update installation instructions

Author: thorstenwagner

docs/changes.rst

@@ -1,11 +1,12 @@
 Changes
 =======
 
-Version 0.2.2 (upcoming)
+Version 0.3.0 (upcoming)
 *************
 
 * Scale heatmaps to the same size as the tomogram, to make them overlay easily. Additionally, make them optional (--write_heatmaps) as they require some space
 * Write Relion 3 STAR files as they are required for WARP (Thanks Tom Dendooven)
+* Reference refinement deactivated by default.
 
 Version 0.2.1
 *************

tomotwin/modules/inference/argparse_map_ui.py

@@ -403,7 +403,7 @@ def run(self, args=None) -> None:
         self.output_pth = args.output
         if "distance" in sys.argv[1]:
             self.mode = MapMode.DISTANCE
-            self.skip_refinement = args.skip_refinement
+            self.skip_refinement = not args.refine
 
     def get_map_configuration(self) -> MapConfiguration:
         conf = MapConfiguration(
@@ -437,10 +437,10 @@ def create_distance_parser(parser):
         )
 
         parser.add_argument(
-            "--skip_refinement",
+            "--refine",
             action='store_true',
             default=False,
-            help="Skip the reference refinement",
+            help="Do reference refinement",
         )
 
         parser.add_argument(