update testing - add symlink for premade run dirs #330

	name: Testing

	on:
	push:
	branches:
	- '**'

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- uses: psf/black@stable
	with:
	src: "./regional_mom6 ./tests"

	testing:
	needs: formatting
	runs-on: ubuntu-latest
	container: ghcr.io/cosima/regional-test-env:updated
	defaults:
	run:
	shell: bash -el {0}
	strategy:
	matrix:
	python-version: ["3.9", "3.10"]

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	auto-update-conda: true
	auto-activate-base: false
	environment-file: environment-ci.yml
	python-version: ${{ matrix.python-version }}
	- name: Install from source
	run: \|
	python -m pip install .
	- name: Install pytest
	run: \|
	python -m pip install pytest pytest-cov nbval
	- name: Test with pytest
	run: \|
	if [[ "${{ matrix.python-version }}" == "3.10" ]]; then
	python -m pytest --cov=regional_mom6 --cov-report=xml tests/
	else
	python -m pytest tests/
	fi
	- name: Test the example notebook
	run: \|
	ln -s /data demos/PATH_TO_GLORYS_DATA
	ln -s /data demos/PATH_TO_GEBCO_FILE
	ln -s /build/FRE-NCtools/tools demos/PATH_TO_FRE_TOOLS
	ln -s /build/regional-mom6 /build/regional-mom6/demos/PATH_TO_REGIONAL_MOM6_CODE
	python -m pytest --nbval demos/reanalysis-forced.ipynb --nbval-current-env

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	if: ${{ matrix.python-version == '3.10' }}
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	directory: ./coverage/reports/
	env_vars: OS,PYTHON
	files: ./coverage.xml
	name: codecov-umbrella

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