Merge pull request #19 from antcc/main

Minor bug fixes
mikekatz04 · Aug 26, 2024 · 5b55f9d · 5b55f9d
2 parents 494f716 + 02a9d8f
commit 5b55f9d
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Showing 3 changed files with 4 additions and 13 deletions.
diff --git a/eryn/backends/backend.py b/eryn/backends/backend.py
@@ -741,7 +741,7 @@ def get_gelman_rubin_convergence_diagnostic(
                 if chains.shape[2] == 1:
                     # If no multiple leaves, we squeeze and transpose to the
                     # right shape to pass to the psrf function, which is  (nwalkers, nsamples, ndim)
-                    chains_in = chains.squeeze().transpose((1, 0, 2))
+                    chains_in = chains.squeeze(axis=2).transpose((1, 0, 2))
                 else:
                     # Project onto the model dim all chains [in case of RJ and multiple leaves per branch]
                     inds = self.get_inds(discard=discard, thin=thin)[branch][

diff --git a/eryn/ensemble.py b/eryn/ensemble.py
@@ -1020,6 +1020,8 @@ def sample(
                         )
 
                     # update after diagnostic and stopping check
+                    # if updating and using burn_in, need to make sure it does not use
+                    # previous chain samples since they are not stored.
                     if (
                         self.update_iterations > 0
                         and self.update_fn is not None
@@ -1068,9 +1070,6 @@ def run_mcmc(
                 )
             initial_state = self._previous_state
 
-        # setup thin_by info
-        thin_by = 1 if "thin_by" not in kwargs else kwargs["thin_by"]
-
         # run burn in
         if burn is not None and burn != 0:
             # prepare kwargs that relate to burn
@@ -1079,14 +1078,6 @@ def run_mcmc(
             burn_kwargs["thin_by"] = 1
             i = 0
             for results in self.sample(initial_state, iterations=burn, **burn_kwargs):
-                # if updating and using burn_in, need to make sure it does not use
-                # previous chain samples since they are not stored.
-                if (
-                    self.update_iterations > 0
-                    and self.update_fn is not None
-                    and (i + 1) % (self.update_iterations * thin_by) == 0
-                ):
-                    self.update_fn(i, results, self)
                 i += 1
 
             # run post-burn update

diff --git a/eryn/moves/combine.py b/eryn/moves/combine.py
@@ -45,7 +45,7 @@ def accepted(self, accepted):
         # set the accepted arrays for all moves
         assert isinstance(accepted, np.ndarray)
         for move in self.moves:
-            move.accepted = accepted
+            move.accepted = accepted.copy()
 
     @property
     def acceptance_fraction(self):