From e5ec764646d6763b7fbe9563dfc1efd11b2ac11c Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Thu, 25 Sep 2025 15:26:26 +0100
Subject: [PATCH 01/27] Removed submodule pybind11

---
 .bettercodehub.yml                            | 21 -------------------
 .gitmodules                                   |  5 +----
 pybind11                                      |  1 -
 src/{ => asmc/preparedecoding}/__init__.py    |  0
 .../preparedecoding}/decoding_quantities.py   |  0
 5 files changed, 1 insertion(+), 26 deletions(-)
 delete mode 100644 .bettercodehub.yml
 delete mode 160000 pybind11
 rename src/{ => asmc/preparedecoding}/__init__.py (100%)
 rename src/{ => asmc/preparedecoding}/decoding_quantities.py (100%)

diff --git a/.bettercodehub.yml b/.bettercodehub.yml
deleted file mode 100644
index 0c919c5..0000000
--- a/.bettercodehub.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-component_depth: 1
-languages:
-  - name: cpp
-    production:
-      include:
-        - /exe/.*\.cpp
-      exclude:
-        - /cmake/.*
-        - /docs/.*
-        - /scripts/.*
-        - /test/.*
-        - /vcpkg/.*
-        - /src/3rd_party/.*
-    test:
-      include:
-        - /test/.*\.cpp
-      exclude:
-        - /cmake/.*
-        - /docs/.*
-        - /scripts/.*
-        - /vcpkg/.*
diff --git a/.gitmodules b/.gitmodules
index 75ff16e..9c10ce8 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,6 +1,3 @@
 [submodule "vcpkg"]
 	path = vcpkg
-	url = https://github.com/microsoft/vcpkg
-[submodule "pybind11"]
-	path = pybind11
-	url = https://github.com/pybind/pybind11
+	url = https://github.com/microsoft/vcpkg
\ No newline at end of file
diff --git a/pybind11 b/pybind11
deleted file mode 160000
index 0bd8896..0000000
--- a/pybind11
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 0bd8896a4010f2d91b2340570c24fa08606ec406
diff --git a/src/__init__.py b/src/asmc/preparedecoding/__init__.py
similarity index 100%
rename from src/__init__.py
rename to src/asmc/preparedecoding/__init__.py
diff --git a/src/decoding_quantities.py b/src/asmc/preparedecoding/decoding_quantities.py
similarity index 100%
rename from src/decoding_quantities.py
rename to src/asmc/preparedecoding/decoding_quantities.py

From a43300ff43810dd31f3e9f3c468b582d60decbcf Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Thu, 25 Sep 2025 15:27:17 +0100
Subject: [PATCH 02/27] Replace setup.py with pyproject.toml

---
 pyproject.toml |  52 ++++++++++++++++++++
 setup.py       | 125 -------------------------------------------------
 2 files changed, 52 insertions(+), 125 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..af74323
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,52 @@
+[build-system]
+requires = [
+    "scikit-build-core>=0.11.6",
+    "pybind11==2.13.6"
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+dynamic = ["readme"]
+name = "asmc-preparedecoding"
+version = "2.2.3"
+description = "Prepare decoding quantities for ASMC & FastSMC"
+authors = [
+    { name = "PalamaraLab (https://palamaralab.github.io/)" }
+]
+requires-python = ">=3.9"
+
+dependencies = [
+    'numpy',
+]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+[tool.scikit-build]
+minimum-version = "build-system.requires"
+build.verbose = true
+cmake.build-type = "Release"
+build.targets = ["preparedecoding_python_bindings"]
+wheel.packages = ["src/asmc"]
+metadata.readme.provider = "scikit_build_core.metadata.fancy_pypi_readme"
+
+[tool.scikit-build.cmake.define]
+PREPARE_DECODING_PYTHON_BINDINGS = "ON"
+PREPARE_DECODING_BUILDING_FROM_PYPROJECT = "ON"
+
+[tool.hatch.metadata.hooks.fancy-pypi-readme]
+content-type = "text/markdown"
+
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+path = "PyPI_README.md"
+
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+path = "RELEASE_NOTES.md"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index a5141d1..0000000
--- a/setup.py
+++ /dev/null
@@ -1,125 +0,0 @@
-# Based on https://github.com/pybind/cmake_example
-
-import os
-import sys
-import subprocess
-
-from setuptools import setup, Extension, find_namespace_packages
-from setuptools.command.build_ext import build_ext
-
-# Convert distutils Windows platform specifiers to CMake -A arguments
-PLAT_TO_CMAKE = {
-    "win32": "Win32",
-    "win-amd64": "x64",
-    "win-arm32": "ARM",
-    "win-arm64": "ARM64",
-}
-
-
-# A CMakeExtension needs a sourcedir instead of a file list.
-# The name must be the _single_ output extension from the CMake build.
-# If you need multiple extensions, see scikit-build.
-class CMakeExtension(Extension):
-    def __init__(self, name, sourcedir=""):
-        Extension.__init__(self, name, sources=[])
-        self.sourcedir = os.path.abspath(sourcedir)
-
-
-class CMakeBuild(build_ext):
-
-    def build_extension(self, ext):
-        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
-
-        # required for auto-detection of auxiliary "native" libs
-        if not extdir.endswith(os.path.sep):
-            extdir += os.path.sep
-
-        cfg = "Debug" if self.debug else "Release"
-
-        # CMake lets you override the generator - we need to check this.
-        # Can be set with Conda-Build, for example.
-        cmake_generator = os.environ.get("CMAKE_GENERATOR", "")
-
-        # Set Python_EXECUTABLE instead if you use PYBIND11_FINDPYTHON
-        # EXAMPLE_VERSION_INFO shows you how to pass a value into the C++ code
-        # from Python.
-        cmake_args = [
-            f"-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={extdir}",
-            f"-DPYTHON_EXECUTABLE={sys.executable}",
-            f"-DCMAKE_BUILD_TYPE={cfg}",
-            f"-DWARNINGS_AS_ERRORS=OFF",
-            f"-DENABLE_TESTING=OFF",
-            f"-DMAKE_DOCS=OFF",
-        ]
-        build_args = []
-
-        if self.compiler.compiler_type != "msvc":
-            # Using Ninja-build since it a) is available as a wheel and b)
-            # multithreads automatically. MSVC would require all variables be
-            # exported for Ninja to pick it up, which is a little tricky to do.
-            # Users can override the generator with CMAKE_GENERATOR in CMake
-            # 3.15+.
-            if not cmake_generator:
-                cmake_args += ["-GNinja"]
-
-        else:
-
-            # Single config generators are handled "normally"
-            single_config = any(x in cmake_generator for x in {"NMake", "Ninja"})
-
-            # CMake allows an arch-in-generator style for backward compatibility
-            contains_arch = any(x in cmake_generator for x in {"ARM", "Win64"})
-
-            # Specify the arch if using MSVC generator, but only if it doesn't
-            # contain a backward-compatibility arch spec already in the
-            # generator name.
-            if not single_config and not contains_arch:
-                cmake_args += ["-A", PLAT_TO_CMAKE[self.plat_name]]
-
-            # Multi-config generators have a different way to specify configs
-            if not single_config:
-                cmake_args += [
-                    "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}".format(cfg.upper(), extdir)
-                ]
-                build_args += ["--config", cfg]
-
-        # Set CMAKE_BUILD_PARALLEL_LEVEL to control the parallel build level
-        # across all generators.
-        if "CMAKE_BUILD_PARALLEL_LEVEL" not in os.environ:
-            # self.parallel is a Python 3 only way to set parallel jobs by hand
-            # using -j in the build_ext call, not supported by pip or PyPA-build.
-            if hasattr(self, "parallel") and self.parallel:
-                # CMake 3.12+ only.
-                build_args += ["-j{}".format(self.parallel)]
-
-        if not os.path.exists(self.build_temp):
-            os.makedirs(self.build_temp)
-
-        subprocess.check_call(
-            ["cmake", ext.sourcedir] + cmake_args, cwd=self.build_temp
-        )
-        subprocess.check_call(
-            ["cmake", "--build", "."] + build_args, cwd=self.build_temp
-        )
-
-
-with open('PyPI_README.md', encoding='utf-8') as f:
-    long_description = f.read()
-
-with open('RELEASE_NOTES.md', encoding='utf-8') as f:
-    release_notes = f.read()
-
-setup(
-    name='asmc-preparedecoding',
-    version='2.2.3',
-    author='PalamaraLab (https://palamaralab.github.io/)',
-    url='https://github.com/PalamaraLab/PrepareDecoding/',
-    install_requires=['numpy'],
-    description='Prepare decoding quantities for ASMC & FastSMC',
-    packages=find_namespace_packages(include=['asmc.*']),
-    long_description='\n'.join([long_description, release_notes]),
-    long_description_content_type='text/markdown',
-    ext_modules=[CMakeExtension('asmc/preparedecoding')],
-    cmdclass=dict(build_ext=CMakeBuild),
-    zip_safe=False,
-)

