lecrapaud 0.18.9__py3-none-any.whl → 0.19.0__py3-none-any.whl

lecrapaud/db/alembic/versions/2025_08_28_1516-c36e9fee22b9_add_avg_precision_to_score.py

@@ -0,0 +1,34 @@
+"""add avg precision to score
+
+Revision ID: c36e9fee22b9
+Revises: 7ed9963e732f
+Create Date: 2025-08-28 15:16:34.657593
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from lecrapaud.config import LECRAPAUD_TABLE_PREFIX
+
+# revision identifiers, used by Alembic.
+revision: str = "c36e9fee22b9"
+down_revision: Union[str, None] = "7ed9963e732f"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column(
+        f"{LECRAPAUD_TABLE_PREFIX}_scores",
+        sa.Column("avg_precision", sa.Float(), nullable=True),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column(f"{LECRAPAUD_TABLE_PREFIX}_scores", "avg_precision")
+    # ### end Alembic commands ###

lecrapaud/db/alembic/versions/2025_08_28_1622-8b11c1ba982e_change_name_column.py

@@ -0,0 +1,44 @@
+"""change name column
+
+Revision ID: 8b11c1ba982e
+Revises: c36e9fee22b9
+Create Date: 2025-08-28 16:22:45.528296
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import mysql
+from lecrapaud.config import LECRAPAUD_TABLE_PREFIX
+
+# revision identifiers, used by Alembic.
+revision: str = "8b11c1ba982e"
+down_revision: Union[str, None] = "c36e9fee22b9"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        f"{LECRAPAUD_TABLE_PREFIX}_experiments",
+        "name",
+        existing_type=mysql.VARCHAR(length=50),
+        type_=sa.String(length=255),
+        existing_nullable=False,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column(
+        f"{LECRAPAUD_TABLE_PREFIX}_experiments",
+        "name",
+        existing_type=sa.String(length=255),
+        type_=mysql.VARCHAR(length=50),
+        existing_nullable=False,
+    )
+    # ### end Alembic commands ###

lecrapaud/db/models/experiment.py

@@ -49,7 +49,7 @@ class Experiment(Base):
         onupdate=func.now(),
         nullable=False,
     )
-    name = Column(String(50), nullable=False)
+    name = Column(String(255), nullable=False)
     path = Column(String(255))  # we do not have this at creation time
     type = Column(String(50), nullable=False)
     size = Column(Integer, nullable=False)

lecrapaud/db/models/score.py

@@ -45,6 +45,7 @@ class Score(Base):
     recall = Column(Float)
     f1 = Column(Float)
     roc_auc = Column(Float)
+    avg_precision = Column(Float)
     thresholds = Column(JSON)
     precision_at_threshold = Column(Float)
     recall_at_threshold = Column(Float)

lecrapaud/db/session.py

@@ -12,6 +12,7 @@ from lecrapaud.config import DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME, DB
 
 _engine = None
 _SessionLocal = None
+
 if DB_URI:
     if "mysql://" in DB_URI and "pymysql://" not in DB_URI:
         DB_URI = DB_URI.replace("mysql://", "mysql+pymysql://")
@@ -72,7 +73,6 @@ def init_db(uri: str = None):
         autocommit=False,
         autoflush=False,
         bind=_engine,
-        expire_on_commit=False,  # Don't expire objects on commit
     )
 
     # Step 5: Apply Alembic migrations programmatically

lecrapaud/model_selection.py

@@ -14,8 +14,6 @@ import pickle
 from pydantic import BaseModel
 import ast
 
-os.environ["COVERAGE_FILE"] = str(Path(".coverage").resolve())
-
 # ML models
 from sklearn.model_selection import TimeSeriesSplit
 from sklearn.calibration import CalibratedClassifierCV
@@ -80,6 +78,8 @@ from lecrapaud.db import (
     Experiment,
 )
 
