physbo 2.0.0__tar.gz → 2.0.2__tar.gz

{physbo-2.0.0 → physbo-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: physbo
-Version: 2.0.0
+Version: 2.0.2
 Summary: optimization tool for PHYSics based on Bayesian Optimization
 Home-page: https://github.com/issp-center-dev/PHYSBO
 Author: PHYSBO developers
@@ -18,7 +18,7 @@ A standard implementation (e.g., scikit-learn), however, can accommodate only sm
 PHYSBO is highly scalable due to an efficient protocol that employs Thompson sampling, random feature maps, one-rank Cholesky update and automatic hyperparameter tuning. Technical features are described in [COMBO's document](https://github.com/tsudalab/combo/blob/master/docs/combo_document.pdf) and [PHYSBO's report](https://doi.org/10.1016/j.cpc.2022.108405) (open access).
 PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for academic use.
 
-## Document
+## Documentation
 
 - Stable (master branch)
     - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
@@ -27,7 +27,7 @@ PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for aca
     - [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)
 
-## Required Packages
+## Dependencies
 
 - Python >= 3.6
     - No longer tested with Python 3.6
@@ -74,7 +74,9 @@ python3 -m pip uninstall physbo
 
 ## Usage
 
-['examples/simple.py'](https://github.com/issp-center-dev/PHYSBO/examples/simple.py) is a simple example.
+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
 

{physbo-2.0.0 → physbo-2.0.2}/README.md

@@ -5,7 +5,7 @@ A standard implementation (e.g., scikit-learn), however, can accommodate only sm
 PHYSBO is highly scalable due to an efficient protocol that employs Thompson sampling, random feature maps, one-rank Cholesky update and automatic hyperparameter tuning. Technical features are described in [COMBO's document](https://github.com/tsudalab/combo/blob/master/docs/combo_document.pdf) and [PHYSBO's report](https://doi.org/10.1016/j.cpc.2022.108405) (open access).
 PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for academic use.
 
-## Document
+## Documentation
 
 - Stable (master branch)
     - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
@@ -14,7 +14,7 @@ PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for aca
     - [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)
 
-## Required Packages
+## Dependencies
 
 - Python >= 3.6
     - No longer tested with Python 3.6
@@ -61,7 +61,9 @@ python3 -m pip uninstall physbo
 
 ## Usage
 
-['examples/simple.py'](https://github.com/issp-center-dev/PHYSBO/examples/simple.py) is a simple example.
+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
 

{physbo-2.0.0 → physbo-2.0.2}/physbo/__init__.py

@@ -14,4 +14,4 @@ from . import predictor
 from .predictor import base_predictor
 from .variable import variable
 
-__version__ = "2.0.0"
+__version__ = "2.0.2"

{physbo-2.0.0 → physbo-2.0.2}/physbo/search/discrete/policy.py

@@ -138,11 +138,15 @@ class policy:
             time_run_simulator=time_run_simulator,
         )
         self.training.add(X=X, t=t, Z=Z)
-        local_index = np.searchsorted(self.actions, action)
-        local_index = local_index[
-            np.take(self.actions, local_index, mode="clip") == action
-        ]
-        self.actions = self._delete_actions(local_index)
+
+        # remove the selected actions from the list of candidates if exists
+        if len(self.actions) > 0:
+            local_index = np.searchsorted(self.actions, action)
+            local_index = local_index[
+                np.take(self.actions, local_index, mode="clip") == action
+            ]
+            self.actions = self._delete_actions(local_index)
+
         if self.new_data is None:
             self.new_data = variable(X=X, t=t, Z=Z)
         else:
@@ -690,7 +694,13 @@ class policy:
                 self.predictor = pickle.load(f)
 
         N = self.history.total_num_search
-        self.actions = self._delete_actions(self.history.chosen_actions[:N])
+
+        visited = self.history.chosen_actions[:N]
+        local_index = np.searchsorted(self.actions, visited)
+        local_index = local_index[
+            np.take(self.actions, local_index, mode="clip") == visited
+        ]
+        self.actions = self._delete_actions(local_index)
 
     def export_predictor(self):
         """

{physbo-2.0.0 → physbo-2.0.2}/physbo/search/discrete/results.py

@@ -183,8 +183,8 @@ class history:
 
         """
         data = np.load(filename)
-        M = data["num_runs"]
-        N = data["total_num_search"]
+        M = int(data["num_runs"])
+        N = int(data["total_num_search"])
         self.num_runs = M
         self.total_num_search = N
         self.fx[0:N] = data["fx"]

