Autologging functionality for scikit-learn integration with LightGBM …

…(Part 1) (#5130)

* init commit

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* restore test

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* fix doc

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* address review: use cloudpickle

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* remove prev folders

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* address review

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

* a better soln

Signed-off-by: Junwen Yao <jwyiao@gmail.com>

mlflow/lightgbm.py

@@ -33,6 +33,7 @@
 from mlflow.models.signature import ModelSignature
 from mlflow.models.utils import ModelInputExample, _save_example
 from mlflow.tracking.artifact_utils import _download_artifact_from_uri
+from mlflow.utils import _get_fully_qualified_class_name
 from mlflow.utils.environment import (
     _mlflow_conda_env,
     _validate_env_arguments,
@@ -67,21 +68,24 @@
 _logger = logging.getLogger(__name__)
 
 
-def get_default_pip_requirements():
+def get_default_pip_requirements(include_cloudpickle=False):
     """
     :return: A list of default pip requirements for MLflow Models produced by this flavor.
              Calls to :func:`save_model()` and :func:`log_model()` produce a pip environment
              that, at minimum, contains these requirements.
     """
-    return [_get_pinned_requirement("lightgbm")]
+    pip_deps = [_get_pinned_requirement("lightgbm")]
+    if include_cloudpickle:
+        pip_deps.append(_get_pinned_requirement("cloudpickle"))
+    return pip_deps
 
 
-def get_default_conda_env():
+def get_default_conda_env(include_cloudpickle=False):
     """
     :return: The default Conda environment for MLflow Models produced by calls to
              :func:`save_model()` and :func:`log_model()`.
     """
-    return _mlflow_conda_env(additional_pip_deps=get_default_pip_requirements())
+    return _mlflow_conda_env(additional_pip_deps=get_default_pip_requirements(include_cloudpickle))
 
 
 @format_docstring(LOG_MODEL_PARAM_DOCS.format(package_name=FLAVOR_NAME))
@@ -132,7 +136,7 @@ def save_model(
     path = os.path.abspath(path)
     if os.path.exists(path):
         raise MlflowException("Path '{}' already exists".format(path))
-    model_data_subpath = "model.lgb"
+    model_data_subpath = "model.lgb" if isinstance(lgb_model, lgb.Booster) else "model.pkl"
     model_data_path = os.path.join(path, model_data_subpath)
     os.makedirs(path)
     if mlflow_model is None:
@@ -143,20 +147,28 @@ def save_model(
         _save_example(mlflow_model, input_example, path)
 
     # Save a LightGBM model
-    lgb_model.save_model(model_data_path)
+    _save_model(lgb_model, model_data_path)
 
+    lgb_model_class = _get_fully_qualified_class_name(lgb_model)
     pyfunc.add_to_model(
         mlflow_model,
         loader_module="mlflow.lightgbm",
         data=model_data_subpath,
         env=_CONDA_ENV_FILE_NAME,
     )
-    mlflow_model.add_flavor(FLAVOR_NAME, lgb_version=lgb.__version__, data=model_data_subpath)
+    mlflow_model.add_flavor(
+        FLAVOR_NAME,
+        lgb_version=lgb.__version__,
+        data=model_data_subpath,
+        model_class=lgb_model_class,
+    )
     mlflow_model.save(os.path.join(path, MLMODEL_FILE_NAME))
 
     if conda_env is None:
         if pip_requirements is None:
-            default_reqs = get_default_pip_requirements()
+            default_reqs = get_default_pip_requirements(
+                include_cloudpickle=not isinstance(lgb_model, lgb.Booster)
+            )
             # To ensure `_load_pyfunc` can successfully load the model during the dependency
             # inference, `mlflow_model.save` must be called beforehand to save an MLmodel file.
             inferred_reqs = mlflow.models.infer_pip_requirements(
@@ -186,6 +198,22 @@ def save_model(
     write_to(os.path.join(path, _REQUIREMENTS_FILE_NAME), "\n".join(pip_requirements))
 
