diff --git a/CHANGELOG.md b/CHANGELOG.md index 205ba5020..27d035954 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Unreleased ### Added -- +- Add `ClearMLLogger` ([#568](https://github.com/etna-team/etna/pull/568)) - - - diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 21c558ff1..7095d6ae5 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -116,7 +116,7 @@ Useful links: 1. [ReST Quickref](https://docutils.sourceforge.io/docs/user/rst/quickref.html) 2. [ReST Roles](https://www.sphinx-doc.org/en/master/usage/restructuredtext/roles.html) 3. [ReST Cross-referencing Python objects](https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html#cross-referencing-python-objects) -4. [Matplotlib Cheetsheet](https://matplotlib.org/sampledoc/cheatsheet.html) +4. [Matplotlib Cheatsheet](https://matplotlib.org/sampledoc/cheatsheet.html) 5. [Sklearn example](https://github.com/scikit-learn/scikit-learn/blob/37ac6788c/sklearn/linear_model/_ridge.py#L321) The simplest way to check how documentation is rendered is to make a pull request. diff --git a/docs/source/api_reference/loggers.rst b/docs/source/api_reference/loggers.rst index 0ad6a2b55..98a697cfb 100644 --- a/docs/source/api_reference/loggers.rst +++ b/docs/source/api_reference/loggers.rst @@ -22,6 +22,7 @@ Loggers: LocalFileLogger S3FileLogger WandbLogger + ClearMLLogger There is global object :code:`tslogger` that can be imported. It has a class: diff --git a/docs/source/api_reference/settings.rst b/docs/source/api_reference/settings.rst index 6e2a346d7..f772e32b3 100644 --- a/docs/source/api_reference/settings.rst +++ b/docs/source/api_reference/settings.rst @@ -19,9 +19,12 @@ All available installation options: pip install "etna[prophet]" pip install "etna[torch]" pip install "etna[wandb]" + pip install "etna[clearml]" pip install "etna[auto]" pip install "etna[classification]" pip install "etna[statsforecast]" + pip install "etna[chronos]" + pip install "etna[timesfm]" pip install "etna[all]" .. note:: diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 90ac3d214..50256fbd3 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -26,6 +26,7 @@ Available user extensions are the following: - ``classiciation``: adds time series classification functionality, - ``chronos``: adds Chronos-like pretrained models, - ``timesfm``: adds TimesFM pretrained models. +- ``clearml``: adds ClearML logger with tensorboard support Install extension: diff --git a/etna/datasets/tsdataset.py b/etna/datasets/tsdataset.py index 892db50e7..db42ff64e 100644 --- a/etna/datasets/tsdataset.py +++ b/etna/datasets/tsdataset.py @@ -786,7 +786,7 @@ def to_flatten(df: pd.DataFrame, features: Union[Literal["all"], Sequence[str]] features: List of features to return. If "all", return all the features in the dataset. - Always return columns with timestamp and segemnt. + Always return columns with timestamp and segment. Returns ------- pd.DataFrame: diff --git a/etna/loggers/__init__.py b/etna/loggers/__init__.py index b70b8d8cf..48c4217ed 100644 --- a/etna/loggers/__init__.py +++ b/etna/loggers/__init__.py @@ -17,11 +17,12 @@ """ from etna import SETTINGS from etna.loggers.base import _Logger +from etna.loggers.base import tslogger from etna.loggers.console_logger import ConsoleLogger from etna.loggers.file_logger import LocalFileLogger from etna.loggers.file_logger import S3FileLogger if SETTINGS.wandb_required: from etna.loggers.wandb_logger import WandbLogger - -tslogger = _Logger() +if SETTINGS.clearml_required: + from etna.loggers.clearml_logger import ClearMLLogger diff --git a/etna/loggers/base.py b/etna/loggers/base.py index c0a8847cb..88ae449fa 100644 --- a/etna/loggers/base.py +++ b/etna/loggers/base.py @@ -186,3 +186,14 @@ def disable(self): self.loggers = [] yield self.loggers = temp_loggers + + @contextmanager + def capture_tslogger(self): + """Context manager to capture global logger.""" + parent_loggers = tslogger.loggers + tslogger.loggers = self.loggers + yield + tslogger.loggers = parent_loggers + + +tslogger = _Logger() diff --git a/etna/loggers/clearml_logger.py b/etna/loggers/clearml_logger.py new file mode 100644 index 000000000..c550c0c86 --- /dev/null +++ b/etna/loggers/clearml_logger.py @@ -0,0 +1,301 @@ +import base64 +import logging +from typing import TYPE_CHECKING +from typing import Any +from typing import Dict +from typing import Mapping +from typing import Optional +from typing import Sequence +from typing import Union +from uuid import uuid4 + +import pandas as pd + +from etna.loggers.base import BaseLogger + +if TYPE_CHECKING: + from clearml.task import Task + + from etna.datasets import TSDataset + + +class ClearMLLogger(BaseLogger): + """ClearML logger. + + Note + ---- + This logger requires ``clearml`` extension to be installed. + Read more about this at :ref:`installation page `. + + Warning + ------- + There is a possibility, that aggregated metrics charts may log incorrectly. + For more details see `issue `_. + """ + + def __init__( + self, + project_name: Optional[str] = None, + task_name: Optional[str] = None, + task_name_prefix: str = "", + task_type: str = "training", + tags: Optional[Sequence[str]] = None, + output_uri: Optional[Union[str, bool]] = None, + auto_connect_frameworks: Union[bool, Mapping[str, Union[bool, str, list]]] = False, + auto_resource_monitoring: Union[bool, Mapping[str, Any]] = True, + auto_connect_streams: Union[bool, Mapping[str, bool]] = True, + plot: bool = True, + table: bool = True, + config: Optional[Dict[str, Any]] = None, + save_dir: Optional[str] = None, + ): + """Create instance of ``ClearMLLogger``. + + Parameters + ---------- + project_name: + The name of the project in which the experiment will be created. + task_name + The name of Task (experiment). + task_name_prefix: + Prefix for the Task name field. + task_type: + The task type. + tags: + Add a list of tags (str) to the created Task. + output_uri: + The default location for output models and other artifacts. + auto_connect_frameworks: + Automatically connect frameworks. + auto_resource_monitoring: + Automatically create machine resource monitoring plots. + auto_connect_streams: + Control the automatic logging of stdout and stderr. + plot: + Indicator for making and sending plots. + table: + Indicator for making and sending tables. + config: + A dictionary-like object for saving inputs to your job, + like hyperparameters for a model or settings for a data preprocessing job. + save_dir: + Path to the directory for saving intermediate data. Used only when logging DL models. + Defaults to ``./tb_save`` + + Notes + ----- + For more details see `documentation `_ + + """ + super().