physbo 2.1.0__tar.gz → 3.0.0__tar.gz

{physbo-2.1.0 → physbo-3.0.0}/PKG-INFO

@@ -1,14 +1,16 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: physbo
-Version: 2.1.0
+Version: 3.0.0
 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: scipy
 
 # optimization tools for PHYsics based on Bayesian Optimization ( PHYSBO )
@@ -21,19 +23,25 @@ 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
 
+### About Cython
+
+From v3.0.0, PHYSBO no longer uses Cython in order to simplify installation process particularly on Windows.
+This means that the performance of PHYSBO is slightly degraded from older versions.
+If you need more performance, you can install ``physbo-core-cython`` additionally.
+This package offers Cythonized version of some functions of PHYSBO.
+
 ## Install
 
 - From PyPI (recommended)
@@ -43,15 +51,10 @@ 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
         ```
 
@@ -64,7 +67,11 @@ 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.
+- To install ``physbo-core-cython`` ::
+
+  ```bash
+  python3 -m pip install physbo-core-cython
+  ```
 
 ## Uninstall
 
@@ -74,25 +81,25 @@ 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).
 
 ## 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 → physbo-3.0.0}/README.md

@@ -8,19 +8,25 @@ 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
 
+### About Cython
+
+From v3.0.0, PHYSBO no longer uses Cython in order to simplify installation process particularly on Windows.
+This means that the performance of PHYSBO is slightly degraded from older versions.
+If you need more performance, you can install ``physbo-core-cython`` additionally.
+This package offers Cythonized version of some functions of PHYSBO.
+
 ## Install
 
 - From PyPI (recommended)
@@ -30,15 +36,10 @@ 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
         ```
 
@@ -51,7 +52,11 @@ 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.
+- To install ``physbo-core-cython`` ::
+
+  ```bash
+  python3 -m pip install physbo-core-cython
+  ```
 
 ## Uninstall
 
@@ -61,25 +66,25 @@ 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).
 
 ## 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-3.0.0/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "physbo"
+version = "3.0.0"
+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",
+    "scipy",
+]
+
+[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-3.0.0/setup.cfg

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

physbo-3.0.0/src/physbo/__init__.py

@@ -0,0 +1,33 @@
+# 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 ._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__ = "3.0.0"
+
+# __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"]

physbo-2.1.0/physbo/variable.py → physbo-3.0.0/src/physbo/_variable.py

@@ -8,7 +8,12 @@
 import numpy as np
 
 
-class variable(object):
+class Variable(object):
+    """ Variable class
+
+    Variable class represents a set of pairs of input (X) and output (t).
+
+    """
     def __init__(self, X=None, t=None, Z=None):
         """
 
@@ -18,13 +23,19 @@ class variable(object):
             N x d dimensional matrix. Each row of X denotes the d-dimensional feature vector of each search candidate.
         t:  numpy array
             N dimensional array. The negative energy of each search candidate (value of the objective function to be optimized).
-        Z:
+        Z: numpy array
 
         """
         self.X = X
         self.Z = Z
         self.t = t
 
+    def __len__(self):
+        if self.X is not None:
+            return self.X.shape[0]
+        else:
+            return 0
+
     def get_subset(self, index):
         """
         Getting subset of variables.
@@ -41,7 +52,7 @@ class variable(object):
         temp_t = self.t[index] if self.t is not None else None
         temp_Z = self.Z[index, :] if self.Z is not None else None
 