From 665225021c68053a58d551d291c4b7e43668c8b6 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Thu, 25 Sep 2025 15:27:40 +0100
Subject: [PATCH 03/27] Get pybind either from build system or from fetch
 content

---
 src/CMakeLists.txt | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 28be6f7..595e158 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -117,8 +117,25 @@ if (BUILD_WITH_SMCPP_SUPPORT)
 endif ()
 
 
-if (PYTHON_BINDINGS)
+if (PREPARE_DECODING_PYTHON_BINDINGS)
+    option(PREPARE_DECODING_BUILDING_FROM_PYPROJECT "Are we building from pyproject.toml (pip install)?" OFF)
+
+    if(PREPARE_DECODING_BUILDING_FROM_PYPROJECT)
+        message(STATUS "Using pybind11 from pyproject.toml build environment")
+        find_package(pybind11 REQUIRED)
+    else()
+        message(STATUS "Using FetchContent to get pybind11")
+        include(FetchContent)
+        FetchContent_Declare(
+                pybind11
+                GIT_REPOSITORY https://github.com/pybind/pybind11.git
+                GIT_TAG a2e59f0e7065404b44dfe92a28aca47ba1378dc4 # Version 2.13.6
+        )
+        FetchContent_MakeAvailable(pybind11)
+    endif()
+
     set_target_properties(prepare_decoding_lib PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
     pybind11_add_module(preparedecoding_python_bindings pybind.cpp)
     target_link_libraries(preparedecoding_python_bindings PRIVATE Eigen3::Eigen fmt::fmt prepare_decoding_lib project_settings)
+    install(TARGETS preparedecoding_python_bindings LIBRARY DESTINATION asmc/preparedecoding)
 endif ()

From db1ab9724d9090f24e00f467b3fdaaa699a78fed Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Thu, 25 Sep 2025 15:31:55 +0100
Subject: [PATCH 04/27] Add standard python .gitignores

---
 .gitignore | 141 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 141 insertions(+)

diff --git a/.gitignore b/.gitignore
index a57e72c..9bbb52a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,3 +51,144 @@ __pycache__/
 
 # Directory containing output generated for ASMC
 utils/dq_for_asmc
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+#######################
+# Custom ASMC-related #
+#######################
+
+.vscode
+.idea
+cmake-build-*
+build
+
+**/.uuid

From 893ec52e9893e5b0efae768758eef84c718168ce Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Thu, 25 Sep 2025 16:43:38 +0100
Subject: [PATCH 05/27] Commit WIP

---
 .github/workflows/python-wheels.yml  | 53 ++++++++++++++++++++--------
 src/asmc/preparedecoding/__init__.py | 12 +++----
 2 files changed, 44 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index b871447..efa5129 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -11,31 +11,54 @@ on:
     types:
       - published
 
-env:
-  CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
-  CIBW_SKIP: cp3*-musllinux_*
-  CIBW_ARCHS_MACOS: x86_64
-  CIBW_ARCHS_LINUX: auto64
-  CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-  CIBW_BEFORE_ALL_LINUX: "yum -y groupinstall 'Development Tools' && yum -y install git"
-  CIBW_BEFORE_ALL_MACOS: brew install libomp pkg-config automake autoconf autoconf-archive libtool
-  CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
-  CIBW_ENVIRONMENT_MACOS: CXX="$(brew --prefix llvm@15)/bin/clang++"
-  MACOSX_DEPLOYMENT_TARGET: 10.15
-
 jobs:
-  build_wheels:
+  build_wheels_cloud:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-22.04, macos-12]
+        include:
+          - os: ubuntu-24.04
+            arch: x86_64
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            before-all: ""
+            extra-env: ""
+            mdt: ""
+          - os: ubuntu-24.04-arm
+            arch: aarch64
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            before-all: dnf -y install boost-devel zlib
+            extra-env: ""
+            mdt: ""
+          - os: macos-15-intel
+            arch: x86_64
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
+            extra-env: CC=clang CXX=clang++
+            mdt: ""
+          - os: macos-15
+            arch: arm64
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
+            extra-env: CC=clang CXX=clang++
+            mdt: ""
+
+    env:
+      CIBW_BUILD: ${{ matrix.py-vers }}
+      CIBW_SKIP: cp3*-musllinux_*
+      CIBW_ARCHS: ${{ matrix.arch }}
+      CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+      CIBW_BEFORE_ALL: ${{ matrix.before-all }}
+      CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
+      CIBW_ENVIRONMENT: ${{ matrix.extra-env }}
+    #      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
+
 
     steps:
 
       - name: checkout repo & submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
diff --git a/src/asmc/preparedecoding/__init__.py b/src/asmc/preparedecoding/__init__.py
index f03065c..1f022de 100644
--- a/src/asmc/preparedecoding/__init__.py
+++ b/src/asmc/preparedecoding/__init__.py
@@ -1,9 +1,9 @@
-from asmc.preparedecoding_python_bindings import DecodingQuantities
-from asmc.preparedecoding_python_bindings import prepareDecoding
-from asmc.preparedecoding_python_bindings import Demography
-from asmc.preparedecoding_python_bindings import Discretization
-from asmc.preparedecoding_python_bindings import Frequencies
-from asmc.preparedecoding_python_bindings import save_demography
+from .preparedecoding_python_bindings import DecodingQuantities
+from .preparedecoding_python_bindings import prepareDecoding
+from .preparedecoding_python_bindings import Demography
+from .preparedecoding_python_bindings import Discretization
+from .preparedecoding_python_bindings import Frequencies
+from .preparedecoding_python_bindings import save_demography
 
 from typing import Iterable, Union
 import numbers

From f4dd2a918c7eefc5b354a32eddb7740ad978ba79 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <3770306+fcooper8472@users.noreply.github.com>
Date: Thu, 25 Sep 2025 23:15:09 +0100
Subject: [PATCH 06/27] Update workflows, remove caching and windows

---
 .github/workflows/coverage.yml        | 25 ++++--------
 .github/workflows/python-wheels.yml   | 28 +++++---------
 .github/workflows/regression.yml      | 23 +++--------
 .github/workflows/sanitisers.yml      | 24 ++++--------
 .github/workflows/static-analysis.yml | 18 ++-------
 .github/workflows/unit-macos.yml      | 20 +++-------
 .github/workflows/unit-ubuntu.yml     | 22 +++--------
 .github/workflows/unit-windows.yml    | 56 ---------------------------
 asmc/preparedecoding                  |  1 -
 9 files changed, 45 insertions(+), 172 deletions(-)
 delete mode 100644 .github/workflows/unit-windows.yml
 delete mode 120000 asmc/preparedecoding

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 1e4f560..b81e0ef 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -12,41 +12,30 @@ jobs:
 
   build-and-test:
     name: Unit test coverage
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
-      CXX: g++-10
+      CXX: g++-13
 
     steps:
 