__init__() + self.project_name = project_name + self.task_name = ( + task_name_prefix + base64.urlsafe_b64encode(uuid4().bytes).decode("utf8").rstrip("=\n")[:8] + if task_name is None + else task_name + ) + self.task_name_prefix = task_name_prefix + self.task_type = task_type + self.tags = tags + self.output_uri = output_uri + self.auto_connect_frameworks = auto_connect_frameworks + self.auto_resource_monitoring = auto_resource_monitoring + self.auto_connect_streams = auto_connect_streams + self.plot = plot + self.table = table + self.config = config + self.save_dir = "./tb_save" if save_dir is None else save_dir + + self._pl_logger = None + self._job_type: Optional[str] = None + self._fold_id: Optional[Union[str, int]] = None + + self._task: Optional["Task"] = None + self.init_task() + + def log(self, msg: Union[str, Dict[str, Any]], **kwargs): + """Log any event. + + This class logs string representation of a message. + + Parameters + ---------- + msg: + Message or dict to log + kwargs: + Additional parameters for particular implementation + """ + level = kwargs.get("level", logging.INFO) + print_console = kwargs.get("print_console", True) + self._get_logger().report_text( + msg=str(msg) if not isinstance(msg, str) else msg, level=level, print_console=print_console + ) + + def log_backtest_metrics( + self, ts: "TSDataset", metrics_df: pd.DataFrame, forecast_df: pd.DataFrame, fold_info_df: pd.DataFrame + ): + """Write metrics to logger. + + Parameters + ---------- + ts: + TSDataset to with backtest data + metrics_df: + Dataframe produced with :py:meth:`etna.pipeline.Pipeline._get_backtest_metrics` + forecast_df: + Forecast from backtest + fold_info_df: + Fold information from backtest + """ + from etna.analysis import plot_backtest_interactive + from etna.metrics.utils import aggregate_metrics_df + + if self._job_type is None: + raise ValueError( + "Experiment is not properly initialized! Ensure that ``start_experiment`` is called before logging backtest results." + ) + + logger = self._get_logger() + + if self.table: + logger.report_table(title="Fold info", series=self._job_type, table_plot=fold_info_df) + + if self.plot: + fig = plot_backtest_interactive(forecast_df, ts, history_len=100) + logger.report_plotly(title="Backtest forecast", series=self._job_type, figure=fig) + + metrics_dict = aggregate_metrics_df(metrics_df) + for metric, value in metrics_dict.items(): + logger.report_single_value(name=metric, value=value) + + def log_backtest_run(self, metrics: pd.DataFrame, forecast: pd.DataFrame, test: pd.DataFrame): + """Backtest metrics from one fold to logger. + + Parameters + ---------- + metrics: + Dataframe with metrics from backtest fold + forecast: + Dataframe with forecast + test: + Dataframe with ground truth + """ + from etna.datasets import TSDataset + from etna.metrics.utils import aggregate_metrics_df + + if self._job_type is None or self._fold_id is None: + raise ValueError( + "Experiment is not properly initialized! Ensure that ``start_experiment`` is called before logging backtest run." + ) + + columns_name = list(metrics.columns) + metrics = metrics.reset_index() + metrics.columns = ["segment"] + columns_name + + logger = self._get_logger() + if self.table: + logger.report_table( + title="Metrics per fold", series=f"{self._job_type} Fold - {self._fold_id}", table_plot=metrics + ) + logger.report_table( + title="Forecasts per fold", + series=f"{self._job_type} Fold - {self._fold_id}", + table_plot=TSDataset.to_flatten(forecast), + ) + logger.report_table( + title="Test folds", + series=f"{self._job_type} Fold - {self._fold_id}", + table_plot=TSDataset.to_flatten(test), + ) + + if isinstance(self._fold_id, int): + metrics_dict = aggregate_metrics_df(metrics) + for metric, value in metrics_dict.items(): + logger.report_scalar(title=metric, series=self._job_type, iteration=self._fold_id, value=value) + else: + self.log( + msg="Logging of scalars requires integer fold ids! Aggregated metrics logging would be skipped!", + level=logging.WARNING, + ) + + def start_experiment(self, job_type: Optional[str] = None, group: Optional[str] = None, *args, **kwargs): + """Start ``Task``. + + Complete logger initialization or reinitialize it before the next experiment with the same name. + + Parameters + ---------- + job_type: + Specify the type of task, which is useful when you're grouping runs together + into larger experiments using group. + group: + Specify a group to organize individual tasks into a larger experiment. + """ + self._job_type = job_type + + if group is not None: + try: + self._fold_id = int(group) + except ValueError: + self._fold_id = group + + # Overwrites current pl_logger if any + self._pl_logger = None + + if self._task is None: + self.init_task() + + def init_task(self): + """Reinit ``Task``.""" + from clearml import Task + from clearml import TaskTypes + + auto_connect_frameworks = { + "tensorboard": True, # for DL models, that use pytorch lightning + "joblib": True, # for backtest with multiple jobs + } + if isinstance(self.auto_connect_frameworks, Mapping): + auto_connect_frameworks = {**auto_connect_frameworks, **self.auto_connect_frameworks} + + self._task = Task.init( + project_name=self.project_name, + task_name=self.task_name, + task_type=TaskTypes[self.task_type], + tags=self.tags, + output_uri=self.output_uri, + auto_connect_frameworks=auto_connect_frameworks, + auto_resource_monitoring=self.auto_resource_monitoring, + auto_connect_streams=self.auto_connect_streams, + reuse_last_task_id=False, + ) + if self.config is not None: + self._task.connect(mutable=self.config) + + def finish_experiment(self, *args, **kwargs): + """Finish ``Task``.""" + # flush all data for additionally spawned tasks + if (self._task is not None) and (not self._task.is_main_task()): + self._task.flush(wait_for_uploads=True) + + self._job_type = None + self._fold_id = None + self._pl_logger = None + + def _get_logger(self): + """Return internal task logger.""" + if self._task is None: + raise ValueError("ClearML task is not initialized!") + return self._task.current_task().get_logger() + + @property + def pl_logger(self): + """Pytorch lightning loggers.""" + if self._pl_logger is None: + from pytorch_lightning.loggers import TensorBoardLogger + + prefix = "" if self._fold_id is None else f"Fold-{self._fold_id}" + self._pl_logger = TensorBoardLogger( + save_dir=self.save_dir, name=self.task_name, prefix=prefix, version=prefix + ) + + return self._pl_logger diff --git a/etna/models/sarimax.py b/etna/models/sarimax.py index fd1ad92f3..4bc53136b 100644 --- a/etna/models/sarimax.py +++ b/etna/models/sarimax.py @@ -406,7 +406,7 @@ def forecast_components(self, df: pd.DataFrame) -> pd.DataFrame: state = forecast_results.predicted_state[:, :-1] if model.mle_regression: - # If there are no exog variales `mle_regression` will be set to `False` + # If there are no exog variables `mle_regression` will be set to `False` # even if user set to `True`. components = self._mle_regression_decomposition( state=state, ssm=forecast_results.model, exog=exog_future.values # type: ignore diff --git a/etna/pipeline/base.py b/etna/pipeline/base.py index 28173086f..7230c4454 100644 --- a/etna/pipeline/base.py +++ b/etna/pipeline/base.py @@ -28,6 +28,7 @@ from etna.datasets.utils import _check_timestamp_param from etna.datasets.utils import timestamp_range from etna.distributions import BaseDistribution +from etna.loggers import _Logger from etna.loggers import