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Merge pull request optuna#5246 from y0z/feature/migrate-mlflow
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Remove MLflow integration
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@nabenabe0928
nabenabe0928 committed Feb 16, 2024
2 parents 32f5ce9 + b5d4dfb commit 323519d
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9 changes: 0 additions & 9 deletions docs/source/reference/integration.rst
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Expand Up @@ -18,15 +18,6 @@ For most of the ML frameworks supported by Optuna, the corresponding Optuna inte

For scikit-learn, an integrated :class:`~optuna.integration.OptunaSearchCV` estimator is available that combines scikit-learn BaseEstimator functionality with access to a class-level ``Study`` object.

MLflow
------

.. autosummary::
:toctree: generated/
:nosignatures:

optuna.integration.MLflowCallback

Dependencies of each integration
--------------------------------

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324 changes: 2 additions & 322 deletions optuna/integration/mlflow.py
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@@ -1,324 +1,4 @@
import functools
import threading
from typing import Any
from typing import Callable
from typing import Dict
from typing import List
from typing import Optional
from typing import Sequence
from typing import Union
from optuna_integration.mlflow import MLflowCallback

import optuna
from optuna._experimental import experimental_class
from optuna._experimental import experimental_func
from optuna._imports import try_import
from optuna.study.study import ObjectiveFuncType


with try_import() as _imports:
import mlflow

RUN_ID_ATTRIBUTE_KEY = "mlflow_run_id"


@experimental_class("1.4.0")
class MLflowCallback:
"""Callback to track Optuna trials with MLflow.
This callback adds relevant information that is
tracked by Optuna to MLflow.
Example:
Add MLflow callback to Optuna optimization.
.. testsetup::
import pathlib
import tempfile
tempdir = tempfile.mkdtemp()
YOUR_TRACKING_URI = pathlib.Path(tempdir).as_uri()
.. testcode::
import optuna
from optuna.integration.mlflow import MLflowCallback
def objective(trial):
x = trial.suggest_float("x", -10, 10)
return (x - 2) ** 2
mlflc = MLflowCallback(
tracking_uri=YOUR_TRACKING_URI,
metric_name="my metric score",
)
study = optuna.create_study(study_name="my_study")
study.optimize(objective, n_trials=10, callbacks=[mlflc])
.. testcleanup::
import shutil
shutil.rmtree(tempdir)
Args:
tracking_uri:
The URI of the MLflow tracking server.
Please refer to `mlflow.set_tracking_uri
<https://www.mlflow.org/docs/latest/python_api/mlflow.html#mlflow.set_tracking_uri>`_
for more details.
metric_name:
Name assigned to optimized metric. In case of multi-objective optimization,
list of names can be passed. Those names will be assigned
to metrics in the order returned by objective function.
If single name is provided, or this argument is left to default value,
it will be broadcasted to each objective with a number suffix in order
returned by objective function e.g. two objectives and default metric name
will be logged as ``value_0`` and ``value_1``. The number of metrics must be
the same as the number of values an objective function returns.
create_experiment:
When :obj:`True`, new MLflow experiment will be created for each optimization run,
named after the Optuna study. Setting this argument to :obj:`False` lets user run
optimization under existing experiment, set via `mlflow.set_experiment
<https://www.mlflow.org/docs/latest/python_api/mlflow.html#mlflow.get_tracking_uri>`_,
by passing ``experiment_id`` as one of ``mlflow_kwargs`` or under default MLflow
experiment, when no additional arguments are passed. Note that this argument
must be set to :obj:`False` when using Optuna with this callback within
Databricks Notebook.
mlflow_kwargs:
Set of arguments passed when initializing MLflow run.
Please refer to `MLflow API documentation
<https://www.mlflow.org/docs/latest/python_api/mlflow.html#mlflow.start_run>`_
for more details.
.. note::
``nest_trials`` argument added in v2.3.0 is a part of ``mlflow_kwargs``
since v3.0.0. Anyone using ``nest_trials=True`` should migrate to
``mlflow_kwargs={"nested": True}`` to avoid raising :exc:`TypeError`.
tag_study_user_attrs:
Flag indicating whether or not to add the study's user attrs
to the mlflow trial as tags. Please note that when this flag is
set, key value pairs in :attr:`~optuna.study.Study.user_attrs`
will supersede existing tags.
tag_trial_user_attrs:
Flag indicating whether or not to add the trial's user attrs
to the mlflow trial as tags. Please note that when both trial and
study user attributes are logged, the latter will supersede the former
in case of a collision.
"""

def __init__(
self,
tracking_uri: Optional[str] = None,
metric_name: Union[str, Sequence[str]] = "value",
create_experiment: bool = True,
mlflow_kwargs: Optional[Dict[str, Any]] = None,
tag_study_user_attrs: bool = False,
tag_trial_user_attrs: bool = True,
) -> None:
_imports.check()

if not isinstance(metric_name, Sequence):
raise TypeError(
"Expected metric_name to be string or sequence of strings, got {}.".format(
type(metric_name)
)
)

self._tracking_uri = tracking_uri
self._metric_name = metric_name
self._create_experiment = create_experiment
self._mlflow_kwargs = mlflow_kwargs or {}
self._tag_study_user_attrs = tag_study_user_attrs
self._tag_trial_user_attrs = tag_trial_user_attrs
self._lock = threading.Lock()

def __call__(self, study: optuna.study.Study, trial: optuna.trial.FrozenTrial) -> None:
with self._lock:
self._initialize_experiment(study)

with mlflow.start_run(
run_id=trial.system_attrs.get(RUN_ID_ATTRIBUTE_KEY),
experiment_id=self._mlflow_kwargs.get("experiment_id"),
run_name=self._mlflow_kwargs.get("run_name") or str(trial.number),
nested=self._mlflow_kwargs.get("nested") or False,
tags=self._mlflow_kwargs.get("tags"),
):
# This sets the metrics for MLflow.
self._log_metrics(trial.values)