-      - name: checkout repo & vcpkg submodule
-        uses: actions/checkout@v3
+      - name: checkout repo & submodules
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ env.CXX }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
       - name: install tools
         run: |
-          sudo apt -y update
-          sudo apt -y install g++-10 lcov libcurl4-openssl-dev
+          sudo apt -y install lcov libcurl4-openssl-dev
 
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: run unit tests with coverage
         run: |
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_COVERAGE=ON
-          cmake --build . --parallel 2 --target unit_tests
-          ctest -j2 --output-on-failure
+          cmake --build . --parallel 4 --target unit_tests
+          ctest -j4 --output-on-failure
         working-directory: build_dir
 
       - name: upload coverage results
diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index efa5129..0bf5218 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -54,7 +54,6 @@ jobs:
       CIBW_ENVIRONMENT: ${{ matrix.extra-env }}
     #      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
 
-
     steps:
 
       - name: checkout repo & submodules
@@ -63,37 +62,30 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v3
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.12.0
-
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
+        uses: pypa/cibuildwheel@v3.2.0
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-cloud-${{ matrix.os }}
           path: ./wheelhouse/*.whl
           retention-days: 1
 
   upload_all:
     name: Upload to PyPI
-    needs: build_wheels
+    needs: [build_wheels_cloud]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
 
     steps:
-      - uses: actions/setup-python@v3
-
-      - name: Download wheels
-        uses: actions/download-artifact@v3
+      - name: Download wheels from cloud runners
+        uses: actions/download-artifact@v4
         with:
-          name: wheels
+          pattern: wheels-cloud-*
+          merge-multiple: true
           path: wheels
 
-      - uses: pypa/gh-action-pypi-publish@v1.6.4
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/regression.yml b/.github/workflows/regression.yml
index 5d5d792..67da0ee 100644
--- a/.github/workflows/regression.yml
+++ b/.github/workflows/regression.yml
@@ -17,30 +17,20 @@ jobs:
       CXX: g++-10
 
     steps:
-      - uses: actions/checkout@v3
+      - name: checkout repo & submodules
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ env.CXX }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-          architecture: x64
+          python-version: 3.13
 
       - name: install python dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install ninja numpy cython
 
       - name: install python bindings
         run: |
@@ -48,12 +38,11 @@ jobs:
 
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: compile prepare decoding
         run: |
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Release
-          cmake --build . --parallel 2 --target prepare_decoding_exe
+          cmake --build . --parallel 4 --target prepare_decoding_exe
         working-directory: build_dir
 
       - name: generate & check decoding quantities (executable)
diff --git a/.github/workflows/sanitisers.yml b/.github/workflows/sanitisers.yml
index a826320..f362d5b 100644
--- a/.github/workflows/sanitisers.yml
+++ b/.github/workflows/sanitisers.yml
@@ -12,36 +12,26 @@ jobs:
 
   build-and-test:
     name: Sanitiser checks
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
-      CXX: clang++-10
+      CXX: clang++-18
 
     steps:
 
       - name: checkout repo & submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ env.CXX }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: address sanitiser
         run: |
           mv vcpkg_installed .. && rm -rf * && mv ../vcpkg_installed .
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_SANITISER_ADDRESS=ON
-          cmake --build . --parallel 2 --target unit_tests
+          cmake --build . --parallel 4 --target unit_tests
           ./test/unit_tests ~"Test prepare decoding"
         working-directory: build_dir
 
@@ -49,7 +39,7 @@ jobs:
         run: |
           mv vcpkg_installed .. && rm -rf * && mv ../vcpkg_installed .
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_SANITISER_LEAK=ON
-          cmake --build . --parallel 2 --target unit_tests
+          cmake --build . --parallel 4 --target unit_tests
           ./test/unit_tests
         working-directory: build_dir
 
@@ -57,7 +47,7 @@ jobs:
         run: |
           mv vcpkg_installed .. && rm -rf * && mv ../vcpkg_installed .
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_SANITISER_UNDEFINED_BEHAVIOUR=ON
-          cmake --build . --parallel 2 --target unit_tests
+          cmake --build . --parallel 4 --target unit_tests
           ./test/unit_tests
         working-directory: build_dir
 
@@ -65,6 +55,6 @@ jobs:
         run: |
           mv vcpkg_installed .. && rm -rf * && mv ../vcpkg_installed .
           cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug -DENABLE_SANITISER_THREAD=ON
-          cmake --build . --parallel 2 --target unit_tests
+          cmake --build . --parallel 4 --target unit_tests
           ./test/unit_tests ~"Test prepare decoding"
         working-directory: build_dir
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 46c2051..9a7b69b 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -12,35 +12,25 @@ jobs:
 
   build-and-test:
     name: Static analysis checks
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
-      CXX: clang++-10
+      CXX: clang++-18
 
     steps:
 
       - name: checkout repo & submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ env.CXX }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: install analysers
         run: |
           sudo apt -y update
-          sudo apt -y install cppcheck clang-tidy-10
+          sudo apt -y install cppcheck
 
       - name: compile with cppcheck
         run: |
diff --git a/.github/workflows/unit-macos.yml b/.github/workflows/unit-macos.yml
index acd0535..c70e900 100644
--- a/.github/workflows/unit-macos.yml
+++ b/.github/workflows/unit-macos.yml
@@ -12,40 +12,30 @@ jobs:
 
   build-and-test:
     name: Unit tests on macOS
-    runs-on: macos-12
+    runs-on: macos-15
 
     steps:
 
       - name: checkout repo & submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
       - name: install system packages
         run: brew install libomp pkg-config automake autoconf autoconf-archive libtool
 
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: cmake configure
-        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=$(brew --prefix llvm@15)/bin/clang++
+        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=clang++
         working-directory: build_dir
 
       - name: cmake build
-        run: cmake --build . --parallel 2 --target unit_tests
+        run: cmake --build . --parallel 4 --target unit_tests
         working-directory: build_dir
 
       - name: cmake test
-        run: ctest -j2 --output-on-failure
+        run: ctest -j4 --output-on-failure
         working-directory: build_dir
diff --git a/.github/workflows/unit-ubuntu.yml b/.github/workflows/unit-ubuntu.yml
index 3704f4c..6239a8e 100644
--- a/.github/workflows/unit-ubuntu.yml
+++ b/.github/workflows/unit-ubuntu.yml
@@ -12,39 +12,29 @@ jobs:
 
   build-and-test:
     name: Unit tests on Ubuntu
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
-      CXX: g++-9
+      CXX: g++-13
 
     steps:
 
-      - name: checkout repo & vcpkg submodule
-        uses: actions/checkout@v3
+      - name: checkout repo & submodules
+        uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ env.CXX }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
       - name: make build directory
         run: mkdir build_dir
-        if: steps.cache.outputs.cache-hit != 'true'
 
       - name: cmake configure
         run: cmake .. -DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug
         working-directory: build_dir
 
       - name: cmake build
-        run: cmake --build . --parallel 2 --target unit_tests
+        run: cmake --build . --parallel 4 --target unit_tests
         working-directory: build_dir
 
