From e9101ab57f9fb4ab076ff9eb2a3b5e85aaafc21b Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 19 Jul 2024 01:25:36 +0100
Subject: [PATCH 01/29] draft scikit build core wheel

---
 CMakeLists.txt        | 10 ++++++++++
 openmc/__init__.py    |  1 +
 openmc/openmc_exec.py | 22 ++++++++++++++++++++++
 pyproject.toml        |  9 ++++++++-
 setup.py              | 11 +++++++++--
 5 files changed, 50 insertions(+), 3 deletions(-)
 create mode 100644 openmc/openmc_exec.py

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0f4cc1b527b..d7fa6cb2a2f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,6 +16,11 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 # Set module path
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
 
+# Conditionally find Python if building with scikit-build-core
+if(SKBUILD)
+  find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+endif()
+
 # Enable correct usage of CXX_EXTENSIONS
 if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
   cmake_policy(SET CMP0128 NEW)
@@ -614,3 +619,8 @@ install(FILES man/man1/openmc.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 install(FILES LICENSE DESTINATION "${CMAKE_INSTALL_DOCDIR}" RENAME copyright)
 install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 install(FILES "${CMAKE_BINARY_DIR}/include/openmc/version.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/openmc)
+
+if(SKBUILD)
+  install(TARGETS openmc RUNTIME DESTINATION openmc/bin)
+  install(TARGETS libopenmc LIBRARY DESTINATION openmc/lib)
+endif()
diff --git a/openmc/__init__.py b/openmc/__init__.py
index 566d287068f..32320365d58 100644
--- a/openmc/__init__.py
+++ b/openmc/__init__.py
@@ -34,6 +34,7 @@
 from openmc.polynomial import *
 from openmc.tracks import *
 from .config import *
+from .openmc_exec import main
 
 # Import a few names from the model module
 from openmc.model import Model
diff --git a/openmc/openmc_exec.py b/openmc/openmc_exec.py
new file mode 100644
index 00000000000..72cd283beff
--- /dev/null
+++ b/openmc/openmc_exec.py
@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+
+# helper script that launches the openmc binary
+
+import os
+import sys
+import sysconfig
+from pathlib import Path
+
+
+def main():
+    lib_path = sysconfig.get_path("platlib") + "openmc/lib/openmc"
+    os.environ["LD_LIBRARY_PATH"] = (
+        lib_path + ":" + os.environ.get("LD_LIBRARY_PATH", "")
+    )
+    os.execv(
+        Path(sysconfig.get_path("platlib")) / "openmc" / "bin" / "openmc", sys.argv
+    )
+
+
+if __name__ == "__main__":
+    main()
diff --git a/pyproject.toml b/pyproject.toml
index d1b2c335cd7..08bc9ad1313 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,6 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy", "cython"]
+requires = ["setuptools", "wheel", "numpy", "cython", "scikit-build-core"]
+build-backend = "scikit_build_core.build"
 
 [project]
 name = "openmc"
@@ -72,3 +73,9 @@ openmc-track-to-vtk = "scripts.openmc_track_to_vtk:main"
 openmc-update-inputs = "scripts.openmc_update_inputs:main"
 openmc-update-mgxs = "scripts.openmc_update_mgxs:main"
 openmc-voxel-to-vtk = "scripts.openmc_voxel_to_vtk:main"
+openmc-exec = "openmc.openmc_exec:main"
+
+[tool.scikit-build]
+cmake.verbose = true
+# cmake args can be passed in here or in the command line via exports or inline with the pip install
+cmake.args = ["-DCMAKE_BUILD_TYPE=RELEASE"]
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 4e24f48a123..32cf2483ce0 100755
--- a/setup.py
+++ b/setup.py
@@ -1,13 +1,20 @@
 #!/usr/bin/env python
 
+import os
 import numpy as np
-from setuptools import setup
+from setuptools import setup, Extension
 from Cython.Build import cythonize
 
