modified gh action to test itsxpress #331

	name: GitHub Actions Weekly Build (V2)

	on:
	push:
	pull_request:
	schedule:
	- cron: "0 0 /7 *"

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.9
	uses: actions/setup-python@v2
	with:
	python-version: 3.9
	- name: Install dependencies
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	- run: \|
	#sudo apt update
	#sudo apt install gcc-10 g++-10
	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	echo $CONDA_PREFIX
	$CONDA/bin/conda list
	$CONDA/bin/conda info --base
	#CONDA_PREFIX=/usr/share/miniconda/envs/testenv


	- name: Initiate conda channels
	uses: conda-incubator/setup-miniconda@v2
	with:
	channels: conda-forge,bioconda,default
	activate-environment: testenv
	auto-activate-base: false


	- name: Set up environment
	run: \|
	$CONDA/bin/conda env create -n testenv --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
	- name: Install Dependencies
	run: \|
	echo $CONDA_PREFIX
	source activate testenv
	$CONDA/bin/conda install biopython
	pip install pyzstd
	pip install pytest
	pip install .
	qiime
	#itsxpress
	#qiime itsxpress
	#ls

	- name: Test with pytest
	run: \|
	source activate testenv
	pytest

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