       - name: cmake test
-        run: ctest -j2 --output-on-failure
+        run: ctest -j4 --output-on-failure
         working-directory: build_dir
diff --git a/.github/workflows/unit-windows.yml b/.github/workflows/unit-windows.yml
deleted file mode 100644
index c4cc483..0000000
--- a/.github/workflows/unit-windows.yml
+++ /dev/null
@@ -1,56 +0,0 @@
-name: "Unit tests: Windows"
-
-on:
-  push:
-    branches:
-      - none
-  pull_request:
-    branches:
-      - none
-
-jobs:
-
-  build-and-test:
-    name: Unit tests on Windows
-    runs-on: windows-latest
-
-    steps:
-
-      - name: checkout repo & vcpkg submodule
-        uses: actions/checkout@v3
-        with:
-          submodules: true
-          fetch-depth: 0
-
-      - name: cache vcpkg installed packages
-        uses: actions/cache@v2
-        id: cache
-        with:
-          path: |
-            vcpkg/
-            build_dir/vcpkg_installed/
-          key: ${{ runner.os }}-${{ hashFiles('vcpkg.json', 'vcpkg/CHANGELOG.md') }}
-
-      - name: make build directory
-        run: |
-          mkdir build_dir
-          mkdir build_dir\vcpkg_installed
-        if: steps.cache.outputs.cache-hit != 'true'
-
-      - name: install system packages
-        run: |
-          .\bootstrap-vcpkg.bat
-          .\vcpkg --x-install-root=${{ github.workspace }}\build_dir\vcpkg_installed install yasm-tool:x86-windows
-        working-directory: vcpkg
-
-      - name: cmake configure
-        run: cmake .. -DCMAKE_TOOLCHAIN_FILE=${{ github.workspace }}\vcpkg\scripts\buildsystems\vcpkg.cmake -DCMAKE_BUILD_TYPE=Debug
-        working-directory: build_dir
-
-      - name: cmake build
-        run: cmake --build . --parallel 2 --target unit_tests
-        working-directory: build_dir
-
-      - name: cmake test
-        run: ctest -j2 --output-on-failure
-        working-directory: build_dir
diff --git a/asmc/preparedecoding b/asmc/preparedecoding
deleted file mode 120000
index 5cd551c..0000000
--- a/asmc/preparedecoding
+++ /dev/null
@@ -1 +0,0 @@
-../src
\ No newline at end of file

From 11c33ba7524e028db73824da12bb173da6e7dc44 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <3770306+fcooper8472@users.noreply.github.com>
Date: Fri, 26 Sep 2025 00:36:20 +0100
Subject: [PATCH 07/27] Update vcpkg

---
 vcpkg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcpkg b/vcpkg
index f14984a..e6e4bc7 160000
--- a/vcpkg
+++ b/vcpkg
@@ -1 +1 @@
-Subproject commit f14984af3738e69f197bf0e647a8dca12de92996
+Subproject commit e6e4bc74aaf5c63dfc358810594f662f7e9bc4d4

From dd7f294d6cffe557a9c2087bba5d938259448648 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <3770306+fcooper8472@users.noreply.github.com>
Date: Fri, 26 Sep 2025 00:58:02 +0100
Subject: [PATCH 08/27] Upgrade deps

---
 vcpkg.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/vcpkg.json b/vcpkg.json
index 6e2b720..55a3908 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -15,9 +15,9 @@
   "builtin-baseline": "f14984af3738e69f197bf0e647a8dca12de92996",
   "overrides": [
     { "name": "cereal", "version": "1.3.2#1" },
-    { "name": "eigen3", "version": "3.3.9" },
-    { "name": "fmt", "version": "7.1.3#5" },
-    { "name": "gmp", "version": "6.2.1#14" },
-    { "name": "mpfr", "version": "4.1.1" }
+    { "name": "eigen3", "version": "3.3.9#1" },
+    { "name": "fmt", "version": "12.0.0" },
+    { "name": "gmp", "version": "6.3.0#2" },
+    { "name": "mpfr", "version": "4.2.2" }
   ]
 }

From 78251d6f45eca8e23cd6872073d5bd24f0cc40c0 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 12:03:45 +0100
Subject: [PATCH 09/27] Roll back cmake version

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index af74323..a17e444 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,7 @@
 [build-system]
 requires = [
     "scikit-build-core>=0.11.6",
+    "cmake<4",
     "pybind11==2.13.6"
 ]
 build-backend = "scikit_build_core.build"

From efb1b64680dc4c8abaeca527ec20fb11f90b4d72 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 12:03:55 +0100
Subject: [PATCH 10/27] Roll back fmt version

---
 vcpkg.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcpkg.json b/vcpkg.json
index 55a3908..3491e79 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -16,7 +16,7 @@
   "overrides": [
     { "name": "cereal", "version": "1.3.2#1" },
     { "name": "eigen3", "version": "3.3.9#1" },
-    { "name": "fmt", "version": "12.0.0" },
+    { "name": "fmt", "version": "7.1.3#5" },
     { "name": "gmp", "version": "6.3.0#2" },
     { "name": "mpfr", "version": "4.2.2" }
   ]

From 448f030c739bd78676038157a0491c1785a47f38 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 12:04:21 +0100
Subject: [PATCH 11/27] Only build vcpkg release binaries for wheels

---
 .github/workflows/python-wheels.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index 0bf5218..47c5f8a 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -23,25 +23,25 @@ jobs:
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: ""
-            extra-env: ""
+            extra-env: VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: ubuntu-24.04-arm
             arch: aarch64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: dnf -y install boost-devel zlib
-            extra-env: ""
+            extra-env: VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: macos-15-intel
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
-            extra-env: CC=clang CXX=clang++
+            extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: macos-15
             arch: arm64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
-            extra-env: CC=clang CXX=clang++
+            extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
             mdt: ""
 
     env:

From e3baeda0ed16643c54c7ed9d3227e411d28761f4 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 13:35:32 +0100
Subject: [PATCH 12/27] Upgrade runner to newer ubuntu

---
 .github/workflows/regression.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/regression.yml b/.github/workflows/regression.yml
index 67da0ee..b1b7b4d 100644
--- a/.github/workflows/regression.yml
+++ b/.github/workflows/regression.yml
@@ -12,9 +12,9 @@ jobs:
 
   build-and-test:
     name: Test decoding quantities can be generated
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
-      CXX: g++-10
+      CXX: g++-13
 
     steps:
       - name: checkout repo & submodules

From d85db01ca0af8c3c8a07206493fb89e82ba12842 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 13:35:42 +0100
Subject: [PATCH 13/27] Ignore errors with coverage command

---
 .github/workflows/coverage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index b81e0ef..50d5bb5 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -41,7 +41,7 @@ jobs:
       - name: upload coverage results
         run: |
           lcov --directory . --capture --output-file coverage.info
-          lcov --remove coverage.info '/usr/*' '*/vcpkg/*' '*/test/*' --output-file coverage.info
+          lcov --remove coverage.info '/usr/*' '*/vcpkg/*' '*/test/*' --output-file coverage.info --ignore-errors unused
           lcov --list coverage.info
           bash <(curl https://codecov.io/bash) -f coverage.info
         env:

From 28d4335e1ff2bc9efb18351a900327341f207431 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 13:39:08 +0100
Subject: [PATCH 14/27] Bump zlib

---
 vcpkg.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vcpkg.json b/vcpkg.json
index 3491e79..c8f94e7 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -14,6 +14,7 @@
   ],
   "builtin-baseline": "f14984af3738e69f197bf0e647a8dca12de92996",
   "overrides": [
+    { "name": "zlib", "version": "1.3.1#0" },
     { "name": "cereal", "version": "1.3.2#1" },
     { "name": "eigen3", "version": "3.3.9#1" },
     { "name": "fmt", "version": "7.1.3#5" },

From b4f239d0422113f630315e919b031c4dec8752c6 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 13:43:11 +0100
Subject: [PATCH 15/27] Add openmp, needed for clang compilation

---
 .github/workflows/sanitisers.yml      | 4 ++++
 .github/workflows/static-analysis.yml | 5 ++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/sanitisers.yml b/.github/workflows/sanitisers.yml
index f362d5b..462d81c 100644
--- a/.github/workflows/sanitisers.yml
+++ b/.github/workflows/sanitisers.yml
@@ -24,6 +24,10 @@ jobs:
           submodules: true
           fetch-depth: 0
 
+      - name: install tools
+        run: |
+          sudo apt -y install libomp-dev
+
       - name: make build directory
         run: mkdir build_dir
 