 
+class OpenMCExtension(Extension):
+    def __init__(self, name, cmake_lists_dir=".", sources=[], **kwa):
+        Extension.__init__(self, name, sources=sources, **kwa)
+        self.cmake_lists_dir = os.path.abspath(cmake_lists_dir)
+
+
 kwargs = {
     # Cython is used to add resonance reconstruction and fast float_endf
-    'ext_modules': cythonize('openmc/data/*.pyx'),
+    'ext_modules': cythonize('openmc/data/*.pyx') + [OpenMCExtension('libopenmc')],
     'include_dirs': [np.get_include()]
 }
 

From e857f4529cd8833c475ee1cecbf6af7e48a61493 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 19 Jul 2024 01:31:11 +0100
Subject: [PATCH 02/29] renamed executable

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 08bc9ad1313..69090111b33 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,7 +73,7 @@ openmc-track-to-vtk = "scripts.openmc_track_to_vtk:main"
 openmc-update-inputs = "scripts.openmc_update_inputs:main"
 openmc-update-mgxs = "scripts.openmc_update_mgxs:main"
 openmc-voxel-to-vtk = "scripts.openmc_voxel_to_vtk:main"
-openmc-exec = "openmc.openmc_exec:main"
+openmc = "openmc.openmc_exec:main"
 
 [tool.scikit-build]
 cmake.verbose = true

From 61b7035681230cb0c94e8b819584ee104873faed Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Fri, 19 Jul 2024 10:02:52 +0100
Subject: [PATCH 03/29] linking libopenmc with openmc in cmakelists

---
 CMakeLists.txt        | 7 ++++++-
 openmc/openmc_exec.py | 4 ----
 pyproject.toml        | 4 ++--
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d7fa6cb2a2f..7c86c391521 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -332,6 +332,11 @@ if("${isSystemDir}" STREQUAL "-1")
   set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
 endif()
 
+if(SKBUILD)
+  set(CMAKE_INSTALL_RPATH "$ORIGIN")
+  set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+endif()
+
 #===============================================================================
 # libopenmc
 #===============================================================================
@@ -622,5 +627,5 @@ install(FILES "${CMAKE_BINARY_DIR}/include/openmc/version.h" DESTINATION ${CMAKE
 
 if(SKBUILD)
   install(TARGETS openmc RUNTIME DESTINATION openmc/bin)
-  install(TARGETS libopenmc LIBRARY DESTINATION openmc/lib)
+  install(TARGETS libopenmc LIBRARY DESTINATION openmc/bin)
 endif()
diff --git a/openmc/openmc_exec.py b/openmc/openmc_exec.py
index 72cd283beff..579eeced24f 100644
--- a/openmc/openmc_exec.py
+++ b/openmc/openmc_exec.py
@@ -9,10 +9,6 @@
 
 
 def main():
-    lib_path = sysconfig.get_path("platlib") + "openmc/lib/openmc"
-    os.environ["LD_LIBRARY_PATH"] = (
-        lib_path + ":" + os.environ.get("LD_LIBRARY_PATH", "")
-    )
     os.execv(
         Path(sysconfig.get_path("platlib")) / "openmc" / "bin" / "openmc", sys.argv
     )
diff --git a/pyproject.toml b/pyproject.toml
index 08bc9ad1313..c236b968035 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,9 +73,9 @@ openmc-track-to-vtk = "scripts.openmc_track_to_vtk:main"
 openmc-update-inputs = "scripts.openmc_update_inputs:main"
 openmc-update-mgxs = "scripts.openmc_update_mgxs:main"
 openmc-voxel-to-vtk = "scripts.openmc_voxel_to_vtk:main"
-openmc-exec = "openmc.openmc_exec:main"
+openmc = "openmc.openmc_exec:main"
 
 [tool.scikit-build]
 cmake.verbose = true
 # cmake args can be passed in here or in the command line via exports or inline with the pip install
-cmake.args = ["-DCMAKE_BUILD_TYPE=RELEASE"]
\ No newline at end of file
+cmake.args = ["-DCMAKE_BUILD_TYPE=RELEASE"]

From 2541d50e557653ba6dc17e70c47db8431edc72a4 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Sat, 20 Jul 2024 00:08:42 +0100
Subject: [PATCH 04/29] updated docs for pip install that compiles