-        return variable(X=temp_X, t=temp_t, Z=temp_Z)
+        return Variable(X=temp_X, t=temp_t, Z=temp_Z)
 
     def delete(self, num_row):
         """

physbo-3.0.0/src/physbo/blm/__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/.
+
+"""Bayesian Linear Model"""
+
+from . import basis
+from . import prior
+from . import lik
+from . import inf
+from . import core
+
+from .core import Model
+from ._predictor import Predictor
+
+from ..misc import deprecated_warning
+
+
+def model(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.model", new="physbo.blm.Model")
+    return Model(*args, **kwargs)
+
+
+def predictor(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.predictor", new="physbo.blm.Predictor")
+    return Predictor(*args, **kwargs)
+
+
+__all__ = ["basis", "prior", "lik", "inf", "core", "Model", "Predictor"]

physbo-2.1.0/physbo/blm/predictor.py → physbo-3.0.0/src/physbo/blm/_predictor.py

@@ -8,13 +8,13 @@
 import physbo.predictor
 
 
-class predictor(physbo.predictor.base_predictor):
+class Predictor(physbo.predictor.BasePredictor):
     """Predictor using Baysean linear model
 
     Attributes
     ==========
-    blm: physbo.blm.core.model
-    config: physbo.misc.set_config
+    blm: physbo.blm.core.Model
+    config: physbo.misc.SetConfig
         configuration
     """
 
@@ -23,18 +23,18 @@ class predictor(physbo.predictor.base_predictor):
 
         Parameters
         ==========
-        config: physbo.misc.set_config
+        config: physbo.misc.SetConfig
             configuration
-        model: physbo.gp.core.model
+        model: physbo.gp.core.Model
 
         See also
         ========
-        physbo.base_predictor
+        physbo.predictor.BasePredictor
         """
-        super(predictor, self).__init__(config, model)
+        super(Predictor, self).__init__(config, model)
         self.blm = None
 
-    def fit(self, training, num_basis=None):
+    def fit(self, training, num_basis=None, comm=None):
         """
         fit model to training dataset
 
@@ -44,14 +44,16 @@ class predictor(physbo.predictor.base_predictor):
             dataset for training
         num_basis: int
             the number of basis (default: self.config.predict.num_basis)
+        comm: MPI.Comm
+            MPI communicator
         """
         if num_basis is None:
             num_basis = self.config.predict.num_basis
 
         if self.model.prior.cov.num_dim is None:
             self.model.prior.cov.num_dim = training.X.shape[1]
-        self.model.fit(training.X, training.t, self.config)
-        self.blm = self.model.export_blm(num_basis)
+        self.model.fit(training.X, training.t, self.config, comm=comm)
+        self.blm = self.model.export_blm(num_basis, comm=comm)
         self.delete_stats()
 
     def prepare(self, training):

physbo-3.0.0/src/physbo/blm/basis/__init__.py

@@ -0,0 +1,18 @@
+# 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 ._fourier import Fourier
+
+from ...misc import deprecated_warning
+
+
+def fourier(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.basis.fourier", new="physbo.blm.basis.Fourier")
+    return Fourier(*args, **kwargs)
+
+__all__ = ["Fourier"]

physbo-2.1.0/physbo/blm/basis/fourier.py → physbo-3.0.0/src/physbo/blm/basis/_fourier.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 
-class fourier:
+class Fourier:
     """
     random feature maps
     ``Psi(X; W,b) = cos[X * Wt + b] * alpha``

{physbo-2.1.0/physbo/blm/lik/_src → physbo-3.0.0/src/physbo/blm/core}/__init__.py

@@ -5,4 +5,6 @@
 # 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 .cov import cov
+from ._model import Model
+
+__all__ = ["Model"]

physbo-2.1.0/physbo/blm/core/model.py → physbo-3.0.0/src/physbo/blm/core/_model.py

@@ -7,17 +7,18 @@
 
 import numpy as np
 from .. import inf
+from ...misc.permutation_importance import get_permutation_importance
 
 
-class model:
+class Model:
     """
     Baysean Linear Model
 
     Attributes
     ==========
-    prior: physbo.blm.prior.gauss
+    prior: physbo.blm.prior.Gauss
         prior distribution of weights
-    lik: physbo.blm.lik.gauss
+    lik: physbo.blm.lik.Gauss
         kernel
     nbasis: int
         number of features in random feature map
@@ -123,7 +124,7 @@ class model:
 
