physbo 2.0.2__tar.gz → 2.1.0__tar.gz

{physbo-2.0.2 → physbo-2.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: physbo
-Version: 2.0.2
+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

{physbo-2.0.2 → physbo-2.1.0}/physbo/__init__.py

@@ -14,4 +14,4 @@ from . import predictor
 from .predictor import base_predictor
 from .variable import variable
 
-__version__ = "2.0.2"
+__version__ = "2.1.0"

{physbo-2.0.2 → physbo-2.1.0}/physbo/blm/core/model.py

@@ -218,13 +218,15 @@ class model:
         Returns
         =======
         numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in X.
 
         See also
         ========
         physbo.blm.inf.exact.get_post_fcov
         """
         if self.method == "exact":
-            fcov = inf.exact.get_post_fcov(self, X, Psi, diag=True)
+            fcov = inf.exact.get_post_fcov(self, X, Psi, diag=diag)
         else:
             pass
         return fcov

{physbo-2.0.2 → physbo-2.1.0}/physbo/blm/inf/exact.py

@@ -170,6 +170,8 @@ def get_post_fcov(blm, X, Psi=None, diag=True):
     Returns
     =======
     numpy.ndarray
+        Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+        where num_points is the number of points in X.
     """
     if Psi is None:
         Psi = blm.lik.linear.basis.get_basis(X)

{physbo-2.0.2 → physbo-2.1.0}/physbo/blm/predictor.py

@@ -101,12 +101,14 @@ class predictor(physbo.predictor.base_predictor):
         Returns
         =======
         numpy.ndarray
+            Returned shape is (num_points),
+            where num_points is the number of points in test.
         """
         if self.blm.stats is None:
             self.prepare(training)
         return self.blm.get_post_fmean(test.X, test.Z)
 
-    def get_post_fcov(self, training, test):
+    def get_post_fcov(self, training, test, diag=True):
         """
         calculates posterior variance-covariance matrix of model
 
@@ -116,14 +118,17 @@ class predictor(physbo.predictor.base_predictor):
             training dataset. If already trained, the model does not use this.
         test: physbo.variable
             inputs
-
+        diag: bool
+            If true, only variances (diagonal elements) are returned.
         Returns
         =======
         numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in test.
         """
         if self.blm.stats is None:
             self.prepare(training)
-        return self.blm.get_post_fcov(test.X, test.Z)
+        return self.blm.get_post_fcov(test.X, test.Z, diag)
 
     def get_post_params(self, training, test):
         """

{physbo-2.0.2 → physbo-2.1.0}/physbo/gp/core/model.py

@@ -269,11 +269,13 @@ class model:
         params: numpy.ndarray
             Parameters
         diag: bool
-            If X is the diagonalization matrix, true.
+            If true, only variances (diagonal elements) are returned.
 
         Returns
         -------
-        physbo.gp.inf.exact.get_post_fcov
+        numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in X.
 
         """
         if params is None:

{physbo-2.0.2 → physbo-2.1.0}/physbo/gp/core/prior.py

@@ -19,7 +19,7 @@ class prior:
         ----------
         mean: numpy.ndarray
             mean values of prior
-        cov: numpy.ndarray
+        cov: physbo.gp.cov.gauss
             covariance matrix of priors
         """
         self.mean = mean
@@ -94,10 +94,13 @@ class prior:
         params: numpy.ndarray
            Parameters.
         diag: bool
-            If X is the diagonalization matrix, true.
+            If true, only variances (diagonal elements) are returned.
+
         Returns
         -------
         numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in X.
         """
         if params is None:
             params = np.copy(self.params)

{physbo-2.0.2 → physbo-2.1.0}/physbo/gp/cov/gauss.py

@@ -149,12 +149,14 @@ class gauss:
             Parameters
 
         diag: bool
-            If X is the diagonalization matrix, true.
+            If true, only variances (diagonal elements) are returned.
 
         Returns
         -------
         G: numpy.ndarray
             covariant matrix
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in X.
         """
         params, width, scale = self.prepare(params)
         scale2 = scale**2

{physbo-2.0.2 → physbo-2.1.0}/physbo/gp/inf/exact.py

@@ -203,10 +203,13 @@ def get_post_fcov(gp, X, Z, params=None, diag=True):
     params: numpy.ndarray
         Parameters.
     diag: bool
-        If X is the diagonalization matrix, true.
+        If true, only variances (diagonal elements) are returned.
+
     Returns
     -------
         numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in X.
     """
 
     lik_params, prior_params = gp.decomp_params(params)

{physbo-2.0.2 → physbo-2.1.0}/physbo/gp/predictor.py

@@ -115,10 +115,13 @@ class predictor(physbo.predictor.base_predictor):
         test: physbo.variable
             inputs
         diag: bool
-            Diagonlization flag in physbo.exact.get_post_fcov function.
+            If true, only variances (diagonal elements) are returned.
+
         Returns
         -------
         numpy.ndarray
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false,
+            where num_points is the number of points in test.
 
