SEC61A1 additional publication #581

	name: Deploy documentation

	on:
	push:
	branches:
	- main

	permissions:
	contents: write

	env:
	# Path to directory that contains the cohorts, one cohort per folder.
	NOTEBOOK_DIR: notebooks

	jobs:
	deploy:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: actions/setup-python@v4
	with:
	python-version: '3.12'
	- uses: actions/cache@v2
	with:
	key: ${{ github.ref }}
	path: .cache

	- name: Install docs dependencies
	run: \|
	python3 -m pip install phenopacket-store-toolkit[release] mkdocstrings[python] mkdocs-material[imaging] mkdocs-material-extensions pillow cairosvg

	- name: Generate reports
	run: \|
	python3 -m ppktstore report collections --notebook-dir ${NOTEBOOK_DIR} --output docs/collections.md

	- name: Deploy docs
	run: \|
	mkdocs gh-deploy --force

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