Merge pull request #236 from golobor/master

bump pairtools version and changes.md

.github/workflows/python-package.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

CHANGES.md

@@ -1,3 +1,35 @@
+### 1.1.0 (2024-04-23) ###
+Major bugfixes:
+- Fix a major bug in sort that previously broke the sorting order. This bug was introduced in recent versions of pairtools #230
+- Fix a major bug in dedup that caused pair duplication and broken sorting order in non-Cython backends
+
+New features:
+- stats: calculate the distance of P(s) divergence between pairs of different directionalities #222
+- dedup: allow column names in all backends, and allow sorting by arbitrary columns #162
+
+New behavior and default settings:
+- dedup: turn mark-dups on by default #211
+- parse: change the default --walks-policy to 5unique
+- parse: pair types are now always in upper case. Previously, letters in pair types were converted to lowercase if the corresponding side contained chimeric alignments.
+
+Minor bugfixes:
+- dedup: allow inputs with quotes #194
+- dedup: allow empty input pairs file #201
+- stats: minor bugfixes #200
+
+Documentation:
+- a new notebook with the statistics of distances between PCR duplicates #233
+- clean up phase walkthrough #218
+- a new chapter on building workflows with pairtools #219 #226 #231
+- a major cleanup
+
+Code updates:
+- make pairsio.py to read (and, in the future, write) .pairs files #195
+- minor refactoring of parse #223
+
+New Contributors:
+- @hkariti made their first contribution in #194
+
 ### 1.0.3 (2023-11-20) ###
 - [x] `pairtools dedup`: update default chunksize to 10,000 to prevent memory overflow on datasets with high duplication rate 
 

pairtools/__init__.py

@@ -4,12 +4,12 @@
 
 CLI tools to process mapped Hi-C data
 
-:copyright: (c) 2017-2023 Open2C
+:copyright: (c) 2017-2024 Open2C
 :author: Open2C
 :license: MIT
 
 """
 
-__version__ = "1.0.3"
+__version__ = "1.1.0"
 
 # from . import lib