 
+def _save_model(lgb_model, model_path):
+    """
+    LightGBM Boosters are saved using the built-in method `save_model()`,
+    whereas LightGBM scikit-learn models are serialized using Cloudpickle.
+    """
+    import lightgbm as lgb
+
+    if isinstance(lgb_model, lgb.Booster):
+        lgb_model.save_model(model_path)
+    else:
+        import cloudpickle
+
+        with open(model_path, "wb") as out:
+            cloudpickle.dump(lgb_model, out)
+
+
 @format_docstring(LOG_MODEL_PARAM_DOCS.format(package_name=FLAVOR_NAME))
 def log_model(
     lgb_model,
@@ -251,9 +279,31 @@ def log_model(
 
 
 def _load_model(path):
-    import lightgbm as lgb
+    """
+    Load Model Implementation.
+    :param path: Local filesystem path to
+                    the MLflow Model with the ``lightgbm`` flavor (MLflow < 1.23.0) or
+                    the top-level MLflow Model directory (MLflow >= 1.23.0).
+    """
+
+    model_dir = os.path.dirname(path) if os.path.isfile(path) else path
+    flavor_conf = _get_flavor_configuration(model_path=model_dir, flavor_name=FLAVOR_NAME)
+
+    model_class = flavor_conf.get("model_class", "lightgbm.basic.Booster")
+    lgb_model_path = os.path.join(model_dir, flavor_conf.get("data"))
+
+    if model_class == "lightgbm.basic.Booster":
+        import lightgbm as lgb
+
+        model = lgb.Booster(model_file=lgb_model_path)
+    else:
+        # LightGBM scikit-learn models are deserialized using Cloudpickle.
+        import cloudpickle
+
+        with open(lgb_model_path, "rb") as f:
+            model = cloudpickle.load(f)
 
-    return lgb.Booster(model_file=path)
+    return model
 
 
 def _load_pyfunc(path):
@@ -283,12 +333,11 @@ def load_model(model_uri, dst_path=None):
                      This directory must already exist. If unspecified, a local output
                      path will be created.
 
-    :return: A LightGBM model (an instance of `lightgbm.Booster`_).
+    :return: A LightGBM model (an instance of `lightgbm.Booster`_) or a LightGBM scikit-learn
+             model, depending on the saved model class specification.
     """
     local_model_path = _download_artifact_from_uri(artifact_uri=model_uri, output_path=dst_path)
-    flavor_conf = _get_flavor_configuration(model_path=local_model_path, flavor_name=FLAVOR_NAME)
-    lgb_model_file_path = os.path.join(local_model_path, flavor_conf.get("data", "model.lgb"))
-    return _load_model(path=lgb_model_file_path)
+    return _load_model(path=local_model_path)
 
 
 class _LGBModelWrapper:

tests/lightgbm/test_lightgbm_model_export.py

@@ -50,6 +50,18 @@ def lgb_model():
     return ModelWithData(model=model, inference_dataframe=X)
 
 
+@pytest.fixture(scope="session")
+def lgb_sklearn_model():
+    iris = datasets.load_iris()
+    X = pd.DataFrame(
+        iris.data[:, :2], columns=iris.feature_names[:2]  # we only take the first two features.
+    )
+    y = iris.target
+    model = lgb.LGBMClassifier(n_estimators=10)
+    model.fit(X, y)
+    return ModelWithData(model=model, inference_dataframe=X)
+
+
 @pytest.fixture
 def model_path(tmpdir):
     return os.path.join(str(tmpdir), "model")
@@ -68,7 +80,7 @@ def test_model_save_load(lgb_model, model_path):
 
     mlflow.lightgbm.save_model(lgb_model=model, path=model_path)
     reloaded_model = mlflow.lightgbm.load_model(model_uri=model_path)
-    reloaded_pyfunc = pyfunc.load_pyfunc(model_uri=model_path)
+    reloaded_pyfunc = pyfunc.load_model(model_uri=model_path)
 
     np.testing.assert_array_almost_equal(
         model.predict(lgb_model.inference_dataframe),
@@ -81,6 +93,24 @@ def test_model_save_load(lgb_model, model_path):
     )
 
