Merge pull request #33 from Becksteinlab/prep-111

prepare 1.1.1 release

Author: orbeckst

CHANGELOG.md

@@ -15,6 +15,20 @@ The rules for this file:
     * YYYY-MM-DD date format (following ISO 8601)
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
+## [1.1.1] - 2025-07-18
+
+### Authors
+* @rsexton2
+* @orbeckst
+
+## Changed
+* The default name for the contacts file changed from "contacts.pkl" to
+  "contacts_max10.0.pkl" as it now embeds the max_cutoff (Issue #27, PR #31)
+
+## Fixed
+* distinguished max_cutoff from cutoff in contact file metadata (Issues #27
+  and #32) 
+
 
 ## [1.1.0] - 2025-07-04
 
@@ -30,7 +44,6 @@ The rules for this file:
   and trajectory source tracking (Issue #16)
 
 ### Changed
-* distinguished max_cutoff from cutoff in contact file metadata (Issues #27 #32) 
 * package has final paper citation
 
 

docs/source/tutorial.rst

@@ -13,7 +13,7 @@ The basicrta workflow starts with collecting contacts between two atom groups
   python -m basicrta.contacts --top top.pdb --traj traj.xtc --sel1 "protein" 
   --sel2 "resname CHOL" --cutoff 7.0 --nproc 4
 
-This will create two contact maps: ``contacts.pkl`` and ``contacts_7.0.pkl``.
+This will create two contact maps: ``contacts_max10.0.pkl`` and ``contacts_7.0.pkl``.
 The first is used to map all contacts defined with a 10 |AA| cutoff, upon which
 the cutoff is imposed and a new contact map is created for each desired cutoff
 value (for storage reasons this may change in the future). The protein residues