         Parameters
         ==========
-        blm: physbo.blm.core.model
+        blm: physbo.blm.core.Model
             model
         w_mu: numpy.ndarray
             mean of weight
@@ -231,6 +232,40 @@ class model:
             pass
         return fcov
 
+    def get_permutation_importance(
+        self, X, t, n_perm: int, comm=None, split_features_parallel=False
+    ):
+        """
+        Calculating permutation importance of model
+
+        Parameters
+        ==========
+        X: numpy.ndarray
+            inputs
+        t: numpy.ndarray
+            target (label)
+        n_perm: int
+            number of permutations
+        comm: MPI.Comm
+            MPI communicator
+
+        Returns
+        =======
+        numpy.ndarray
+            importance_mean
+        numpy.ndarray
+            importance_std
+        """
+
+        return get_permutation_importance(
+            self,
+            X,
+            t,
+            n_perm,
+            comm=comm,
+            split_features_parallel=split_features_parallel,
+        )
+
     def _set_options(self, options):
         """
         read options
@@ -251,9 +286,9 @@ class model:
 
         Parameters
         ==========
-        prior: physbo.blm.prior.gauss
-            if None, prior.gauss(self.nbasis)
+        prior: physbo.blm.prior.Gauss
+            if None, prior.Gauss(self.nbasis)
         """
         if prior is None:
-            prior = prior.gauss(self.nbasis)
+            prior = prior.Gauss(self.nbasis)
         self.prior = prior

{physbo-2.1.0 → physbo-3.0.0/src}/physbo/blm/inf/__init__.py

@@ -6,3 +6,5 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 
 from . import exact
+
+__all__ = ["exact"]

{physbo-2.1.0 → physbo-3.0.0/src}/physbo/blm/inf/exact.py

@@ -19,7 +19,7 @@ def prepare(blm, X, t, Psi=None):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
         model
     X: numpy.ndarray
         inputs
@@ -45,7 +45,7 @@ def update_stats(blm, x, t, psi=None):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
         model
     x: numpy.ndarray
         input
@@ -78,7 +78,7 @@ def sampling(blm, w_mu=None, N=1, alpha=1.0):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
         model
     w_mu: numpy.ndarray
         mean of weight
@@ -114,7 +114,7 @@ def get_post_params_mean(blm):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
 
     Returns
     =======
@@ -129,7 +129,7 @@ def get_post_fmean(blm, X, Psi=None, w=None):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
     X: numpy.ndarray
         inputs
     Psi: numpy.ndarray
@@ -157,7 +157,7 @@ def get_post_fcov(blm, X, Psi=None, diag=True):
 
     Parameters
     ==========
-    blm: physbo.blm.core.model
+    blm: physbo.blm.core.Model
     X: numpy.ndarray
         inputs
     Psi: numpy.ndarray

physbo-3.0.0/src/physbo/blm/lik/__init__.py

@@ -0,0 +1,33 @@
+# 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 ._cov import Cov
+from ._gauss import Gauss
+from ._linear import Linear
+
+from ...misc import deprecated_warning
+
+
+def cov(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.lik.cov", new="physbo.blm.lik.Cov")
+    return Cov(*args, **kwargs)
+
+
+def gauss(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.lik.gauss", new="physbo.blm.lik.Gauss")
+    return Gauss(*args, **kwargs)
+
+
+def linear(*args, **kwargs):
+    ":meta private:"
+    deprecated_warning(old="physbo.blm.lik.linear", new="physbo.blm.lik.Linear")
+    return Linear(*args, **kwargs)
+
+
+__all__ = ["Cov", "Gauss", "Linear"]

physbo-2.1.0/physbo/blm/lik/_src/cov.py → physbo-3.0.0/src/physbo/blm/lik/_cov.py

@@ -8,7 +8,7 @@
 import numpy as np
 
 
-class cov:
+class Cov:
     """
     Covariance