hoppMCMC 2.2.0__tar.gz → 2.2.1__tar.gz

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1}/NEWS.txt

@@ -1,14 +1,13 @@
 News
 ====
 
-2.2.0
+2.2.1
 -----
 
 *Release date: 13-Jul-2026*
 
 inferFun is now updated to include ABCModel and inferABCModels as the main ABC-SMC inference tools
 
-2.1.0
 1.2.1
 1.2
 1.1 *13-Sep-2018*

{hoppmcmc-2.2.0/src/hoppMCMC.egg-info → hoppmcmc-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoppMCMC
-Version: 2.2.0
+Version: 2.2.1
 Summary: An adaptive basin-hopping Markov-chain Monte Carlo algorithm for Bayesian optimisation
 Author: Kamil Erguler
 Author-email: Kamil Erguler <kerguler@gmail.com>

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hoppMCMC"
-version = "2.2.0"
+version = "2.2.1"
 description = "An adaptive basin-hopping Markov-chain Monte Carlo algorithm for Bayesian optimisation"
 authors = [{ name = "Kamil Erguler", email = "kerguler@gmail.com" }]
 license = { text = "GPLv3" }

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = hoppMCMC
-version = 2.2.0
+version = 2.2.1
 description = Adaptive basin-hopping MCMC and ABC inference with MPI support
 author = Kamil Erguler
 author_email = k.erguler@cyi.ac.cy

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1}/src/hoppMCMC/__init__.py

@@ -6,7 +6,7 @@ This is the python (v2.7) implementation of the hoppMCMC algorithm aiming to ide
 
 """
 
-__version__ = '2.2.0'
+__version__ = '2.2.1'
 
 import os
 import sys

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1/src/hoppMCMC.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoppMCMC
-Version: 2.2.0
+Version: 2.2.1
 Summary: An adaptive basin-hopping Markov-chain Monte Carlo algorithm for Bayesian optimisation
 Author: Kamil Erguler
 Author-email: Kamil Erguler <kerguler@gmail.com>

{hoppmcmc-2.2.0 → hoppmcmc-2.2.1}/src/inferFun/__init__.py

@@ -488,6 +488,52 @@ class inferABCModels:
         # Add small jitter to avoid singular covariance problems.
         kernel = kernel + numpy.eye(kernel.shape[0]) * self.jitter
 
+        eigvals, eigvecs = numpy.linalg.eigh(kernel)
+        if numpy.any(eigvals <= 0):
+            raise ValueError(
+                f"Kernel is not positive definite for model {model_id} "
+                f"({self.model_names[model_id]}), even after jitter. "
+                f"Eigenvalues={eigvals}\nKernel:\n{kernel}"
+            )
+
+        condition_number = eigvals[-1] / eigvals[0]
+        if condition_number > 1e10 and self.verbose:
+            smallest = numpy.argmin(eigvals)
+            bad_direction = eigvecs[:, smallest]
+            culprit_order = numpy.argsort(numpy.abs(bad_direction))[::-1]
+            print(
+                f"Warning: near-singular kernel for model {model_id} "
+                f"({self.model_names[model_id]}). "
+                f"condition_number={condition_number:g}, "
+                f"eigenvalues={eigvals}",
+                flush=True
+            )
+            print("  Dominant dimensions in smallest-eigenvalue direction:", flush=True)
+            for k in culprit_order:
+                print(
+                    f"    kernel dim {k}, parameter index {inferpar[k]}, "
+                    f"loading={bad_direction[k]:g}, "
+                    f"variance={kernel[k, k]:g}",
+                    flush=True
+                )
+
+        sd = numpy.sqrt(numpy.diag(kernel))
+        corr = kernel / numpy.outer(sd, sd)
+        if self.verbose:
+            print("  correlation matrix:", flush=True)
+            print(corr, flush=True)
+
+            high = numpy.where(numpy.abs(corr) > 0.98)
+
+            for a, b in zip(high[0], high[1]):
+                if a < b:
+                    print(
+                        f"  high correlation: kernel dims {a}-{b}, "
+                        f"parameter indices {inferpar[a]}-{inferpar[b]}, "
+                        f"corr={corr[a, b]:g}",
+                        flush=True
+                    )
+
         return multivariate_normal.logpdf(x_inf, mean=mean_inf, cov=kernel, allow_singular=False)
 
     def calc_weights(self, mat_new, mat_old, kernels):