add codecov action and config file #1

	name: Build msmbuilder2022 codecov

	on:
	push:
	branches:
	- main
	# ignore changes to docs
	paths-ignore:
	- ./docs/*
	pull_request:
	branches:
	- main
	# ignore changes to docs
	paths-ignore:
	- ./docs/*
	workflow_dispatch:

	jobs:
	build-code:
	runs-on: ${{ matrix.os }}
	strategy:
	max-parallel: 6
	matrix:
	python-version: ["3.12"]
	include:
	- os: ubuntu-latest
	path: ~/.cache/pip
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- uses: actions/checkout@v4
	- uses: actions/cache@v4
	with:
	path: ${{ matrix.path }}
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	- uses: conda-incubator/setup-miniconda@v3
	with:
	auto-activate-base: true
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	activate-environment: test
	- name: Install required packages
	run: \|
	conda config --add channels conda-forge
	# conda install -yq conda-build jinja2 conda-verify
	conda install -yq zlib
	conda install h5py
	python -m pip install --upgrade pip
	# conda update conda-build
	- name: Pip install
	run: \|
	python -m pip install .
	- name: Test with pytest
	run: \|
	conda install -yq numdifftools hmmlearn
	pip install pytest
	pip install pytest-cov
	mkdir ../../pkgs
	cp -r msmbuilder/tests ../../pkgs/
	cd ../../pkgs
	python tests/data_init.py
	pytest tests --cov=msmbuilder --cov-report=xml:coverage.xml
	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ../../pkgs/coverage.xml
	fail_ci_if_error: True
	verbose: True

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