eryn 1.2.2__tar.gz → 1.2.4__tar.gz

{eryn-1.2.2 → eryn-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: eryn
-Version: 1.2.2
+Version: 1.2.4
 Summary: Eryn: an omni-MCMC sampling package.
 Author: Michael Katz
 Author-email: Michael Katz <mikekatz04@gmail.com>

{eryn-1.2.2 → eryn-1.2.4}/pyproject.toml

@@ -8,7 +8,7 @@ requires = [
 [project]
 name = "eryn" #@NAMESUFFIX@
 
-version = "1.2.2"
+version = "1.2.4"
 
 description = "Eryn: an omni-MCMC sampling package."
 

{eryn-1.2.2 → eryn-1.2.4}/src/eryn/backends/backend.py

@@ -703,8 +703,11 @@ class Backend(object):
             "thermo",
             "ti",
         ]:
-            logls = np.mean(logls_all, axis=(0, -1))
-            logZ, dlogZ = thermodynamic_integration_log_evidence(betas, logls)
+            logls = logls_all.copy()
+            logls[~np.isfinite(logls)] = np.nan
+            meanlogls = np.nanmean(logls, axis=(0, -1))
+            logZ, dlogZ = thermodynamic_integration_log_evidence(betas, meanlogls)
+            
         elif method.lower() in [
             "stepping stone",
             "ss",

{eryn-1.2.2 → eryn-1.2.4}/src/eryn/ensemble.py

@@ -1208,6 +1208,9 @@ class EnsembleSampler(object):
                 # vectorized because everything is rectangular (no groups to indicate model difference)
                 prior_out += prior_out_temp.sum(axis=-1)
 
+        if np.any(np.isnan(prior_out)):
+            raise ValueError("The prior function is returning Nan.")
+        
         return prior_out
 
     def compute_log_like(
@@ -1493,8 +1496,9 @@ class EnsembleSampler(object):
             ll[inds_fix_zeros] = self.fill_zero_leaves_val
 
             # deal with blobs
-            blobs_out = np.zeros((nwalkers_all, results.shape[1] - 1))
-            blobs_out[unique_groups] = results[:, 1:]
+            _blobs_out = np.zeros((nwalkers_all, results.shape[1] - 1))
+            _blobs_out[unique_groups] = results[:, 1:]
+            blobs_out = _blobs_out.reshape(ntemps, nwalkers)
 
         elif results.dtype == "object":
             # TODO: check blobs and add this capability
@@ -1531,6 +1535,9 @@ class EnsembleSampler(object):
                                 for key in branch_supps_in_2[name_i]
                             }
 
+        if np.any(np.isnan(ll)):
+            raise ValueError("The likelihood function is returning Nan.")
+        
         # return Likelihood and blobs
         return ll.reshape(ntemps, nwalkers), blobs_out
 

{eryn-1.2.2 → eryn-1.2.4}/src/eryn/moves/gaussian.py

@@ -137,7 +137,12 @@ class _isotropic_proposal(object):
     def __init__(self, scale, factor, mode):
         self.index = 0
         self.scale = scale
-        self.invscale = np.linalg.inv(np.linalg.cholesky(scale))
+        
+        if isinstance(scale, float):
+            self.invscale = 1. / scale
+        else:
+            self.invscale = np.linalg.inv(np.linalg.cholesky(scale))
+
         if factor is None:
             self._log_factor = None
         else:

{eryn-1.2.2 → eryn-1.2.4}/src/eryn/utils/utility.py

@@ -237,11 +237,12 @@ def stepping_stone_log_evidence(betas, logls, block_len=50, repeats=100):
 
     def calculate_stepping_stone(betas, logls):
         n = logls.shape[0]
-        delta_betas = betas[1:] - betas[:-1]
         n_T = betas.shape[0]
-        log_ratio = logsumexp(delta_betas * logls[:, :-1], axis=0) - np.log(n)
+        delta_betas = betas[1:] - betas[:-1]
+        throwaways = np.any(~np.isfinite(logls), axis=1) # a safeguard against non-finite entries
+        log_ratio = logsumexp(delta_betas * logls[~throwaways, :-1], axis=0) - (n_T - 1.0)*np.log(n - np.sum(throwaways))
         return np.sum(log_ratio), log_ratio
-
+    
     # make sure they are the same length
     if len(betas) != logls.shape[1]:
         raise ValueError(