutations"
	run: \|
	mkdir -p data
	curl -o data/auto_generated.json https://raw.githubusercontent.com/corneliusroemer/pango-sequences/refs/heads/main/data/pango-consensus-sequences_summary.json

	- name: "merge files and update web data"
	run: \|
	python3 -m scripts.defining_mutations.merge_defining_mutations defining_mutations data web/public/data/definingMutations

	- name: "Commit and push update"
	run: \|
	git config --local user.email "github-actions[bot]@users.noreply.github.com"
	git config --local user.name "github-actions"
	git add web/public/data/definingMutations
	git diff --staged --quiet \|\| git commit -m "chore: Update defining mutations"
	git push

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