Periodic Save Freq

orbitize/results.py

@@ -115,7 +115,8 @@ def save_results(self, filename):
         hf.attrs['version_number'] = self.version_number
 
         # Now add post and lnlike from the results object as datasets
-        hf.create_dataset('post', data=self.post)
+        if self.post is not None:
+            hf.create_dataset('post', data=self.post)
         # hf.create_dataset('data', data=self.data)
         if self.lnlike is not None:
             hf.create_dataset('lnlike', data=self.lnlike)
@@ -151,8 +152,12 @@ def load_results(self, filename, append=False):
             version_number = str(hf.attrs['version_number'])
         except KeyError:
             version_number = "<= 1.13"
-        post = np.array(hf.get('post'))
-        lnlike = np.array(hf.get('lnlike'))
+        post = hf.get('post')
+        if post is not None:
+            post = np.array(post)
+        lnlike = hf.get('lnlike')
+        if lnlike is not None:
+            lnlike = np.array(lnlike)
 
 
         try:

tests/test_mcmc.py

@@ -44,21 +44,23 @@ def test_mcmc_runs(num_temps=0, num_threads=1):
         }
     )
 
-    # run it a little (tests 0 burn-in steps)
-    myDriver.sampler.run_sampler(100)
-    assert myDriver.sampler.results.post.shape[0] == 100
-
-    # run it a little more
-    myDriver.sampler.run_sampler(1000, burn_steps=1)
-    assert myDriver.sampler.results.post.shape[0] == 1100
-
-    # run it a little more (tests adding to results object, and periodic saving)
+    # run it some (tests adding to results object, and periodic saving)
     output_filename = os.path.join(orbitize.DATADIR, 'test_mcmc.hdf5')
     myDriver.sampler.run_sampler(
-        400, burn_steps=1, output_filename=output_filename, periodic_save_freq=2
+        400, burn_steps=10, output_filename=output_filename, periodic_save_freq=2
     )
 
-    # test results object exists and has 2100*100 steps
+    # TODO: Add test for restarting from saved results when burn-in is interrupted (i.e. no regular steps have been done) 
+
+    # run it a little more (tests 0 burn-in steps)
+    myDriver.sampler.run_sampler(100)
+    assert myDriver.sampler.results.post.shape[0] == 500
+
+    # run it a little more and save
+    myDriver.sampler.run_sampler(1000, burn_steps=1, output_filename=output_filename, periodic_save_freq=2)
+    assert myDriver.sampler.results.post.shape[0] == 1500
+
+    # test results object exists and has 1500*100 steps
     assert os.path.exists(output_filename)
     saved_results = results.Results()
     saved_results.load_results(output_filename)