build

Create basic integration test #140

	name: build

	on:
	pull_request:
	branches:
	- main

	permissions:
	contents: write

	jobs:
	build:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	ref: ${{ github.event.pull_request.head.ref }}
	- uses: mamba-org/setup-micromamba@v2
	with:
	environment-file: workflow/envs/github-actions.yml
	cache-environment: true
	- name: git config
	run: \|
	git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
	git config --local user.name "github-actions[bot]"

	- name: Style R code
	shell: bash -el {0}
	run: \|
	R -e 'usethis::use_tidy_style()'
	git add workflow/scripts
	git diff-index --quiet HEAD \
	\|\| git commit \
	-m '🎨 Style R code'
	- name: Style Python code
	shell: bash -el {0}
	run: \|
	black workflow/
	snakefmt workflow/
	git add workflow/scripts workflow/rules workflow/Snakefile
	git diff-index --quiet HEAD \
	\|\| git commit \
	-m '🎨 Style Python & Snakemake code 🐍'
	- name: Build graphs
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: "--use-conda --conda-frontend mamba --cores 2 make_graph_figures --configfile config/test.yaml"
	- name: Update container file
	uses: snakemake/snakemake-github-action@v1
	with:
	directory: .
	snakefile: 'workflow/Snakefile'
	task: 'containerize'

	- name: Commit
	run: \|
	git add figures/graphviz
	git commit -m "📊 Update graph figures" \
	\|\| echo "No changes in figures/graphviz to commit"

	git add Dockerfile
	git commit -m "🐳 Update Dockerfile" \
	\|\| echo "No changes in Dockerfile to commit"

	git push
	env:
	GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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