# This sets the params for MLflow.
self._log_params(trial.params)

# This sets the tags for MLflow.
self._set_tags(trial, study)

@experimental_func("2.9.0")
def track_in_mlflow(self) -> Callable:
"""Decorator for using MLflow logging in the objective function.
This decorator enables the extension of MLflow logging provided by the callback.
All information logged in the decorated objective function will be added to the MLflow
run for the trial created by the callback.
Example:
Add additional logging to MLflow.
.. testcode::
import optuna
import mlflow
from optuna.integration.mlflow import MLflowCallback
mlflc = MLflowCallback(
tracking_uri=YOUR_TRACKING_URI,
metric_name="my metric score",
)
@mlflc.track_in_mlflow()
def objective(trial):
x = trial.suggest_float("x", -10, 10)
mlflow.log_param("power", 2)
mlflow.log_metric("base of metric", x - 2)
return (x - 2) ** 2
study = optuna.create_study(study_name="my_other_study")
study.optimize(objective, n_trials=10, callbacks=[mlflc])
Returns:
Objective function with tracking to MLflow enabled.
"""

def decorator(func: ObjectiveFuncType) -> ObjectiveFuncType:
@functools.wraps(func)
def wrapper(trial: optuna.trial.Trial) -> Union[float, Sequence[float]]:
with self._lock:
study = trial.study
self._initialize_experiment(study)
nested = self._mlflow_kwargs.get("nested")

with mlflow.start_run(run_name=str(trial.number), nested=nested) as run:
trial.storage.set_trial_system_attr(
trial._trial_id, RUN_ID_ATTRIBUTE_KEY, run.info.run_id
)

return func(trial)

return wrapper

return decorator

def _initialize_experiment(self, study: optuna.study.Study) -> None:
"""Initialize an MLflow experiment with the study name.
If a tracking uri has been provided, MLflow will be initialized to use it.
Args:
study: Study to be tracked in MLflow.
"""

# This sets the `tracking_uri` for MLflow.
if self._tracking_uri is not None:
mlflow.set_tracking_uri(self._tracking_uri)

if self._create_experiment:
mlflow.set_experiment(study.study_name)

def _set_tags(self, trial: optuna.trial.FrozenTrial, study: optuna.study.Study) -> None:
"""Sets the Optuna tags for the current MLflow run.
Args:
trial: Trial to be tracked.
study: Study to be tracked.
"""

tags: Dict[str, Union[str, List[str]]] = {}
tags["number"] = str(trial.number)
tags["datetime_start"] = str(trial.datetime_start)

tags["datetime_complete"] = str(trial.datetime_complete)

# Set trial state.
if trial.state.is_finished():
tags["state"] = trial.state.name

# Set study directions.
directions = [d.name for d in study.directions]
tags["direction"] = directions if len(directions) != 1 else directions[0]

distributions = {(k + "_distribution"): str(v) for (k, v) in trial.distributions.items()}
tags.update(distributions)

if self._tag_trial_user_attrs:
tags.update(trial.user_attrs)

if self._tag_study_user_attrs:
tags.update(study.user_attrs)

# This is a temporary fix on Optuna side. It avoids an error with user
# attributes that are too long. It should be fixed on MLflow side later.
# When it is fixed on MLflow side this codeblock can be removed.
# see https://github.com/optuna/optuna/issues/1340
# see https://github.com/mlflow/mlflow/issues/2931
for key, value in tags.items():
value = str(value) # make sure it is a string
max_val_length = mlflow.utils.validation.MAX_TAG_VAL_LENGTH
if len(value) > max_val_length:
tags[key] = "{}...".format(value[: max_val_length - 3])

mlflow.set_tags(tags)

def _log_metrics(self, values: Optional[List[float]]) -> None:
"""Log the trial results as metrics to MLflow.
Args:
values: Results of a trial.
"""
if values is None:
return

if isinstance(self._metric_name, str):
if len(values) > 1:
# Broadcast default name for multi-objective optimization.
names = ["{}_{}".format(self._metric_name, i) for i in range(len(values))]

else:
names = [self._metric_name]

else:
if len(self._metric_name) != len(values):
raise ValueError(
"Running multi-objective optimization "
"with {} objective values, but {} names specified. "
"Match objective values and names, or use default broadcasting.".format(
len(values), len(self._metric_name)
)
)

else:
names = [*self._metric_name]

metrics = {name: val for name, val in zip(names, values)}
mlflow.log_metrics(metrics)

@staticmethod
def _log_params(params: Dict[str, Any]) -> None:
"""Log the parameters of the trial to MLflow.
Args:
params: Trial params.
"""
mlflow.log_params(params)
__all__ = ["MLflowCallback"]
2 changes: 0 additions & 2 deletions pyproject.toml
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Expand Up @@ -68,7 +68,6 @@ document = [
"fvcore",
"lightgbm",
"matplotlib!=3.6.0",
"mlflow",
"pandas",
"pillow",
"plotly>=4.9.0", # optuna/visualization.
Expand All @@ -82,7 +81,6 @@ document = [
"torchvision",
]
integration = [
"mlflow",
"scikit-learn>=0.24.2",
"shap",
"tensorflow",
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