Merge branch 'optuna:master' into fix-lightGBM-argument

.github/workflows/checks-integration.yml

@@ -30,7 +30,6 @@ jobs:
         sudo apt-get -y install openmpi-bin libopenmpi-dev libopenblas-dev
 
     # TODO(Shinichi): Remove the version constraint on SQLAlchemy
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
     - name: Install
       run: |
         python -m pip install -U pip
@@ -42,7 +41,6 @@ jobs:
         pip install --progress-bar off -U bayesmark
         pip install --progress-bar off -U kurobako
         pip install "sqlalchemy<2.0.0"
-        pip install "pytorch-lightning<2.0.0"
 
     - name: Output installed packages
       run: |

.github/workflows/coverage.yml

@@ -42,7 +42,7 @@ jobs:
         sudo apt-get update
         sudo apt-get -y install openmpi-bin libopenmpi-dev libopenblas-dev
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
+    # TODO(Shinichi): Remove the version constraint on Numpy
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -56,7 +56,7 @@ jobs:
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
         pip install --progress-bar off .[integration] --extra-index-url https://download.pytorch.org/whl/cpu
-        pip install "pytorch-lightning<2.0.0"
+        pip install "numpy<1.24.0"
         pip install "fakeredis<2.11.1"
 
         echo 'import coverage; coverage.process_startup()' > sitecustomize.py

.github/workflows/mac-tests.yml

@@ -41,7 +41,6 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-3.8-${{ env.cache-name }}-${{ hashFiles('**/pyproject.toml') }}
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -53,7 +52,6 @@ jobs:
         optuna --version
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
-        pip install "pytorch-lightning<2.0.0"
         pip install "fakeredis<2.11.1"
 
     - name: Output installed packages
@@ -105,7 +103,7 @@ jobs:
         brew install open-mpi
         brew install openblas
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
+    # TODO(Shinichi): Remove the version constraint on Numpy
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -119,7 +117,7 @@ jobs:
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
         pip install --progress-bar off .[integration]
-        pip install "pytorch-lightning<2.0.0"
+        pip install "numpy<1.24.0"
         pip install "fakeredis<2.11.1"
 
     - name: Output installed packages

.github/workflows/tests-integration.yml

@@ -20,7 +20,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
     - name: Checkout
@@ -46,7 +46,7 @@ jobs:
         sudo apt-get update
         sudo apt-get -y install openmpi-bin libopenmpi-dev libopenblas-dev
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
+    # TODO(Shinichi): Remove the version constraint on Numpy
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -60,7 +60,7 @@ jobs:
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
         pip install --progress-bar off .[integration] --extra-index-url https://download.pytorch.org/whl/cpu
-        pip install "pytorch-lightning<2.0.0"
+        pip install "numpy<1.24.0"
         pip install "fakeredis<2.11.1"
 
     - name: Output installed packages

.github/workflows/tests-storage.yml

@@ -53,7 +53,7 @@ jobs:
           --health-timeout 5s
           --health-retries 5
       redis:
-        image: redis:6.2.6
+        image: redis
         ports:
           - 6379:6379
 

.github/workflows/windows-tests.yml

@@ -41,7 +41,6 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-3.9-${{ env.cache-name }}-${{ hashFiles('**/pyproject.toml') }}
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -53,7 +52,6 @@ jobs:
         optuna --version
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
-        pip install "pytorch-lightning<2.0.0"
         pip install PyQt6 # Install PyQT for using QtAgg as matplotlib backend.
         pip install "fakeredis<2.11.1"
 
@@ -109,7 +107,7 @@ jobs:
       with:
         mpi: "msmpi"
 
-    # TODO(Shinichi): Remove the version constraint on PyTorch Lightning
+    # TODO(Shinichi): Remove the version constraint on Numpy
     # TODO(c-bata): Remove the version constraint on fakeredis
     - name: Install
       run: |
@@ -122,7 +120,7 @@ jobs:
         pip install --progress-bar off .[test]
         pip install --progress-bar off .[optional]
         pip install --progress-bar off .[integration]
-        pip install "pytorch-lightning<2.0.0"
+        pip install "numpy<1.24.0"
         pip install "distributed<2023.3.2"
         pip install "fakeredis<2.11.1"
 

benchmarks/asv/optimize.py

@@ -63,7 +63,11 @@ def time_optimize(self, args: str) -> None:
         "inmemory, tpe, 1000",
         "inmemory, cmaes, 1000",
         "sqlite, random, 1000",
-        "cached_sqlite, random, 1000",
+        "sqlite, tpe, 1000",
+        "sqlite, cmaes, 1000",
+        "journal, random, 1000",
+        "journal, tpe, 1000",
+        "journal, cmaes, 1000",
     )
     param_names = ["storage, sampler, n_trials"]
     timeout = 600

docs/source/conf.py

@@ -16,14 +16,14 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
-import pkg_resources
 import warnings
 
 import plotly.io as pio
 from sklearn.exceptions import ConvergenceWarning
 from sphinx_gallery.sorting import FileNameSortKey
 
-__version__ = pkg_resources.get_distribution("optuna").version
+import optuna
+
 
 # -- Project information -----------------------------------------------------
 
@@ -32,9 +32,9 @@
 author = "Optuna Contributors."
 
