Add docs for NelderMeadSampler (#397)

* uploaded installation.md

* fixed descriptions wrt Linux and ABCI.

* fixed links.

* added descriptions wrt macOS.

* fixed installation.md

* mkdir installation
mv installation.md installation

* added auto_formatting_guide.md to contribution_guide directory.

* deleted black space

* added Makefile

* added installation_en.md

* fixed installation_en.md

* added auto_formatting_guide_en.md

* fixed error wrt ruff

* fixed errors wrt ruff

* Add docs for nm.(WIP)

* Add docs/source/hpo.

* Add Sphinx documents.

* Delete docs/source/api_reference.

* Add docs/source/api_reference in .gitignore.

* Add publish_pages.yaml.

* Delete japanese in docstring.

* Change html_theme to pydata.

* Delete japanese.

* Remove files.

* Split API reference.

* Add logo.

* Fix for ruff and mypy.

* Update hpo.md

* Fix typo.

* Add --maxdepth option.

* Delete html.

* Remove sphinx_rtd_theme.

* Resize logo.

* Fixed to upper case.

* Change document structure.

* Add contribution_guide(WIP).

* Add api_reference/index.rst.

* Add user_guide(WIP)

* Remove unnecessary sentences.

* Remove docs/source/api_reference/*.md.

* Integrate contribution_guide.

* Split user_guide.

* Adjust html_sidebars.

* Fix for ruff.

* Update installation.md

* Update index.rst

* Update and rename docs/source/installation/installation.md to docs/source/getting_started.md

* Update aiaccel/hpo/algorithms/nelder_mead_algorithm.py

Co-authored-by: Yoshiaki Bando <yoshipon@users.noreply.github.com>

* Add logo_aiaccel_padding.png.

* Integrate neldermeadsampler_en.md.

* Delete unnecessary files.

* Add sphinx.ext.doctest.

* Remove cp index.html .

---------

Co-authored-by: 3bisuoka <ebisuoka-ryoya@aist.go.jp>
Co-authored-by: Yoshiaki Bando <yoshipon@users.noreply.github.com>

.github/workflows/publish_pages.yaml

@@ -0,0 +1,31 @@
+name: Publish on GitHub Pages
+
+on:
+  [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[dev,github-actions,test]
+      - name: Sphinx build
+        run: |
+          sphinx-apidoc --maxdepth 2 -f -o ./docs/source/api_reference/ ./aiaccel/
+          cd docs
+          make html
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/feature/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          force_orphan: true

.gitignore

@@ -113,6 +113,8 @@ work_aiaccel/
 
 # document
 docs/build/html
+docs/source/api_reference/*.rst
+!docs/source/api_reference/index.rst
 
 # IntelliJ
 .idea

aiaccel/hpo/algorithms/nelder_mead_algorithm.py

@@ -33,48 +33,31 @@ class NelderMeadAlgorism:
     Uses a queue to receive results and advance the NelderMead algorithm.
     Return parameters within the normalization range by referring only to the number of dimensions.
 
-    NelderMead アルゴリズムを管理するクラス
-
-    queue を用いて結果を受け取り、NelderMead のアルゴリズムを進める
-    次元数のみを参照して、正規化範囲でパラメータを返す
-
     Args:
         dimensions: int | None = None
             The number of dimensions in the search space.
-            探索範囲の次元数
         coeff: NelderMeadCoefficient | None = None
             Parameters used in NelderMead.
-            NelderMead で用いられるパラメータ
         rng: np.random.RandomState | None = None
             RandomState used for calculating initial points.
-            初期点計算に用いられる RandomState
         block: bool = False
             Sets whether to block the queue used internally.
-            内部で用いられる queue を block するかどうかを設定する
         timeout: int | None = None
             Time to block the queue.
-            queue を block する時間
     Attributes:
         vertices: list[npt.NDArray[np.float64]]
             List of simplex parameters.
-            simplex のパラメータのリスト
         values: list[float]
             List of simplex calculation results.
-            simplex の計算結果のリスト
         generator: iterator
             Generator for NelderMead parameters.
-            neldermead のパラメータのジェネレータ
         lock: threading.Lock
             threading.Lock variable used for thread-safe processing.
-             スレッドセーフ処理に用いる threading.Lock 変数
         results: queue.Queue[tuple[npt.NDArray[np.float64], float, bool]]
             Queue to receive tuples of parameters, calculation results,
             and a boolean indicating whether the parameters were output by NelderMead.
-            外部からパラメータ・計算結果・nelder mead から出力されたパラメータか否かを示す bool 変数
-            のタプルを受け取る queue
         simplex_size: int
             Number of vertices in the simplex.
-            simplex の頂点の個数
     """
 
     vertices: list[npt.NDArray[np.float64]]
@@ -107,14 +90,9 @@ def get_vertex(self, dimensions: int | None = None) -> npt.NDArray[np.float64]:
 
         Thread-safe due to parallel processing requirements.
 