+os.environ["COVERAGE_FILE"] = str(Path(".coverage").resolve())
+
 # Reproducible result
 keras.utils.set_random_seed(42)
 np.random.seed(42)
@@ -157,8 +157,10 @@ class ModelEngine:
     def fit(self, *args):
         if self.recurrent:
             fit = self.fit_recurrent
-        elif (self.create_model == "lgb") or (self.create_model == "xgb"):
+        elif (self.model_name == "lgb") or (self.model_name == "xgb"):
             fit = self.fit_boosting
+        elif self.model_name == "catboost":
+            fit = self.fit_catboost
         else:
             fit = self.fit_sklearn
         model = fit(*args)
@@ -201,17 +203,110 @@ class ModelEngine:
 
         return model
 
-    def fit_boosting(self, x_train, y_train, x_val, y_val, params):
+    def fit_catboost(self, x_train, y_train, x_val, y_val, params):
         """
-        This is using lightGBM or XGboost C++ librairies
+        Train CatBoost models with native early stopping and log metrics to TensorBoard.
+        Also supports plotting of the primary eval metric if self.plot is True.
         """
-        lightGBM = self.create_model == "lgb"
+        # Prepare constructor parameters
+        ctor_params = dict(params) if params else {}
+        early_stopping_rounds = ctor_params.pop("early_stopping_rounds", None)
+        # Alias support: num_boost_round -> iterations
+        num_boost_round = ctor_params.pop("num_boost_round", None)
+        if num_boost_round is not None and "iterations" not in ctor_params:
+            ctor_params["iterations"] = num_boost_round
+
+        # Determine classification/regression setup
+        labels = np.unique(y_train)
+        num_class = (
+            labels.size
+            if self.target_type == "classification" and labels.size > 2
+            else 1
+        )
+
+        if self.target_type == "regression":
+            ctor_params.setdefault("loss_function", "RMSE")
+            eval_metric = ctor_params.get("eval_metric", "RMSE")
+        else:
+            if num_class <= 2:
+                ctor_params.setdefault("loss_function", "Logloss")
+                eval_metric = ctor_params.get("eval_metric", "Logloss")
+            else:
+                ctor_params.setdefault("loss_function", "MultiClass")
+                eval_metric = ctor_params.get("eval_metric", "MultiClass")
+        ctor_params.setdefault("eval_metric", eval_metric)
+
+        # Instantiate CatBoost model from provided constructor
+        model = self.create_model(**ctor_params, allow_writing_files=False)
+
+        # Train with eval_set and early stopping
+        logger.info(f"Fitting the model {self.model_name}...")
+        logger.info(f"x_train shape: {x_train.shape}, x_val shape: {x_val.shape}")
+        logger.info(f"y_train shape: {y_train.shape}, y_val shape: {y_val.shape}")
+
+        model.fit(
+            x_train,
+            y_train,
+            eval_set=[(x_val, y_val)],
+            use_best_model=True,
+            early_stopping_rounds=early_stopping_rounds,
+            verbose=False,
+        )
+
+        # Retrieve evaluation results
+        evals_result = model.get_evals_result()
+        # CatBoost commonly uses 'learn' and 'validation' (or 'validation_0')
+        learn_key = "learn"
+        val_key = None
+        for k in evals_result.keys():
+            if k != learn_key:
+                val_key = k
+                break
+
+        # Ensure eval_metric exists; otherwise fallback to first available metric
+        if eval_metric not in evals_result.get(learn_key, {}):
+            if evals_result.get(learn_key):
+                eval_metric = next(iter(evals_result[learn_key].keys()))
+
+        # TensorBoard logging
+        writer = SummaryWriter(self.log_dir)
+        try:
+            # learn_scores = evals_result.get(learn_key, {}).get(eval_metric, [])
+            val_scores = (
+                evals_result.get(val_key, {}).get(eval_metric, []) if val_key else []
+            )
+            # for i, v in enumerate(learn_scores):
+            #     writer.add_scalar(f"CatBoost/train/{eval_metric}", v, i)
+            for i, v in enumerate(val_scores):
+                writer.add_scalar(f"CatBoost/{eval_metric}", v, i)
+        finally:
+            writer.close()
+
+        # Optional plotting of training progress
+        if self.plot and eval_metric and learn_key in evals_result and val_key:
+            logs = {
+                "train": evals_result[learn_key].get(eval_metric, []),
+                "val": evals_result[val_key].get(eval_metric, []),
+            }
+            plot_training_progress(
+                logs=logs,
+                model_name=self.model_name,
+                target_number=self.target_number,
+                title_suffix=f"Training Progress - {eval_metric}",
+            )
+
+        # Attach metadata for consistency with sklearn path
+        model.model_name = self.model_name
+        model.target_type = self.target_type
+        logger.info(f"Successfully created a {model.model_name} at {datetime.now()}")
 
