Compress output image files #30

	name: CI
	on: [push, pull_request, workflow_dispatch]

	jobs:
	test:
	runs-on: ubuntu-latest
	env:
	IMG: exemplar-001-cycle6.ome.tif
	PMAP: exemplar-001-cycle6_Probabilities_1.tif
	steps:
	- uses: actions/checkout@v3

	- name: Build the Docker container
	run: \|
	docker build -t s3seg:test .
	docker build -t s3seg:test-large large/

	# Cache test data to avoid repeated download
	- uses: actions/cache@v3
	id: cache-data
	with:
	path: ~/data/*.tif
	key: testdata-2022-05-12

	# Download test data only if no cache is present
	- name: Test data download
	if: steps.cache-data.outputs.cache-hit != 'true'
	run: \|
	mkdir ~/data
	cd ~/data
	curl -f -o $IMG "https://mcmicro.s3.amazonaws.com/ci/$IMG"
	curl -f -o $PMAP "https://mcmicro.s3.amazonaws.com/ci/$PMAP"

	- name: Test the default container
	run: \|
	cd ~/data
	rm -rf exemplar-001-cycle6
	docker run -v "$PWD":/data s3seg:test /bin/bash -c "cd /data; \
	python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath ."

	- name: Test the large container
	run: \|
	cd ~/data
	rm -rf large
	docker run -v "$PWD":/data s3seg:test-large /bin/bash -c "cd /data; \
	python /app/S3segmenter.py --imagePath $IMG --stackProbPath $PMAP --outputPath large"

	# If the action is successful, the output will be available as a downloadable artifact
	- name: Upload processed result
	uses: actions/upload-artifact@v2
	with:
	name: ex001-s3seg
	path: \|
	~/data/exemplar-001-cycle6/**
	~/data/large/**

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