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Test active learning in drug discovery

Update test.yml #37

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Update test.yml

Update test.yml #37

Workflow file for this run

.github/workflows/test.yml at e7a36e4
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: |
cd active_learning_dd/utils
python generate_bt_clustering.py --csv_file_or_dir=./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