add pathogenome to list of docker images #240

	name: ci

	on:
	pull_request:
	push:
	branches:
	- master

	jobs:
	lint:
	runs-on: ubuntu-latest
	steps:
	- name: checkout source
	uses: actions/checkout@v2

	- name: set up python 3.9
	uses: actions/setup-python@v1
	with:
	python-version: 3.9

	- name: install dependencies
	run: python -m pip install --upgrade pip

	- name: lint
	run: \|
	pip install -q flake8
	flake8

	verify:
	runs-on: ubuntu-latest
	steps:
	- name: checkout source
	uses: actions/checkout@v2

	- name: install QIIME 2 amplicon distro
	run: \|
	envFile=qiime2-amplicon-ubuntu-latest-conda.yml
	wget https://raw.githubusercontent.com/qiime2/distributions/dev/2024.10/amplicon/released/$envFile
	conda env create -q -p ./test-env --file $envFile

	- name: install conda dependencies
	shell: bash -l {0}
	run: \|
	source "$CONDA/etc/profile.d/conda.sh"
	conda install -p ./test-env -q pip

	- name: install pip dependencies
	shell: bash -l {0}
	run: \|
	source "$CONDA/etc/profile.d/conda.sh"
	conda activate ./test-env
	pip install -r requirements.txt

	- name: build docs
	shell: bash -l {0}
	env:
	SPHINXOPTS: -q
	run: \|
	source "$CONDA/etc/profile.d/conda.sh"
	conda activate ./test-env
	make clean && make dummy && make preview

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