.. Generated by tools/update_cli_reference.py; do not edit.

.. code-block:: text

   surfacia ml-analysis



   options:
     -h, --help
       show this help message and exit
     -i, --input INPUT (required)
       Input CSV file (FinalFull.csv from feature extraction)
     --test-samples TEST_SAMPLES
       Comma-separated test sample names or numbers (e.g., "79,22,82,36,70,80")
     --nan-handling NAN_HANDLING
       How to handle NaN values (default: drop_columns)
       choices: drop_rows, drop_columns
     --manual
       Use manual feature selection mode (default: automatic workflow mode)

   Manual Mode Options:
     --manual-features MANUAL_FEATURES
       Comma-separated feature names for manual mode, or "Full" for all features
     --no-generate-fitting
       Disable generation of fitting plots for manual mode

   Workflow Mode Options (Default):
     --max-features MAX_FEATURES
       Maximum features for automatic selection (default: 5)
     --stepreg-runs STEPREG_RUNS
       Number of stepwise regression runs (default: 3)
     --initial-features INITIAL_FEATURES
       Comma-separated initial features for stepwise regression
     --shap-fit-threshold SHAP_FIT_THRESHOLD
       SHAP R² threshold for feature recommendation (default: 0.3)

   Common Options:
     --train-test-split TRAIN_TEST_SPLIT
       Train/test split ratio (default: 0.85)
     --epoch EPOCH
       Number of training epochs (default: 64)
     --cores CORES
       Number of CPU cores to use (default: 32)

   Examples:
     # Automatic workflow mode (default) - uses stepwise regression for feature selection
     surfacia ml-analysis -i ./Surfacia*/FinalFull.csv --test-samples "79,22,82,36,70,80" --max-features 5 --stepreg-runs 3

     # Manual feature selection mode
     surfacia ml-analysis -i ./Surfacia*/FinalFull.csv --manual --manual-features "S_ALIE_min,C_LEAE_min,Fun_ESP_delta"

     # Use all features in manual mode
     surfacia ml-analysis -i ./Surfacia*/FinalFull.csv --manual --manual-features "Full"

     # Custom training parameters
     surfacia ml-analysis -i ./Surfacia*/FinalFull.csv --epoch 128 --cores 64 --train-test-split 0.8

   Modes:
     - Default (workflow): Automatic feature selection using stepwise regression
     - Manual (--manual): Use specific features you provide
