Merge branch '345-resume-file-removed-before-result-file-output' into 'master'

Resolve "Resume file removed before result file output"

Closes #345

See merge request !417

bilby/core/result.py

@@ -412,12 +412,17 @@ class Result(object):
             default=False
         outdir: str, optional
             Path to the outdir. Default is the one stored in the result object.
-        extension: str, optional {json, hdf5}
-            Determines the method to use to store the data
+        extension: str, optional {json, hdf5, True}
+            Determines the method to use to store the data (if True defaults
+            to json)
         gzip: bool, optional
             If true, and outputing to a json file, this will gzip the resulting
             file and add '.gz' to the file extension.
         """
+
+        if extension is True:
+            extension = "json"
+
         outdir = self._safe_outdir_creation(outdir, self.save_to_file)
         file_name = result_file_name(outdir, self.label, extension, gzip)
 

bilby/core/sampler/__init__.py

@@ -167,6 +167,10 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
     else:
         result = sampler.run_sampler()
 
+    # Initial save of the sampler in case of failure in post-processing
+    if save:
+        result.save_to_file(extension=save, gzip=gzip)
+
     end_time = datetime.datetime.now()
     result.sampling_time = (end_time - start_time).total_seconds()
     logger.info('Sampling time: {}'.format(end_time - start_time))
@@ -188,12 +192,11 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
 
     result.samples_to_posterior(likelihood=likelihood, priors=result.priors,
                                 conversion_function=conversion_function)
-    if save == 'hdf5':
-        result.save_to_file(extension='hdf5')
-        logger.info("Results saved to {}/".format(outdir))
-    elif save:
-        result.save_to_file(gzip=gzip)
-        logger.info("Results saved to {}/".format(outdir))
+
+    if save:
+        # The overwrite here ensures we overwrite the initially stored data
+        result.save_to_file(overwrite=True, extension=save, gzip=gzip)
+
     if plot:
         result.plot_corner()
     logger.info("Summary of results:\n{}".format(result))

bilby/core/sampler/dynesty.py

@@ -189,7 +189,10 @@ class Dynesty(NestedSampler):
         if self.kwargs["verbose"]:
             print("")
 
-        # self.result.sampler_output = out
+        dynesty_result = "{}/{}_dynesty.pickle".format(self.outdir, self.label)
+        with open(dynesty_result, 'wb') as file:
+            pickle.dump(out, file)
+
         weights = np.exp(out['logwt'] - out['logz'][-1])
         nested_samples = DataFrame(
             out.samples, columns=self.search_parameter_keys)