tslogger from etna.metrics import Metric from etna.metrics import MetricAggregationMode @@ -783,25 +784,28 @@ def _compute_metrics( metrics_values[metric.name] = metric(y_true=y_true, y_pred=y_pred) # type: ignore return metrics_values - def _fit_backtest_pipeline( - self, - ts: TSDataset, - fold_number: int, - ) -> "BasePipeline": + def _fit_backtest_pipeline(self, ts: TSDataset, fold_number: int, logger: _Logger) -> "BasePipeline": """Fit pipeline for a given data in backtest.""" - tslogger.start_experiment(job_type="training", group=str(fold_number)) - pipeline = deepcopy(self) - pipeline.fit(ts=ts, save_ts=False) - tslogger.finish_experiment() + with logger.capture_tslogger(): + logger.start_experiment(job_type="training", group=str(fold_number)) + pipeline = deepcopy(self) + pipeline.fit(ts=ts, save_ts=False) + logger.finish_experiment() return pipeline def _forecast_backtest_pipeline( - self, pipeline: "BasePipeline", ts: TSDataset, fold_number: int, forecast_params: Dict[str, Any] + self, + pipeline: "BasePipeline", + ts: TSDataset, + fold_number: int, + forecast_params: Dict[str, Any], + logger: _Logger, ) -> TSDataset: """Make a forecast with a given pipeline in backtest.""" - tslogger.start_experiment(job_type="forecasting", group=str(fold_number)) - forecast = pipeline.forecast(ts=ts, **forecast_params) - tslogger.finish_experiment() + with logger.capture_tslogger(): + logger.start_experiment(job_type="forecasting", group=str(fold_number)) + forecast = pipeline.forecast(ts=ts, **forecast_params) + logger.finish_experiment() return forecast def _process_fold_forecast( @@ -813,24 +817,26 @@ def _process_fold_forecast( fold_number: int, mask: FoldMask, metrics: List[Metric], + logger: _Logger, ) -> Dict[str, Any]: """Process forecast made for a fold.""" - tslogger.start_experiment(job_type="crossval", group=str(fold_number)) + with logger.capture_tslogger(): + logger.start_experiment(job_type="crossval", group=str(fold_number)) - fold: Dict[str, Any] = {} - for stage_name, stage_df in zip(("train", "test"), (train, test)): - fold[f"{stage_name}_timerange"] = {} - fold[f"{stage_name}_timerange"]["start"] = stage_df.index.min() - fold[f"{stage_name}_timerange"]["end"] = stage_df.index.max() + fold: Dict[str, Any] = {} + for stage_name, stage_df in zip(("train", "test"), (train, test)): + fold[f"{stage_name}_timerange"] = {} + fold[f"{stage_name}_timerange"]["start"] = stage_df.index.min() + fold[f"{stage_name}_timerange"]["end"] = stage_df.index.max() - forecast.df = forecast.df.loc[mask.target_timestamps] - test.df = test.df.loc[mask.target_timestamps] + forecast.df = forecast.df.loc[mask.target_timestamps] + test.df = test.df.loc[mask.target_timestamps] - fold["forecast"] = forecast - fold["metrics"] = deepcopy(pipeline._compute_metrics(metrics=metrics, y_true=test, y_pred=forecast)) + fold["forecast"] = forecast + fold["metrics"] = deepcopy(pipeline._compute_metrics(metrics=metrics, y_true=test, y_pred=forecast)) - tslogger.log_backtest_run(pd.DataFrame(fold["metrics"]), forecast.to_pandas(), test.to_pandas()) - tslogger.finish_experiment() + logger.log_backtest_run(pd.DataFrame(fold["metrics"]), forecast.to_pandas(), test.to_pandas()) + logger.finish_experiment() return fold @@ -947,7 +953,9 @@ def _run_all_folds( train for train, _ in self._generate_folds_datasets(ts=ts, masks=fit_masks, horizon=self.horizon) ) pipelines = parallel( - delayed(self._fit_backtest_pipeline)(ts=fit_ts, fold_number=fold_groups[group_idx]["train_fold_number"]) + delayed(self._fit_backtest_pipeline)( + ts=fit_ts, fold_number=fold_groups[group_idx]["train_fold_number"], logger=tslogger + ) for group_idx, fit_ts in enumerate(fit_datasets) ) @@ -968,6 +976,7 @@ def _run_all_folds( pipeline=pipelines[group_idx], fold_number=fold_groups[group_idx]["forecast_fold_numbers"][idx], forecast_params=forecast_params, + logger=tslogger, ) for group_idx, group_forecast_datasets in enumerate(forecast_datasets) for idx, forecast_ts in enumerate(group_forecast_datasets) @@ -995,6 +1004,7 @@ def _run_all_folds( fold_number=fold_groups[group_idx]["forecast_fold_numbers"][idx], mask=fold_groups[group_idx]["forecast_masks"][idx], metrics=metrics, + logger=tslogger, ) for group_idx, (train, group_fold_process_test_datasets) in enumerate( zip(fold_process_train_datasets, fold_process_test_datasets) diff --git a/etna/settings.py b/etna/settings.py index afbcc5d8a..3672f2cc8 100644 --- a/etna/settings.py +++ b/etna/settings.py @@ -109,6 +109,15 @@ def _is_statsforecast_available(): return False +def _is_clearml_available(): + true_case = _module_available("clearml") & _module_available("tensorboard") + if true_case: + return True + else: + warnings.warn("etna[clearml] is not available, to install it, run `pip install etna[clearml]`") + return False + + def _get_optional_value(is_required: Optional[bool], is_available_fn: Callable, assert_msg: str) -> bool: if is_required is None: return is_available_fn() @@ -133,6 +142,7 @@ def __init__( # noqa: D107 classification_required: Optional[bool] = None, auto_required: Optional[bool] = None, statsforecast_required: Optional[bool] = None, + clearml_required: Optional[bool] = None, ): # True – use the package # None – use the package if available @@ -175,6 +185,11 @@ def __init__( # noqa: D107 _is_statsforecast_available, "etna[statsforecast] is not available, to install it, run `pip install etna[statsforecast]`.", ) + self.clearml_required: bool = _get_optional_value( + clearml_required, + _is_clearml_available, + "etna[clearml] is not available, to install it, run `pip install etna[clearml]`.", + ) @staticmethod def parse() -> "Settings": diff --git a/examples/205-automl.ipynb b/examples/205-automl.ipynb index dc6dbcbd4..eec083dd6 100644 --- a/examples/205-automl.ipynb +++ b/examples/205-automl.ipynb @@ -3,11 +3,7 @@ { "cell_type": "markdown", "id": "c855b45e", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "# AutoML\n", "\n", @@ -17,11 +13,7 @@ { "cell_type": "markdown", "id": "bca01a6c", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "This notebooks covers AutoML utilities of ETNA library.\n", "\n", @@ -41,11 +33,7 @@ "cell_type": "code", "execution_count": 1, "id": "45f65253", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "!pip install \"etna[auto, prophet]\" -q" @@ -55,11 +43,7 @@ "cell_type": "code", "execution_count": 2, "id": "6f70e872", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "import warnings\n", @@ -71,11 +55,7 @@ "cell_type": "code", "execution_count": 3, "id": "b858a832", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", @@ -93,11 +73,7 @@ "cell_type": "code", "execution_count": 4, "id": "e50060f6", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "HORIZON = 14" @@ -106,11 +82,7 @@ { "cell_type": "markdown", "id": "33ad7417", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "## 1. Hyperparameters tuning " ] @@ -118,11 +90,7 @@ { "cell_type": "markdown", "id": "4542c8eb", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "It is a common task to tune hyperparameters of existing pipeline to improve its quality. For this purpose there is an `etna.auto.Tune` class, which is responsible for creating [optuna](https://github.com/optuna/optuna) study to solve this problem.