physbo 2.1.0__tar.gz → 3.2.0__tar.gz

{physbo-2.1.0/physbo.egg-info → physbo-3.2.0}/PKG-INFO

@@ -1,15 +1,35 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: physbo
-Version: 2.1.0
+Version: 3.2.0
 Summary: optimization tool for PHYSics based on Bayesian Optimization
-Home-page: https://github.com/issp-center-dev/PHYSBO
-Author: PHYSBO developers
-Author-email: physbo-dev@issp.u-tokyo.ac.jp
-License: MPLv2
-Requires-Python: >=3.6
+Author-email: PHYSBO developers <physbo-dev@issp.u-tokyo.ac.jp>
+License-Expression: MPL-2.0
+Project-URL: homepage, https://www.pasums.issp.u-tokyo.ac.jp/physbo/en
+Project-URL: source, https://github.com/issp-center-dev/PHYSBO
+Project-URL: documentation, https://issp-center-dev.github.io/PHYSBO/
+Project-URL: releasenotes, https://github.com/issp-center-dev/PHYSBO/releases
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-Requires-Dist: numpy<2.0
+Requires-Dist: numpy
+Requires-Dist: odat-se>=3.2.0
 Requires-Dist: scipy
+Provides-Extra: odat-se
+Requires-Dist: odat-se; extra == "odat-se"
+Provides-Extra: docs
+Requires-Dist: gitpython>=3.1.45; extra == "docs"
+Requires-Dist: jupyter>=1.1.1; extra == "docs"
+Requires-Dist: matplotlib>=3.9.4; extra == "docs"
+Requires-Dist: nbsphinx>=0.9.7; extra == "docs"
+Requires-Dist: sphinx>=7.4.7; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=3.0.2; extra == "docs"
+Provides-Extra: tutorials
+Requires-Dist: jupyter>=1.1.1; extra == "tutorials"
+Requires-Dist: matplotlib>=3.9.4; extra == "tutorials"
+Requires-Dist: odat-se>=3.2.0; extra == "tutorials"
+Requires-Dist: pandas>=2.3.3; extra == "tutorials"
+Provides-Extra: tests
+Requires-Dist: pytest>=8.4.2; extra == "tests"
+Requires-Dist: pytest-mock>=3.15.1; extra == "tests"
 
 # optimization tools for PHYsics based on Bayesian Optimization ( PHYSBO )
 
@@ -21,37 +41,39 @@ PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for aca
 ## Documentation
 
 - Stable (master branch)
-    - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
-    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/master/ja/index.html)
+  - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
+  - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/master/ja/index.html)
 - Latest (develop branch)
-    - [English](https://issp-center-dev.github.io/PHYSBO/manual/develop/en/index.html)
-    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/index.html)
+  - [English](https://issp-center-dev.github.io/PHYSBO/manual/develop/en/index.html)
+  - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/index.html)
 
 ## Dependencies
 
-- Python >= 3.6
-    - No longer tested with Python 3.6
-- NumPy < 2.0.0
+- Python >= 3.9
+- NumPy
 - SciPy
 
+### Optional dependencies
+
+- [ODAT-SE](https://github.com/issp-center-dev/ODAT-SE) (for continuous space optimization)
+
+  ``` bash
+  python3 -m pip install odat-se
+  ```
+
 ## Install
 
 - From PyPI (recommended)
 
-```bash
-python3 -m pip install physbo
-```
+  ```bash
+  python3 -m pip install physbo
+  ```
 
 - From source (for developers)
-    1. Update pip (>= 19.0)
-
-        ```bash
-        python3 -m pip install -U pip
-        ```
 
     1. Download or clone the github repository
 
-        ```
+        ```bash
         git clone https://github.com/issp-center-dev/PHYSBO
         ```
 
@@ -64,8 +86,6 @@ python3 -m pip install physbo
         python3 -m pip install ./PHYSBO
         ```
 
