Linux

Fix test of CLI tool across OSes and Python versions #4

	name: Linux
	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]
	jobs:
	Test-CLI:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
	steps:
	- name: Cache sample WSI
	uses: actions/cache@v3
	with:
	path: ~/wsi/
	key: sample-wsi
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install WSInfer-CLI
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	python -m pip install torch torchvision --extra-index-url https://download.pytorch.org/whl/cpu
	python -m pip install .
	- name: Download sample WSI
	run: \|
	mkdir -p ~/wsi
	cd ~/wsi
	wget -nc -q https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs
	cd -
	- name: Run tests
	# Go to a different directory to test that WSInfer-MIL still finds everything it needs.
	# Test it twice so the second time we get cache hits.
	run: \|
	cd /tmp
	wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs
	wsinfer-mil run -m kaczmarj/pancancer-tissue-classifier.tcga -i ~/wsi/CMU-1.svs

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