\n", "\n", @@ -132,11 +100,7 @@ { "cell_type": "markdown", "id": "73194640", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "### 1.1 How `Tune` works " ] @@ -144,11 +108,7 @@ { "cell_type": "markdown", "id": "c7777ea3", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "During init `Tune` accepts `pipeline`, its tuning parameters (`params_to_tune`), optimization metric (`target_metric`), parameters of backtest and parameters of optuna study.\n", "\n", @@ -158,11 +118,7 @@ { "cell_type": "markdown", "id": "09e6cb8e", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's look closer at `params_to_tune` parameter. It expects dictionary with parameter names and its distributions. But how this parameter names should be chosen?" ] @@ -170,11 +126,7 @@ { "cell_type": "markdown", "id": "5d7a777a", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "#### 1.1.1 `set_params`" ] @@ -182,11 +134,7 @@ { "cell_type": "markdown", "id": "cc05b85b", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "We are going to make a little detour to explain the `set_params` method, which is supported by ETNA pipelines, models and transforms. Given a dictionary with parameters it allows to create from existing object a new one with changed parameters." ] @@ -194,11 +142,7 @@ { "cell_type": "markdown", "id": "b291efa4", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "First, we define some objects for our future examples." ] @@ -207,11 +151,7 @@ "cell_type": "code", "execution_count": 5, "id": "9d6893b8", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "model = LinearPerSegmentModel()\n", @@ -225,11 +165,7 @@ { "cell_type": "markdown", "id": "01a57e5c", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's look at simple example, when we want to change `fit_intercept` parameter of the `model`." ] @@ -238,11 +174,7 @@ "cell_type": "code", "execution_count": 6, "id": "32c51370", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -261,11 +193,7 @@ "cell_type": "code", "execution_count": 7, "id": "60bc963f", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -285,11 +213,7 @@ { "cell_type": "markdown", "id": "383931c2", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Great! On the next step we want to change the `fit_intercept` of `model` inside the `pipeline`." ] @@ -298,11 +222,7 @@ "cell_type": "code", "execution_count": 8, "id": "7ff49f9a", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -321,11 +241,7 @@ "cell_type": "code", "execution_count": 9, "id": "497662b6", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -345,11 +261,7 @@ { "cell_type": "markdown", "id": "8eba262b", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Ok, it looks like we managed to do this. On the last step we are going to change `is_weekend` flag of `DateFlagsTransform` inside our `pipeline`." ] @@ -358,11 +270,7 @@ "cell_type": "code", "execution_count": 10, "id": "28a1ac00", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -382,11 +290,7 @@ { "cell_type": "markdown", "id": "50c2bf0d", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "As we can see, we managed to do this." ] @@ -394,11 +298,7 @@ { "cell_type": "markdown", "id": "4deb8b8b", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "#### 1.1.2 `params_to_tune`" ] @@ -406,11 +306,7 @@ { "cell_type": "markdown", "id": "8c732645", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's get back to our initial question about `params_to_tune`. In our optuna study we are going to sample each parameter value from its distribution and pass it into `pipeline.set_params` method. So, the keys for `params_to_tune` should be a valid for `set_params` method.\n", "\n", @@ -420,11 +316,7 @@ { "cell_type": "markdown", "id": "f6a39f16", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "For example, something like this will be valid for our `pipeline` defined above:" ] @@ -442,10 +334,7 @@ "}" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -454,10 +343,7 @@ "This custom dict could be passed into `Tune` class. This will be shown in the [Example](#custom_params) below." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -466,10 +352,7 @@ "There are some good news: it isn't necessary for our users to define `params_to_tune`, because we have a default grid for many of our classes. The default grid is available by calling `params_to_tune` method on pipeline, model or transform. Let's check our `pipeline`:" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -489,10 +372,7 @@ "pipeline.params_to_tune()" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -501,10 +381,7 @@ "Now we are ready to use it in practice." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -513,10 +390,7 @@ "### 1.2 Example " ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -525,10 +399,7 @@ "#### 1.2.1 Loading data" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -537,10 +408,7 @@ "Let's start by loading example data." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -562,10 +430,7 @@ "df.head()" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -586,10 +451,7 @@ "full_ts.plot()" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -598,10 +460,7 @@ "Let's divide current dataset into train and validation parts. We will use validation part later to check final results." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -612,10 +471,7 @@ "ts, _ = full_ts.train_test_split(test_size=HORIZON * 5)" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -624,10 +480,7 @@ "#### 1.2.2 Running `Tune`" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -636,10 +489,7 @@ "We are going to define our `Tune` object:" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -652,10 +502,7 @@ "tune = Tune(pipeline=pipeline, target_metric=SMAPE(), horizon=HORIZON, backtest_params=dict(n_folds=5))" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -668,10 +515,7 @@ "For a full list of parameters we advise you to check our documentation." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -680,10 +524,7 @@ "Let's hide the logs of optuna, there are too many of them for a notebook." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -696,10 +537,7 @@ "optuna.logging.set_verbosity(optuna.logging.CRITICAL)" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -708,10 +546,7 @@ "Let's run the tuning" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -723,10 +558,7 @@ "best_pipeline = tune.fit(ts=ts, n_trials=20)" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -735,10 +567,7 @@ "Command `%%capture` just hides the output." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -747,10 +576,7 @@ "#### 1.2.3 Running `Tune` with custom `params_to_tune`" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -766,10 +592,7 @@ "Now we can use these parameters when initializing `Tune`." