Reproduce Paper #407
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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 |