fix(pybind): pinned pybind to 3.0.0 for ABI compatibility

updated to the version of libcomposition which fixes the atomic header installation directory

.gitignore

@@ -110,3 +110,5 @@ output/
 scratch/
 
 node_modules/
+
+*.whl

meson.build

@@ -1,4 +1,4 @@
-project('fourdst', 'cpp', version: 'v0.10.4', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
+project('fourdst', 'cpp', version: 'v0.10.6', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
 
 add_project_arguments('-fvisibility=default', language: 'cpp')
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["meson-python>=0.19,<0.20", "meson>=1.9.1,<1.10", "pybind11>=2.10"]
+requires = ["meson-python>=0.19,<0.20", "meson>=1.9.1,<1.10", "pybind11==3.0.0"]
 build-backend = "mesonpy"
 
 [project]
@@ -34,6 +34,7 @@ fourdst-include-dirs = "fourdst:get_include_dirs"
 fourdst-lib-dirs = "fourdst:get_lib_dirs"
 fourdst-rpath-flags = "fourdst:get_rpath_flags"
 fourdst-version = "fourdst:print_fourdst_version"
+fourdst-extra-flags = "fourdst:get_extra_flags"
 
 [tool.meson-python.args]
 setup = [

src-pybind/fourdst/__init__.py

@@ -54,8 +54,12 @@ def get_include_flags() -> List[str]:
 def get_compiler_flags() -> List[str]:
     return get_include_flags() + get_lib_flags()
 
+def get_extra_flags() -> List[str]:
+    return ['-fPIC', '-std=c++23']
+
 def get_compiler_flags_formatted() -> int:
     flags = get_compiler_flags()
+    flags.extend(get_extra_flags())
     print(' '.join(flags))
     return 0
 

subprojects/libcomposition.wrap

@@ -1,4 +1,4 @@
 [wrap-git]
 url = https://github.com/4D-STAR/libcomposition.git
-revision = v2.4.8
+revision = v2.4.9
 depth = 1

subprojects/packagefiles/pybind11/LICENSE.build

@@ -0,0 +1,19 @@
+Copyright (c) 2021 The Meson development team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

subprojects/packagefiles/pybind11/meson.build

@@ -0,0 +1,8 @@
+project('pybind11', 'cpp',
+        version : 'v3.0.0',
+        license : 'BSD-3-Clause')
+
+pybind11_incdir = include_directories('include')
+
+pybind11_dep = declare_dependency(
+  include_directories : pybind11_incdir)

subprojects/pybind11.wrap

@@ -1,13 +1,8 @@
-[wrap-file]
-directory = pybind11-2.13.5
-source_url = https://github.com/pybind/pybind11/archive/refs/tags/v2.13.5.tar.gz
-source_filename = pybind11-2.13.5.tar.gz
-source_hash = b1e209c42b3a9ed74da3e0b25a4f4cd478d89d5efbb48f04b277df427faf6252
-patch_filename = pybind11_2.13.5-1_patch.zip
-patch_url = https://wrapdb.mesonbuild.com/v2/pybind11_2.13.5-1/get_patch
-patch_hash = ecb031b830481560b3d8487ed63ba4f5509a074be42f5d19af64d844c795e15b
-source_fallback_url = https://github.com/mesonbuild/wrapdb/releases/download/pybind11_2.13.5-1/pybind11-2.13.5.tar.gz
-wrapdb_version = 2.13.5-1
+[wrap-git]
+url = https://github.com/pybind/pybind11.git
+revision = v3.0.0
+depth = 1
+patch_directory = pybind11
 
