Merge pull request #406 from prophyle/pyup-scheduled-update-2024-10-01 #111

	name: Testing

	on:
	push:
	branches:
	- master
	pull_request:

	jobs:
	#build:
	build_and_test:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	compiler: [gcc]
	#compiler: [gcc, clang]
	steps:

	- name: Checkout ProPhyle
	uses: actions/checkout@v2

	- name: Setup apt dependencies
	run: \|
	sudo apt install -y texinfo zlib1g-dev

	- name: Compile with ${{ matrix.compiler }}
	run: \|
	make CC=${{ matrix.compiler }}

	# bioconda:
	#runs-on: ubuntu-latest
	#needs: build
	#steps:

	- name: Setup ProPhyle environment
	run: \|
	export PATH="/usr/share/miniconda/bin:$PATH"
	conda install -c conda-forge -q mamba
	mamba create -c conda-forge -c bioconda --name prophyle -y "python>=3.8" ete3 bitarray parallel psutil scipy sphinx codecov pysam samtools

	#test:
	#runs-on: ubuntu-latest
	#needs: bioconda
	#steps:

	- name: Run tests
	env:
	CI: true
	run: \|
	export PATH="/usr/share/miniconda/bin:$PATH"
	source activate prophyle

	make test

Provide feedback