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 9a7b69b..0625292 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -27,9 +27,12 @@ jobs:
       - name: make build directory
         run: mkdir build_dir
 
+      - name: install tools
+        run: |
+          sudo apt -y install libomp-dev
+
       - name: install analysers
         run: |
-          sudo apt -y update
           sudo apt -y install cppcheck
 
       - name: compile with cppcheck

From cc2074d213b7d05fbcf29290b728cf26a928792a Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 13:52:04 +0100
Subject: [PATCH 16/27] Beef up system packages needed for bootstrapping vcpkg

---
 .github/workflows/python-wheels.yml | 8 ++++----
 .github/workflows/unit-macos.yml    | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index 47c5f8a..191ebe7 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -22,25 +22,25 @@ jobs:
           - os: ubuntu-24.04
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: ""
+            before-all: dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
             extra-env: VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: ubuntu-24.04-arm
             arch: aarch64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: dnf -y install boost-devel zlib
+            before-all: dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
             extra-env: VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: macos-15-intel
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
+            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
             extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
             mdt: ""
           - os: macos-15
             arch: arm64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool
+            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
             extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
             mdt: ""
 
diff --git a/.github/workflows/unit-macos.yml b/.github/workflows/unit-macos.yml
index c70e900..4ffe9fc 100644
--- a/.github/workflows/unit-macos.yml
+++ b/.github/workflows/unit-macos.yml
@@ -23,7 +23,7 @@ jobs:
           fetch-depth: 0
 
       - name: install system packages
-        run: brew install libomp pkg-config automake autoconf autoconf-archive libtool
+        run: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
 
       - name: make build directory
         run: mkdir build_dir

From 12b2e79e783e7dbda1ac28530ecf070b7c43755a Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 14:14:37 +0100
Subject: [PATCH 17/27] Treat clang tidy as warnings for time being

---
 .clang-tidy | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.clang-tidy b/.clang-tidy
index 30a3f4e..06b5b1e 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -1,5 +1,5 @@
 ---
 Checks:          '*,-android-*,-bugprone-bool-pointer-implicit-conversion,-bugprone-exception-escape,-bugprone-infinite-loop,-bugprone-signed-char-misuse,-cert-dcl16-c,-cert-dcl37-c,-cert-dcl50-cpp,-cert-dcl51-cpp,-cert-dcl54-cpp,-cert-dcl59-cpp,-cert-env33-c,-cert-err09-cpp,-cert-err61-cpp,-cert-fio38-c,-cert-flp30-c,-cert-mem57-cpp,-cert-msc30-c,-cert-msc32-c,-cert-oop11-cpp,-cert-oop57-cpp,-cert-oop58-cpp,-cert-pos44-c,-clang-analyzer-*,-cppcoreguidelines-avoid-magic-numbers,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-vararg,-darwin-*,-fuchsia-*,-google-*,google-default-arguments,google-explicit-constructor,google-runtime-operator,-hicpp-*,hicpp-exception-baseclass,hicpp-multiway-paths-covered,hicpp-signed-bitwise,-linuxkernel-*,-llvm-*,-llvmlibc-*,-misc-definitions-in-headers,-misc-non-private-member-variables-in-classes,-misc-unused-alias-decls,-misc-unused-parameters,-misc-unused-using-decls,-modernize-use-trailing-return-type,-objc-*,-openmp-exception-escape,-readability-braces-around-statements,-readability-else-after-return,-readability-function-size,-readability-identifier-naming,-readability-implicit-bool-conversion,-readability-isolate-declaration,-readability-magic-numbers,-readability-named-parameter,-readability-qualified-auto,-readability-redundant-access-specifiers,-readability-redundant-member-init,-readability-redundant-preprocessor,-readability-simplify-boolean-expr,-readability-uppercase-literal-suffix,-zircon-*'
-WarningsAsErrors: '*'
+WarningsAsErrors: ''
 HeaderFilterRegex: ''
 FormatStyle:     none

From 8e666b347fa2205f2ab07b3cef974b9b2f7ea62e Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 14:14:46 +0100
Subject: [PATCH 18/27] Specify clang compiler

---
 .github/workflows/unit-macos.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/unit-macos.yml b/.github/workflows/unit-macos.yml
index 4ffe9fc..6dd7a7a 100644
--- a/.github/workflows/unit-macos.yml
+++ b/.github/workflows/unit-macos.yml
@@ -13,6 +13,9 @@ jobs:
   build-and-test:
     name: Unit tests on macOS
     runs-on: macos-15
+    env:
+      CC: clang
+      CXX: clang++
 
     steps:
 

From b5418a1adc4501d1dbf4a3003f0581a28c1764df Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 15:02:58 +0100
Subject: [PATCH 19/27] Explicitly specify omp location and install dev tools

---
 .github/workflows/python-wheels.yml | 14 +++++++-------
 .github/workflows/unit-macos.yml    |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index 191ebe7..fedd6b7 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -22,26 +22,26 @@ jobs:
           - os: ubuntu-24.04
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
-            extra-env: VCPKG_BUILD_TYPE=release
+            before-all: yum groupinstall -y "Development Tools" && dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
+            extra-env: ""
             mdt: ""
           - os: ubuntu-24.04-arm
             arch: aarch64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
-            before-all: dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
-            extra-env: VCPKG_BUILD_TYPE=release
+            before-all: yum groupinstall -y "Development Tools" && dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
+            extra-env: ""
             mdt: ""
           - os: macos-15-intel
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
-            extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
+            extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
             mdt: ""
           - os: macos-15
             arch: arm64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
-            extra-env: CC=clang CXX=clang++ VCPKG_BUILD_TYPE=release
+            extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
             mdt: ""
 
     env:
@@ -51,7 +51,7 @@ jobs:
       CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
       CIBW_BEFORE_ALL: ${{ matrix.before-all }}
       CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
-      CIBW_ENVIRONMENT: ${{ matrix.extra-env }}
+      CIBW_ENVIRONMENT: VCPKG_BUILD_TYPE=release ${{ matrix.extra-env }}
     #      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
 
     steps:
diff --git a/.github/workflows/unit-macos.yml b/.github/workflows/unit-macos.yml
index 6dd7a7a..d4be979 100644
--- a/.github/workflows/unit-macos.yml
+++ b/.github/workflows/unit-macos.yml
@@ -32,7 +32,7 @@ jobs:
         run: mkdir build_dir
 
       - name: cmake configure
-        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=clang++
+        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_PREFIX_PATH=$(brew --prefix libomp)
         working-directory: build_dir
 
       - name: cmake build

From 8d7cdab76c002270f225617b57f2fbc63a7a88e6 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 15:49:42 +0100
Subject: [PATCH 20/27] Add mac deployment target 11 (Big Sur) and build py
 3.14 wheels

---
 .github/workflows/python-wheels.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index fedd6b7..3920cf8 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -21,28 +21,28 @@ jobs:
         include:
           - os: ubuntu-24.04
             arch: x86_64
-            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             before-all: yum groupinstall -y "Development Tools" && dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
             extra-env: ""
             mdt: ""
           - os: ubuntu-24.04-arm
             arch: aarch64
-            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             before-all: yum groupinstall -y "Development Tools" && dnf -y install ninja-build pkgconf openssl-devel zlib-devel bzip2-devel xz-devel
             extra-env: ""
             mdt: ""
           - os: macos-15-intel
             arch: x86_64
-            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
             extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
-            mdt: ""
+            mdt: 11
           - os: macos-15
             arch: arm64
-            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
+            py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
             before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
             extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
-            mdt: ""
+            mdt: 11
 
     env:
       CIBW_BUILD: ${{ matrix.py-vers }}
@@ -52,7 +52,7 @@ jobs:
       CIBW_BEFORE_ALL: ${{ matrix.before-all }}
       CIBW_BEFORE_BUILD: pip install --upgrade pip setuptools wheel ninja numpy cython
       CIBW_ENVIRONMENT: VCPKG_BUILD_TYPE=release ${{ matrix.extra-env }}
-    #      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
+      MACOSX_DEPLOYMENT_TARGET: ${{ matrix.mdt }}
 
     steps:
 

