Merge pull request #53 from msk-access/release/0.2.7 #210

	name: Document package
	on:
	push:
	branches: [main]
	jobs:
	update_cli_doc:
	# The type of runner that the job will run on
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.9"]
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- name: Extract branch name
	shell: bash
	run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
	id: extract_branch
	# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
	- name: setup python
	uses: actions/setup-python@v4
	with:
	python-version: "3.10" # install the python version needed
	- name: Document CLI and write to folder
	run: \|
	git checkout ${{ steps.extract_branch.outputs.branch }}
	make deps-install
	mkdir -p docs
	poetry run typer postprocessing_variant_calls.main utils docs > docs/cli.md
	- uses: EndBug/add-and-commit@v9
	with:
	default_author: github_actions
	message: "add doc for cli"
	add: '["docs/*.md --force"]'
	- name: Write Docs
	id: write_docs
	run: \|
	git checkout docs --
	git checkout ${{ steps.extract_branch.outputs.branch }} -- README.md
	git checkout ${{ steps.extract_branch.outputs.branch }} -- docs/cli.md
	mv docs/cli.md cli.md
	- uses: EndBug/add-and-commit@v9
	with:
	default_author: github_actions
	message: "add doc for cli"
	add: '["*.md --force"]'
	push: 'origin docs --set-upstream --force'

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