 [provide]
 pybind11 = pybind11_dep

utils/wheels/build-wheels-linux_aarch64.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Must be run on an aarch64 Linux host (uses docker so arm macos is fine so long as as the daemon is running)
+
+if [[ $# -ne 1 ]]; then
+  echo "Usage: $0 <git-repo-url>"
+  echo "Example: $0 https://github.com/4D-STAR/fourdst"
+  exit 1
+fi
+
+REPO_URL="$1"
+WORK_DIR="$(pwd)"
+WHEEL_DIR="${WORK_DIR}/wheels_linux_aarch64"
+
+echo "➤ Creating wheel output directory at ${WHEEL_DIR}"
+mkdir -p "${WHEEL_DIR}"
+
+TMPDIR="$(mktemp -d)"
+echo "➤ Cloning ${REPO_URL} → ${TMPDIR}/project"
+git clone --depth 1 "${REPO_URL}" "${TMPDIR}/project"
+
+IMAGE="tboudreaux/manylinux_2_28_aarch64_boost_1_88_0:latest"
+
+docker run --rm \
+  -v "${WHEEL_DIR}":/io/wheels \
+  -v "${TMPDIR}/project":/io/project \
+  "${IMAGE}" \
+  /bin/bash -eux -c '
+    cd /io/project
+    RAW=/tmp/raw_wheels
+
+    for PY in /opt/python/*/bin/python; do
+      "$PY" -m pip install --upgrade pip
+
+      rm -rf "$RAW"; mkdir -p "$RAW"
+
+       CC=clang CXX=clang++ "$PY" -m pip wheel . \
+        --no-deps \
+        -w "$RAW" -vv
+
+      for whl in "$RAW"/*.whl; do
+        auditwheel repair "$whl" -w /io/wheels
+      done
+    done
+
+    echo "Linux aarch64 wheels ready in /io/wheels"
+  '
+
+echo "Done. Repaired wheels in ${WHEEL_DIR}"
+rm -rf "${TMPDIR}"

utils/wheels/build-wheels-linux_x86_64.sh

@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ $# -ne 1 ]]; then
+  echo "Usage: $0 <git-repo-url>"
+  echo "Example: $0 https://github.com/4D-STAR/fourdst"
+  exit 1
+fi
+
+REPO_URL="$1"
+WORK_DIR="$(pwd)"
+WHEEL_DIR="${WORK_DIR}/wheels_linux_x86_64"
+
+echo "➤ Creating wheel output directory at ${WHEEL_DIR}"
+mkdir -p "${WHEEL_DIR}"
+
+TMPDIR="$(mktemp -d)"
+echo "➤ Cloning ${REPO_URL} → ${TMPDIR}/project"
+git clone --depth 1 "${REPO_URL}" "${TMPDIR}/project"
+
+IMAGE="tboudreaux/manylinux_2_28_x86_64_boost_1_88_0:latest"
+
+docker run --rm \
+  -v "${WHEEL_DIR}":/io/wheels \
+  -v "${TMPDIR}/project":/io/project \
+  "${IMAGE}" \
+  /bin/bash -eux -c '
+    cd /io/project
+    RAW=/tmp/raw_wheels
+
+    for PY in /opt/python/*/bin/python; do
+      "$PY" -m pip install --upgrade pip
+
+      rm -rf "$RAW"; mkdir -p "$RAW"
+
+      CC=clang CXX=clang++ "$PY" -m pip wheel . \
+        --no-deps \
+        --config-settings=setup-args=-Dunity=on \
+        -w "$RAW" -vv
+
+      # Repair only the freshly built wheel into the shared output dir.
+      for whl in "$RAW"/*.whl; do
+        auditwheel repair "$whl" -w /io/wheels
+      done
+    done
+
+    echo "Linux x86_64 wheels ready in /io/wheels"
+  '
+
+echo "Done. Repaired wheels in ${WHEEL_DIR}"
+rm -rf "${TMPDIR}"