---
 docs/source/quickinstall.rst       | 25 ++++++------------
 docs/source/usersguide/install.rst | 42 +++++++++++++++++++++++-------
 2 files changed, 40 insertions(+), 27 deletions(-)

diff --git a/docs/source/quickinstall.rst b/docs/source/quickinstall.rst
index 7f222f77cb8..3e0778a9eca 100644
--- a/docs/source/quickinstall.rst
+++ b/docs/source/quickinstall.rst
@@ -160,28 +160,19 @@ download and install OpenMC by entering the following commands in a terminal:
 
     git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
     cd openmc
-    mkdir build && cd build
-    cmake ..
-    make
-    sudo make install
+    python -m pip install .
 
-This will build an executable named ``openmc`` and install it (by default in
-/usr/local/bin). If you do not have administrator privileges, the cmake command
-should specify an installation directory where you have write access, e.g.
+The easiest way to install it is using `pip <https://pip.pypa.io/en/stable/>`_.
+This `pip` command will install the `openmc` Python package and compile an executable named ``openmc``
+and install it (by default in the bin folder of the Python package directory).
 
 .. code-block:: sh
 
-    cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local ..
-
-The :mod:`openmc` Python package must be installed separately. The easiest way
-to install it is using `pip <https://pip.pypa.io/en/stable/>`_.
-From the root directory of the OpenMC repository, run:
+    python -m pip install . --global-option="build_ext" --global-option="--" --global-option="-DOPENMC_USE_MPI=ON"
 
-.. code-block:: sh
-
-    python -m pip install .
 
+The compilion of the ``openmc`` can be customised by specifying CMake arguments.
 By default, OpenMC will be built with multithreading support. To build
-distributed-memory parallel versions of OpenMC using MPI or to configure other
-options, directions can be found in the :ref:`detailed installation instructions
+distributed-memory parallel versions of OpenMC using MPI the above command can be run.
+There are other options that can be set, more details can be found in the :ref:`detailed installation instructions
 <usersguide_build>`.
diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst
index 130e96c0ae6..203ec879430 100644
--- a/docs/source/usersguide/install.rst
+++ b/docs/source/usersguide/install.rst
@@ -175,9 +175,9 @@ feature can be used to access the installed packages.
 
 .. _install_source:
 
-----------------------
-Installing from Source
-----------------------
+--------------------------------
+Compiling from Source with CMake
+--------------------------------
 
 .. _prerequisites:
 
@@ -367,6 +367,8 @@ Note that first a build directory is created as a subdirectory of the source
 directory. The Makefile in the top-level directory will automatically perform an
 out-of-source build with default options.
 
+.. _cmake_arguemnts:
+
 CMakeLists.txt Options
 ++++++++++++++++++++++
 
@@ -505,15 +507,15 @@ To run the test suite, you will first need to download a pre-generated cross
 section library along with windowed multipole data. Please refer to our
 :ref:`devguide_tests` documentation for further details.
 
----------------------
-Installing Python API
----------------------
+-----------------------------------------------
+Installing Python API and compiling from source
+-----------------------------------------------
 
 If you installed OpenMC using :ref:`Conda <install_conda>`, no further steps are
 necessary in order to use OpenMC's :ref:`Python API <pythonapi>`. However, if
-you are :ref:`installing from source <install_source>`, the Python API is not
-installed by default when ``make install`` is run because in many situations it
-doesn't make sense to install a Python package in the same location as the
+you are :ref:`Compiling from Source with CMake <install_source>`, the Python API
+is not installed by default when ``make install`` is run because in many situations
+it doesn't make sense to install a Python package in the same location as the
 ``openmc`` executable (for example, if you are installing the package into a
 `virtual environment <https://docs.python.org/3/tutorial/venv.html>`_). The
 easiest way to install the :mod:`openmc` Python package is to use pip_, which is
@@ -527,7 +529,27 @@ distribution/repository, run:
 pip will first check that all :ref:`required third-party packages
 <usersguide_python_prereqs>` have been installed, and if they are not present,
 they will be installed by downloading the appropriate packages from the Python
-Package Index (`PyPI <https://pypi.org/>`_).
+Package Index (`PyPI <https://pypi.org/>`_). The pip command will also compile
+an executable named ``openmc`` and install it (by default in the bin folder of
+the Python package directory).
+
+Passing CMake Options to via pip
+--------------------------------
+
+If you need to pass CMake options to the build process, you can do so by
+running pip install with some additional options. All the CMake arguments
+covered in the :ref:`CMakeLists.txt Options<cmake_arguemnts>` are supported.
+For example, to build OpenMC with MPI support, you can run:
+
+.. code-block:: sh
+
+    python -m pip install . --global-option="build_ext" --global-option="--" --global-option="-DOPENMC_USE_MPI=ON"
+
+To build OpenMC with DAGMC support two CMake arguments are needed, you can run:
+
+.. code-block:: sh
+
+    python -m pip install . --global-option="build_ext" --global-option="--" --global-option="-DOPENMC_USE_DAGMC=ON" --global-option="-DDAGMC_ROOT=/path/to/dagmc/installation"
 
