Changing tmpfile used, changed precedence of the slide_mpp and magnif… #29

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: PathoPatcher Build Workflow

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest
	# https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v3
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	channels: conda-forge, defaults
	python-version: 3.10.12
	environment-file: environment_build.yaml
	activate-environment: pathopatch_env
	use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
	auto-update-conda: true
	auto-activate-base: false
	- name : Run CLI Tests
	run: python -m pytest -vv -s ./tests/test_cli
	- name : Run Util Tests
	run: python -m pytest -vv -s ./tests/test_utils
	- name : Run Macenko Tests
	run: python -m pytest -vv -s ./tests/test_macenko_module
	- name : Run Core Tests
	run: python -m pytest -vv -s ./tests/test_core_modules
	- name : Run Dataset and Dataloader Tests
	run: python -m pytest -vv -s ./tests/test_pytorch_dataset

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