-    1. Note: Do not `import physbo` at the root directory of the repository because `import physbo` does not try to import the installed PHYSBO but one in the repository, which includes Cython codes not compiled.
-
 ## Uninstall
 
 ```bash
@@ -74,25 +94,50 @@ python3 -m pip uninstall physbo
 
 ## Usage
 
-For an introductory tutorial please consult the documentation. ([English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/notebook/tutorial_basic.html) / [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/install.html#id2))  
+For an introductory tutorial please consult the documentation. ([English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/notebook/tutorial_basic.html) / [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/install.html#id2))
 
 ['examples/simple.py'](./examples/simple.py) is a simple example.
 
 ## Data repository
 
-A tutorial and a dataset of a paper about PHYSBO can be found in [PHYSBO Gallery](http://isspns-container.issp.u-tokyo.ac.jp/repo/12).
+A tutorial and a dataset of a paper about PHYSBO can be found in [PHYSBO Gallery](https://isspns-gitlab.issp.u-tokyo.ac.jp/physbo-dev/physbo-gallery).
+
+## For developers
+
+[UV](https://docs.astral.sh/uv/) is recommended to make a virtual environment and install dependencies for development.
+
+### Run tests
+
+When using UV, the command `uv sync --extra tests` will install the dependencies to run tests like `pytest`.
+Test files are in `tests/` directory, and use `pytest` to run tests.
+
+``` bash
+uv run pytest tests
+```
+
+### Build documentation
+
+When using UV, the command `uv sync --extra docs` will install the dependencies for building the documentation like `sphinx`.
+
+The command
+
+```bash
+uv run bash docs/make_docs.sh
+```
+
+will build the documentation into `docs/built`.
 
 ## License
 
 PHYSBO was developed based on [COMBO](https://github.com/tsudalab/COMBO) for academic use.
-PHYSBO v2 is distributed under Mozilla Public License version 2.0 (MPL v2).
+PHYSBO is distributed under Mozilla Public License version 2.0 (MPL v2).
 We hope that you cite the following reference when you publish the results using PHYSBO:
 
 [“Bayesian optimization package: PHYSBO”, Yuichi Motoyama, Ryo Tamura, Kazuyoshi Yoshimi, Kei Terayama, Tsuyoshi Ueno, Koji Tsuda, Computer Physics Communications Volume 278, September 2022, 108405.](https://doi.org/10.1016/j.cpc.2022.108405)
 
 Bibtex
 
-```
+```bibtex
 @misc{@article{MOTOYAMA2022108405,
 title = {Bayesian optimization package: PHYSBO},
 journal = {Computer Physics Communications},

physbo-2.1.0/PKG-INFO → physbo-3.2.0/README.md

@@ -1,16 +1,3 @@
-Metadata-Version: 2.2
-Name: physbo
-Version: 2.1.0
-Summary: optimization tool for PHYSics based on Bayesian Optimization
-Home-page: https://github.com/issp-center-dev/PHYSBO
-Author: PHYSBO developers
-Author-email: physbo-dev@issp.u-tokyo.ac.jp
-License: MPLv2
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-Requires-Dist: numpy<2.0
-Requires-Dist: scipy
-
 # optimization tools for PHYsics based on Bayesian Optimization ( PHYSBO )
 
 Bayesian optimization has been proven as an effective tool in accelerating scientific discovery.
@@ -21,37 +8,39 @@ PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for aca
 ## Documentation
 
 - Stable (master branch)
-    - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
-    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/master/ja/index.html)
+  - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
+  - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/master/ja/index.html)
 - Latest (develop branch)
-    - [English](https://issp-center-dev.github.io/PHYSBO/manual/develop/en/index.html)
-    - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/index.html)
+  - [English](https://issp-center-dev.github.io/PHYSBO/manual/develop/en/index.html)
+  - [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/index.html)
 
 ## Dependencies
 
-- Python >= 3.6
-    - No longer tested with Python 3.6
-- NumPy < 2.0.0
+- Python >= 3.9
+- NumPy
 - SciPy
 
+### Optional dependencies
+
+- [ODAT-SE](https://github.com/issp-center-dev/ODAT-SE) (for continuous space optimization)
+
+  ``` bash
+  python3 -m pip install odat-se
+  ```
+
 ## Install
 
 - From PyPI (recommended)
 
-```bash
-python3 -m pip install physbo
-```
+  ```bash
+  python3 -m pip install physbo
+  ```
 
 - From source (for developers)
-    1. Update pip (>= 19.0)
-
-        ```bash
-        python3 -m pip install -U pip
-        ```
 
     1. Download or clone the github repository
 
-        ```
+        ```bash
         git clone https://github.com/issp-center-dev/PHYSBO
         ```
 
@@ -64,8 +53,6 @@ python3 -m pip install physbo
         python3 -m pip install ./PHYSBO
         ```
 
-    1. Note: Do not `import physbo` at the root directory of the repository because `import physbo` does not try to import the installed PHYSBO but one in the repository, which includes Cython codes not compiled.
-
 ## Uninstall
 
 ```bash
@@ -74,25 +61,50 @@ python3 -m pip uninstall physbo
 
 ## Usage
 
-For an introductory tutorial please consult the documentation. ([English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/notebook/tutorial_basic.html) / [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/install.html#id2))  
+For an introductory tutorial please consult the documentation. ([English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/notebook/tutorial_basic.html) / [日本語](https://issp-center-dev.github.io/PHYSBO/manual/develop/ja/install.html#id2))
 
 ['examples/simple.py'](./examples/simple.py) is a simple example.
 