 Installing in "Development" Mode
 --------------------------------

From f15e80f00537660919b2d8ff9d8b66f65562953b Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Tue, 23 Jul 2024 19:04:34 +0100
Subject: [PATCH 05/29] pip install with cmake args in ci

---
 tools/ci/gha-install.py | 33 ++++++++++++++++-----------------
 tools/ci/gha-install.sh |  3 ---
 2 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index f4b2fbb3187..5cf46baa24c 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -26,48 +26,47 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
     os.chdir('build')
 
     # Build in debug mode by default with support for MCPL
-    cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DOPENMC_USE_MCPL=on']
+    pip_command = ['pip' 'install' '.[test,vtk]']
+    pip_suffix = ['--config-settings=cmake.args=-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
 
     # Turn off OpenMP if specified
     if not omp:
-        cmake_cmd.append('-DOPENMC_USE_OPENMP=off')
+        pip_suffix.append('-DOPENMC_USE_OPENMP=off')
 
     # Use MPI wrappers when building in parallel
     if mpi:
-        cmake_cmd.append('-DOPENMC_USE_MPI=on')
+        pip_suffix.append('-DOPENMC_USE_MPI=on')
 
     # Tell CMake to prefer parallel HDF5 if specified
     if phdf5:
         if not mpi:
             raise ValueError('Parallel HDF5 must be used in '
                              'conjunction with MPI.')
-        cmake_cmd.append('-DHDF5_PREFER_PARALLEL=ON')
+        pip_suffix.append('-DHDF5_PREFER_PARALLEL=ON')
     else:
-        cmake_cmd.append('-DHDF5_PREFER_PARALLEL=OFF')
+        pip_suffix.append('-DHDF5_PREFER_PARALLEL=OFF')
 
     if dagmc:
-        cmake_cmd.append('-DOPENMC_USE_DAGMC=ON')
-        cmake_cmd.append('-DCMAKE_PREFIX_PATH=~/DAGMC')
+        pip_suffix.append('-DOPENMC_USE_DAGMC=ON')
+        pip_suffix.append('-DCMAKE_PREFIX_PATH=~/DAGMC')
 
     if libmesh:
-        cmake_cmd.append('-DOPENMC_USE_LIBMESH=ON')
+        pip_suffix.append('-DOPENMC_USE_LIBMESH=ON')
         libmesh_path = os.environ.get('HOME') + '/LIBMESH'
-        cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + libmesh_path)
+        pip_suffix.append('-DCMAKE_PREFIX_PATH=' + libmesh_path)
 
     if ncrystal:
-        cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON')
+        pip_suffix.append('-DOPENMC_USE_NCRYSTAL=ON')
         ncrystal_cmake_path = os.environ.get('HOME') + '/ncrystal_inst/lib/cmake'
-        cmake_cmd.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
+        pip_suffix.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
 
     # Build in coverage mode for coverage testing
-    cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on')
+    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=on')
 
