Auto Generate `environment.yml` #998

	name: unit-tests

	on:
	workflow_dispatch:
	push:
	branches:
	- main
	- dev
	pull_request:
	branches:
	- main
	- dev
	- breaking-improvments

	jobs:
	unit-tests:
	runs-on: ubuntu-20.04
	container:
	image: hopkinsidd/flepimop:latest-dev
	options: --user root
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	with:
	lfs: true
	- name: Set up Rprofile
	run: \|
	cp build/docker/Docker.Rprofile $HOME/.Rprofile
	cp /home/app/.bashrc $HOME/.bashrc
	shell: bash
	- name: Install the gempyor package
	run: \|
	source /var/python/3.10/virtualenv/bin/activate
	python -m pip install --upgrade pip
	python -m pip install "flepimop/gempyor_pkg[test]"
	shell: bash
	- name: Install local R packages
	run: Rscript build/local_install.R
	shell: bash
	- name: Run gempyor tests
	run: \|
	source /var/python/3.10/virtualenv/bin/activate
	cd flepimop/gempyor_pkg
	pytest -s
	shell: bash
	- name: Run gempyor-cli integration tests from examples
	run: \|
	source /var/python/3.10/virtualenv/bin/activate
	cd examples
	pytest -s
	shell: bash
	- name: Run flepicommon tests
	run: \|
	setwd("flepimop/R_packages/flepicommon")
	devtools::test(stop_on_failure=TRUE)
	shell: Rscript {0}
	- name: Run inference tests
	run: \|
	setwd("flepimop/R_packages/inference")
	devtools::test(stop_on_failure=TRUE)
	shell: Rscript {0}
	# - name: Run integration tests
	# env:
	# CENSUS_API_KEY: ${{ secrets.CENSUS_API_KEY }}
	# run: \|
	# Rscript build/local_install.R
	# cd test
	# source /var/python/3.10/virtualenv/bin/activate
	# pytest run_tests.py
	# shell: bash

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