Ensure DeepDISC has all dependencies installed #16

	# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: Unit test and code coverage

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

	jobs:
	build:

	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}
	strategy:
	matrix:
	python-version: ['3.9', '3.10', '3.11']

	steps:
	- uses: actions/checkout@v3

	- uses: conda-incubator/setup-miniconda@v2
	with:
	python-version: ${{ matrix.python-version }}
	channels: conda-forge,defaults
	channel-priority: strict
	show-channel-urls: true
	use-mamba: true
	environment-file: ci-environment.yml
	activate-environment: deepdisc

	- name: Install dependencies
	run: \|
	sudo apt-get update
	python -m pip install --upgrade pip
	pip install .
	pip install .[dev]
	pip install 'git+https://github.com/facebookresearch/detectron2.git'
	pip install 'git+https://github.com/pmelchior/scarlet.git'
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Run unit tests with pytest
	run: \|
	python -m pytest tests --cov=deepdisc --cov-report=xml
	- name: Upload coverage report to codecov
	uses: codecov/codecov-action@v3

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