+    pip_command.append(';'.join(pip_suffix))
     # Build and install
-    cmake_cmd.append('..')
-    print(' '.join(cmake_cmd))
-    subprocess.check_call(cmake_cmd)
-    subprocess.check_call(['make', '-j4'])
-    subprocess.check_call(['sudo', 'make', 'install'])
+    print(' '.join(pip_command))
+    subprocess.check_call(pip_command)
 
 def main():
     # Convert Travis matrix environment variables into arguments for install()
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 2cef974d346..1673edd4ada 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -47,9 +47,6 @@ fi
 # Build and install OpenMC executable
 python tools/ci/gha-install.py
 
-# Install Python API in editable mode
-pip install -e .[test,vtk]
-
 # For coverage testing of the C++ source files
 pip install cpp-coveralls
 

From 3c98d8a8346746d1c0cd90dd60ed33c4799d5b39 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Tue, 23 Jul 2024 19:59:07 +0100
Subject: [PATCH 06/29] added missing ,

---
 tools/ci/gha-install.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index 5cf46baa24c..f8c9ebe7e53 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -26,7 +26,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
     os.chdir('build')
 
     # Build in debug mode by default with support for MCPL
-    pip_command = ['pip' 'install' '.[test,vtk]']
+    pip_command = ['pip', 'install', '.[test,vtk]']
     pip_suffix = ['--config-settings=cmake.args=-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
 
     # Turn off OpenMP if specified

From 0aafd44dda9cdaffca73e83fd42c201eec0fbae5 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Tue, 23 Jul 2024 20:02:44 +0100
Subject: [PATCH 07/29] no need for manual creation of build dir

---
 tools/ci/gha-install.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index f8c9ebe7e53..536df1f9377 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -1,5 +1,4 @@
 import os
-import shutil
 import subprocess
 
 def which(program):
@@ -20,10 +19,6 @@ def is_exe(fpath):
 
 
 def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False):
-    # Create build directory and change to it
-    shutil.rmtree('build', ignore_errors=True)
-    os.mkdir('build')
-    os.chdir('build')
 
     # Build in debug mode by default with support for MCPL
     pip_command = ['pip', 'install', '.[test,vtk]']

From 9ef3beb1603bd286467dccbfa13eca87f29c9bf2 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 26 Jul 2024 13:05:41 +0100
Subject: [PATCH 08/29] [skip ci] adding apt packages for read the docs

---
 .readthedocs.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index b7b69f9fe59..fb49db819e5 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -4,6 +4,11 @@ build:
   os: "ubuntu-20.04"
   tools:
     python: "3.10"
+  apt_package:
+    - g++
+    - cmake
+    - libhdf5-dev
+    - libpng-dev
 
 sphinx:
   configuration: docs/source/conf.py

From 40ceaadea68b02e6758b4ef0a66194371095456c Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 26 Jul 2024 13:17:20 +0100
Subject: [PATCH 09/29] [skip ci] trying ubuntu 22.04

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index fb49db819e5..e5d69973b34 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
     python: "3.10"
   apt_package:

From 2c8cf714a716d77bcf9363d4e93abd73bb93defa Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 26 Jul 2024 13:18:08 +0100
Subject: [PATCH 10/29] [skip ci] added missing s

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index e5d69973b34..bcbea55994e 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -4,7 +4,7 @@ build:
   os: "ubuntu-22.04"
   tools:
     python: "3.10"
-  apt_package:
+  apt_packages:
     - g++
     - cmake
     - libhdf5-dev

From 4c0075f0f3fdb7562beff590a71de2da7ad0f9d7 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 26 Jul 2024 17:52:37 +0100
Subject: [PATCH 11/29] adding gha actions

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9293e319b42..1415074ad71 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -145,9 +145,7 @@ jobs:
 
       - name: test
         shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash

From 4de0d948f0feceaa5c3fa1e4c1119f6db2224697 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Fri, 26 Jul 2024 23:30:11 +0100
Subject: [PATCH 12/29] upper case ON for cmake args

---
 tools/ci/gha-install.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index cb1b23b2433..a03c89712b1 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -14,7 +14,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
 
     # Use MPI wrappers when building in parallel
     if mpi:
-        pip_suffix.append('-DOPENMC_USE_MPI=on')
+        pip_suffix.append('-DOPENMC_USE_MPI=ON')
 
     # Tell CMake to prefer parallel HDF5 if specified
     if phdf5:
@@ -40,7 +40,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
         pip_suffix.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
 
