Drop bacteria_reg (not being used anywhere and doesn't really do anyt… #7

	name: R-test

	on:
	push:
	branches:
	[main, new_release_0-3-8]
	pull_request:
	branches:
	[main]
	schedule:
	- cron: '11 1 1 * *'
	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	jobs:
	R-test:
	name: python ${{ matrix.python-version }}, ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	env:
	REPO_NAME: ${{ github.event.repository.name }}

	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest]
	python-version: ['3.7', '3.8', '3.9', '3.10']
	include:
	- os: windows-latest
	python-version: "3.9"
	steps:
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}

	- name: Set up R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: 'release'

	- uses: r-lib/actions/setup-pandoc@v2

	- name: Update pip and install testing pkgs
	run: \|
	python -VV
	python -m pip install --upgrade pip
	pip install pytest

	# fiona doesn't have wheels for windows
	- if: matrix.os == 'windows-latest'
	run: \|
	pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/GDAL-3.7.1-cp39-cp39-win_amd64.whl
	pip install https://github.com/cgohlke/geospatial-wheels/releases/download/v2023.7.16/Fiona-1.9.4.post1-cp39-cp39-win_amd64.whl

	- name: Install package and dependencies
	run: \|
	python -m pip install --no-deps .
	pip install -r requirements.txt

	- name: Run pip env using R reticulate
	run: \|
	install.packages("reticulate")
	reticulate::import("harmonize_wq")
	shell: Rscript {0}

	- name: Run pytest
	run: pytest -v harmonize_wq

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