Reproduce Paper #413
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name: Reproduce Paper | |
# This action runs a Jupyter notebook in the examples folder that uses astartes to generate | |
# train/val/test splits on two datasets (RDB7 and QM9). These dynamically generated splits | |
# are then compared to the splits which were created at the time of paper writing, to ensure | |
# that subsequent releases of astartes have backwards compatibility. | |
on: | |
schedule: | |
- cron: "0 8 * * 1-5" | |
workflow_dispatch: | |
concurrency: | |
group: actions-id-${{ github.workflow }} | |
cancel-in-progress: true | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -el {0} | |
name: Reproduce Paper Data Splits | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: mamba-org/setup-micromamba@main | |
with: | |
environment-name: temp | |
condarc: | | |
channels: | |
- defaults | |
- conda-forge | |
channel_priority: flexible | |
create-args: | | |
python=3.11 | |
- name: Install Dependencies | |
run: | | |
python -m pip install -e .[molecules] | |
python -m pip install scikit-learn==1.2.2 | |
python -m pip install notebook | |
python -m pip install "numpy<2" | |
- name: Backup Reference Splits | |
run: | | |
cd examples/reproduce_paper_splits | |
cp QM9_splits/QM9_splits_kmeans.pkl REFERENCE_QM9_splits_kmeans.pkl | |
cp QM9_splits/QM9_splits_random.pkl REFERENCE_QM9_splits_random.pkl | |
cp QM9_splits/QM9_splits_scaffold.pkl REFERENCE_QM9_splits_scaffold.pkl | |
cp RDB7_splits/RDB7_splits_kmeans.pkl REFERENCE_RDB7_splits_kmeans.pkl | |
cp RDB7_splits/RDB7_splits_random.pkl REFERENCE_RDB7_splits_random.pkl | |
cp RDB7_splits/RDB7_splits_scaffold.pkl REFERENCE_RDB7_splits_scaffold.pkl | |
- name: Execute Splitting Notebooks | |
run: | | |
cd examples/reproduce_paper_splits | |
ipython QM9_make_splits.ipynb | |
ipython RDB7_make_splits.ipynb | |
- name: Upload New Splits as Artifacts | |
uses: actions/upload-artifact@v3 | |
with: | |
name: dynamically-generated-splits | |
path: | | |
examples/reproduce_paper_splits/QM9_splits/ | |
examples/reproduce_paper_splits/RDB7_splits/ | |
- name: Compare Reference to Current | |
run: | | |
cd examples/reproduce_paper_splits | |
python validate_splits.py |