Test Tutorial #183
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name: Test Tutorial | |
# following example: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/ | |
on: | |
push: | |
branches: | |
- main | |
tags: | |
- "[0-9]+.[0-9]+.[0-9]+" | |
schedule: | |
# Weekly on saturday 23:59 | |
- cron: "59 23 * * 6" | |
jobs: | |
test-tutorial: | |
runs-on: [self-hosted, linux, x64, gpu] | |
container: | |
image: continuumio/miniconda3 | |
options: --runtime=nvidia --gpus all | |
defaults: | |
run: | |
working-directory: ./docs/tutorials | |
steps: | |
- name: Pull code | |
uses: actions/checkout@v4 | |
- name: Install dependencies, code, and list everything | |
working-directory: ./ | |
run: | | |
conda install -y -c conda-forge python=3 cupy cuda-version=11.8 curl unzip | |
python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later | |
python -m pip install .[all] | |
conda list | |
- name: Grab files needed for tests | |
run: | | |
mkdir dataset | |
mkdir templates | |
mkdir results_80S | |
mkdir results_60S | |
cd templates | |
cp ../data/6qzp_60S.mrc . | |
curl https://files.wwpdb.org/pub/emdb/structures/EMD-2938/map/emd_2938.map.gz -o emd_2938.map.gz | |
gunzip emd_2938.map.gz | |
cd ../dataset | |
curl -L -O -J -H "X-Dataverse-key:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718 | |
unzip dataverse_files.zip | |
# this inflates into a 'tutorial' folder, moving everything out | |
mv tutorial/* . | |
- name: Set TQDM_MININTERVAL | |
run: echo "TQDM_MININTERVAL=10" >> "$GITHUB_ENV" | |
- name: Run Tutorial test | |
run: | | |
# Hardcode the conversion line | |
for x in dataset/*.mrc; do python -c "import mrcfile; mrc = mrcfile.mmap('$x', 'r+'); mrc.voxel_size = 13.79"; done | |
python -u tests/test_tutorial.py |