ENH: tracked R2 metric (#28) #265

	name: Test and build

	on:
	pull_request:
	branches:
	- main
	push:
	branches:
	- main

	jobs:
	lint:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up python 3.8
	uses: actions/setup-python@v5
	with:
	python-version: 3.8

	- name: Install dependencies
	run: \|
	pip install -q https://github.com/qiime2/q2lint/archive/master.zip
	pip install -q flake8

	- name: Lint
	run: make lint

	build-and-test:
	needs: lint
	strategy:
	matrix:
	# todo: include macos once repos is public
	# os: [ubuntu-latest, macos-latest]
	os: [ubuntu-latest]
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v4
	with:
	# necessary for versioneer
	fetch-depth: 0
	- uses: actions/setup-python@v5
	with:
	python-version: 3.8
	- uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	python-version: 3.8
	- name: Run tests
	# ugly because I wanted to keep one location of dependencies
	run: \|
	python -m pip install --upgrade pip
	make create-env
	conda activate ritme && make dev && make test-cov

	- name: Hack - template coverage output path
	run: echo "COV=coverage xml -o $GITHUB_WORKSPACE/coverage.xml" >> $GITHUB_ENV

	# # TODO: include this once this is a Q2 plugin and remove above run tests
	# - uses: qiime2/action-library-packaging@alpha1
	# with:
	# package-name: q2-ritme
	# additional-tests: ${{ env.COV }}
	# build-target: dev
	# library-token: ${{ secrets.LIBRARY_TOKEN }}

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	# TODO: remove token when repos is public
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: true

Provide feedback