Bump version to 3.1.0

Author: dcjones

.gitignore

@@ -1,5 +1,6 @@
 Cargo.lock
 /target
 /debug
+/benches
 /.zed
 /.vscode

CHANGES.md

@@ -1,4 +1,13 @@
 
+# 3.1.0
+  - Fix a significant bug in the factorization scheme which degraded segmentation quality on data with large gene panels.
+  - Extensive optimization work leading to around 1.5x-4x faster run times and 5-10% less memory usage. Changes include:
+    - Redesign sparse count matrix data structure (now using csr with B+-tree rows, and row-level read/write locks)
+    - New optimized Binomial and Multinomial samplers.
+    - Parallelize some additional loops, and tune rayon min lengths for better cpu utilization.
+    - Use ahash in place of HashMap and BTreeMap in some places.
+    - Many other minor optimizations.
+
 # 3.0.12
   - Fix numerical error crash occurring in some Visium HD data.
   - Fix an incompatibility with spatialdata zarr output and newer versions of the python package.

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "proseg"
 description = "Probabilistic cell segmentation for in situ spatial transcriptomics"
-version = "3.0.12"
+version = "3.1.0"
 rust-version = "1.88.0"
 edition = "2024"
 authors = ["Daniel C. Jones <djones3@fredhutch.org>"]