-        nelder mead の次のパラメータを返すメソッド
-
-        並列処理の都合でスレッドセーフとなっている
-
         Returns:
             npt.NDArray[np.float64]:
                 The next parameters for NelderMead.
-                nelder mead の次のパラメータ
         """
 
         if dimensions is not None:
@@ -151,14 +129,11 @@ def put_value(
     ) -> None:
         """Method to pass a pair of parameters and results to NelderMead
 
-        nelder mead にパラメータと結果の組を渡すメソッド
-
         Args:
-            vertex: npt.NDArray[np.float64]: Parameters パラメータ
-            value: float: Calculation result 計算結果
+            vertex: npt.NDArray[np.float64]: Parameters
+            value: float: Calculation result
             enqueue: bool = False:
                 Boolean indicating whether the parameters were output by NelderMead.
-                nelder mead から出力されたパラメータか否かを示す bool 変数
         """
 
         if self.dimensions is None:

aiaccel/hpo/optuna/samplers/nelder_mead_sampler.py

@@ -35,52 +35,48 @@ class NelderMeadSampler(optuna.samplers.BaseSampler):
     The enqueued parameters are calculated in parallel
     with the parameters determined by NelderMead if parallelisation is enabled.
 
-    NelderMead アルゴリズムを用いた Sampler
+    Example:
 
-    パラメータ数-1個の初期点計算と shrink 時のみ並列化可能で、
-    それ以外は基本的には直列計算になる(optuna.optimize(n_jobs=2)等で設定しても、前述の時以外は直列で計算する)
-    並列化を有効にする場合は、引数 block = True にする必要がある。
+        An example of a single-objective optimization is as follows:
 
-    optuna.enqueue_trial() 利用時は、NelderMeadSampler が決定するパラメータとは個別に計算され、
-    良い結果が出れば NelderMead に取り込まれる。(Simplexの再構成を行う)
-    また、optuna.enqueue_trial() で決定されたパラメータは、
-    並列化が有効であれば NelderMead の決定するパラメータと並列で計算される。
+        .. testcode::
+
+            import optuna
+            from aiaccel.hpo.optuna.samplers.nelder_mead_sampler import NelderMeadSampler
+
+
+            def objective(trial):
+                x = trial.suggest_float("x", -10, 10)
+                return x**2
+
+
+            search_space = {"x": {"low": -10, "high": 10}}
+            sampler = NelderMeadSampler(search_space=search_space, seed=42)
+            study.optimize(objective, n_trials=10)
 
     Args:
         search_space: dict[str, tuple[float, float]]
             Parameter names and corresponding lower and upper limits.
             Must be set separately from suggest_uniform
             (as the parameters must be determined at the time of before_trial).
-            パラメータ名と対応した lower, upper
-            suggest_uniform 等とは個別に設定する必要がある(before_trial 時点でパラメータを決定する必要があるため)
         seed: int | None = None
             Random seed used for initial point calculation.
-            初期点計算をランダムで決定する際に利用されるシード値
         rng: np.random.RandomState | None = None
             RandomState used for initial point calculation.
             If specified with seed, rng takes precedence.
-            初期点計算に用いられる RandomState
-            seed と同時に指定された場合、 rng が優先される
         coeff: NelderMeadCoefficient | None = None
             Parameters used in NelderMead Algorism.
-            NelderMead で用いられるパラメータ
         block: bool = False
             Indicates whether the queue used internally is blocked or not.
             If parallelisation by optuna.optimize is enabled, it must be set with block = True
-            内部で用いられる queue を block するかどうかを設定する
-            optuna.optimize による並列化を有効にする場合は、 block = Trueで設定する必要がある
         sub_sampler: optuna.samplers.BaseSampler | None = None
             Sampler to output parameters when NelderMead cannot output parameters.
             Mainly intended for use on free computation nodes in parallel.
             If the sub_sampler function is enabled, it must be set with block = False.
-            NelderMead がパラメータを出力出来ない時に、代わりにパラメータを出力する Sampler
-            主に並列化時に空いている計算ノードで利用することを想定している
-            sub_sampler 機能を有効にする場合は、 block = False で設定する必要がある
 
     Attributes:
         nm: NelderMeadAlgorism
             Instance of a class that manages the NelderMead algorithm.
-            NelderMead のアルゴリズムを管理するクラスのインスタンス
 
     """
 
@@ -171,14 +167,6 @@ def before_trial(self, study: Study, trial: FrozenTrial) -> None:
         If sub_sampler is specified, sub_sampler.before_trial() is executed,
         and trial.user_attr["sub_trial"] is set to True.
 
