add params json #58

	name: notebooks-gambiae

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

	jobs:

	run:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	matrix:
	python-version: ['3.8', '3.11']

	steps:

	- name: Checkout source
	uses: actions/checkout@v3

	- name: Install poetry
	run: pipx install poetry==1.4.2

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'poetry'

	- name: Install dependencies
	run: \|
	poetry install
	poetry run python -m ipykernel install --user --name AnoPrimer

	- id: 'auth'
	name: 'Set up Google Cloud authentication'
	uses: 'google-github-actions/auth@v2'
	with:
	credentials_json: '${{ secrets.GOOGLE_CREDENTIALS }}'

	- name: 'Set up Google Cloud SDK'
	uses: 'google-github-actions/setup-gcloud@v2'
	with:
	version: '>= 363.0.0'

	- name: 'Check gcloud CLI'
	run: 'gcloud info'

	- name: Run notebooks
	run: \|
	poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params.json
	poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2.json
	poetry run papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params.json
	poetry run papermill notebooks/AnoPrimer-long.ipynb probe_run.ipynb -k AnoPrimer -f tests/probe_Params.json
	poetry run papermill notebooks/AnoPrimer-short.ipynb short_run.ipynb -k AnoPrimer

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