         """
         if self.model.stats is None:

{physbo-2.0.2 → physbo-2.1.0}/physbo/search/discrete/policy.py

@@ -348,7 +348,21 @@ class policy:
         print("         before calling {}.".format(method_name))
 
     def get_post_fmean(self, xs):
-        """Calculate mean value of predictor (post distribution)"""
+        """
+        Calculate mean value of predictor (post distribution)
+
+        Parameters
+        ----------
+        xs: physbo.variable or np.ndarray
+            input parameters to calculate mean value
+            shape is (num_points, num_parameters)
+
+        Returns
+        -------
+        fmean: numpy.ndarray
+            Mean value of the post distribution.
+            Returned shape is (num_points).
+        """
         X = self._make_variable_X(xs)
         if self.predictor is None:
             self._warn_no_predictor("get_post_fmean()")
@@ -360,18 +374,34 @@ class policy:
             self._update_predictor()
             return self.predictor.get_post_fmean(self.training, X)
 
-    def get_post_fcov(self, xs):
-        """Calculate covariance of predictor (post distribution)"""
+    def get_post_fcov(self, xs, diag=True):
+        """
+        Calculate covariance of predictor (post distribution)
+
+        Parameters
+        ----------
+        xs: physbo.variable or np.ndarray
+            input parameters to calculate covariance
+            shape is (num_points, num_parameters)
+        diag: bool
+            If true, only variances (diagonal elements) are returned.
+
+        Returns
+        -------
+        fcov: numpy.ndarray
+            Covariance matrix of the post distribution.
+            Returned shape is (num_points) if diag=true, (num_points, num_points) if diag=false.
+        """
         X = self._make_variable_X(xs)
         if self.predictor is None:
             self._warn_no_predictor("get_post_fcov()")
             predictor = gp_predictor(self.config)
             predictor.fit(self.training, 0)
             predictor.prepare(self.training)
-            return predictor.get_post_fcov(self.training, X)
+            return predictor.get_post_fcov(self.training, X, diag)
         else:
             self._update_predictor()
-            return self.predictor.get_post_fcov(self.training, X)
+            return self.predictor.get_post_fcov(self.training, X, diag)
 
     def get_score(
         self,

{physbo-2.0.2 → physbo-2.1.0}/physbo/search/discrete_multi/policy.py

@@ -294,6 +294,23 @@ class policy(discrete.policy):
         return np.array(chosen_actions)
 
     def get_post_fmean(self, xs):
+        """
+        Calculate mean value of predictors (post distribution)
+
+        Parameters
+        ----------
+        xs: physbo.variable or np.ndarray
+            input parameters to calculate covariance
+            shape is (num_points, num_parameters)
+        diag: bool
+            If true, only variances (diagonal elements) are returned.
+
+        Returns
+        -------
+        fcov: numpy.ndarray
+            Covariance matrix of the post distribution.
+            Returned shape is (num_points, num_objectives).
+        """
         if self.predictor_list == [None] * self.num_objectives:
             self._warn_no_predictor("get_post_fmean()")
             predictor_list = []
@@ -312,7 +329,24 @@ class policy(discrete.policy):
         ]
         return np.array(fmean).T
 
-    def get_post_fcov(self, xs):
+    def get_post_fcov(self, xs, diag=True):
+        """
+        Calculate covariance of predictors (post distribution)
+
+        Parameters
+        ----------
+        xs: physbo.variable or np.ndarray
+            input parameters to calculate covariance
+            shape is (num_points, num_parameters)
+        diag: bool
+            If true, only variances (diagonal elements) are returned.
+
+        Returns
+        -------
+        fcov: numpy.ndarray
+            Covariance matrix of the post distribution.
+            Returned shape is (num_points, num_objectives) if diag=true, (num_points, num_points, num_objectives) if diag=false.
+        """
         if self.predictor_list == [None] * self.num_objectives:
             self._warn_no_predictor("get_post_fcov()")
             predictor_list = []
@@ -326,10 +360,14 @@ class policy(discrete.policy):
             predictor_list = self.predictor_list[:]
         X = self._make_variable_X(xs)
         fcov = [
-            predictor.get_post_fcov(training, X)
+            predictor.get_post_fcov(training, X, diag)
             for predictor, training in zip(predictor_list, self.training_list)
         ]
-        return np.array(fcov).T
+        arr = np.array(fcov)
+        if diag:
+            return arr.T
+        else:
+            return np.einsum("nij->ijn", arr)
 
     def get_score(
         self,

{physbo-2.0.2 → physbo-2.1.0}/physbo.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: physbo
-Version: 2.0.2
+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

{physbo-2.0.2 → physbo-2.1.0}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = physbo
-version = 2.0.2
+version = 2.1.0
 description = optimization tool for PHYSics based on Bayesian Optimization
 long_description = file: README.md
 long_description_content_type = text/markdown