Bump version to 3.5.1 for PyPI re-release

v3.5.0 was published to PyPI before bugfixes landed. Bump all version
strings so the fixed code can be published as 3.5.1.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: TimoLassmann

CITATION.cff

@@ -6,7 +6,7 @@ authors:
     family-names: "Lassmann"
     orcid: "https://orcid.org/0000-0002-0138-2691"
 title: "Kalign 3: multiple sequence alignment of large datasets"
-version: 3.5.0
+version: 3.5.1
 date-released: 2026-02-27
 url: "https://github.com/TimoLassmann/kalign"
 repository-code: "https://github.com/TimoLassmann/kalign"

CMakeLists.txt

@@ -13,7 +13,7 @@ include(GenerateExportHeader)
 
 set(KALIGN_LIBRARY_VERSION_MAJOR 3)
 set(KALIGN_LIBRARY_VERSION_MINOR 5)
-set(KALIGN_LIBRARY_VERSION_PATCH 0)
+set(KALIGN_LIBRARY_VERSION_PATCH 1)
 set(KALIGN_LIBRARY_VERSION_STRING ${KALIGN_LIBRARY_VERSION_MAJOR}.${KALIGN_LIBRARY_VERSION_MINOR}.${KALIGN_LIBRARY_VERSION_PATCH})
 
 

ChangeLog

@@ -1,5 +1,11 @@
 2026-02-27  Timo Lassmann  <timolassmann@icloud.com>
 
+	* version 3.5.1 - Bugfix release
+	- Fix memory leak in build_tree_from_pairwise (realign/ensemble)
+	- Move seaborn from core to optional dependency
+	- Fix benchmark workflow to handle unavailable datasets gracefully
+	- Black formatting fixes
+
 	* version 3.5.0 - Three modes
 	Kalign now has three modes: default (best general-purpose), fast
 	(same as v3.4), and precise (ensemble, highest accuracy, ~10x slower).

build.zig

@@ -2,7 +2,7 @@ const std = @import("std");
 const builtin = @import("builtin");
 const ArrayList = std.ArrayList;
 
-const kalignPackageVersion = "3.5.0";
+const kalignPackageVersion = "3.5.1";
 
 const targets: []const std.Target.Query = &.{
     .{ .cpu_arch = .aarch64, .os_tag = .macos },

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "kalign-python"
-version = "3.5.0"
+version = "3.5.1"
 description = "Python wrapper for the Kalign multiple sequence alignment engine"
 readme = "README-python.md"
 license = "Apache-2.0"