utils/wheels/build-wheels-macos_aarch64.sh

@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Must be run on an Apple Silicon (arm64) Mac.
+
+if [[ $(uname -m) != "arm64" ]]; then
+  echo "Error: This script is intended to run on an Apple Silicon (arm64) Mac."
+  exit 1
+fi
+
+if [[ $# -ne 1 ]]; then
+  echo "Usage: $0 <git-repo-url>"
+  echo "Example: $0 https://github.com/4D-STAR/fourdst"
+  exit 1
+fi
+
+REPO_URL="$1"
+WORK_DIR="$(pwd)"
+WHEEL_DIR="${WORK_DIR}/wheels_macos_aarch64_tmp"
+FINAL_WHEEL_DIR="${WORK_DIR}/wheels_macos_aarch64"
+
+echo "➤ Creating wheel output directories"
+mkdir -p "${WHEEL_DIR}"
+mkdir -p "${FINAL_WHEEL_DIR}"
+
+TMPDIR="$(mktemp -d)"
+echo "➤ Cloning ${REPO_URL} → ${TMPDIR}/project"
+git clone --depth 1 "${REPO_URL}" "${TMPDIR}/project"
+cd "${TMPDIR}/project"
+
+export MACOSX_DEPLOYMENT_TARGET=15.0
+
+PYTHON_VERSIONS=("3.9.23" "3.10.18" "3.11.13" "3.12.11" "3.13.5" "3.13.5t" "3.14.0rc1" "3.14.0rc1t" "3.14-dev" "3.14t-dev" )
+
+if ! command -v pyenv &> /dev/null; then
+    echo "Error: pyenv not found. Please install it to manage Python versions."
+    echo "       Then run installPyEnvVersions.sh to install the interpreters above."
+    exit 1
+fi
+eval "$(pyenv init -)"
+
+for PY_VERSION in "${PYTHON_VERSIONS[@]}"; do
+  (
+    set -e
+
+    pyenv shell "${PY_VERSION}"
+    PY="$(pyenv which python)"
+
+    echo "----------------------------------------------------------------"
+    echo "➤ Building for $($PY --version) on macOS arm64"
+    echo "----------------------------------------------------------------"
+
+    "$PY" -m pip install --upgrade pip
+    "$PY" -m pip install "meson>=1.9.1,<1.10" "meson-python>=0.19,<0.20" "pybind11>=2.10" delocate
+
+    echo "➤ Building wheel with ccache enabled"
+    echo "➤ Found meson version $(meson --version)"
+
+    CC="ccache clang" CXX="ccache clang++" "$PY" -m pip wheel . \
+      --no-deps --no-build-isolation -w "${WHEEL_DIR}" -v
+
+    CURRENT_WHEEL=$(find "${WHEEL_DIR}" -name "*.whl" | head -n 1)
+
+    echo "➤ Repairing wheel with delocate"
+    delocate-wheel -w "${FINAL_WHEEL_DIR}" "$CURRENT_WHEEL"
+
+    rm "$CURRENT_WHEEL"
+  )
+done
+
+rm -rf "${TMPDIR}"
+rm -rf "${WHEEL_DIR}"
+
+echo "➤ All builds complete. Artifacts in ${FINAL_WHEEL_DIR}"

utils/wheels/installPyEnvVersions.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+# Install every interpreter the macOS arm64 build matrix iterates over.
+# Run once before build-wheels-macos_aarch64.sh.
+
+pyenv install -s 3.9.23
+pyenv install -s 3.10.18
+pyenv install -s 3.11.13
+pyenv install -s 3.12.11
+pyenv install -s 3.13.5
+pyenv install -s 3.13.5t
+pyenv install -s 3.14.0rc1
+pyenv install -s 3.14.0rc1t
+pyenv install -s 3.14-dev
+pyenv install -s 3.14t-dev
+pyenv install -s 3.15-dev
+pyenv install -s 3.15t-dev

utils/wheels/readme.md

@@ -0,0 +1,42 @@
+# Wheel Generation
+
+This directory contains scripts to generate precompiled Python wheels for **fourdst**.
+
+## Notes
+
+- macOS wheels can only be generated on macOS.
+- aarch64 wheels can only be generated on an aarch64 machine.
+- x86_64 wheels can only be generated on an x86_64 machine.
+- Linux wheels can be generated on any Linux machine, but the target architecture must match the host architecture (Docker runs natively, there is no emulation here).
+- Running each script takes **a very long time** (potentially most of a day, depending on the machine) and needs roughly 2 GB of disk space.
+- For the macOS build you must have all the listed Python versions installed via `pyenv`. Run `installPyEnvVersions.sh` first to install them.
+- The old duplicate-RPATH workaround (`repair_wheel_macos.sh` + `fix_rpaths.py`) is **no longer needed** — the meson-python bug that caused it has been fixed, so the macOS script repairs with a plain `delocate-wheel` pass. Those two files can be deleted.
+
+## Usage
+
+Once you are on the correct machine, run the script for your target platform, passing the repository URL. For example, to build the macOS arm64 wheels:
+
+```bash
+./build-wheels-macos_aarch64.sh https://github.com/4D-STAR/fourdst
+```
+
+For Linux:
+
+```bash
+./build-wheels-linux_x86_64.sh  https://github.com/4D-STAR/fourdst   # on an x86_64 host
+./build-wheels-linux_aarch64.sh https://github.com/4D-STAR/fourdst   # on an aarch64 host
+```
+
+Each script writes its repaired, redistributable wheels to a per-platform directory (e.g. `wheels_macos_aarch64/`, `wheels_linux_x86_64/`).
+
+## Publishing
+
+Once every platform's wheels are generated (which generally requires multiple machines), copy them all into a single directory — assume it is called `wheels/` at the repository root — then, from the repository root:
+
+```bash
+python -m pip install --upgrade build twine
+python -m build --sdist --outdir wheels   # adds the source distribution
+twine upload wheels/*
+```
+
+This uploads every wheel plus the sdist to PyPI (also slow, since it has to upload all of them).