 # The short X.Y version
-version = __version__
+version = optuna.version.__version__
 # The full version, including alpha/beta/rc tags
-release = __version__
+release = optuna.version.__version__
 
 # -- General configuration ---------------------------------------------------
 

docs/source/reference/integration.rst

@@ -26,6 +26,7 @@ BoTorch
    :nosignatures:
 
    optuna.integration.BoTorchSampler
+   optuna.integration.botorch.logei_candidates_func
    optuna.integration.botorch.qei_candidates_func
    optuna.integration.botorch.qnei_candidates_func
    optuna.integration.botorch.qehvi_candidates_func

optuna/artifacts/__init__.py

@@ -0,0 +1,4 @@
+from optuna.artifacts._filesystem import FileSystemArtifactStore
+
+
+__all__ = ["FileSystemArtifactStore"]

optuna/artifacts/_filesystem.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+
+import os
+import shutil
+from typing import TYPE_CHECKING
+
+from optuna.artifacts.exceptions import ArtifactNotFound
+
+
+if TYPE_CHECKING:
+    from typing import BinaryIO
+
+
+class FileSystemArtifactStore:
+    """An artifact backend for file systems.
+
+    Example:
+       .. code-block:: python
+
+           import optuna
+           from optuna_dashboard.artifact import upload_artifact
+           from optuna_dashboard.artifact.file_system import FileSystemBackend
+
+           artifact_backend = FileSystemBackend("./artifacts")
+
+
+           def objective(trial: optuna.Trial) -> float:
+               ... = trial.suggest_float("x", -10, 10)
+               file_path = generate_example_png(...)
+               upload_artifact(artifact_backend, trial, file_path)
+               return ...
+    """
+
+    def __init__(self, base_path: str) -> None:
+        self._base_path = base_path
+
+    def open_reader(self, artifact_id: str) -> BinaryIO:
+        filepath = os.path.join(self._base_path, artifact_id)
+        try:
+            f = open(filepath, "rb")
+        except FileNotFoundError as e:
+            raise ArtifactNotFound("not found") from e
+        return f
+
+    def write(self, artifact_id: str, content_body: BinaryIO) -> None:
+        filepath = os.path.join(self._base_path, artifact_id)
+        with open(filepath, "wb") as f:
+            shutil.copyfileobj(content_body, f)
+
+    def remove(self, artifact_id: str) -> None:
+        filepath = os.path.join(self._base_path, artifact_id)
+        try:
+            os.remove(filepath)
+        except FileNotFoundError as e:
+            raise ArtifactNotFound("not found") from e
+
+
+if TYPE_CHECKING:
+    # A mypy-runtime assertion to ensure that LocalArtifactBackend
+    # implements all abstract methods in ArtifactBackendProtocol.
+    from ._protocol import ArtifactStore
+
+    _: ArtifactStore = FileSystemArtifactStore("")

optuna/artifacts/_protocol.py

@@ -0,0 +1,59 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+
+try:
+    from typing import Protocol
+except ImportError:
+    from typing_extensions import Protocol  # type: ignore
+
+
+if TYPE_CHECKING:
+    from typing import BinaryIO
+
+
+class ArtifactStore(Protocol):
+    """A protocol defining the interface for an artifact backend.
+
+    An artifact backend is responsible for managing the storage and retrieval
+    of artifact data. The backend should provide methods for opening, writing
+    and removing artifacts.
+    """
+
+    def open_reader(self, artifact_id: str) -> BinaryIO:
+        """Open the artifact identified by the artifact_id.
+
+        This method should return a binary file-like object in read mode, similar to
+        ``open(..., mode="rb")``. If the artifact does not exist, an
+        :exc:`~optuna_dashboard.artifact.exceptions.ArtifactNotFound` exception
+        should be raised.
+
+        Args:
+            artifact_id: The identifier of the artifact to open.
+
+        Returns:
+            BinaryIO: A binary file-like object that can be read from.
+        """
+        ...
+
+    def write(self, artifact_id: str, content_body: BinaryIO) -> None:
+        """Save the content to the backend.
+
+        Args:
+            artifact_id: The identifier of the artifact to write to.
+            content_body: The content to write to the artifact.
+        """
+        ...
+
+    def remove(self, artifact_id: str) -> None:
+        """Remove the artifact identified by the artifact_id.
+
+        This method should delete the artifact from the backend. If the artifact does not
+        exist, an :exc:`~optuna_dashboard.artifact.exceptions.ArtifactNotFound` exception
+        may be raised.
+
+        Args:
+            artifact_id: The identifier of the artifact to remove.
+        """
+        ...

optuna/artifacts/exceptions.py

@@ -0,0 +1,12 @@
+from optuna.exceptions import OptunaError
+
+
+class ArtifactNotFound(OptunaError):
+    """Exception raised when an artifact is not found.
+
+    It is typically raised while calling
+    :meth:`~optuna_dashboard.artifact.protocol.ArtifactBackend.open` or
+    :meth:`~optuna_dashboard.artifact.protocol.ArtifactBackend.remove` methods.
+    """
+
+    ...