{physbo-2.0.0 → physbo-2.0.2}/physbo/search/discrete_multi/policy.py

@@ -58,7 +58,7 @@ class policy(discrete.policy):
                 msg = "ERROR: len(initial_data[0]) != initial_data[1].shape[0]"
                 raise RuntimeError(msg)
             self.write(actions, fs)
-            self.actions = sorted(list(set(self.actions) - set(actions)))
+            self.actions = np.array(sorted(list(set(self.actions) - set(actions))))
 
         if comm is None:
             self.mpicomm = None
@@ -106,11 +106,14 @@ class policy(discrete.policy):
             else:
                 self.new_data_list[i].add(X=X, t=t[:, i], Z=Z)
             self.training_list[i].add(X=X, t=t[:, i], Z=Z)
-        local_index = np.searchsorted(self.actions, action)
-        local_index = local_index[
-            np.take(self.actions, local_index, mode="clip") == action
-        ]
-        self.actions = self._delete_actions(local_index)
+        
+        # remove action from candidates if exists
+        if len(self.actions) > 0:
+            local_index = np.searchsorted(self.actions, action)
+            local_index = local_index[
+                np.take(self.actions, local_index, mode="clip") == action
+            ]
+            self.actions = self._delete_actions(local_index)
 
     def _model(self, i):
         training = self.training_list[i]
@@ -487,7 +490,13 @@ class policy(discrete.policy):
             self.load_predictor_list(file_predictor_list)
 
         N = self.history.total_num_search
-        self.actions = self._delete_actions(self.history.chosen_actions[:N])
+
+        visited = self.history.chosen_actions[:N]
+        local_index = np.searchsorted(self.actions, visited)
+        local_index = local_index[
+            np.take(self.actions, local_index, mode="clip") == visited
+        ]
+        self.actions = self._delete_actions(local_index)
 
     def save_predictor_list(self, file_name):
         with open(file_name, "wb") as f:

{physbo-2.0.0 → physbo-2.0.2}/physbo/search/discrete_multi/results.py

@@ -118,8 +118,8 @@ class history(object):
         with open(filename, "rb") as f:
             data = pickle.load(f)
 
-        M = data["num_runs"]
-        N = data["total_num_search"]
+        M = int(data["num_runs"])
+        N = int(data["total_num_search"])
         self.num_runs = M
         self.total_num_search = N
         self.fx[0:N] = data["fx"]

{physbo-2.0.0 → physbo-2.0.2}/physbo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: physbo
-Version: 2.0.0
+Version: 2.0.2
 Summary: optimization tool for PHYSics based on Bayesian Optimization
 Home-page: https://github.com/issp-center-dev/PHYSBO
 Author: PHYSBO developers
@@ -18,7 +18,7 @@ A standard implementation (e.g., scikit-learn), however, can accommodate only sm
 PHYSBO is highly scalable due to an efficient protocol that employs Thompson sampling, random feature maps, one-rank Cholesky update and automatic hyperparameter tuning. Technical features are described in [COMBO's document](https://github.com/tsudalab/combo/blob/master/docs/combo_document.pdf) and [PHYSBO's report](https://doi.org/10.1016/j.cpc.2022.108405) (open access).
 PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for academic use.
 
-## Document
+## Documentation
 
 - Stable (master branch)
     - [English](https://issp-center-dev.github.io/PHYSBO/manual/master/en/index.html)
@@ -27,7 +27,7 @@ PHYSBO was developed based on [COMBO](https://github.com/tsudalab/combo) for aca
     - [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)
 
-## Required Packages
+## Dependencies
 
 - Python >= 3.6
     - No longer tested with Python 3.6
@@ -74,7 +74,9 @@ python3 -m pip uninstall physbo
 
 ## Usage
 
-['examples/simple.py'](https://github.com/issp-center-dev/PHYSBO/examples/simple.py) is a simple example.
+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
 

physbo-2.0.2/pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel", "cython", "numpy<2.0"]
+build-backend = "setuptools.build_meta"

{physbo-2.0.0 → physbo-2.0.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = physbo
-version = 2.0.0
+version = 2.0.2
 description = optimization tool for PHYSics based on Bayesian Optimization
 long_description = file: README.md
 long_description_content_type = text/markdown

physbo-2.0.0/pyproject.toml

@@ -1,3 +0,0 @@
-[build-system]
-requires = ["setuptools", "wheel", "cython", "numpy<1.20; python_version<'3.10'", "numpy; python_version>='3.10'"]
-build-backend = "setuptools.build_meta"