ci: add docker workflow #31
Workflow file for this run
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| name: Design pipeline | |
| on: | |
| push: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build Docker image | |
| run: docker build -t my-image:latest . | |
| - name: Run Docker container | |
| run: docker run my-image:latest | |
| # defaults: | |
| # run: | |
| # shell: bash -el {0} | |
| # | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # | |
| # - name: Clone GT4SD | |
| # run: | | |
| # git clone https://github.com/GT4SD/gt4sd-core.git | |
| # | |
| # - uses: conda-incubator/setup-miniconda@v3 | |
| # with: | |
| # activate-environment: gt4sd | |
| # environment-file: gt4sd-core/conda_cpu_linux.yml | |
| # python-version: 3.8 | |
| # auto-activate-base: false | |
| # use-only-tar-bz2: true | |
| # | |
| # - name: Install dependencies | |
| # run: | | |
| # conda activate gt4sd | |
| # cd gt4sd-core | |
| # pip install --no-deps . | |
| # pip uninstall --yes toxsmi && pip install toxsmi | |
| # | |
| # - name: Load datasets | |
| # run: | | |
| # conda activate gt4sd | |
| # mkdir data | |
| # python scripts/load_data.py \ | |
| # --uniprot P05067 \ | |
| # --affinity_type IC50 \ | |
| # --affinity_cutoff 10000 \ | |
| # --output_dir data/ \ | |
| # --train_size 0.8 \ | |
| # --binary_labels | |
| # | |
| # - name: Train toxsmi model | |
| # run: | | |
| # conda activate gt4sd | |
| # python scripts/train_toxsmi.py \ | |
| # --train data/train.csv \ | |
| # --test data/valid.csv \ | |
| # --smi data/mols.smi \ | |
| # --language tokenizer \ | |
| # --params config/toxsmi_conf.json \ | |
| # --model models \ | |
| # --name toxsmi_model | |
| # | |
| # - name: Generate molecules with MoLeR | |
| # run: | | |
| # conda activate gt4sd | |
| # head -n 5 data/mols.smi > data/good_docks.smi | |
| # python scripts/moler_generate_toxsmi.py \ | |
| # --smi_path data/good_docks.smi \ | |
| # --param_path config/moler_conf.json \ | |
| # --output_path data/moler_filtered \ | |
| # --predictor_path models/toxsmi_model/weights/best_F1.pt | |
| # | |
| # - name: Generate more diverse molecules with Regression Transformer | |
| # run: | | |
| # conda activate gt4sd | |
| # python scripts/prepare_rt_data.py \ | |
| # --smi_path data/moler_filtered/generated.csv \ | |
| # --output_path data/moler_filtered/generated_qed.csv | |
| # head -n 10 data/moler_filtered/generated_qed.csv > data/moler_filtered/generated_qed_selected.csv | |
| # python scripts/rt_generate.py \ | |
| # --smi_path data/moler_filtered/generated_qed_selected.csv \ | |
| # --param_path config/rt_conf.json \ | |
| # --output_path data/rt | |
| # | |
| # | |
| # |