Exiting before discarding Phase1 samples if phase 3 not meant to be run

Codes/main.py

@@ -1203,6 +1203,14 @@ if __name__ == '__main__':
 
 
     if not(phase3_ongoing):
+        # Check whether user only wants to run Phases I and II,
+        # in which case we don't discard Phase I samples yet otherwise
+        # an empty file will be saved and the future load will see
+        # sampler.samples = [] which will bug the derivations of scales
+        # from the covariance matrix
+        if n_traj_already_run == sampler.n_traj_fit:
+            cut.logger.info(f"Only Phase I and II were asked to be run as n_traj_fit = {sampler.n_traj_fit}. Quitting here.")
+            sys.exit()
         cut.logger.info("----------------------------------------------------------------------------")
         cut.logger.info("PHASE 2.3 : SCALES")
         old_scales = sampler.scales.copy()