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Merge pull request #116 from monarch-initiative/feature/use-fasthpocr #82

Merge pull request #116 from monarch-initiative/feature/use-fasthpocr

Merge pull request #116 from monarch-initiative/feature/use-fasthpocr #82

name: Generate phenopackets
env:
# We generate the phenopackets from this state
# of the `phenopacket-store` repository.
PHENOPACKET_STORE_TAG: pyphe-ci-wip
# PHENOPACKET_STORE_TAG: c06a52e0 # State from Mar 5th, 2024
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/Comeglio_isolated_ectopia_lentis.ipynb"
"FBN1/FBN1_lipodystrophy_Lin_2020.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