Merge pull request #16 from gavinevans/mobt_877_implement_qrf_7

Alter saving of QRF model

Author: Kat-90

improver/calibration/load_and_train_quantile_regression_random_forest.py

@@ -43,7 +43,6 @@ def __init__(
         random_state: Optional[int] = None,
         transformation: Optional[str] = None,
         pre_transform_addition: float = 0,
-        compression: int = 5,
     ):
         """Initialise the LoadAndTrainQRF plugin."""
         self.feature_config = feature_config
@@ -59,7 +58,6 @@ def __init__(
         self.random_state = random_state
         self.transformation = transformation
         self.pre_transform_addition = pre_transform_addition
-        self.compression = compression
         self.quantile_forest_installed = quantile_forest_package_available()
 
     def _split_cubes_and_parquet_files(
@@ -355,7 +353,7 @@ def process(
         forecast_df = self._add_features_to_df(forecast_df, cube_inputs)
         forecast_df, truth_df = self.filter_bad_sites(forecast_df, truth_df)
 
-        TrainQuantileRegressionRandomForests(
+        result = TrainQuantileRegressionRandomForests(
             target_name=self.target_cf_name,
             feature_config=self.feature_config,
             n_estimators=self.n_estimators,
@@ -364,6 +362,6 @@ def process(
             random_state=self.random_state,
             transformation=self.transformation,
             pre_transform_addition=self.pre_transform_addition,
-            compression=self.compression,
             model_output=model_output,
         )(forecast_df, truth_df)
+        return result

improver/calibration/quantile_regression_random_forest.py

@@ -6,7 +6,6 @@
 
 from typing import Optional
 
-import joblib
 import numpy as np
 import pandas as pd
 
@@ -206,8 +205,6 @@ def __init__(
         random_state: Optional[int] = None,
         transformation: Optional[str] = None,
         pre_transform_addition: np.float32 = 0,
-        compression: int = 5,
-        model_output: Optional[str] = None,
         **kwargs,
     ) -> None:
         """Initialise the plugin.
@@ -246,10 +243,6 @@ def __init__(
                 Transformation to be applied to the data before fitting.
             pre_transform_addition (float):
                 Value to be added before transformation.
-            compression (int):
-                Compression level for saving the model.
-            model_output (str):
-                Full path including model file name that will store the pickled model.
             kwargs:
                 Additional keyword arguments for the quantile regression model.
 
@@ -264,8 +257,6 @@ def __init__(
         self.transformation = transformation
         _check_valid_transformation(self.transformation)
         self.pre_transform_addition = pre_transform_addition
-        self.compression = compression
-        self.output = model_output
         self.kwargs = kwargs
         self.expected_coordinate_order = ["forecast_reference_time", "forecast_period"]
 
@@ -353,9 +344,7 @@ def process(
         target_values = combined_df["ob_value"].values
 
         # Fit the quantile regression model
-        qrf_model = self.fit_qrf(feature_values, target_values)
-
-        joblib.dump(qrf_model, self.output, compress=self.compression)
+        return self.fit_qrf(feature_values, target_values)
 
 
 class ApplyQuantileRegressionRandomForests(PostProcessingPlugin):

improver/cli/__init__.py

@@ -312,6 +312,7 @@ def with_output(
     pass_through_output=False,
     compression_level=1,
     least_significant_digit: int = None,
+    output_file_type="netCDF",
     **kwargs,
 ):
     """Add `output` keyword only argument.
@@ -346,15 +347,20 @@ def with_output(
     Returns:
         Result of calling `wrapped` or None if `output` is given.
     """
+    import joblib
+
     from improver.utilities.save import save_netcdf
 
     result = wrapped(*args, **kwargs)
 
-    if output and result:
+    if output and output.endswith(".nc"):
         save_netcdf(result, output, compression_level, least_significant_digit)
         if pass_through_output:
             return ObjectAsStr(result, output)
         return
+    elif output and output.endswith((".pickle", ".pkl")):
+        joblib.dump(result, output, compress=compression_level)
+        return
     return result
 
 

improver/cli/train_quantile_regression_random_forest.py

@@ -9,6 +9,7 @@
 
 
 @cli.clizefy
+@cli.with_output
 def process(
     *file_paths: cli.inputpath,
     feature_config: cli.inputjson,
@@ -24,8 +25,6 @@ def process(
     random_state: int = None,
     transformation: str = None,
     pre_transform_addition: float = 0,
-    compression: int = 5,
-    output: str = None,
 ):
     """Training a model using Quantile Regression Random Forest.
 
@@ -92,10 +91,6 @@ def process(
             Transformation to be applied to the data before fitting.
         pre_transform_addition (float):
             Value to be added before transformation.
-        compression (int):
-            Compression level for saving the model.
-        output (str):
-            Full path including model file name that will store the pickled model.
     Returns:
         None:
             The function creates a pickle file.
@@ -119,9 +114,7 @@ def process(
         random_state=random_state,
         transformation=transformation,
         pre_transform_addition=pre_transform_addition,
-        compression=compression,
     )(
         file_paths,
-        model_output=output,
     )
     return result

improver_tests/acceptance/test_train_quantile_regression_random_forest.py

@@ -59,7 +59,7 @@ def test_basic(
         "5",
         "--random-state",
         "42",
-        "--compression",
+        "--compression-level",
         "5",
         "--output",
         output_path,

improver_tests/calibration/quantile_regression_random_forests_calibration/test_load_and_apply_quantile_regression_random_forest.py

