Switch to containerized CI using Conda #63

	name: Regression tests

	on:
	workflow_dispatch:
	pull_request:
	branches: ['develop']
	paths:
	- .github/workflows/regressiontests.yml
	- superdsm/**
	- examples/**
	- superdsm.yml
	- tests/regression
	- requirements.txt

	jobs:

	regression_tests:
	name: "Test: ${{ matrix.taskdir }}"
	timeout-minutes: 1440
	runs-on: gpuagrohr-01
	container:
	image: ubuntu:22.04
	defaults:
	run:
	shell: bash -el {0}
	strategy:
	fail-fast: false
	matrix:
	taskdir:
	- U2OS
	- NIH3T3
	- GOWT1-1
	- GOWT1-2

	steps:

	- name: Checkout
	uses: actions/checkout@v2

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: 'latest'
	channels: conda-forge, bioconda, defaults
	auto-update-conda: true
	auto-activate-base: false
	activate-environment: superdsm
	environment-file: superdsm.yml

	- name: Download image data
	run: \|
	cd examples
	python load_data.py

	- name: Run SuperDSM
	run: \|
	python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}"
	python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}" --run
	env:
	SUPERDSM_INTERMEDIATE_OUTPUT: false
	SUPERDSM_NUM_CPUS: 20

	- name: Validate results
	id: validation
	run: \|
	mkdir "actual_csv"
	sh "tests/regression/validate-${{ matrix.taskdir }}.sh" "actual_csv"

	- name: Upload artifact
	if: failure() && steps.validation.outcome != 'success'
	uses: actions/upload-artifact@v3 ## v4 requires GLIBC_2.28 which is not found on host
	with:
	name: Results ${{ matrix.taskdir }}
	path: actual_csv/${{ matrix.taskdir }}

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