add test to main workflow #240

	name: Combined Workflow

	on: [push]

	defaults:
	run:
	shell: bash -el {0} # use default shell
	jobs:
	build-and-dryrun:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 2


	steps:
	- name: Checkout
	uses: actions/[email protected]

	- name: Get current month
	id: date
	run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}"

	- uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: atlasenv.yml
	environment-name: atlasenv
	# persist on the same month.
	cache-environment-key: environment-${{ steps.date.outputs.date }}
	cache-downloads-key: downloads-${{ steps.date.outputs.date }}

	- name: Install atlas
	run: \|
	python -m pip install . --no-deps -vv

	- name: Test atlas
	run: \|
	atlas --help
	atlas --version

	- name: test import modules atlas
	run: \|
	python -c "from atlas import utils"

	- name: Dryrun
	run: test/dryrun.sh

	- name: Test init many samples
	run: ./test/test_init_many_samples.sh

	# full-test:
	# runs-on: ubuntu-latest
	# needs: build-and-dryrun
	# strategy:
	# max-parallel: 1

	# steps:
	- name: Clone Example Data Repository
	run: git clone https://github.com/metagenome-atlas/example_data.git

	- name: Run Test
	run: \|
	ls -l
	ls -l example_data
	chmod +x test/test_ci.sh
	test/test_ci.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2

	- name: Store Logs
	uses: actions/upload-artifact@v2
	with:
	name: logs
	path: test_ci/logs

	- name: Store Sample Logs
	uses: actions/upload-artifact@v2
	with:
	name: sample_logs
	path: test_ci/Streptococcus/logs

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