From 8afec91bca8acee96c78fce75e2161e7f6c7a7bd Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 15:57:13 +0100
Subject: [PATCH 21/27] Bump pybind version

---
 CMakeLists.txt     | 8 --------
 pyproject.toml     | 3 +--
 src/CMakeLists.txt | 2 +-
 3 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 51a2c6d..ae0f0e1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,14 +33,6 @@ include(cmake/StaticAnalysers.cmake)
 option(BUILD_SHARED_LIBS "Enable compilation of shared libraries" OFF)
 option(ENABLE_TESTING "Enable Test Builds" ON)
 
-option(PYTHON_BINDINGS "Whether to build the python bindings" OFF)
-if (EXISTS ${CMAKE_SOURCE_DIR}/pybind11/LICENSE)
-    set(PYTHON_BINDINGS ON)
-endif()
-if (PYTHON_BINDINGS)
-    add_subdirectory(pybind11)
-endif ()
-
 add_subdirectory(src)
 add_subdirectory(exe)
 
diff --git a/pyproject.toml b/pyproject.toml
index a17e444..c57ec97 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,8 +1,7 @@
 [build-system]
 requires = [
     "scikit-build-core>=0.11.6",
-    "cmake<4",
-    "pybind11==2.13.6"
+    "pybind11==3.0.1"
 ]
 build-backend = "scikit_build_core.build"
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 595e158..923d41c 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -129,7 +129,7 @@ if (PREPARE_DECODING_PYTHON_BINDINGS)
         FetchContent_Declare(
                 pybind11
                 GIT_REPOSITORY https://github.com/pybind/pybind11.git
-                GIT_TAG a2e59f0e7065404b44dfe92a28aca47ba1378dc4 # Version 2.13.6
+                GIT_TAG f5fbe867d2d26e4a0a9177a51f6e568868ad3dc8 # Version 3.0.1
         )
         FetchContent_MakeAvailable(pybind11)
     endif()

From e757912b391b33de5b43bfdf68ee8629586d836d Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 16:29:00 +0100
Subject: [PATCH 22/27] Remove openmp completely

---
 .github/workflows/python-wheels.yml   |  8 ++++----
 .github/workflows/sanitisers.yml      |  4 ----
 .github/workflows/static-analysis.yml |  4 ----
 .github/workflows/unit-macos.yml      |  4 ++--
 PyPI_README.md                        | 10 ++++++++++
 cmake/AsmcPrepareDecodingConfig.cmake |  1 -
 src/CMakeLists.txt                    |  4 +---
 7 files changed, 17 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
index 3920cf8..a9bea68 100644
--- a/.github/workflows/python-wheels.yml
+++ b/.github/workflows/python-wheels.yml
@@ -34,14 +34,14 @@ jobs:
           - os: macos-15-intel
             arch: x86_64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
-            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
-            extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
+            before-all: brew install pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
+            extra-env: CC=clang CXX=clang++
             mdt: 11
           - os: macos-15
             arch: arm64
             py-vers: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
-            before-all: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
-            extra-env: CC=clang CXX=clang++ CMAKE_PREFIX_PATH="$(brew --prefix libomp)"
+            before-all: brew install pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
+            extra-env: CC=clang CXX=clang++
             mdt: 11
 
     env:
diff --git a/.github/workflows/sanitisers.yml b/.github/workflows/sanitisers.yml
index 462d81c..f362d5b 100644
--- a/.github/workflows/sanitisers.yml
+++ b/.github/workflows/sanitisers.yml
@@ -24,10 +24,6 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - name: install tools
-        run: |
-          sudo apt -y install libomp-dev
-
       - name: make build directory
         run: mkdir build_dir
 
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 0625292..52a64e6 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -27,10 +27,6 @@ jobs:
       - name: make build directory
         run: mkdir build_dir
 
-      - name: install tools
-        run: |
-          sudo apt -y install libomp-dev
-
       - name: install analysers
         run: |
           sudo apt -y install cppcheck
diff --git a/.github/workflows/unit-macos.yml b/.github/workflows/unit-macos.yml
index d4be979..0820681 100644
--- a/.github/workflows/unit-macos.yml
+++ b/.github/workflows/unit-macos.yml
@@ -26,13 +26,13 @@ jobs:
           fetch-depth: 0
 
       - name: install system packages
-        run: brew install libomp pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
+        run: brew install pkg-config automake autoconf autoconf-archive libtool ninja openssl zlib bzip2 xz
 
       - name: make build directory
         run: mkdir build_dir
 
       - name: cmake configure
-        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_PREFIX_PATH=$(brew --prefix libomp)
+        run: cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_CXX_COMPILER=clang++
         working-directory: build_dir
 
       - name: cmake build
diff --git a/PyPI_README.md b/PyPI_README.md
index 5413584..84c5964 100644
--- a/PyPI_README.md
+++ b/PyPI_README.md
@@ -12,6 +12,16 @@
 
 Tool to compute decoding quantities.
 
+This is a Python-wrapped C++ project with prebuilt CPython wheels targeting manylinux_2_28 on Linux and macOS 11.0+.
+
+| 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
 
 ### Install the Python module from PyPI
diff --git a/cmake/AsmcPrepareDecodingConfig.cmake b/cmake/AsmcPrepareDecodingConfig.cmake
index c936b18..d3ce992 100644
--- a/cmake/AsmcPrepareDecodingConfig.cmake
+++ b/cmake/AsmcPrepareDecodingConfig.cmake
@@ -4,7 +4,6 @@ find_dependency(cereal)
 find_dependency(Eigen3)
 find_dependency(fmt)
 find_dependency(GMP)
-find_dependency(OpenMP)
 find_dependency(ZLIB)
 
 include(${CMAKE_CURRENT_LIST_DIR}/AsmcPrepareDecoding_Runtime.cmake)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 923d41c..e99d5e5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -99,8 +99,6 @@ if (BUILD_WITH_SMCPP_SUPPORT)
     find_package(cereal CONFIG REQUIRED)
     message(STATUS "Found cereal ${cereal_VERSION}")
 
-    find_package(OpenMP REQUIRED)
-
     add_library(smcpp_lib 3rd_party/smcpp.cpp 3rd_party/smcpp.hpp 3rd_party/mpreal.h)
 
     target_include_directories(
@@ -109,7 +107,7 @@ if (BUILD_WITH_SMCPP_SUPPORT)
             $<INSTALL_INTERFACE:3rd_party>
     )
 
-    target_link_libraries(smcpp_lib PRIVATE Eigen3::Eigen fmt::fmt PkgConfig::gmpxx PkgConfig::mpfr cereal::cereal OpenMP::OpenMP_CXX)
+    target_link_libraries(smcpp_lib PRIVATE Eigen3::Eigen fmt::fmt PkgConfig::gmpxx PkgConfig::mpfr cereal::cereal)
     set_target_properties(smcpp_lib PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
     set_target_properties(smcpp_lib PROPERTIES CXX_CLANG_TIDY "")
     set_target_properties(smcpp_lib PROPERTIES CXX_CPPCHECK "")

From 828148ef4362127cde1edbd5559885e4e31836c3 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 16:42:00 +0100
Subject: [PATCH 23/27] Begin preparing 2.2.4

