Minor adjustments to dynesty

1) Print the progress to STDOUT rather than STDERR - this will keep the
log file clean
2) Add SIGALRM to checkpoint signals
3) Change some logging messages to help diagnose checkpointing issues
4) Remove write current state when it has just been read
5) Improve documentation on how the periodic/reflective boundaries are
implemented

CHANGELOG.md

@@ -13,6 +13,7 @@ Periodic boundaries are supported as before.
 Reflective boundaries are supported in `dynesty` and `cpnest`.  
 - Added state plotting for dynesty. Use `check_point_plot=True` in the `run_sampler` 
 function to create trace plots during the dynesty checkpoints
+- Dynesty now prints the progress to STDOUT rather than STDERR
 
 ### Removed
 -

bilby/core/sampler/dynesty.py

@@ -119,6 +119,7 @@ class Dynesty(NestedSampler):
 
         signal.signal(signal.SIGTERM, self.write_current_state_and_exit)
         signal.signal(signal.SIGINT, self.write_current_state_and_exit)
+        signal.signal(signal.SIGALRM, self.write_current_state_and_exit)
 
     @property
     def sampler_function_kwargs(self):
@@ -181,8 +182,8 @@ class Dynesty(NestedSampler):
             niter, key, logz, logzerr, delta_logz, dlogz)
 
         # Printing.
-        sys.stderr.write(print_str)
-        sys.stderr.flush()
+        sys.stdout.write(print_str)
+        sys.stdout.flush()
 
     def _apply_dynesty_boundaries(self):
         if self.kwargs['periodic'] is None:
@@ -294,12 +295,12 @@ class Dynesty(NestedSampler):
             state is mostly written back to disk.
         """
 
-        logger.debug("Reading resume file {}".format(self.resume_file))
+        logger.info("Reading resume file {}".format(self.resume_file))
 
         if os.path.isfile(self.resume_file):
             with open(self.resume_file, 'rb') as file:
                 saved = pickle.load(file)
-            logger.debug(
+            logger.info(
                 "Succesfuly read resume file {}".format(self.resume_file))
 
             self.sampler.saved_u = list(saved['unit_cube_samples'])
@@ -325,8 +326,6 @@ class Dynesty(NestedSampler):
             self.sampler.live_bound = saved['live_bound']
             self.sampler.live_it = saved['live_it']
             self.sampler.added_live = saved['added_live']
-            if continuing:
-                self.write_current_state(plot=False)
             return True
 
         else:
@@ -452,11 +451,13 @@ class Dynesty(NestedSampler):
 
         Notes
         -----
-        Since dynesty allows periodic parameters to wander outside the unit
-        We also allow parameters with reflective boundaries to wander outside
+        Since dynesty allows periodic parameters to wander outside the unit,
+        here we transform them depending of if they should be periodic or
+        reflective. For reflective boundaries, theta < 0 you shift to |theta|
+        and when theta > 1 you return 2 - theta. For periodic boundaries,
+        if theta < 0, you shift to 1-|theta| and when theta > 1 you shift to
+        |theta| - 1 (i.e. wrap around).
 
-        The logic ensures that when theta < 0 you shift to |theta| and when
-        theta > 1 you return 2 - theta
         """
         theta[self._periodic] = np.mod(theta[self._periodic], 1)
         theta_ref = theta[self._reflective]