 ## Data repository
 
-A tutorial and a dataset of a paper about PHYSBO can be found in [PHYSBO Gallery](http://isspns-container.issp.u-tokyo.ac.jp/repo/12).
+A tutorial and a dataset of a paper about PHYSBO can be found in [PHYSBO Gallery](https://isspns-gitlab.issp.u-tokyo.ac.jp/physbo-dev/physbo-gallery).
+
+## For developers
+
+[UV](https://docs.astral.sh/uv/) is recommended to make a virtual environment and install dependencies for development.
+
+### Run tests
+
+When using UV, the command `uv sync --extra tests` will install the dependencies to run tests like `pytest`.
+Test files are in `tests/` directory, and use `pytest` to run tests.
+
+``` bash
+uv run pytest tests
+```
+
+### Build documentation
+
+When using UV, the command `uv sync --extra docs` will install the dependencies for building the documentation like `sphinx`.
+
+The command
+
+```bash
+uv run bash docs/make_docs.sh
+```
+
+will build the documentation into `docs/built`.
 
 ## License
 
 PHYSBO was developed based on [COMBO](https://github.com/tsudalab/COMBO) for academic use.
-PHYSBO v2 is distributed under Mozilla Public License version 2.0 (MPL v2).
+PHYSBO is distributed under Mozilla Public License version 2.0 (MPL v2).
 We hope that you cite the following reference when you publish the results using PHYSBO:
 
 [“Bayesian optimization package: PHYSBO”, Yuichi Motoyama, Ryo Tamura, Kazuyoshi Yoshimi, Kei Terayama, Tsuyoshi Ueno, Koji Tsuda, Computer Physics Communications Volume 278, September 2022, 108405.](https://doi.org/10.1016/j.cpc.2022.108405)
 
 Bibtex
 
-```
+```bibtex
 @misc{@article{MOTOYAMA2022108405,
 title = {Bayesian optimization package: PHYSBO},
 journal = {Computer Physics Communications},

physbo-3.2.0/pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "physbo"
+version = "3.2.0"
+description = "optimization tool for PHYSics based on Bayesian Optimization"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = "MPL-2.0"
+authors = [ { name = "PHYSBO developers", email = "physbo-dev@issp.u-tokyo.ac.jp" } ]
+
+requires-python = ">=3.9"
+dependencies = [
+    "numpy",
+    "odat-se>=3.2.0",
+    "scipy",
+]
+
+[project.optional-dependencies]
+odat-se = [ "odat-se" ]
+docs = [
+    "gitpython>=3.1.45",
+    "jupyter>=1.1.1",
+    "matplotlib>=3.9.4",
+    "nbsphinx>=0.9.7",
+    "sphinx>=7.4.7",
+    "sphinx-rtd-theme>=3.0.2",
+]
+tutorials = [
+    "jupyter>=1.1.1",
+    "matplotlib>=3.9.4",
+    "odat-se>=3.2.0",
+    "pandas>=2.3.3",
+]
+tests = [
+    "pytest>=8.4.2",
+    "pytest-mock>=3.15.1",
+]
+
+[project.urls]
+homepage = "https://www.pasums.issp.u-tokyo.ac.jp/physbo/en"
+source = "https://github.com/issp-center-dev/PHYSBO"
+documentation = "https://issp-center-dev.github.io/PHYSBO/"
+releasenotes = "https://github.com/issp-center-dev/PHYSBO/releases"
+
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+
+[tool.ruff.lint]
+ignore = ["E741"]

physbo-3.2.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

physbo-3.2.0/src/physbo/__init__.py

@@ -0,0 +1,34 @@
+# SPDX-License-Identifier: MPL-2.0
+# Copyright (C) 2020- The University of Tokyo
+#
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+from . import gp
+from . import opt
+from . import blm
+from . import misc
+from . import search
+from . import predictor
+from . import test_functions
+from ._variable import Variable
+
+
+def base_predictor(*args, **kwargs):
+    ":meta private:"
+    misc.deprecated_warning(old="physbo.base_predictor", new="physbo.predictor.BasePredictor")
+    return predictor.BasePredictor(*args, **kwargs)
+
+
+def variable(*args, **kwargs):
+    ":meta private:"
+    misc.deprecated_warning(old="physbo.variable", new="physbo.Variable")
+    return Variable(*args, **kwargs)
+
+
+__version__ = "3.2.0"
+
+# __all__ is used to specify the public API of the package
+# and is used by sphinx to generate the API documentation
+__all__ = ["gp", "opt", "blm", "misc", "search", "predictor", "Variable", "test_functions"]