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -786,10 +609,7 @@ ")" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -798,10 +618,7 @@ "Let's run the tuning with our custom parameters." ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { @@ -813,10 +630,7 @@ "best_pipeline_custom_params = tune_custom_params.fit(ts=ts, n_trials=20)" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%%\n" - } + "collapsed": false } }, { @@ -825,20 +639,13 @@ "#### 1.2.4 Analysis" ], "metadata": { - "collapsed": false, - "pycharm": { - "name": "#%% md\n" - } + "collapsed": false } }, { "cell_type": "markdown", "id": "1fd09627", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "In the last section dedicated to `Tune` we will look at methods for result analysis." ] @@ -846,11 +653,7 @@ { "cell_type": "markdown", "id": "3faf63b9", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "First of all there is `summary` method that shows us the results of optuna trials." ] @@ -859,11 +662,7 @@ "cell_type": "code", "execution_count": 21, "id": "14525b55", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -882,11 +681,7 @@ { "cell_type": "markdown", "id": "cf987a2e", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's show only the columns we are interested in." ] @@ -895,11 +690,7 @@ "cell_type": "code", "execution_count": 22, "id": "b650bfc7", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -918,11 +709,7 @@ { "cell_type": "markdown", "id": "95721277", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "As we can see, we have duplicate lines according to the `hash` column. Some trials have the same sampled hyperparameters and they have the same results. We have a special handling for such duplicates: they are skipped during optimization and the previously computed metric values are returned.\n", "\n", @@ -933,11 +720,7 @@ "cell_type": "code", "execution_count": 23, "id": "7506fe96", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -956,11 +739,7 @@ { "cell_type": "markdown", "id": "a642c361", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "The second method `top_k` is useful when you want to check out best tried pipelines without duplicates." ] @@ -969,11 +748,7 @@ "cell_type": "code", "execution_count": 24, "id": "6f707553", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "top_3_pipelines = tune.top_k(k=3)" @@ -983,11 +758,7 @@ "cell_type": "code", "execution_count": 25, "id": "7fd2b238", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -1005,11 +776,7 @@ { "cell_type": "markdown", "id": "15ef8f10", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "## 2. General AutoML " ] @@ -1017,11 +784,7 @@ { "cell_type": "markdown", "id": "fef33f7e", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Hyperparameters tuning is useful, but can be too narrow. In this section we move our attention to general AutoML pipeline.\n", "In ETNA we have an `etna.auto.Auto` class for making automatic pipeline selection. It can be useful to quickly create a good baseline for your forecasting task." @@ -1030,11 +793,7 @@ { "cell_type": "markdown", "id": "8c1763e2", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "### 2.1 How `Auto` works " ] @@ -1042,11 +801,7 @@ { "cell_type": "markdown", "id": "4e20092d", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "`Auto` init has similar parameters to `Tune`, but instead of `pipeline` it works with `pool`. Pool, in general, is just a list of pipelines.\n", "\n", @@ -1057,7 +812,7 @@ "\n", "Pool stage is responsible for checking every pipeline suggested in a given `pool`. For each pipeline we run a backtest and compute `target_metric`. Results are saved in optuna study.\n", "\n", - "Tuning stage takes `tune_size` best pipelines according to the resuls of the pool stage. And then runs `Tune` with default `params_to_tune` for them sequentially from best to the worst. \n", + "Tuning stage takes `tune_size` best pipelines according to the results of the pool stage. And then runs `Tune` with default `params_to_tune` for them sequentially from best to the worst.\n", "\n", "Limit parameters `n_trials` and `timeout` are shared between pool and tuning stages. First, we run pool stage with given `n_trials` and `timeout`. After that, the remaining values are divided equally among `tune_size` tuning steps." ] @@ -1065,11 +820,7 @@ { "cell_type": "markdown", "id": "96b2fb38", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "### 2.2 Example " ] @@ -1077,11 +828,7 @@ { "cell_type": "markdown", "id": "02b2c527", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "We will move stright to the example." ] @@ -1090,11 +837,7 @@ "cell_type": "code", "execution_count": 26, "id": "ea97e2f7", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "from etna.auto import Auto\n", @@ -1105,11 +848,7 @@ { "cell_type": "markdown", "id": "83fe5077", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "We used mostly default parameters, even pool. There is also a default `sampler`, but to make results more reproducible we fixed the `seed`." ] @@ -1117,11 +856,7 @@ { "cell_type": "markdown", "id": "aa87e050", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's start the fitting. We can start by running only pool stage." ] @@ -1130,11 +865,7 @@ "cell_type": "code", "execution_count": 27, "id": "47ccd63b", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "%%capture\n", @@ -1145,11 +876,7 @@ "cell_type": "code", "execution_count": 28, "id": "d972dfb5", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -1168,11 +895,7 @@ { "cell_type": "markdown", "id": "ff62ced9", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "We can continue our training. The pool stage is over and there will be only the tuning stage. If we don't want to wait forever we should limit the tuning by fixing `n_trials` or `timeout`. \n", "\n", @@ -1186,11 +909,7 @@ "cell_type": "code", "execution_count": 29, "id": "13a1861a", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "%%capture\n", @@ -1200,11 +919,7 @@ { "cell_type": "markdown", "id": "09f78f63", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "Let's look at the results." ] @@ -1213,11 +928,7 @@ "cell_type": "code", "execution_count": 30, "id": "95c854eb", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -1239,11 +950,7 @@ "cell_type": "code", "execution_count": 31, "id": "640269ba", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -1261,11 +968,7 @@ { "cell_type": "markdown", "id": "7451f135", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "If we look at `study` column we will see that best trial from tuning stage is better then best trial from pool stage. It means, that tuning stage was successful and improved the final result. \n", "\n", @@ -1276,11 +979,7 @@ "cell_type": "code", "execution_count": 32, "id": "ce8953ab", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "%%capture\n", @@ -1292,11 +991,7 @@ "cell_type": "code", "execution_count": 33, "id": "7a42cc84", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "name": "stdout", @@ -1317,11 +1012,7 @@ { "cell_type": "markdown", "id": "3f41537f", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "As we can