pmc_maqc-ml/dvc.yaml at develop · babelomics/pmc_maqc-ml · GitHub

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stages:
  retrieve_raw_data:
    cmd: pixi run python src/retrieve_raw_data.py
    deps:
    - src/retrieve_raw_data.py
    params:
    - raw_data_folder
    - outcome_data_folder
    - dataset
    outs:
    - ${repo_data_folder}/raw/
  train_baseline:
    cmd: pixi run python src/train_baseline.py
    deps:
    - ${repo_data_folder}/raw/
    - src/train_baseline.py
    outs:
    - ${repo_data_folder}/models/baseline/
  predict_baseline:
    cmd: pixi run python src/predict_baseline.py
    deps:
    - ${repo_data_folder}/models/baseline/
    - src/predict_baseline.py
    params:
    - predict_params
    outs:
    - ${repo_data_folder}/results/baseline/
  feature_master:
    cmd: pixi run python src/feature_master.py
    deps:
    - ${repo_data_folder}/raw/
    - src/feature_master.py
    params:
    - master_params
    outs:
    - ${repo_data_folder}/${master_params.output_folder}/
  feature_diag:
    cmd: pixi run python src/featurize_table.py --table diag
    deps:
    - ${repo_data_folder}/raw/
    - src/featurize_table.py
    - src/featurization/diag.py
    params:
    - feature_params.diag_params
    outs:
    - ${repo_data_folder}/features/diag/
  feature_procdr:
    cmd: pixi run python src/featurize_table.py --table procdr
    deps:
    - ${repo_data_folder}/raw/
    - src/featurize_table.py
    - src/featurization/procdr.py
    params:
    - feature_params.procdr_params
    outs:
    - ${repo_data_folder}/features/procdr/
  feature_moltest:
    cmd: pixi run python src/featurize_table.py --table moltest
    deps:
    - ${repo_data_folder}/raw/
    - src/featurize_table.py
    - src/featurization/moltest.py
    params:
    - feature_params.moltest_params
    outs:
    - ${repo_data_folder}/features/moltest/
  feature_test:
    cmd: pixi run python src/featurize_table.py --table test
    deps:
    - ${repo_data_folder}/raw/
    - src/featurize_table.py
    - src/featurization/test.py
    params:
    - feature_params.test_params
    outs:
    - ${repo_data_folder}/features/test/
  feature_drug:
    cmd: pixi run python src/featurize_table.py --table drug
    deps:
    - ${repo_data_folder}/raw/
    - src/featurize_table.py
    - src/featurization/drug.py
    params:
    - feature_params.drug_params
    outs:
    - ${repo_data_folder}/features/drug/
  train:
    cmd: pixi run python src/train.py
    deps:
    - ${repo_data_folder}/features/
    - src/train.py
    - src/preprocessing.py
    - src/models.py
    params:
    - train_params
    outs:
    - ${repo_data_folder}/models/current/
  predict:
    cmd: pixi run python src/predict.py
    deps:
    - ${repo_data_folder}/models/current/
    - src/predict.py
    params:
    - predict_params
    outs:
    - ${repo_data_folder}/results/current/
metrics:
- data/models/baseline/metrics.json
- data/models/current/metrics.json
artifacts:
  baseline:
    path: data/models/baseline/best_model.pkl
    type: model
  best_model:
    path: data/models/current/best_model.pkl
    type: model