Bump version to 3.5.2 and add ChangeLog entry

Updated in all four locations so the build artefacts agree:
  pyproject.toml (PyPI metadata)
  CMakeLists.txt (KALIGN_LIBRARY_VERSION_PATCH)
  build.zig (zig cross-compile package version)
  ChangeLog (release notes summary)

Release theme: this is the first version that ships the four-mode
preset system as the stable public interface (fast / default / recall
/ accurate), with the Chase-Lev threadpool replacing OpenMP as the
default parallelism backend and macOS wheels no longer linking
libomp.dylib — closing the conda-forge / numpy OpenMP runtime
conflict reported on the issue tracker.

Verified: kalign --version reports 3.5.2; kalign.__version__ reports
3.5.2; pre-push checklist (tests/check-local.sh --quick) green
prior to this commit.

Author: TimoLassmann

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 1)
+set(KALIGN_LIBRARY_VERSION_PATCH 2)
 set(KALIGN_LIBRARY_VERSION_STRING ${KALIGN_LIBRARY_VERSION_MAJOR}.${KALIGN_LIBRARY_VERSION_MINOR}.${KALIGN_LIBRARY_VERSION_PATCH})
 
 

ChangeLog

@@ -1,4 +1,57 @@
-2026-02-27  Timo Lassmann  <timolassmann@icloud.com>
+2026-05-16  Timo Lassmann  <timolassmann@icloud.com>
+
+	* version 3.5.2 - Four-mode preset system, threadpool, hardening
+	Algorithm and presets
+	- Four mode presets stable for protein and nucleotide:
+	  fast, default, recall, accurate. Per-mode configurations
+	  derived by NSGA-III multi-objective optimisation on
+	  BAliBASE v4 (protein) and BRAliBASE (RNA).
+	- Unified nucleotide preset (DNA and RNA share one path).
+	- Ensemble alignment with POAR consensus and per-column /
+	  per-residue confidence scores.
+	- New --add mode: append sequences to an existing alignment.
+	- Sparse consistency-bonus matrix for large MSAs (avoids
+	  quadratic memory in column count).
+	- Removed deprecated 'precise' mode alias (Python only;
+	  never shipped as a wheel).
+
+	Parallelism
+	- Chase-Lev work-stealing thread pool is now the default
+	  parallelism backend; OpenMP is optional (USE_OPENMP=ON).
+	- macOS wheels no longer link libomp.dylib, resolving the
+	  conda-forge / numpy OpenMP runtime conflict.
+
+	Security / robustness
+	- POAR file parsing now rejects malformed inputs that would
+	  cause integer overflow in pair-count or per-pair entry
+	  count (lib/src/poar.c). Limited threat model (requires
+	  explicit --load-poar) but tightened anyway.
+	- finalise_alignment is now atomic w.r.t. msa->sequences:
+	  validates all per-sequence linear lengths before swapping
+	  any pointer, so a failure leaves the MSA unchanged.
+	- kalign_msa_compare wraps finalise_alignment in RUN(); a
+	  failure surfaces cleanly instead of producing a half-
+	  finalised MSA.
+	- DSSIM stress test now uses KALIGN_MATRIX_AUTO so it
+	  exercises both protein and DNA biotypes correctly.
+	- Bumped locked dependencies (cryptography, flask, werkzeug,
+	  pillow, pygments, pytest, urllib3, requests, mako, black)
+	  past their CVE fix versions.
+
+	Build / tooling
+	- build.zig updated for zig 0.16 (four cross-compile targets).
+	- tests/check-local.sh: one-command pre-push gate that runs
+	  zig build + native ctest + Linux ASAN container + pytest.
+	- Containerfile.memcheck (Ubuntu + ASAN + Valgrind) for local
+	  Linux memory-bug reproduction.
+	- Removed paper-side benchmark machinery, optimizer scripts,
+	  and design-rationale PRDs from the public tree (preserved
+	  in the manuscript repository for reproducibility).
+	- Cleaned up ~550 lines of dead code (coretralign,
+	  bitShiftRight256ymm, unused split() in bisectingKmeans).
+	- Build is now warning-free on clang and GCC.
+	- Dropped the broken benchmark CI workflow (BAliBASE download
+	  endpoint has been gone for months).
 
 	* version 3.5.1 - Bugfix release
 	- Fix memory leak in build_tree_from_pairwise (realign/ensemble)

build.zig

@@ -1,6 +1,6 @@
 const std = @import("std");
 
-const kalignPackageVersion = "3.5.1";
+const kalignPackageVersion = "3.5.2";
 
 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 = "3.5.1"
+version = "3.5.2"
 description = "Python wrapper for the Kalign multiple sequence alignment engine"
 readme = "README-python.md"
 license = "Apache-2.0"