-        # Experiments
-        boosting_dataset = lgb.Dataset if lightGBM else xgb.DMatrix
-        train_data = boosting_dataset(x_train, label=y_train)
-        val_data = boosting_dataset(x_val, label=y_val)
+        self._model = model
+        return model
 
+    def fit_boosting(self, x_train, y_train, x_val, y_val, params):
+        """
+        This is using lightGBM or XGboost C++ librairies
+        """
         # Create a TensorBoardX writer
         writer = SummaryWriter(self.log_dir)
         evals_result = {}
@@ -223,11 +318,13 @@ class ModelEngine:
             if self.target_type == "classification" and labels.size > 2
             else 1
         )
-        logger.info("Fitting the model...")
+        logger.info(f"Fitting the model {self.model_name}...")
         logger.info(f"x_train shape: {x_train.shape}, x_val shape: {x_val.shape}")
         logger.info(f"y_train shape: {y_train.shape}, y_val shape: {y_val.shape}")
 
-        if lightGBM:
+        if self.model_name == "lgb":
+            train_data = lgb.Dataset(x_train, label=y_train)
+            val_data = lgb.Dataset(x_val, label=y_val)
 
             def tensorboard_callback(env):
                 for i, metric in enumerate(env.evaluation_result_list):
@@ -252,18 +349,23 @@ class ModelEngine:
                     "objective": loss,
                     "metric": eval_metric,
                     "num_class": num_class,
+                    "verbose": -1,
                 },
                 num_boost_round=params["num_boost_round"],
                 train_set=train_data,
                 valid_sets=[train_data, val_data],
                 valid_names=["train", "val"],
                 callbacks=[
-                    lgb.early_stopping(stopping_rounds=params["early_stopping_rounds"]),
+                    lgb.early_stopping(
+                        stopping_rounds=params["early_stopping_rounds"], verbose=False
+                    ),
                     lgb.record_evaluation(evals_result),
                     tensorboard_callback,
                 ],
             )
         else:
+            train_data = xgb.DMatrix(x_train, label=y_train)
+            val_data = xgb.DMatrix(x_val, label=y_val)
 
             class TensorBoardCallback(xgb.callback.TrainingCallback):
 
@@ -300,6 +402,7 @@ class ModelEngine:
                 if self.target_type == "regression"
                 else ("logloss" if num_class <= 2 else "mlogloss")
             )
+            xgb.set_config(verbosity=0)
             model = xgb.train(
                 params={
                     **params["model_params"],
@@ -318,7 +421,7 @@ class ModelEngine:
                     tensorboard_callback,
                 ],
                 evals_result=evals_result,  # Record evaluation result
-                verbose_eval=0,
+                verbose_eval=10000,
             )
 
         model.model_name = self.create_model
@@ -1365,6 +1468,9 @@ def evaluate(
             average=("binary" if num_classes == 2 else "macro"),
         )
         score["ROC_AUC"] = float(roc_auc_score(y_true, y_pred_proba, multi_class="ovr"))
+        score["AVG_PRECISION"] = average_precision_score(
+            y_true, y_pred_proba, average="macro"
+        )
 
         # Store the complete thresholds dictionary
         if len(target_clf_thresholds.keys()) > 1:

lecrapaud/search_space.py

@@ -15,6 +15,7 @@ from sklearn.naive_bayes import GaussianNB
 # Ensemble models
 from lightgbm import LGBMRegressor, LGBMClassifier
 from xgboost import XGBRegressor, XGBClassifier
+from catboost import CatBoostRegressor, CatBoostClassifier
 from sklearn.ensemble import (
     RandomForestRegressor,
     AdaBoostRegressor,
@@ -464,6 +465,41 @@ ml_models = [
             },
         },
     },
+    {
+        "model_name": "catboost",
+        "recurrent": False,
+        "need_scaling": False,
+        "classification": {
+            "create_model": CatBoostClassifier,
+            "search_params": {
+                "iterations": tune.randint(50, 1000),
+                "num_boost_round": tune.randint(50, 1000),
+                "early_stopping_rounds": tune.randint(5, 50),
+                "learning_rate": tune.loguniform(1e-4, 0.5),
+                "depth": tune.randint(3, 10),
+                "l2_leaf_reg": tune.loguniform(1e-5, 10),
+                "bagging_temperature": tune.uniform(0.0, 1.0),
+                "rsm": tune.quniform(0.6, 1.0, 0.05),
+                "random_state": 42,
+                "verbose": False,
+            },
+        },
+        "regression": {
+            "create_model": CatBoostRegressor,
+            "search_params": {
+                "iterations": tune.randint(50, 1000),
+                "num_boost_round": tune.randint(50, 1000),
+                "early_stopping_rounds": tune.randint(5, 50),
+                "learning_rate": tune.loguniform(1e-4, 0.5),
+                "depth": tune.randint(3, 10),
+                "l2_leaf_reg": tune.loguniform(1e-5, 10),
+                "bagging_temperature": tune.uniform(0.0, 1.0),
+                "rsm": tune.quniform(0.6, 1.0, 0.05),
+                "random_state": 42,
+                "verbose": False,
+            },
+        },
+    },
 ]
 