see, the results are slightly better after the tuning stage, but it can be statistically insignificant. For your datasets the results could be different." ] @@ -1329,11 +1020,7 @@ { "cell_type": "markdown", "id": "6b340a85", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "### 2.3 Using custom pipeline pool " ] @@ -1341,11 +1028,7 @@ { "cell_type": "markdown", "id": "0e27cd91", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "We can define our own set of pipelines for the search." ] @@ -1354,11 +1037,7 @@ "cell_type": "code", "execution_count": 34, "id": "3da863a4", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "pool = [\n", @@ -1375,11 +1054,7 @@ "cell_type": "code", "execution_count": 35, "id": "6feef342", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [], "source": [ "%%capture\n", @@ -1397,11 +1072,7 @@ "cell_type": "code", "execution_count": 36, "id": "149ecb63", - "metadata": { - "pycharm": { - "name": "#%%\n" - } - }, + "metadata": {}, "outputs": [ { "data": { @@ -1420,11 +1091,7 @@ { "cell_type": "markdown", "id": "3322d9c2", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "## 3. Summary " ] @@ -1432,11 +1099,7 @@ { "cell_type": "markdown", "id": "39b4a081", - "metadata": { - "pycharm": { - "name": "#%% md\n" - } - }, + "metadata": {}, "source": [ "In this notebook we discussed how AutoML works in ETNA library and how to use it. There are two supported scenarios:\n", "\n", @@ -1466,4 +1129,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/examples/208-forecasting_strategies.ipynb b/examples/208-forecasting_strategies.ipynb index 67425ffe8..d6f91fade 100644 --- a/examples/208-forecasting_strategies.ipynb +++ b/examples/208-forecasting_strategies.ipynb @@ -222,7 +222,7 @@ "`Pipeline` implements the version of direct strategy, where the only one model is fitted to forecast all the points in the future. This implies the several things:\n", "\n", "* `Pipeline` doesn't accept lags less than `horizon`\n", - "* This is the most time-efficient method: both in traning and in forecasting\n", + "* This is the most time-efficient method: both in training and in forecasting\n", "* This method might lose the quality with the growth of horizon when using the lags, as the only horizon-far lags are available for all the points\n", "\n", "**Note:**\n", diff --git a/examples/clearml/pytorch_lightning_example.py b/examples/clearml/pytorch_lightning_example.py new file mode 100644 index 000000000..7226d0bb6 --- /dev/null +++ b/examples/clearml/pytorch_lightning_example.py @@ -0,0 +1,60 @@ +import random +from pathlib import Path + +import numpy as np +import pandas as pd + +from etna.datasets import TSDataset +from etna.loggers import ClearMLLogger +from etna.loggers import tslogger +from etna.metrics import MAE +from etna.models.nn import MLPModel +from etna.pipeline import Pipeline +from etna.transforms import LagTransform +from etna.transforms import StandardScalerTransform + +FILE_PATH = Path(__file__) + + +def set_seed(seed: int = 42): + random.seed(seed) + np.random.seed(seed) + + +def dataloader(file_path: Path, freq: str) -> TSDataset: + df = pd.read_csv(file_path) + df = TSDataset.to_dataset(df) + ts = TSDataset(df=df, freq=freq) + return ts + + +def backtest(): + set_seed() + + ts = dataloader(file_path=Path("../data/example_dataset.csv"), freq="D") + + pipeline = Pipeline( + model=MLPModel( + input_size=8, + decoder_length=14, + hidden_size=[7, 7], + trainer_params=dict(max_epochs=30, enable_checkpointing=False), + split_params=dict(train_size=0.75), + ), + transforms=[ + StandardScalerTransform(in_column="target"), + LagTransform(in_column="target", lags=list(range(5, 13)), out_column="lag"), + ], + horizon=5, + ) + + cml_logger = ClearMLLogger( + project_name="test/clearml_basic", tags=["test", "clearml", "concurrency"], config=pipeline.to_dict() + ) + tslogger.add(cml_logger) + + pipeline.backtest(ts, n_jobs=5, metrics=[MAE()]) + + +if __name__ == "__main__": + backtest() diff --git a/examples/wandb/sweeps/sweeps_example.py b/examples/wandb/sweeps/sweeps_example.py index d96d15141..3437f082e 100644 --- a/examples/wandb/sweeps/sweeps_example.py +++ b/examples/wandb/sweeps/sweeps_example.py @@ -1,4 +1,5 @@ import random +from pathlib import Path from typing import Optional import hydra @@ -8,8 +9,6 @@ from omegaconf import DictConfig from omegaconf import OmegaConf -from pathlib import Path - from etna.datasets import TSDataset from etna.loggers import WandbLogger from etna.loggers import tslogger @@ -21,6 +20,7 @@ FILE_PATH = Path(__file__) + def set_seed(seed: int = 42): random.seed(seed) np.random.seed(seed) @@ -42,7 +42,7 @@ def dataloader(file_path: Path, freq: str) -> TSDataset: @hydra.main(config_name="config.yaml") def objective(cfg: DictConfig): config = OmegaConf.to_container(cfg, resolve=True) - + # Set seed for reproducibility set_seed(cfg.seed) @@ -51,7 +51,7 @@ def objective(cfg: DictConfig): # Init pipeline pipeline: Pipeline = hydra_slayer.get_from_params(**config["pipeline"]) - + # Init backtest parameters like metrics and e.t.c. backtest_params = hydra_slayer.get_from_params(**config["backtest"]) diff --git a/poetry.lock b/poetry.lock index fc9d286c4..da51ea17c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,35 +1,46 @@ # This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +[[package]] +name = "absl-py" +version = "2.1.0" +description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." +optional = true +python-versions = ">=3.7" +files = [ + {file = "absl-py-2.1.0.tar.gz", hash = "sha256:7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff"}, + {file = "absl_py-2.1.0-py3-none-any.whl", hash = "sha256:526a04eadab8b4ee719ce68f204172ead1027549089702d99b9059f129ff1308"}, +] + [[package]] name = "accelerate" -version = "0.32.1" +version = "0.34.2" description = "Accelerate" optional = true python-versions = ">=3.8.0" files = [ - {file = "accelerate-0.32.1-py3-none-any.whl", hash = "sha256:71fcf4be00872194071de561634268b71417d7f5b16b178e2fa76b6f117c52b0"}, - {file = "accelerate-0.32.1.tar.gz", hash = "sha256:3999acff0237cd0d4f9fd98b42d5a3163544777b53fc4f1eec886b77e992d177"}, + {file = "accelerate-0.34.2-py3-none-any.whl", hash = "sha256:d69159e2c4e4a473d14443b27d2d732929254e826b3ab4813b3785b5ac616c7c"}, + {file = "accelerate-0.34.2.tar.gz", hash = "sha256:98c1ebe1f5a45c0a3af02dc60b5bb8b7d58d60c3326a326a06ce6d956b18ca5b"}, ] [package.dependencies] -huggingface-hub = "*" -numpy = ">=1.17,<2.0.0" +huggingface-hub = ">=0.21.0" +numpy = ">=1.17,<3.0.0" packaging = ">=20.0" psutil = "*" pyyaml = "*" -safetensors = ">=0.3.1" +safetensors = ">=0.4.3" torch = ">=1.10.0" [package.extras] -deepspeed = ["deepspeed (<=0.14.0)"] -dev = ["bitsandbytes", "black (>=23.1,<24.0)", "datasets", "diffusers", "evaluate", 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(>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [extras] -all = ["accelerate", "einops", "huggingface-hub", "jax", "jaxlib", "optuna", "prophet", "pytorch-forecasting", "pytorch-lightning", "pyts", "sqlalchemy", "statsforecast", "torch", "transformers", "tsfresh", "utilsforecast", "wandb"] -all-dev = ["GitPython", "Sphinx", "accelerate", "black", "click", "click", "codespell", "einops", "flake8", "flake8-bugbear", "flake8-comprehensions", "flake8-docstrings", "huggingface-hub", "ipywidgets", "isort", "jax", "jaxlib", "jupyter", "mypy", "myst-parser", "nbconvert", "nbqa", "nbsphinx", "optuna", "pep8-naming", "prophet", "pydata-sphinx-theme", "pytest", "pytest-cov", "pytest-shard", "pytorch-forecasting", "pytorch-lightning", "pyts", "semver", "semver", "sphinx-design", "sphinx-mathjax-offline", "sqlalchemy", "statsforecast", "torch", "transformers", "tsfresh", "types-PyYAML", "types-setuptools", "utilsforecast", "wandb"] +all = ["accelerate", "clearml", "einops", "huggingface-hub", "jax", "jaxlib", "optuna", "prophet", "pytorch-forecasting", "pytorch-lightning", "pyts", "sqlalchemy", "statsforecast", "tensorboard", "torch", "transformers", "tsfresh", "utilsforecast", "wandb"] +all-dev = ["GitPython", "Sphinx", "accelerate", "black", "clearml", "click", "click", "codespell", "einops", "flake8", "flake8-bugbear", "flake8-comprehensions", "flake8-docstrings", "huggingface-hub", "ipywidgets", "isort", "jax", "jaxlib", "jupyter", "mypy", "myst-parser", "nbconvert", "nbqa", "nbsphinx", "optuna", "pep8-naming", "prophet", "pydata-sphinx-theme", "pytest", "pytest-cov", "pytest-shard", "pytorch-forecasting", "pytorch-lightning", "pyts", "semver", "semver", "sphinx-design", "sphinx-mathjax-offline", "sqlalchemy", "statsforecast", "tensorboard", "torch", "transformers", "tsfresh", "types-PyYAML", "types-setuptools", "utilsforecast", "wandb"] auto = ["optuna", "sqlalchemy"] chronos = ["accelerate", "huggingface-hub", "torch", "transformers"] classification = ["pyts", "tsfresh"] +clearml = ["clearml", "tensorboard"] docs = ["GitPython", "Sphinx", "jupyter", "myst-parser", "nbsphinx", "pydata-sphinx-theme", "sphinx-design", "sphinx-mathjax-offline"] jupyter = ["black", "ipywidgets", "jupyter", "nbconvert"] prophet = ["prophet"] @@ -6497,4 +7565,4 @@ wandb = ["wandb"] [metadata] lock-version = "2.0" python-versions = ">=3.8.0, <3.11.0" -content-hash = "560122b4e3d4cbbe17fa501f1eb961c3a9605cf52a40b1f9df7129d3ab58f5cf" +content-hash = "c26f4a80cc754da922cf4d13e5a5dfb9bcc75691801c7238c9bec0abb762f94a" diff --git a/pyproject.toml b/pyproject.toml index fa1a0bb97..766d5abe9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -79,6 +79,8 @@ pytorch-lightning = {version = "*", optional = true} einops = {version = "*", optional = true} wandb = {version = "^0.12.2", optional = true} +clearml = {version = "^1.15", optional = true} +tensorboard = {version = "^2.12.0", optional = true} optuna = {version = ">=2.5.0,<3.0.0", optional = true} sqlalchemy = {version = "^1.1.0", optional = true} @@ -132,6 +134,7 @@ types-setuptools = {version = "^65.7.0", optional = true} prophet = ["prophet"] torch = ["torch", "pytorch-forecasting", "pytorch-lightning", "einops"] wandb = ["wandb"] +clearml = ["clearml", "tensorboard"] auto = ["optuna", "sqlalchemy"] classification = ["pyts", "tsfresh"] statsforecast = ["statsforecast"] @@ -148,7 +151,7 @@ style = ["black", "isort", "flake8", "pep8-naming", "flake8-docstrings", "mypy", all = [ "prophet", "torch", "pytorch-forecasting", "pytorch-lightning", "einops", - "wandb", + "wandb", "clearml", "tensorboard", "optuna", "sqlalchemy", "pyts", "tsfresh", "statsforecast", @@ -159,7 +162,7 @@ all = [ all-dev = [ "prophet", "torch", "pytorch-forecasting", "pytorch-lightning", "einops", - "wandb", + "wandb", "clearml", "tensorboard", "optuna", "sqlalchemy", "click", "semver", "Sphinx", "nbsphinx", "sphinx-mathjax-offline", "myst-parser", "GitPython", "pydata-sphinx-theme", "sphinx-design", @@ -244,6 +247,10 @@ filterwarnings = [ "ignore:(.|\n)*A value is trying to be set on a copy of a slice from a DataFrame", # SettingWithCopyWarning "ignore: New behaviour in v1.1.5.* a small bias is added", # ruptures: normal cost "ignore: Dynamic prediction specified to begin during out-of-sample forecasting period, and so has no effect.", + "ignore: `ModuleAvailableCache` is a special case of `RequirementCache`.", # lightning_utilities + "ignore: `sentry_sdk.Hub` is deprecated and will be removed in a future major release.", + "ignore::DeprecationWarning:holidays", + "ignore:This property will be removed in 2.0.0.", # torchmetrics "ignore::pytorch_lightning.utilities.rank_zero.LightningDeprecationWarning", "ignore: numpy.ufunc size changed, may indicate binary incompatibility", "ignore: Jupyter is migrating its paths to use standard platformdirs", diff --git a/tests/test_loggers/test_clearml_logger.py b/tests/test_loggers/test_clearml_logger.py new file mode 100644 index 000000000..141bce834 --- /dev/null +++ b/tests/test_loggers/test_clearml_logger.py @@ -0,0 +1,134 @@ +import os +from unittest.mock import MagicMock +from unittest.mock import call +from unittest.mock import patch + +import pytest +from pytorch_lightning.loggers import TensorBoardLogger + +from etna.loggers import ClearMLLogger +from etna.loggers import tslogger as _tslogger +from etna.metrics import MAE +from etna.models import NaiveModel +from etna.models.nn import MLPModel +from etna.pipeline import Pipeline +from etna.transforms import LagTransform + + +@pytest.fixture() +def tslogger(): + _tslogger.loggers = [] + yield _tslogger + _tslogger.loggers = [] + + +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_task_not_init_error(init_task): + cml_logger = ClearMLLogger() + with pytest.raises(ValueError, match="ClearML task is not initialized!"): + cml_logger.log(msg="test") + + +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_log_backtest_metrics_not_init_error(init_task): + cml_logger = ClearMLLogger() + with pytest.raises(ValueError, match="Experiment is not properly initialized!"): + cml_logger.log_backtest_metrics(ts=None, metrics_df=None, forecast_df=None, fold_info_df=None) + + +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_log_backtest_run_not_init_error(init_task): + cml_logger = ClearMLLogger() + with pytest.raises(ValueError, match="Experiment is not properly initialized!"): + cml_logger.log_backtest_run(metrics=None, forecast=None, test=None) + + +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_correct_experiment_start_finish(init_task): + cml_logger = ClearMLLogger() + + assert cml_logger._job_type is None + assert cml_logger._fold_id is None + assert cml_logger._pl_logger is None + + cml_logger.start_experiment(job_type="test", group="1") + cml_logger.finish_experiment() + + assert cml_logger._job_type is None + assert cml_logger._fold_id is None + assert cml_logger._pl_logger is None + + +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_clearml_logger_log(init_task, tslogger): + cml_logger = ClearMLLogger() + cml_logger._task = MagicMock() + + idx = tslogger.add(cml_logger) + tslogger.log("test") + tslogger.log({"MAE": 0}) + tslogger.log({"MAPE": 1.5}) + tslogger.remove(idx) + + calls = [ + call(msg="test", level=20, print_console=True), + call(msg="{'MAE': 