Increase macOS deployment target for intel, bump macOS arm back to 14

.github/workflows/python-package.yml

@@ -39,30 +39,16 @@ jobs:
             arch: x86_64
             py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             py-vers-pr: cp313-*
-            before-all: MACOSX_DEPLOYMENT_TARGET=11 brew install --build-from-source boost zlib
-            extra-env: >
-              CC=clang
-              CXX=clang++
-              MACOSX_DEPLOYMENT_TARGET=11
-              SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
-              CFLAGS="-mmacosx-version-min=11"
-              CXXFLAGS="-mmacosx-version-min=11"
-              LDFLAGS="-mmacosx-version-min=11"
-            mdt: 11
-          - os: macos-15
+            before-all: brew install boost zlib
+            extra-env: CC=clang CXX=clang++
+            mdt: 15
+          - os: macos-14
             arch: arm64
             py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             py-vers-pr: cp314-*
-            before-all: MACOSX_DEPLOYMENT_TARGET=11 brew install --build-from-source boost zlib
-            extra-env: >
-              CC=clang
-              CXX=clang++
-              MACOSX_DEPLOYMENT_TARGET=11
-              SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
-              CFLAGS="-mmacosx-version-min=11"
-              CXXFLAGS="-mmacosx-version-min=11"
-              LDFLAGS="-mmacosx-version-min=11"
-            mdt: 11
+            before-all: brew install boost zlib
+            extra-env: CC=clang CXX=clang++
+            mdt: 14
 
     env:
       CIBW_BUILD: ${{ github.event_name != 'pull_request' && matrix.py-vers-full || matrix.py-vers-pr }}

CMakeLists.txt

@@ -4,7 +4,7 @@
 cmake_minimum_required(VERSION 3.15)
 message(STATUS "CMake version: ${CMAKE_VERSION}")
 
-project(asmc LANGUAGES CXX VERSION 1.3.1)
+project(asmc LANGUAGES CXX VERSION 1.4.0)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 

COPYING

@@ -1,4 +1,4 @@
-Copyright (c) 2020, University of Oxford.
+Copyright (c) 2025, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

PyPI_README.md

@@ -8,7 +8,15 @@
 
 # ASMC and FastSMC
 
-This repository contains ASMC and an extension, FastSMC, together with python bindings for both.
+This repository provides ASMC and its extension FastSMC, implemented in C++ with Python bindings.
+Prebuilt CPython wheels are available for Linux (compatible with glibc ≥ 2.28) and macOS (built on macOS 15 for x86_64 and macOS 14 for arm64).
+
+| Platform \ CPython          | ≤3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | 3.14 |
+|-----------------------------| ---- | --- | ---- | ---- | ---- | ---- | ---- |
+| Linux x86_64                | ❌    | ✅   | ✅    | ✅    | ✅    | ✅    | ✅    |
+| Linux aarch64               | ❌    | ✅   | ✅    | ✅    | ✅    | ✅    | ✅    |
+| macOS Intel (x86_64)        | ❌    | ✅   | ✅    | ✅    | ✅    | ✅    | ✅    |
+| macOS Apple Silicon (arm64) | ❌    | ✅   | ✅    | ✅    | ✅    | ✅    | ✅    |
 
 ## Quickstart
 

README.md

@@ -59,7 +59,7 @@ This should not have a substantial impact on most downstream analyses.
 
 ## For developers: making a release
 
-- Bump the version number in [pyproject.toml]([pyproject.toml]), [CMakeLists.txt](CMakeLists.txt) and [conf.py](docs/conf.py)
+- Bump the version number in [pyproject.toml](pyproject.toml), [CMakeLists.txt](CMakeLists.txt) and [conf.py](docs/conf.py)
 - Update [RELEASE_NOTES.md](RELEASE_NOTES.md)
 - Push changes and check that all [GitHub workflows](https://github.com/PalamaraLab/ASMC/actions) pass
 - Tag the commit in Git using syntax `vX.Y`

RELEASE_NOTES.md

@@ -1,5 +1,17 @@
 # ASMC Release Notes
 
+## v1.4.0 (2025-10-22)
+
+### Breaking changes
+
+- Dependencies are no longer managed with vcpkg. Boost and zlib should now be obtained from a system package manager, while other dependencies are fetched using CMake's FetchContent during configuration.
+
+### Other changes
+
+- Added support for cross-platform SIMD vectorization using the Google Highway library. This improves performance by dynamically dispatching to the most powerful supported instruction set at runtime (e.g., AVX-512, AVX2, or NEON), ensuring optimal performance on different CPU architectures.
+
+- Python wheels are now available for Linux and macOS on both x86_64 and arm64/AArch64 architectures, for CPython versions 3.9 to 3.14 inclusive.
+
 ## v1.3.1 (2023-06-30)
 
 ### Breaking changes

docs/conf.py

@@ -18,9 +18,9 @@
 # -- Project information -----------------------------------------------------
 
 project = 'ASMC'
-copyright = '2023, ASMC Developers'
+copyright = '2025, ASMC Developers'
 author = 'ASMC Developers, https://palamaralab.github.io/software/asmc/'
-release = 'v1.3.1'
+release = 'v1.4.0'
 
 # -- General configuration ---------------------------------------------------
 

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "scikit_build_core.build"
 [project]
 dynamic = ["readme"]
 name = "asmc-asmc"
-version = "1.3.1"
+version = "1.4.0"
 description = "ASMC is a method to efficiently estimate pairwise coalescence time along the genome"
 authors = [
     { name = "PalamaraLab (https://palamaralab.github.io/)" }