Update test.yml on new branch #42
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| name: Test active learning in drug discovery | |
| on: | |
| - push | |
| - pull_request | |
| jobs: | |
| Test: | |
| name: Test active learning in drug discovery | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: active_learning_dd | |
| environment-file: conda_cpu_env.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| # Activate the installed packages | |
| - name: Install active_learning_dd package | |
| shell: bash --login {0} | |
| run: pip install -e . | |
| # Test Sample Runner | |
| - name: Test sample data runner | |
| shell: bash --login {0} | |
| run: | | |
| cd chtc_runners | |
| python sample_data_runner.py \ | |
| --pipeline_params_json_file=../param_configs/sample_data_config.json \ | |
| --hyperparams_json_file=../param_configs/experiment_PstP_hyperparams/sampled_hyparams/ClusterBasedWCSelector_609.json \ | |
| --iter_max=5 \ | |
| --no-precompute_dissimilarity_matrix \ | |
| --initial_dataset_file=../datasets/sample_data/training_data/iter_0.csv.gz | |
| # Tests the BT clustering | |
| - name: Test BT_Clustering | |
| shell: bash --login {0} | |
| run: | | |
| gzip -dk datasets/sample_data/unlabeled_data/unlabeled_0.csv.gz | |
| python active_learning_dd/utils/generate_bt_clustering.py --csv_file_or_dir=datasets/sample_data/unlabeled_data/unlabeled_0.csv --output_dir=./tmp_test --feature_name="Morgan FP_2_1024" --cutoff=0.4 | |
| # Tests that base Simulation Runner | |
| - name: Test Simulation Runner | |
| shell: bash --login {0} | |
| run: python chtc_runners/simulation_runner.py --pipeline_params_json_file=param_configs/sample_data_config.json --nbs_params_json_file=param_configs/ClusterBasedWCSelector_params_reduced.json --exploration_strategy=weighted --iter_max=5 --process_num=0 --batch_size_index=0 --rnd_seed=0 --no-random_param_sampling --precompute_dissimilarity_matrix |