 

{lecrapaud-0.18.9.dist-info → lecrapaud-0.19.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lecrapaud
-Version: 0.18.9
+Version: 0.19.0
 Summary: Framework for machine and deep learning, with regression, classification and time series analysis
 License: Apache License
 Author: Pierre H. Gallet
@@ -8,6 +8,7 @@ Requires-Python: ==3.12.*
 Classifier: License :: Other/Proprietary License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: catboost (>=1.2.8)
 Requires-Dist: category-encoders (>=2.8.1)
 Requires-Dist: celery (>=5.5.3)
 Requires-Dist: ftfy (>=6.3.1)

{lecrapaud-0.18.9.dist-info → lecrapaud-0.19.0.dist-info}/RECORD

@@ -10,20 +10,22 @@ lecrapaud/db/alembic/versions/2025_06_24_1216-c62251b129ed_.py,sha256=6Pf36HAXEV
 lecrapaud/db/alembic/versions/2025_06_24_1711-86457e2f333f_.py,sha256=KjwjYvFaNqYmBLTYel8As37fyaBtNVWTqN_3M7y_2eI,1357
 lecrapaud/db/alembic/versions/2025_06_25_1759-72aa496ca65b_.py,sha256=MiqooJuZ1etExl2he3MniaEv8G0LrmqY-0m22m9xKmc,943
 lecrapaud/db/alembic/versions/2025_08_25_1434-7ed9963e732f_add_best_score_to_model_selection.py,sha256=gyQDFFHp1dlILuDtXSPdUU_MsLlX-UzTP-E96Aj_Hto,966
+lecrapaud/db/alembic/versions/2025_08_28_1516-c36e9fee22b9_add_avg_precision_to_score.py,sha256=Bpi1zegNGX1qU-8RVzRfwjyv2cVaQ5P9cpKQ1QDJgxs,945
+lecrapaud/db/alembic/versions/2025_08_28_1622-8b11c1ba982e_change_name_column.py,sha256=g6H2Z9MwB6UEiqdGlBoHBXpO9DTaWkwHt8FS6joVOm0,1191
 lecrapaud/db/alembic.ini,sha256=Zw2rdwsKV6c7J1SPtoFIPDX08_oTP3MuUKnNxBDiY8I,3796
 lecrapaud/db/models/__init__.py,sha256=Lhyw9fVLdom0Fc6yIP-ip8FjkU1EwVwjae5q2VM815Q,740
 lecrapaud/db/models/base.py,sha256=Sc6g38LsNsjn9-qpWOMSsZlbUER0Xr56-yLIJLpTMDU,7808
-lecrapaud/db/models/experiment.py,sha256=LjsMTY-PA9HZ27D2sz2fWy7HvwFqiS0dXKaiKF-S3k4,14868
+lecrapaud/db/models/experiment.py,sha256=HlaHnAdjTRo9q87FUWq83YlKw5vB_o1sULxUQdmuCvo,14869
 lecrapaud/db/models/feature.py,sha256=5o77O2FyRObnLOCGNj8kaPSGM3pLv1Ov6mXXHYkmnYY,1136
 lecrapaud/db/models/feature_selection.py,sha256=mk42xuw1Sm_7Pznfg7TNc5_S4hscdw79QgIe3Bt9ZRI,3245
 lecrapaud/db/models/feature_selection_rank.py,sha256=Ydsb_rAT58FoSH13wkGjGPByzsjPx3DITXgJ2jgZmow,2198
 lecrapaud/db/models/model.py,sha256=F0hyMjd4FFHCv6_arIWBEmBCGOfG3b6_uzU8ExtFE90,952
 lecrapaud/db/models/model_selection.py,sha256=tJuICcporf3TxQHbJbHxnKgkaVc02z2kJJoCYS2nDcw,2001
