Added the workflow file for sample data #13
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It is the bt_clustering and simulation runner running on the sample data with most of the default params.
Added the pip install -e . that I forgot in the original update
agitter
requested changes
Nov 28, 2023
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I had forgotten we already had a test script in place that does most of these steps. Rather than overwrite the old test script, can you please modify the existing .yml file to add the new conda list and testing steps that we want? That will retain the history of the old file. You may need to adjust to the whitespace style of the existing .yml file.
.github/workflows/test.yml
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| environment-file: conda_cpu_env.yml | ||
| auto-activate-base: false | ||
| miniconda-version: 'latest' | ||
| # Log conda environment contents |
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Keep this new step after installing the active_learning_dd package
.github/workflows/test.yml
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| # Tests that the regression training code runs in the conda environment | ||
| - name: Test BT_Clustering | ||
| shell: bash --login {0} | ||
| run: python utils/generate_bt_clustering.py --csv_file_or_dir=datasets/sample_data/training_data/iter_{}.csv --output_dir=datasets/sample_data/training_data --feature_name="Morgan FP_2_1024" --cutoff=0.4 --dist_function=tanimoto_dissimilarity --process_count=2 --index_name="Index ID" | ||
| # Tests that inference notebook can execute in the conda environment | ||
| - 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 |
.github/workflows/test.yml
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| # Tests that the regression training code runs in the conda environment | ||
| - name: Test BT_Clustering | ||
| shell: bash --login {0} | ||
| run: python utils/generate_bt_clustering.py --csv_file_or_dir=datasets/sample_data/training_data/iter_{}.csv --output_dir=datasets/sample_data/training_data --feature_name="Morgan FP_2_1024" --cutoff=0.4 --dist_function=tanimoto_dissimilarity --process_count=2 --index_name="Index ID" |
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Does the {} need to be set to some index?
Also note the error from the GitHub Actions log:
python: can't open file 'utils/generate_bt_clustering.py': [Errno 2] No such file or directory
The working directory is the root of the repository.
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Superseded by #14 |
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It is the bt_clustering and simulation runner running on the sample data with most of the default params.