0}", level=20, print_console=True), + call(msg="{'MAPE': 1.5}", level=20, print_console=True), + ] + + assert cml_logger._get_logger().report_text.call_count == 3 + cml_logger._get_logger().report_text.assert_has_calls(calls) + + +@pytest.mark.filterwarnings("ignore:The frame.append method is deprecated") +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_default_pipeline(init_task, tslogger, example_tsds): + cml_logger = ClearMLLogger() + cml_logger._task = MagicMock() + + idx = tslogger.add(cml_logger) + + pipeline = Pipeline(model=NaiveModel(), transforms=[]) + pipeline.backtest(ts=example_tsds, metrics=[MAE()], n_jobs=1) + + tslogger.remove(idx) + + # General checks + assert cml_logger._get_logger().report_text.call_count > 0 + assert cml_logger._get_logger().report_table.call_count == 5 * 3 + 1 # n_folds + summary + assert cml_logger._get_logger().report_plotly.call_count == 1 # single summary + assert cml_logger._get_logger().report_single_value.call_count == 1 * 8 # final aggregated metric with stats + assert cml_logger._get_logger().report_scalar.call_count == 5 * 8 # metric stats per each fold + + +@pytest.mark.filterwarnings("ignore:The frame.append method is deprecated") +@patch("etna.loggers.clearml_logger.ClearMLLogger.init_task") +def test_dl_pytorch_lightning_pipeline(init_task, tslogger, example_tsds): + cml_logger = ClearMLLogger() + cml_logger._task = MagicMock() + + idx = tslogger.add(cml_logger) + + pipeline = Pipeline( + model=MLPModel( + input_size=8, + decoder_length=14, + hidden_size=[7, 7], + trainer_params=dict(max_epochs=3, enable_checkpointing=False, log_every_n_steps=1), + ), + transforms=[LagTransform(in_column="target", lags=list(range(5, 13)), out_column="lag")], + ) + pipeline.backtest(ts=example_tsds, metrics=[MAE()], n_jobs=1) + + tslogger.remove(idx) + + # General checks + assert cml_logger._get_logger().report_text.call_count > 0 + assert cml_logger._get_logger().report_table.call_count == 5 * 3 + 1 # n_folds + summary + assert cml_logger._get_logger().report_plotly.call_count == 1 # single summary + assert cml_logger._get_logger().report_single_value.call_count == 1 * 8 # final aggregated metric with stats + assert cml_logger._get_logger().report_scalar.call_count == 5 * 8 # metric stats per each fold + + # Lightning specific checks + assert isinstance(cml_logger.pl_logger, TensorBoardLogger) + assert os.path.exists(cml_logger.save_dir) diff --git a/tests/test_loggers/test_file_logger.py b/tests/test_loggers/test_file_logger.py index 1e120534f..97b15a442 100644 --- a/tests/test_loggers/test_file_logger.py +++ b/tests/test_loggers/test_file_logger.py @@ -270,7 +270,7 @@ def test_local_file_logger_with_stacking_ensemble(example_df): def test_local_file_logger_with_empirical_prediction_interval(example_df): - """Test that LocalFileLogger correctly works in with empirical predicition intervals via backtest.""" + """Test that LocalFileLogger correctly works in with empirical prediction intervals via backtest.""" with tempfile.TemporaryDirectory() as dirname: cur_dir = pathlib.Path(dirname) logger = LocalFileLogger(experiments_folder=dirname, gzip=False) diff --git a/tests/test_models/test_nn/deepar_native/test_deepar_native.py b/tests/test_models/test_nn/deepar_native/test_deepar_native.py index 3cb298b8a..b3bdbca70 100644 --- a/tests/test_models/test_nn/deepar_native/test_deepar_native.py +++ b/tests/test_models/test_nn/deepar_native/test_deepar_native.py @@ -24,7 +24,7 @@ (13, GaussianLoss(), [StandardScalerTransform(in_column="target")], 100, 1e-3, 0.05), (15, GaussianLoss(), [StandardScalerTransform(in_column="target")], 100, 1e-3, 0.05), (8, NegativeBinomialLoss(), [], 300, 1e-2, 0.05), - (13, NegativeBinomialLoss(), [], 300, 1e-2, 0.06), + (13, NegativeBinomialLoss(), [], 700, 1e-2, 0.06), (15, NegativeBinomialLoss(), [], 300, 1e-2, 0.05), ], ) diff --git a/tests/test_pipeline/test_pipeline.py b/tests/test_pipeline/test_pipeline.py index b1980c32e..76a0365fc 100644 --- a/tests/test_pipeline/test_pipeline.py +++ b/tests/test_pipeline/test_pipeline.py @@ -13,6 +13,7 @@ from etna.distributions import CategoricalDistribution from etna.distributions import FloatDistribution from etna.distributions import IntDistribution +from etna.loggers import _Logger from etna.metrics import MAE from etna.metrics import MSE from etna.metrics import SMAPE @@ -1550,7 +1551,14 @@ def test_process_fold_forecast(ts_process_fold_forecast, mask: FoldMask, expecte pipeline = pipeline.fit(ts=train) forecast = pipeline.forecast() fold = pipeline._process_fold_forecast( - forecast=forecast, train=train, test=test, pipeline=pipeline, fold_number=1, mask=mask, metrics=[MAE()] + forecast=forecast, + train=train, + test=test, + pipeline=pipeline, + fold_number=1, + mask=mask, + metrics=[MAE()], + logger=_Logger(), ) for seg in fold["metrics"]["MAE"].keys(): assert fold["metrics"]["MAE"][seg] == expected[seg] diff --git a/tests/test_transforms/test_timestamp/test_holiday_transform.py b/tests/test_transforms/test_timestamp/test_holiday_transform.py index 3531f3174..cea4c1c11 100644 --- a/tests/test_transforms/test_timestamp/test_holiday_transform.py +++ b/tests/test_transforms/test_timestamp/test_holiday_transform.py @@ -353,7 +353,7 @@ def test_transform_binary_minute(iso_code: str, answer: np.array, two_segments_s @pytest.mark.parametrize( "iso_code,answer", ( - ("RUS", np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])), + ("RUS", np.array([0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1])), ("US", np.array([0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])), ), ) @@ -361,7 +361,7 @@ def test_transform_binary_w_mon(iso_code: str, answer: np.array, two_segments_w_ holidays_finder = HolidayTransform(iso_code=iso_code, mode="binary", out_column="holiday") df = holidays_finder.fit_transform(two_segments_w_mon).to_pandas() for segment in df.columns.get_level_values("segment").unique(): - assert np.array_equal(df[segment]["holiday"].values, answer) + assert np.array_equal(df[segment]["holiday"].to_numpy(), answer) assert df[segment]["holiday"].dtype == "category" @@ -404,7 +404,15 @@ def test_transform_category_day(in_column, ts_name, iso_code, answer, request): @pytest.mark.parametrize( "iso_code,answer", ( - ("RUS", np.array(["NO_HOLIDAY"] * 18)), + ( + "RUS", + np.array( + ["NO_HOLIDAY"] * 6 + + ["Day off (substituted from 02/23/2020)", "NO_HOLIDAY", "Day off (substituted from 03/08/2020)"] + + ["NO_HOLIDAY"] * 7 + + ["Day off (substituted from 01/04/2020)", "Day off (substituted from 05/09/2020)"] + ), + ), ( "US", np.array( @@ -420,7 +428,7 @@ def test_transform_category_w_mon(iso_code: str, answer: np.array, two_segments_ holidays_finder = HolidayTransform(iso_code=iso_code, mode="category", out_column="holiday") df = holidays_finder.fit_transform(two_segments_w_mon).to_pandas() for segment in df.columns.get_level_values("segment").unique(): - assert np.array_equal(df[segment]["holiday"].values, answer) + assert np.array_equal(df[segment]["holiday"].to_numpy(), answer) assert df[segment]["holiday"].dtype == "category"