 
+@pytest.mark.large
+def test_sklearn_model_save_load(lgb_sklearn_model, model_path):
+    model = lgb_sklearn_model.model
+    mlflow.lightgbm.save_model(lgb_model=model, path=model_path)
+    reloaded_model = mlflow.lightgbm.load_model(model_uri=model_path)
+    reloaded_pyfunc = pyfunc.load_model(model_uri=model_path)
+
+    np.testing.assert_array_almost_equal(
+        model.predict(lgb_sklearn_model.inference_dataframe),
+        reloaded_model.predict(lgb_sklearn_model.inference_dataframe),
+    )
+
+    np.testing.assert_array_almost_equal(
+        reloaded_model.predict(lgb_sklearn_model.inference_dataframe),
+        reloaded_pyfunc.predict(lgb_sklearn_model.inference_dataframe),
+    )
+
+
 def test_signature_and_examples_are_saved_correctly(lgb_model):
     model = lgb_model.model
     X = lgb_model.inference_dataframe
@@ -398,3 +428,49 @@ def test_pyfunc_serve_and_score_sklearn(model):
     )
     scores = pd.read_json(resp.content, orient="records").values.squeeze()
     np.testing.assert_array_equal(scores, model.predict(X.head(3)))
+
+
+@pytest.mark.large
+def test_load_pyfunc_succeeds_for_older_models_with_pyfunc_data_field(lgb_model, model_path):
+    """
+    This test verifies that LightGBM models saved in older versions of MLflow are loaded
+    successfully by ``mlflow.pyfunc.load_model``. These older models specify a pyfunc ``data``
+    field referring directly to a LightGBM model file. Newer models also have the
+    ``model_class`` in LightGBM flavor.
+    """
+    model = lgb_model.model
+    mlflow.lightgbm.save_model(lgb_model=model, path=model_path)
+
+    model_conf_path = os.path.join(model_path, "MLmodel")
+    model_conf = Model.load(model_conf_path)
+    pyfunc_conf = model_conf.flavors.get(pyfunc.FLAVOR_NAME)
+    lgb_conf = model_conf.flavors.get(mlflow.lightgbm.FLAVOR_NAME)
+    assert lgb_conf is not None
+    assert "model_class" in lgb_conf
+    assert "data" in lgb_conf
+    assert pyfunc_conf is not None
+    assert "model_class" not in pyfunc_conf
+    assert pyfunc.DATA in pyfunc_conf
+
+    # test old MLmodel conf
+    model_conf.flavors["lightgbm"] = {"lgb_version": lgb.__version__, "data": "model.lgb"}
+    model_conf.save(model_conf_path)
+    model_conf = Model.load(model_conf_path)
+    lgb_conf = model_conf.flavors.get(mlflow.lightgbm.FLAVOR_NAME)
+    assert "data" in lgb_conf
+    assert lgb_conf["data"] == "model.lgb"
+
+    reloaded_pyfunc = pyfunc.load_model(model_uri=model_path)
+    assert isinstance(reloaded_pyfunc._model_impl.lgb_model, lgb.Booster)
+    reloaded_lgb = mlflow.lightgbm.load_model(model_uri=model_path)
+    assert isinstance(reloaded_lgb, lgb.Booster)
+
+    np.testing.assert_array_almost_equal(
+        lgb_model.model.predict(lgb_model.inference_dataframe),
+        reloaded_pyfunc.predict(lgb_model.inference_dataframe),
+    )
+
+    np.testing.assert_array_almost_equal(
+        reloaded_lgb.predict(lgb_model.inference_dataframe),
+        reloaded_pyfunc.predict(lgb_model.inference_dataframe),
+    )