     # Build in coverage mode for coverage testing
-    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=on')
+    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON')
 
     pip_command.append(';'.join(pip_suffix))
     # Build and install

From 688d6882d59e56da6b3f2e191986b788fadf7982 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Sat, 27 Jul 2024 00:09:17 +0100
Subject: [PATCH 13/29] added quotes to cmake args

---
 tools/ci/gha-pip-install.py | 63 +++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 tools/ci/gha-pip-install.py

diff --git a/tools/ci/gha-pip-install.py b/tools/ci/gha-pip-install.py
new file mode 100644
index 00000000000..dde7535e0d6
--- /dev/null
+++ b/tools/ci/gha-pip-install.py
@@ -0,0 +1,63 @@
+import os
+import subprocess
+
+
+def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False):
+
+    # Build in debug mode by default with support for MCPL
+    pip_command = ['pip', 'install', '.[test,vtk]']
+    pip_suffix = ['--config-settings=cmake.args="-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
+
+    # Turn off OpenMP if specified
+    if not omp:
+        pip_suffix.append('-DOPENMC_USE_OPENMP=off')
+
+    # Use MPI wrappers when building in parallel
+    if mpi:
+        pip_suffix.append('-DOPENMC_USE_MPI=ON')
+
+    # Tell CMake to prefer parallel HDF5 if specified
+    if phdf5:
+        if not mpi:
+            raise ValueError('Parallel HDF5 must be used in '
+                             'conjunction with MPI.')
+        pip_suffix.append('-DHDF5_PREFER_PARALLEL=ON')
+    else:
+        pip_suffix.append('-DHDF5_PREFER_PARALLEL=OFF')
+
+    if dagmc:
+        pip_suffix.append('-DOPENMC_USE_DAGMC=ON')
+        pip_suffix.append('-DCMAKE_PREFIX_PATH=~/DAGMC')
+
+    if libmesh:
+        pip_suffix.append('-DOPENMC_USE_LIBMESH=ON')
+        libmesh_path = os.environ.get('HOME') + '/LIBMESH'
+        pip_suffix.append('-DCMAKE_PREFIX_PATH=' + libmesh_path)
+
+    if ncrystal:
+        pip_suffix.append('-DOPENMC_USE_NCRYSTAL=ON')
+        ncrystal_cmake_path = os.environ.get('HOME') + '/ncrystal_inst/lib/cmake'
+        pip_suffix.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
+
+    # Build in coverage mode for coverage testing
+    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON"')
+
+    pip_command.append(';'.join(pip_suffix))
+    # Build and install
+    print(' '.join(pip_command))
+    subprocess.check_call(pip_command)
+
+def main():
+    # Convert Travis matrix environment variables into arguments for install()
+    omp = (os.environ.get('OMP') == 'y')
+    mpi = (os.environ.get('MPI') == 'y')
+    phdf5 = (os.environ.get('PHDF5') == 'y')
+    dagmc = (os.environ.get('DAGMC') == 'y')
+    ncrystal = (os.environ.get('NCRYSTAL') == 'y')
+    libmesh = (os.environ.get('LIBMESH') == 'y')
+
+    # Build and install
+    install(omp, mpi, phdf5, dagmc, libmesh, ncrystal)
+
+if __name__ == '__main__':
+    main()

From 07a4dcd473fc048aeb4baf22bceb22fb203aa9a0 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Sat, 27 Jul 2024 00:26:08 +0100
Subject: [PATCH 14/29] keeping same filename

---
 .github/workflows/ci.yml    |  4 ++-
 tools/ci/gha-install.py     |  4 +--
 tools/ci/gha-pip-install.py | 63 -------------------------------------
 3 files changed, 5 insertions(+), 66 deletions(-)
 delete mode 100644 tools/ci/gha-pip-install.py

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1415074ad71..9293e319b42 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -145,7 +145,9 @@ jobs:
 
       - name: test
         shell: bash
-        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash
diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index a03c89712b1..dde7535e0d6 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -6,7 +6,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
 
