o Add echo and show output, build Trust that the run actually happened #9
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| name: Docker Parsl GraphDRP CSA workflow | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: rajeeja/graphdrp-image:latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install missing libraries | |
| run: | | |
| apt-get update && apt-get install -y libxrender1 libxext6 tree #added tree here | |
| - name: Install and check | |
| run: | | |
| which python | |
| python --version | |
| which conda | |
| conda env list | |
| eval "$(conda shell.bash hook)" | |
| conda activate graphdrp | |
| pip install -e . | |
| export PYTHONPATH=$PYTHONPATH:. | |
| python -c "from improvelib.applications.drug_response_prediction.config import DRPPreprocessConfig; print('Import successful')" | |
| BASE_DIR=$(pwd) | |
| ls -ltrh | |
| cd /app/GraphDRP | |
| ls -ltrh | |
| conda list -n graphdrp | |
| python -c "import sys; print(sys.path)" | |
| cd $BASE_DIR/workflows/csa/parsl/ | |
| pip install cryptography==37.0.1 | |
| pip install pyopenssl==22.0.0 | |
| pip install cffi==1.14.5 | |
| pip install parsl numpy pandas scikit-learn pyyaml | |
| mv /app/GraphDRP/csa_data . | |
| echo "Preprocess started" | |
| ls -ltrh | |
| python workflow_preprocess.py --config_file ./parsl_csa_githubactions.ini | |
| echo "Preprocess done" | |
| python workflow_csa.py --config_file ./parsl_csa_githubactions.ini | |
| echo "Parsl CSA done" | |
| echo "Tree of ./parsl_csa_exp3:" | |
| tree ./parsl_csa_exp3 | |
| echo "Content of ./parsl_csa_exp3/infer/CCLE-CCLE/split_0/test_scores.json:" | |
| cat ./parsl_csa_exp3/infer/CCLE-CCLE/split_0/test_scores.json | |
| echo "Content of ./parsl_csa_exp3/infer/CCLE-CCLE/split_1/test_scores.json:" | |
| cat ./parsl_csa_exp3/infer/CCLE-CCLE/split_1/test_scores.json | |
| echo "Content of ./parsl_csa_exp3/infer/CCLE-gCSI/split_0/test_scores.json:" | |
| cat ./parsl_csa_exp3/infer/CCLE-gCSI/split_0/test_scores.json | |
| echo "Content of ./parsl_csa_exp3/infer/gCSI-CCLE/split_0/test_scores.json:" | |
| cat ./parsl_csa_exp3/infer/gCSI-CCLE/split_0/test_scores.json |