@@ -78,7 +78,6 @@ def test_load_and_apply_qrf(
     feature_config = {"wind_speed_at_10m": ["mean", "std", "latitude", "longitude"]}
 
     model_output = _run_train_qrf(
-        tmp_path,
         feature_config,
         n_estimators,
         max_depth,
@@ -98,6 +97,7 @@ def test_load_and_apply_qrf(
         ],
         realization_data=[2, 6, 10],
         truth_data=[4.2, 6.2, 4.1, 5.1],
+        tmp_path=tmp_path,
     )
 
     frt = "20170103T0000Z"
@@ -182,7 +182,6 @@ def test_unexpected(
     quantiles = [0.5]
 
     model_output = _run_train_qrf(
-        tmp_path,
         feature_config,
         n_estimators,
         max_depth,
@@ -202,6 +201,7 @@ def test_unexpected(
         ],
         realization_data=[2, 6, 10],
         truth_data=[4.2, 6.2, 4.1, 5.1],
+        tmp_path=tmp_path,
     )
 
     frt = "20170103T0000Z"

improver_tests/calibration/quantile_regression_random_forests_calibration/test_load_and_train_quantile_regression_random_forest.py

@@ -5,7 +5,6 @@
 """Unit tests for the LoadAndTrainQRF plugin."""
 
 import iris
-import joblib
 import numpy as np
 import pandas as pd
 import pytest
@@ -380,10 +379,6 @@ def test_load_and_train_qrf(
     truth_path = truth_creation(tmp_path)
     file_paths = [forecast_path, truth_path]
 
-    model_output_dir = tmp_path / "train_qrf"
-    model_output_dir.mkdir(parents=True)
-    model_output = str(model_output_dir / "qrf_model.pkl")
-
     if include_static:
         ancil_path = _create_ancil_file(tmp_path, sorted(list(set(wmo_ids))))
         file_paths.append(ancil_path)
@@ -407,9 +402,7 @@ def test_load_and_train_qrf(
         transformation="log",
         pre_transform_addition=1,
     )
-    plugin(file_paths, model_output=model_output)
-
-    qrf_model = joblib.load(model_output)
+    qrf_model = plugin(file_paths)
 
     assert qrf_model.n_estimators == n_estimators
     assert qrf_model.max_depth == max_depth
@@ -446,10 +439,6 @@ def test_load_and_train_qrf_no_paths(tmp_path, make_files):
         for file_path in file_paths:
             (tmp_path / file_path).mkdir(parents=True, exist_ok=True)
 
-    model_output_dir = tmp_path / "train_qrf"
-    model_output_dir.mkdir(parents=True)
-    model_output = str(model_output_dir / "qrf_model.pkl")
-
     plugin = LoadAndTrainQRF(
         experiment="latestblend",
         feature_config=feature_config,
@@ -464,11 +453,9 @@ def test_load_and_train_qrf_no_paths(tmp_path, make_files):
         transformation="log",
         pre_transform_addition=1,
     )
-    result = plugin(file_paths, model_output=model_output)
+    result = plugin(file_paths)
     # Expecting None since no valid paths are provided
     assert result is None
-    # Check if the model output file is not created
-    assert not (model_output_dir / "qrf_model.pkl").exists()
 
 
 @pytest.mark.parametrize(
@@ -491,10 +478,6 @@ def test_load_and_train_qrf_mismatches(tmp_path, cycletime, forecast_periods):
         tmp_path / "partition" / "truth_table/",
     ]
 
-    model_output_dir = tmp_path / "train_qrf"
-    model_output_dir.mkdir(parents=True)
-    model_output = str(model_output_dir / "qrf_model.pkl")
-
     plugin = LoadAndTrainQRF(
         experiment="latestblend",
         feature_config=feature_config,
@@ -509,11 +492,9 @@ def test_load_and_train_qrf_mismatches(tmp_path, cycletime, forecast_periods):
         transformation="log",
         pre_transform_addition=1,
     )
-    result = plugin(file_paths, model_output=model_output)
+    result = plugin(file_paths)
     # Expecting None since no valid paths are provided
     assert result is None
-    # Check if the model output file is not created
-    assert not (model_output_dir / "qrf_model.pkl").exists()
 
 
 @pytest.mark.parametrize(
@@ -581,10 +562,6 @@ def test_unexpected(
     truth_path = truth_creation(tmp_path)
     file_paths = [forecast_path, truth_path]
 
-    model_output_dir = tmp_path / "train_qrf"
-    model_output_dir.mkdir(parents=True)
-    model_output = str(model_output_dir / "qrf_model.pkl")
-
     # Create an instance of LoadAndTrainQRF with the required parameters
     plugin = LoadAndTrainQRF(
         experiment="latestblend",
@@ -603,7 +580,7 @@ def test_unexpected(
 
     if exception == "non_matching_truth":
         with pytest.raises(IOError, match="The requested filepath"):
-            plugin(file_paths, model_output=model_output)
+            plugin(file_paths)
     elif exception == "missing_static_feature":
         feature_config = {
             "wind_speed_at_10m": ["mean", "std"],
@@ -622,13 +599,13 @@ def test_unexpected(
             plugin.process(file_paths=file_paths)
     elif exception == "no_percentile_realization":
         with pytest.raises(ValueError, match="The forecast parquet file"):
-            plugin(file_paths, model_output=model_output)
+            plugin(file_paths)
     elif exception == "alternative_forecast_period":
         with pytest.raises(ValueError, match="The forecast_periods argument"):
-            plugin(file_paths, model_output=model_output)
+            plugin(file_paths)
     elif exception == "no_quantile_forest_package":
         plugin.quantile_forest_installed = False
-        result = plugin(file_paths, model_output=model_output)
+        result = plugin(file_paths)
         assert result is None
     else:
         raise ValueError(f"Unknown exception type: {exception}")