[build testing] collapse all Docker builds into a single PR check #9

	name: Docker Stack SIPNET

	on:
	pull_request:
	workflow_dispatch:
	schedule:
	- cron: '30 4 * * 4'

	jobs:
	sipnet:
	name: sipnet
	runs-on: ubuntu-latest
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	steps:
	- name: Free Disk Space (Ubuntu)
	uses: jlumbroso/free-disk-space@main
	with:
	tool-cache: false
	android: true
	dotnet: true
	haskell: true
	large-packages: true
	docker-images: false
	swap-storage: true

	- name: Checkout source code
	uses: actions/checkout@v4

	- name: Set up Docker Compose
	run: \|
	sudo apt-get update
	sudo apt-get -y install docker-compose

	- name: Prepare override
	run: \|
	cp docker-compose.dev.yml docker-compose.override.yml
	sed -i'' '/R_library/d' docker-compose.override.yml

	- name: Initialize data volumes
	run: \|
	cp docker/env.example .env
	echo "COMPOSE_PROJECT_NAME=pecan" >> .env
	echo "PECAN_VERSION=develop" >> .env
	echo "UID=$(id -u)" >> .env
	echo "GID=$(id -g)" >> .env
	docker compose up --wait -d postgres
	docker run --rm --network pecan_pecan pecan/db:ci
	docker run --rm --network pecan_pecan --volume pecan_pecan:/data --env FQDN=docker pecan/data:develop
	docker run --rm --network pecan_pecan --volume pecan_pecan:/data pecan/data:develop chown -R "$(id -u):$(id -g)" /data
	docker image rm pecan/db:ci pecan/data:develop \|\| true

	- name: Start required services
	run: \|
	docker compose up --wait -d sipnet executor monitor rabbitmq

	- name: List running containers
	run: \|
	sleep 50
	docker ps

	- name: Run SIPNET workflow
	run: \|
	docker compose exec --workdir /pecan/tests executor R CMD ../web/workflow.R --settings docker-ghaction.sipnet.xml

Provide feedback