-        trial の前処理
-
-        ここで NelderMead のパラメータを決定する
-        trial.user_attr["params"] に決定したパラメータが格納される
-        NelderMead のパラメータが出力出来ないかつ、sub_sampler = None の場合は NelderMeadEmptyError を raise する
-        sub_sampler が指定されている場合は、 sub_sampler.before_trial() を実行し、
-        trial.user_attr["sub_trial"] = True とする
-
         Args:
             study: Study
                 Target study object.
@@ -223,13 +211,6 @@ def sample_independent(
         If trial.user_attr["sub_trial"] = True,
         execute sub_sampler.sample_independent() and return its parameters.
 
-        パラメータを sample する
-
-        NelderMeadSampler の場合は before_trial でパラメータを決定済みなので、
-        trial.user_attr["params"] の対応したパラメータを返り値とする
-        trial.user_attr["sub_trial"] = True の場合は、
-        sub_sampler.sample_independent() を実行し、そのパラメータを返り値とする
-
         Args:
             study: Study
                 Target study object.
@@ -299,11 +280,6 @@ def after_trial(
         Pass the parameter-result pairs to the NelderMead algorithm.
         If trial.user_attr["sub_trial"] = True, execute sub_sampler.after_trial().
 
-        trial の後処理
-
-        パラメータ、計算結果の組を NelderMead アルゴリズムに渡す
-        trial.user_attr["sub_trial"] = True の場合は、 sub_sampler.after_trial() を実行する
-
         Args:
             study: Study
                 Target study object.

docs/Makefile

@@ -0,0 +1,14 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api_reference/index.rst

@@ -0,0 +1,19 @@
+
+*************
+API Reference
+*************
+
+* :ref:`genindex`
+* :ref:`modindex`
+
+----
+
+
+.. toctree::
+   :maxdepth: 2
+
+   aiaccel.app
+   aiaccel.hpo
+   aiaccel.job
+   aiaccel.torch
+   aiaccel.utils

docs/source/conf.py

@@ -0,0 +1,88 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+from pathlib import Path
+import sys
+
+root_path = Path(__file__).parent.parent.parent
+sys.path.insert(0, str(root_path.absolute()))
+
+# -- Project information -----------------------------------------------------
+
+project = "aiaccel"
+project_copyright = "2024, AIST"
+author = "AIST"
+
+# The full version, including alpha/beta/rc tags
+release = "2.0.0"
+html_logo = f"{root_path}/docs/image/logo_aiaccel_padding.png"
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx_fontawesome",
+    "myst_parser",
+    "pydata_sphinx_theme",
+    "sphinx.ext.doctest",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+]
+
+# Auto-generated header anchors
+# The MyST Parser can automatically generate label “slugs” for header anchors
+# so that you can reference them from markdown links. For example, you can use
+# header bookmark links, locally; [](#header-anchor), or cross-file
+# [](path/to/file.md#header-anchor). To achieve this, use the
+# myst_heading_anchors = DEPTH configuration option, where DEPTH is the depth
+# of header levels for which you wish to generate links.
+# (commentout) myst_heading_anchors = 3
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "pydata_sphinx_theme"
+html_show_sourcelink = False
+html_show_sphinx = False
+# (commentout) html_static_path = ["_static"]
+html_sidebars = {"**": ["search-field", "sidebar-nav-bs", "sourcelink.html"]}
+source_suffix = {".rst": "restructuredtext", ".txt": "markdown", ".md": "markdown"}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# (commentout) html_static_path = ['_static']
+
+language = "en"
+
+# -- Extension configuration -------------------------------------------------
+# (commentout) todo_include_todos = True
+# (commentout) autoclass_content = "both"

docs/source/contribution_guide/contribution_guide.md

@@ -0,0 +1,3 @@
+# Contribution Guide
+
+(WIP)