---
 CMakeLists.txt   |  2 +-
 PyPI_README.md   |  9 +++------
 README.md        | 13 ++++++-------
 RELEASE_NOTES.md |  6 ++++++
 pyproject.toml   |  2 +-
 vcpkg.json       |  2 +-
 6 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ae0f0e1..bb1df97 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -7,7 +7,7 @@ include(cmake/AutodetectVcpkgToolchainFile.cmake)
 
 set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
-project(PrepareDecoding LANGUAGES CXX VERSION 2.2.3)
+project(PrepareDecoding LANGUAGES CXX VERSION 2.2.4)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
diff --git a/PyPI_README.md b/PyPI_README.md
index 84c5964..e0dc86d 100644
--- a/PyPI_README.md
+++ b/PyPI_README.md
@@ -24,20 +24,17 @@ This is a Python-wrapped C++ project with prebuilt CPython wheels targeting many
 
 ## Quickstart
 
-### Install the Python module from PyPI
+### Install the Python package from PyPI
 
-Most functionality is available through a Python module which can be installed with:
+Most functionality is available through a Python package which can be installed with:
 
 ```bash
 pip install asmc-preparedecoding
 ```
 
-This Python module is currently available on Linux and macOS.
-We hope it will be available soon on Windows.
-
 ### Example notebook
 
-Examples for using the Python module can be found in the following Jupyter notebook:
+Examples for using the Python package can be found in the following Jupyter notebook:
 - [creating decoding quantities](https://github.com/PalamaraLab/PrepareDecoding/blob/4a206d577a8cd431ab6dd59bbccc4035ab8b1069/notebooks/CreatingDecodingQuantities.ipynb)
 
 Please note that to run the notebook you should first clone the repository and install Jupyter:
diff --git a/README.md b/README.md
index 944d6df..88738a5 100644
--- a/README.md
+++ b/README.md
@@ -13,18 +13,17 @@ Tool to compute decoding quantities.
 
 ## Quickstart
 
-### Install the Python module from PyPI
+### Install the Python package from PyPI
 
-Most functionality is available through a Python module which can be installed with:
+Most functionality is available through a Python package which can be installed with:
 
 ```bash
 pip install asmc-preparedecoding
 ```
 
-This Python module is currently available on Linux and macOS.
-We hope it will be available soon on Windows.
+This Python package is currently available on Linux and macOS, x86_64 and arm64.
 
-Examples for using the Python module can be found in the following Jupyter notebook:
+Examples for using the Python package can be found in the following Jupyter notebook:
 - [creating decoding quantities](notebooks/CreatingDecodingQuantities.ipynb)
 
 Please note that you must install Jupyter in order to view the notebook, and then open it:
@@ -36,7 +35,7 @@ jupyter-notebook notebooks/CreatingDecodingQuantities.ipynb
 
