Including testing tutorial notebooks in PR unit CI workflow #411

	name: pytest

	on:
	push:
	# Action will run when any changes to these paths are pushed or pr'ed to master
	branches: [ main ]
	paths:
	- flowermd/**
	- environment-dev.yml
	- .github/workflows/pytest.yml
	pull_request:
	branches: [ main ]
	paths:
	- flowermd/**
	- environment-dev.yml
	- .github/workflows/pytest.yml
	# Allows workflow to be manually triggered
	workflow_dispatch:

	jobs:
	pytest:
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.9', '3.10', '3.11', '3.12']

	runs-on: ${{ matrix.os }}

	steps:
	- name: Check out repository
	uses: actions/checkout@v2

	- name: Build environment
	uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: environment-dev.yml
	miniforge-variant: Mambaforge
	miniforge-version: 4.9.2-4
	use-mamba: true

	- name: Install package
	shell: bash -l {0}
	run: pip install .

	- name: Run pytest with coverage report
	shell: bash -l {0}
	run: python -m pytest -rs -v --cov=./ --cov-report=xml

	- name: Run pytest on tutorials
	shell: bash -l {0}
	run: python -m pytest -rs -v --nbmake tutorials/

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml

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