Integration Tests #63

	name : Integration Tests
	on :
	# allow manual triggering
	workflow_dispatch:

	schedule:
	# run Thursday 4:30 AM UTC
	- cron: '30 4 * * 4'
	jobs:
	test:
	runs-on: ubuntu-latest

	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	PGHOST: postgres

	services:
	postgres:
	image: mdillon/postgis:9.5
	options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5

	container:
	image: pecan/base:develop

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

	# initialize database
	- name: db setup
	uses: docker://pecan/db:ci

	- name: Run tests
	run: \|
	for FILE in modules/data.atmosphere/inst/integrationTests/*; do
	if echo "$FILE" \| grep -q "ERA5"; then
	echo "Skipping file : $FILE"
	else
	Rscript "$FILE"
	fi
	done

	- name: Run modular pipeline integration test
	run: Rscript modules/uncertainty/inst/integrationTests/test.modular.chain.R

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