 ### Compiling the C++ library and executable
 
-Get the source, together with the [vcpkg](https://github.com/microsoft/vcpkg) and [pybind11](https://github.com/pybind/pybind11) submodules:
+Get the source, together with the [vcpkg](https://github.com/microsoft/vcpkg) submodule:
 
 ```bash
 git clone --recurse-submodules https://github.com/PalamaraLab/PrepareDecoding.git
@@ -144,7 +143,7 @@ where `{{{SANITISER}}}` is one of:
 
 ## For developers: making a release
 
-- Bump the version number in [setup.py](setup.py), [CMakeLists.txt](CMakeLists.txt), and [vcpkg.json](vcpkg.json)
+- Bump the version number in [pyproject.toml](pyproject.toml), [CMakeLists.txt](CMakeLists.txt), and [vcpkg.json](vcpkg.json)
 - Update [RELEASE_NOTES.md](RELEASE_NOTES.md)
 - Update permalink to the notebook in [PyPI_README.md](PyPI_README.md)
 - Push changes and check that all [GitHub workflows](https://github.com/PalamaraLab/PrepareDecoding/actions) pass
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 9dfecc8..cdb4bb5 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,11 @@
 # Release Notes
 
+## v2.2.4 (2023-09-26)
+
+- wheels now available for ARM64 (Linux and macOS)
+- wheels now available for Python 3.9-3.14 (inclusive)
+- no change in functionality
+
 ## v2.2.3 (2023-02-22)
 
 Infrastructure updates and building wheels for newer Python versions.
diff --git a/pyproject.toml b/pyproject.toml
index c57ec97..6abfb60 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ build-backend = "scikit_build_core.build"
 [project]
 dynamic = ["readme"]
 name = "asmc-preparedecoding"
-version = "2.2.3"
+version = "2.2.4"
 description = "Prepare decoding quantities for ASMC & FastSMC"
 authors = [
     { name = "PalamaraLab (https://palamaralab.github.io/)" }
diff --git a/vcpkg.json b/vcpkg.json
index c8f94e7..48e1427 100644
--- a/vcpkg.json
+++ b/vcpkg.json
@@ -1,6 +1,6 @@
 {
   "name": "asmc-prepare-decoding",
-  "version-string": "2.2.3",
+  "version-string": "2.2.4",
   "homepage": "https://github.com/PalamaraLab/PrepareDecoding/",
   "description": "Prepare decoding quantities for ASMC & FastSMC",
   "dependencies": [

From 534adde6a8aa97d35c760312f40fcd0145284783 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 16:44:09 +0100
Subject: [PATCH 24/27] Add 3.14 to pyproject

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 6abfb60..ac7c0a5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,6 +28,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 
 [tool.scikit-build]

From 6fc81360bc88a8474af8bd86ef84fb396e88ace8 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 16:52:53 +0100
Subject: [PATCH 25/27] Add output of notebook cells

---
 notebooks/CreatingDecodingQuantities.ipynb | 163 +++++++++++++++++++--
 1 file changed, 148 insertions(+), 15 deletions(-)

diff --git a/notebooks/CreatingDecodingQuantities.ipynb b/notebooks/CreatingDecodingQuantities.ipynb
index 7663d3f..4f38de3 100644
--- a/notebooks/CreatingDecodingQuantities.ipynb
+++ b/notebooks/CreatingDecodingQuantities.ipynb
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "42f85552",
    "metadata": {},
    "outputs": [],
@@ -47,10 +47,78 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "56e8e52f",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Demography set to file /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_CEU.demo\n",
+      "Discretization file set to file /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_30-100-2000.disc\n",
+      "Frequencies file set to /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq\n",
+      "New CSFS will be calculated\n",
+      "Will read discretization intervals from /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_30-100-2000.disc ...\n",
+      "smcpp: init_cache() successful\n",
+      "smcpp: storing cache: /tmp/smcpp_matrices.dat\n",
+      "smcpp: store_cache() successful\n",
+      "Will use minor allele frequencies from /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq ...\n",
+      "Will use mutation rate mu = 1.65e-08.\n",
+      "Number of samples in CSFS calculations: 50.\n",
+      "Verified 69 CSFS entries.\n",
+      "Probability of a site being monomorphic due to subsampling: 0.222911939663710\n",
+      "\n",
+      "Building decoding quantities...\n",
+      "Genetic distances progress: 100%\t\n",
+      "Physical distances progress: 100%\t\n",
+      "Demography set to file /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_CEU.demo\n",
+      "Frequencies file set to /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq\n",
+      "New CSFS will be calculated\n",
+      "Using the following pre-specified discretization intervals: {0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 550, 650, 750, 850, 950, 1050, 1150, 1250, 1350, 1450, 1550, 1650, 1750, 1850, 1950}\n",
+      " and calculating 39 additional intervals from coalescent distribution.\n",
+      "smcpp: init_cache() successful\n",
+      "Will use minor allele frequencies from /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq ...\n",
+      "Will use mutation rate mu = 1.65e-08.\n",
+      "Number of samples in CSFS calculations: 50.\n",
+      "Verified 70 CSFS entries.\n",
+      "Probability of a site being monomorphic due to subsampling: 0.222911939663710\n",
+      "\n",
+      "Building decoding quantities...\n",
+      "Genetic distances progress: 100%\t\n",
+      "Physical distances progress: 100%\t\n",
+      "Demography set to built-in CEU\n",
+      "Frequencies file set to /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq\n",
+      "New CSFS will be calculated\n",
+      "Using the following pre-specified discretization intervals: {0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 550, 650, 750, 850, 950, 1050, 1150, 1250, 1350, 1450, 1550, 1650, 1750, 1850, 1950}\n",
+      " and calculating 39 additional intervals from coalescent distribution.\n",
+      "smcpp: init_cache() successful\n",
+      "Will use minor allele frequencies from /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/input_UKBB.frq ...\n",
+      "Will use mutation rate mu = 1.65e-08.\n",
+      "Number of samples in CSFS calculations: 50.\n",
+      "Verified 70 CSFS entries.\n",
+      "Probability of a site being monomorphic due to subsampling: 0.222911939663710\n",
+      "\n",
+      "Building decoding quantities...\n",
+      "Genetic distances progress: 100%\t\n",
+      "Physical distances progress: 100%\t\n",
+      "Demography set to built-in CEU\n",
+      "Frequencies set to built-in UKBB with 50 samples\n",
+      "New CSFS will be calculated\n",
+      "Using the following pre-specified discretization intervals: {0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 550, 650, 750, 850, 950, 1050, 1150, 1250, 1350, 1450, 1550, 1650, 1750, 1850, 1950}\n",
+      " and calculating 39 additional intervals from coalescent distribution.\n",
+      "smcpp: init_cache() successful\n",
+      "Using built-in frequency information from UKBB ...\n",
+      "Will use mutation rate mu = 1.65e-08.\n",
+      "Number of samples in CSFS calculations: 50.\n",
+      "Verified 70 CSFS entries.\n",
+      "\n",
+      "Building decoding quantities...\n",
+      "Genetic distances progress: 100%\t\n",
+      "Physical distances progress: 100%\t"
+     ]
+    }
+   ],
    "source": [
     "files_dir = (pathlib.Path('..') / 'test' / 'regression').resolve()\n",
     "\n",
@@ -104,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "e1d704d3",
    "metadata": {},
    "outputs": [],
@@ -133,10 +201,31 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "84e495bb",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Demography set to built-in CEU\n",
+      "Frequencies set to built-in UKBB with 50 samples\n",
+      "Precomputed CSFS will be loaded from file: /home/fcooper/GitRepos/PalamaraLab/PrepareDecoding/test/regression/output.csfs\n",
+      "Using the following pre-specified discretization intervals: {0, 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 550, 650, 750, 850, 950, 1050, 1150, 1250, 1350, 1450, 1550, 1650, 1750, 1850, 1950}\n",
+      " and calculating 39 additional intervals from coalescent distribution.\n",
+      "Using built-in frequency information from UKBB ...\n",
+      "Will use mutation rate mu = 1.65e-08.\n",
+      "Number of samples in CSFS calculations: 50.\n",
+      "Verified 70 CSFS entries.\n",
+      "\n",
+      "Building decoding quantities...\n",
+      "Genetic distances progress: 100%\t\n",
+      "Physical distances progress: 100%\t"
+     ]
+    }
+   ],
    "source": [
     "dq = prepare_decoding(\n",
     "    csfs_file=str(files_dir / 'output.csfs'),\n",
@@ -157,10 +246,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "6ecc7fd7",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'states': 70, 'samples': 50, 'mu': 1.65e-08}"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "{\"states\": dq.states, \"samples\": dq.samples, \"mu\": dq.mu}"
    ]
@@ -175,10 +275,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "fad47cb3",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(numpy.ndarray, (2, 70))"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "X = dq.compressedEmission\n",
     "type(X), X.shape"
@@ -194,20 +305,42 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "aacfc6cd",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "70"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "len([x for x in dq.CSFS])"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "id": "2a1689b4",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(3, 49)"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "c0 = dq.CSFS[0]\n",
     "{\"mu\": c0.mu, \"from\": c0.csfsFrom, \"to\": c0.csfsTo, \"samples\": c0.samples}\n",
@@ -231,7 +364,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.11.11"
   }
  },
  "nbformat": 4,

From 0e08b309a294579fb5c22fdeb39e6f799736aa98 Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 16:54:34 +0100
Subject: [PATCH 26/27] Generic link to notebook with output

---
 PyPI_README.md | 2 +-
 README.md      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/PyPI_README.md b/PyPI_README.md
index e0dc86d..0ad6a29 100644
--- a/PyPI_README.md
+++ b/PyPI_README.md
@@ -35,7 +35,7 @@ pip install asmc-preparedecoding
 ### Example notebook
 
 Examples for using the Python package can be found in the following Jupyter notebook:
-- [creating decoding quantities](https://github.com/PalamaraLab/PrepareDecoding/blob/4a206d577a8cd431ab6dd59bbccc4035ab8b1069/notebooks/CreatingDecodingQuantities.ipynb)
+- [creating decoding quantities](https://github.com/PalamaraLab/PrepareDecoding/blob/main/notebooks/CreatingDecodingQuantities.ipynb)
 
 Please note that to run the notebook you should first clone the repository and install Jupyter:
 
diff --git a/README.md b/README.md
index 88738a5..bd010d4 100644
--- a/README.md
+++ b/README.md
@@ -145,7 +145,7 @@ where `{{{SANITISER}}}` is one of:
 
 - Bump the version number in [pyproject.toml](pyproject.toml), [CMakeLists.txt](CMakeLists.txt), and [vcpkg.json](vcpkg.json)
 - Update [RELEASE_NOTES.md](RELEASE_NOTES.md)
-- Update permalink to the notebook in [PyPI_README.md](PyPI_README.md)
+- Ensure supported python versions are up-to-date in [pyproject.toml](pyproject.toml)
 - Push changes and check that all [GitHub workflows](https://github.com/PalamaraLab/PrepareDecoding/actions) pass
 - Tag the commit in Git using syntax `vX.Y.Z`
 - Make a release on GitHub, which should trigger a new build that will upload Python wheels to PyPI

From 9b138cbb4da23803b5abcc70194dae04eb2d6d5b Mon Sep 17 00:00:00 2001
From: Fergus Cooper <fcooper8472@gmail.com>
Date: Fri, 26 Sep 2025 17:09:13 +0100
Subject: [PATCH 27/27] Update README badges

---
 PyPI_README.md | 2 --
 README.md      | 1 -
 2 files changed, 3 deletions(-)

diff --git a/PyPI_README.md b/PyPI_README.md
index 0ad6a29..1f6d761 100644
--- a/PyPI_README.md
+++ b/PyPI_README.md
@@ -1,4 +1,3 @@
-[![Unit tests: Windows](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20Windows/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Unit tests: Ubuntu](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20Ubuntu/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Unit tests: macOS](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20macOS/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Regression test](https://github.com/PalamaraLab/PrepareDecoding/workflows/Regression%20test/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
@@ -6,7 +5,6 @@
 [![Static analysis checks](https://github.com/PalamaraLab/PrepareDecoding/workflows/Static%20analysis%20checks/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Sanitiser checks](https://github.com/PalamaraLab/PrepareDecoding/workflows/Sanitiser%20checks/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![codecov](https://codecov.io/gh/PalamaraLab/PrepareDecoding/branch/master/graph/badge.svg)](https://codecov.io/gh/PalamaraLab/PrepareDecoding)
-[![BCH compliance](https://bettercodehub.com/edge/badge/PalamaraLab/PrepareDecoding?branch=master)](https://bettercodehub.com/results/PalamaraLab/PrepareDecoding)
 
 # ASMC Prepare Decoding
 
diff --git a/README.md b/README.md
index bd010d4..40dee7d 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,3 @@
-[![Unit tests: Windows](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20Windows/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Unit tests: Ubuntu](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20Ubuntu/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Unit tests: macOS](https://github.com/PalamaraLab/PrepareDecoding/workflows/Unit%20tests:%20macOS/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)
 [![Regression test](https://github.com/PalamaraLab/PrepareDecoding/workflows/Regression%20test/badge.svg)](https://github.com/PalamaraLab/PrepareDecoding/actions)