Execute python notebooks #79

	name: Execute python notebooks

	on:
	pull_request:
	workflow_dispatch:
	# run once a week
	schedule:
	- cron: "0 0 * * 0"

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- id: checkout
	uses: actions/checkout@v3

	- id: python-setup
	name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.11'

	- id: python-dependencies
	name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements_dev.txt
	pip install jupyter

	- id: execute-bioscales
	name: Execute bioscales notebook
	run: \|
	jupyter nbconvert --execute --to notebook --inplace bioscales_biogeochemical_metadata/python/bioscales.ipynb

	- id: execute-neon
	name: Execute neon notebook
	run: \|
	jupyter nbconvert --execute --to notebook --inplace NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb

	- id: execute-taxonomic
	name: Execute taxonomic notebook
	run: \|
	jupyter nbconvert --execute --to notebook --inplace taxonomic_dist_by_soil_layer/python/taxonomic_dist_soil_layer.ipynb

	- id: execute-NOM
	name: Execute NOM notebook
	run: \|
	jupyter nbconvert --execute --to notebook --inplace NOM_visualizations/python/nom_data.ipynb

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