Merge branch 'master' into dev

doc/source/user_guide/new_v2.rst

@@ -12,11 +12,11 @@
 What's new in MacSyFinder v2?
 *****************************
 
-=======
-V 2.1.x
-=======
+======
+master
+======
 
-features
+Features
 ========
 
 Support of *gziped* files
@@ -27,21 +27,21 @@ It will uncompress them on the fly.
 The compressed files must end with the *.gz* extension.
 For the `hmmsearch` step You need to have `gunzip` installed on your system for this to work.
 
-
-=======
-V 2.1.2
-=======
-
+search engine
+-------------
 A group of hits that respect the distance constraints but each hit represent the same
 gene on the model, is **not** considered as a *cluster*.
 
 A group of hits that respect the distance constraints but all hits
 represent a Neutral gene in model, is **not** considered as a *cluster*.
 
+timeout improvement
+-------------------
 If a replicon is skipped due to timeout during best_solution phase.
 The results corresponding to this replicon are not produced,
 but a warning indicating that msf skip this replicon appear in outputs.
 
+
 =======
 V 2.1.1
 =======