 lecrapaud/db/models/model_training.py,sha256=jAIYPdwBln2jf593soLQ730uYrTfNK8zdG8TesOqmh0,1698
-lecrapaud/db/models/score.py,sha256=fSfXLt6Dm-8Fy9ku0urMT5Fa6zNqn4YqVnEO4o3zKVI,1669
+lecrapaud/db/models/score.py,sha256=oo9-IAP8iRgrQYe39W_T1nW4zA_E3cLuTnFaDPAAK1A,1703
 lecrapaud/db/models/target.py,sha256=DKnfeaLU8eT8J_oh_vuFo5-o1CaoXR13xBbswme6Bgk,1649
 lecrapaud/db/models/utils.py,sha256=-a-nWWmpJ2XzidIxo2COVUTrGZIPYCfBzjhcszJj_bM,1109
-lecrapaud/db/session.py,sha256=24vbFhpC2dB3eTMRWc9XFdNOVHdXXt5U6U3_WzXsGA0,3732
+lecrapaud/db/session.py,sha256=87W5AkGRYu8b2rF5FNQ0MFC6wtGc-gGagNJQN_0vnDQ,3667
 lecrapaud/directories.py,sha256=0LrANuDgbuneSLker60c6q2hmGnQ3mKHIztTGzTx6Gw,826
 lecrapaud/experiment.py,sha256=1xLWjOrqAxJh9CdXOx9ppQuRFRRj0GH-xYZqg-ty9hI,2463
 lecrapaud/feature_engineering.py,sha256=ib1afBrwqePiXUaw0Cpe6hY3VNl5afg8YVntb88SCT4,39199
@@ -37,10 +39,10 @@ lecrapaud/misc/tabpfn_tests.ipynb,sha256=VkgsCUJ30d8jaL2VaWtQAgb8ngHPNtPgnXLs7QQ
 lecrapaud/misc/test-gpu-bilstm.ipynb,sha256=4nLuZRJVe2kn6kEmauhRiz5wkWT9AVrYhI9CEk_dYUY,9608
 lecrapaud/misc/test-gpu-resnet.ipynb,sha256=27Vu7nYwujYeh3fOxBNCnKJn3MXNPKZU-U8oDDUbymg,4944
 lecrapaud/misc/test-gpu-transformers.ipynb,sha256=k6MBSs_Um1h4PykvE-LTBcdpbWLbIFST_xl_AFW2jgI,8444
-lecrapaud/model_selection.py,sha256=gP7Jo_JyI7YVKNk7VG5DjGcheUZsir1vNnTlTCM-R40,72480
-lecrapaud/search_space.py,sha256=-JkzuMhaomdwiWi4HvVQY5hiw3-oREemJA16tbwEIp4,34854
+lecrapaud/model_selection.py,sha256=z6sMU6ZGaymZOWdJehPw4yaWdzcYTABWweyH5LvCJwk,76980
+lecrapaud/search_space.py,sha256=FCIEHZBK1pUQ4CphJuxwXY2N_BdrCelRzHsCXnNLlVI,36334
 lecrapaud/utils.py,sha256=ATKu9pbXjYFRa2YzBYjqyLHJrzfnZ7SJrOD_qAnEBYE,8242
-lecrapaud-0.18.9.dist-info/LICENSE,sha256=MImCryu0AnqhJE_uAZD-PIDKXDKb8sT7v0i1NOYeHTM,11350
-lecrapaud-0.18.9.dist-info/METADATA,sha256=h4ahCgmQFRO_B6zF39_TTmFFIhO9VCdgH4XgEpK7T2g,11081
-lecrapaud-0.18.9.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-lecrapaud-0.18.9.dist-info/RECORD,,
+lecrapaud-0.19.0.dist-info/LICENSE,sha256=MImCryu0AnqhJE_uAZD-PIDKXDKb8sT7v0i1NOYeHTM,11350
+lecrapaud-0.19.0.dist-info/METADATA,sha256=VdLOpM5P_sI6pe2UBIcBwcrA8870ZBWUUmjBbZINQbI,11115
+lecrapaud-0.19.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+lecrapaud-0.19.0.dist-info/RECORD,,