From a5c7bcf667e04c1f72ef993f9b67c6e62d7ef70d Mon Sep 17 00:00:00 2001 From: Svyatoslav Date: Thu, 30 Nov 2023 19:02:45 +0300 Subject: [PATCH] Added logging with mlflow --- .gitignore | 1 + README.md | 3 + configs/cb_config.yaml | 9 +- configs/rf_config.yaml | 10 +- mlopscourse/models/base.py | 4 + mlopscourse/models/catboost.py | 24 ++ mlopscourse/models/random_forest.py | 37 ++ mlopscourse/train.py | 17 +- mlopscourse/utils.py | 6 + poetry.lock | 628 +++++++++++++++++++++++++++- pyproject.toml | 1 + 11 files changed, 736 insertions(+), 4 deletions(-) create mode 100644 mlopscourse/utils.py diff --git a/.gitignore b/.gitignore index fccf941..1c68fce 100644 --- a/.gitignore +++ b/.gitignore @@ -161,3 +161,4 @@ cython_debug/ checkpoints predictions catboost_info +mlruns diff --git a/README.md b/README.md index e726468..825d84a 100644 --- a/README.md +++ b/README.md @@ -79,6 +79,9 @@ The available models are `rf` (Random Forest from the `scikit-learn` library) an poetry run python3 commands.py train --config_name cb_config ``` +_N.B. Do not forget to set `logging.mlflow.tracking_uri` before the launch. The logs are +saved in the default directory: `mlruns`._ + ### Evaluation If you want to infer a previously trained model, make sure you've placed the checkpoint in diff --git a/configs/cb_config.yaml b/configs/cb_config.yaml index 9f37ea4..a3f887c 100644 --- a/configs/cb_config.yaml +++ b/configs/cb_config.yaml @@ -9,10 +9,17 @@ model: learning_rate: 0.3 l2_leaf_reg: 3 loss_function: RMSE - metric_period: 100 + metric_period: 10 + logging_level: Verbose training: checkpoint_name: cb_model.p inference: checkpoint_name: cb_model.p + +logging: + commit_id: None # Adding new fields from a script is prohibited by default + mlflow: + exp_name: MLOps hw2 + tracking_uri: http://127.0.0.1:5000 diff --git a/configs/rf_config.yaml b/configs/rf_config.yaml index 82e4efd..30881ac 100644 --- a/configs/rf_config.yaml +++ b/configs/rf_config.yaml @@ -1,11 +1,19 @@ model: name: rf hyperparams: - n_estimators: 500 + n_estimators: 100 random_state: 0 + verbose: 0 + n_jobs: -1 training: checkpoint_name: rf_model.p inference: checkpoint_name: rf_model.p + +logging: + commit_id: None # Adding new fields from a script is prohibited by default + mlflow: + exp_name: MLOps hw2 + tracking_uri: http://127.0.0.1:5000 diff --git a/mlopscourse/models/base.py b/mlopscourse/models/base.py index 07b0f4a..3685547 100644 --- a/mlopscourse/models/base.py +++ b/mlopscourse/models/base.py @@ -35,3 +35,7 @@ def __call__(self, X_sample: pd.DataFrame) -> pd.Series: def save_checkpoint(self, path: str) -> None: with open(path + self.cfg.training.checkpoint_name, "wb") as f: pickle.dump(self, f) + + @abstractmethod + def log_fis_and_metrics(self, exp_id: str) -> None: + raise NotImplementedError() diff --git a/mlopscourse/models/catboost.py b/mlopscourse/models/catboost.py index d8de95c..1a07d59 100644 --- a/mlopscourse/models/catboost.py +++ b/mlopscourse/models/catboost.py @@ -1,5 +1,6 @@ from typing import List, Optional +import mlflow import numpy as np import pandas as pd from catboost import CatBoostRegressor, Pool @@ -68,3 +69,26 @@ def __call__(self, X_sample: pd.DataFrame) -> np.ndarray: feature_names=list(X_sample.columns), ) return self.model.predict(sample_data) + + def log_fis_and_metrics(self, exp_id: str, col_names: List[str]) -> None: + with mlflow.start_run( + experiment_id=exp_id, run_name=f"training-{self.cfg.model.name}" + ): + # Log the model's hyperparameters and the code version + mlflow.log_params(self.cfg.model.hyperparams) + mlflow.log_param("commit_id", self.cfg.logging.commit_id) + # Log feature importances + mlflow.log_metrics( + { + f"fi_of_{col_name}": self.model.feature_importances_[i] + for i, col_name in enumerate(col_names) + } + ) + r2_scores = self.model.evals_result_["learn"]["R2"] + rmse_scores = self.model.evals_result_["learn"]["RMSE"] + assert len(r2_scores) == len(rmse_scores), "Something wrong with metrics!" + for i in range(len(r2_scores)): + mlflow.log_metrics( + {"R2_metric": r2_scores[i], "RMSE_loss": rmse_scores[i]}, + step=i * self.cfg.model.hyperparams.metric_period, + ) diff --git a/mlopscourse/models/random_forest.py b/mlopscourse/models/random_forest.py index 97c16c0..4f25001 100644 --- a/mlopscourse/models/random_forest.py +++ b/mlopscourse/models/random_forest.py @@ -1,12 +1,15 @@ from typing import List, Optional +import mlflow import numpy as np import pandas as pd from omegaconf import DictConfig from sklearn.compose import ColumnTransformer from sklearn.ensemble import RandomForestRegressor +from sklearn.metrics import mean_squared_error, r2_score from sklearn.pipeline import make_pipeline from sklearn.preprocessing import OrdinalEncoder +from tqdm import tqdm from .base import BaseModel @@ -52,3 +55,37 @@ def eval(self, X_test: pd.DataFrame, y_test: pd.Series) -> pd.Series: def __call__(self, X_sample: pd.DataFrame) -> np.ndarray: return self.model.predict(X_sample) + + def log_fis_and_metrics( + self, exp_id: str, X_train: pd.DataFrame, y_train: pd.Series + ) -> None: + with mlflow.start_run( + experiment_id=exp_id, run_name=f"training-{self.cfg.model.name}" + ): + # Log the model's hyperparameters and the code version + mlflow.log_params(self.cfg.model.hyperparams) + mlflow.log_param("commit_id", self.cfg.logging.commit_id) + # Log feature importances + mlflow.log_metrics( + { + f"fi_of_{col_name}": self.model.named_steps[ + "randomforestregressor" + ].feature_importances_[i] + for i, col_name in enumerate(X_train.columns) + } + ) + # Log R2 and RMSE metrics + for i in tqdm(range(0, self.cfg.model.hyperparams.n_estimators)): + model_i = make_pipeline( + self.preprocessor, RandomForestRegressor(**self.cfg.model.hyperparams) + ) + model_i.named_steps["randomforestregressor"].n_estimators = i + 1 + model_i.fit(X_train, y_train) + y_pred = model_i.predict(X_train) + mlflow.log_metrics( + { + "R2_metric": r2_score(y_train, y_pred), + "RMSE_metric": mean_squared_error(y_train, y_pred, squared=False), + }, + step=i, + ) diff --git a/mlopscourse/train.py b/mlopscourse/train.py index b83d4b7..9c7294c 100644 --- a/mlopscourse/train.py +++ b/mlopscourse/train.py @@ -1,11 +1,13 @@ import os import fire +import mlflow from hydra import compose from omegaconf import DictConfig, OmegaConf from .data.prepare_dataset import load_dataset from .models.models_zoo import prepare_model +from .utils import get_git_revision_hash class Trainer: @@ -23,6 +25,7 @@ def __init__(self, config_name: str, **kwargs: dict) -> None: self.cfg: DictConfig = compose( config_name=config_name, overrides=[f"{k}={v}" for k, v in kwargs.items()] ) + self.cfg.logging.commit_id = get_git_revision_hash() print(OmegaConf.to_yaml(self.cfg)) def train(self) -> None: @@ -40,7 +43,19 @@ def train(self) -> None: os.makedirs("checkpoints", exist_ok=True) model.save_checkpoint("checkpoints/") - print("The training was finished successfully!") + print("The training was finished successfully!\nCollecting logs...") + + # Since there is no easy way to log metrics as functions of time during + # the training, they should be collected after it. + mlflow_cfg = self.cfg.logging.mlflow + mlflow.set_tracking_uri(mlflow_cfg.tracking_uri) + exp_id = mlflow.set_experiment(mlflow_cfg.exp_name).experiment_id + # Unfortunately, logging is model dependent, at least because + # RandomForestRegressor doesn't provide the target metric progress. + if self.cfg.model.name == "cb": + model.log_fis_and_metrics(exp_id, X_train.columns) + else: + model.log_fis_and_metrics(exp_id, X_train, y_train) if __name__ == "__main__": diff --git a/mlopscourse/utils.py b/mlopscourse/utils.py new file mode 100644 index 0000000..ea38f52 --- /dev/null +++ b/mlopscourse/utils.py @@ -0,0 +1,6 @@ +import subprocess + + +# Credits to https://stackoverflow.com/a/21901260/12187881 +def get_git_revision_hash() -> str: + return subprocess.check_output(["git", "rev-parse", "HEAD"]).decode("ascii").strip() diff --git a/poetry.lock b/poetry.lock index d7eacb3..310d8c4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -136,6 +136,25 @@ files = [ 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