Changes for external data eval.

  model_cmd.add_argument(

      "--featurize", action="store_true",

      help="Perform the featurization step.")

  model_cmd.add_argument(

      "--generate-dataset", action="store_true",

      help="Generate dataset from featurized data.")

  model_cmd.add_argument(

      "--train-test-split", action="store_true",

      help="Perform the train-test-split step.")

  model_cmd.add_argument(

      "--eval", action="store_true",

      help="Perform model eval step.")

  model_cmd.add_argument(

      "--eval-full", action="store_true",

      help="Evaluate model on full dataset.")

  model_cmd.add_argument(

      "--base-dir", type=str, default=None,

      help="The base directory for the model.")

  model_cmd.add_argument(

      "--model-dir", type=str, default=None,

      help="The model storage directory for the model.")

  model_cmd.add_argument(

      "--eval-train", type=bool, default=True,

      help="Evaluate model on train dataset.")

  model_cmd.add_argument(

      "--eval-test", type=bool, default=True,

      help="Evaluate model on test dataset.")

  model_cmd.add_argument(

      "--eval-full", type=bool, default=False,

      help="Evaluate model on full dataset.")

  add_featurize_group(model_cmd)

  add_transforms_group(model_cmd)

    ensure_exists([feature_dir, data_dir, model_dir])

  if args.featurize:

    print("+++++++++++++++++++++++++++++++++")

    print("Perform featurization")

  if args.featurize:

    featurize_inputs(

        feature_dir, data_dir, args.input_files, args.user_specified_features,

        args.tasks, args.smiles_field, args.split_field, args.id_field,

        args.threshold, args.parallel)

  if args.generate_dataset:

    print("+++++++++++++++++++++++++++++++++")

    print("Generate dataset for featurized samples")

    samples_dir = os.path.join(data_dir, "samples")

    samples = FeaturizedSamples(samples_dir, reload=True)

    print("Generating dataset.")

    full_data_dir = os.path.join(data_dir, "full-data")

    full_dataset = Dataset(full_data_dir, samples, args.feature_types)

    print("Transform data.")

    full_dataset.transform(args.input_transforms, args.output_transforms)

  if args.train_test_split:

    print("+++++++++++++++++++++++++++++++++")

    print("Perform train-test split")

    paths = [feature_dir]

  if args.train_test_split:

    train_test_split(

        paths, args.input_transforms, args.output_transforms, args.feature_types,

        args.splittype, args.mode, data_dir)

  if args.fit:

    print("+++++++++++++++++++++++++++++++++")

    print("Fit model")

  if args.fit:

    model_params = extract_model_params(args)

    fit_model(

        model_name, model_params, model_dir, data_dir)

  print("+++++++++++++++++++++++++++++++++")

  if args.eval:

    if args.eval_train:

    print("+++++++++++++++++++++++++++++++++")

    print("Eval Model on Train")

    print("-------------------")

    train_dir = os.path.join(data_dir, "train-data")

        model_name, model_dir, train_dir, csv_out_train,

        stats_out_train)

    if args.eval_test:

    print("Eval Model on Test")

    print("------------------")

    test_dir = os.path.join(data_dir, "test-data")

        stats_out_test)

  if args.eval_full:

    print("+++++++++++++++++++++++++++++++++")

    print("Eval Model on Full Dataset")

    print("--------------------------")

    full_data_dir = os.path.join(data_dir, "full-data")

    csv_out_full = os.path.join(data_dir, "full.csv")

    stats_out_full = os.path.join(data_dir, "full-stats.txt")

    eval_trained_model(

          model_name, model_dir, data_dir, csv_out_full,

        model_name, model_dir, full_data_dir, csv_out_full,

        stats_out_full)

def parse_args(input_args=None):

      featurize_input_partial(input_file)

  dataset_files = glob.glob(os.path.join(feature_dir, "*.joblib"))

  print("Loading featurized data.")

  print("Writing samples to disk.")

  samples_dir = os.path.join(data_dir, "samples")

  samples = FeaturizedSamples(samples_dir, dataset_files)