Adding installation guide. #81

	name: Generate phenopackets

	env:
	# We generate the phenopackets from this state
	# of the `phenopacket-store` repository.
	# State from May 8th, 2024
	PHENOPACKET_STORE_TAG: 9fe73a29246bce4493d98e85efdd0f9f3cb56856

	on:
	push:
	branches: [ develop ]
	pull_request:
	branches: [ main, develop ]

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2

	- name: Initialize Python 3.8
	uses: actions/[email protected]
	with:
	python-version: "3.8"

	- name: Install pyphetools & dependencies
	run: \|
	python3 -m pip install --editable .

	- name: Install Jupyter and register current Python as kernel
	run: \|
	python3 -m pip install ipykernel notebook
	python3 -m ipykernel install --user --name pp_env --display-name "Pyphetools (Python 3)"

	- name: Check out phenopacket-store
	run: \|
	cd ..
	git clone https://github.com/monarch-initiative/phenopacket-store.git
	cd phenopacket-store
	git checkout $PHENOPACKET_STORE_TAG

	- name: Generate phenopackets
	run: \|
	# phenopacket-store folder
	pps_dir=$(dirname $(pwd))/phenopacket-store

	# Prepare the notebooks to run
	declare -a fbn1_notebooks=(
	"FBN1/FBN1_isolated_ectopia_lentis_individuals.ipynb"
	"FBN1/FBN1_lipodystropy_individuals.ipynb"
	"FBN1/Katzke_2002_Marfan.ipynb"
	"FBN1/LeGoff_FBN1_acromicric_and_geleophysic_dysplasia.ipynb"
	"FBN1/Loeys2010_stiff_skin_syndrome.ipynb"
	"FBN1/Palz_Marfan_2000.ipynb"
	"FBN1/Tiecke_2001_Marfan.ipynb"
	)

	# Run the notebooks
	for nb in ${fbn1_notebooks[@]}
	do
	nb_path=${pps_dir}/notebooks/${nb}
	printf "Running %s\n" ${nb_path}
	jupyter execute --kernel_name=pp_env ${nb_path}
	done

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