     # Build in debug mode by default with support for MCPL
     pip_command = ['pip', 'install', '.[test,vtk]']
-    pip_suffix = ['--config-settings=cmake.args=-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
+    pip_suffix = ['--config-settings=cmake.args="-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
 
     # Turn off OpenMP if specified
     if not omp:
@@ -40,7 +40,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
         pip_suffix.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
 
     # Build in coverage mode for coverage testing
-    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON')
+    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON"')
 
     pip_command.append(';'.join(pip_suffix))
     # Build and install
diff --git a/tools/ci/gha-pip-install.py b/tools/ci/gha-pip-install.py
deleted file mode 100644
index dde7535e0d6..00000000000
--- a/tools/ci/gha-pip-install.py
+++ /dev/null
@@ -1,63 +0,0 @@
-import os
-import subprocess
-
-
-def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False):
-
-    # Build in debug mode by default with support for MCPL
-    pip_command = ['pip', 'install', '.[test,vtk]']
-    pip_suffix = ['--config-settings=cmake.args="-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
-
-    # Turn off OpenMP if specified
-    if not omp:
-        pip_suffix.append('-DOPENMC_USE_OPENMP=off')
-
-    # Use MPI wrappers when building in parallel
-    if mpi:
-        pip_suffix.append('-DOPENMC_USE_MPI=ON')
-
-    # Tell CMake to prefer parallel HDF5 if specified
-    if phdf5:
-        if not mpi:
-            raise ValueError('Parallel HDF5 must be used in '
-                             'conjunction with MPI.')
-        pip_suffix.append('-DHDF5_PREFER_PARALLEL=ON')
-    else:
-        pip_suffix.append('-DHDF5_PREFER_PARALLEL=OFF')
-
-    if dagmc:
-        pip_suffix.append('-DOPENMC_USE_DAGMC=ON')
-        pip_suffix.append('-DCMAKE_PREFIX_PATH=~/DAGMC')
-
-    if libmesh:
-        pip_suffix.append('-DOPENMC_USE_LIBMESH=ON')
-        libmesh_path = os.environ.get('HOME') + '/LIBMESH'
-        pip_suffix.append('-DCMAKE_PREFIX_PATH=' + libmesh_path)
-
-    if ncrystal:
-        pip_suffix.append('-DOPENMC_USE_NCRYSTAL=ON')
-        ncrystal_cmake_path = os.environ.get('HOME') + '/ncrystal_inst/lib/cmake'
-        pip_suffix.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}')
-
-    # Build in coverage mode for coverage testing
-    pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON"')
-
-    pip_command.append(';'.join(pip_suffix))
-    # Build and install
-    print(' '.join(pip_command))
-    subprocess.check_call(pip_command)
-
-def main():
-    # Convert Travis matrix environment variables into arguments for install()
-    omp = (os.environ.get('OMP') == 'y')
-    mpi = (os.environ.get('MPI') == 'y')
-    phdf5 = (os.environ.get('PHDF5') == 'y')
-    dagmc = (os.environ.get('DAGMC') == 'y')
-    ncrystal = (os.environ.get('NCRYSTAL') == 'y')
-    libmesh = (os.environ.get('LIBMESH') == 'y')
-
-    # Build and install
-    install(omp, mpi, phdf5, dagmc, libmesh, ncrystal)
-
-if __name__ == '__main__':
-    main()

From 9253977ac3df5a29b2b021fb6112c509b7794c54 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Sat, 27 Jul 2024 00:37:54 +0100
Subject: [PATCH 15/29] running just pytest

---
 .github/workflows/ci.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9293e319b42..1415074ad71 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -145,9 +145,7 @@ jobs:
 
       - name: test
         shell: bash
-        run: |
-          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
-          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
       - name: after_success
         shell: bash

From 1f016940ee9e6c0c6e2eba5bf71912729ee2bf63 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Sat, 27 Jul 2024 00:39:43 +0100
Subject: [PATCH 16/29] [skip ci] corrected cmake arg passing example

---
 docs/source/usersguide/install.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst
index 203ec879430..c0ad2fdcd48 100644
--- a/docs/source/usersguide/install.rst
+++ b/docs/source/usersguide/install.rst
@@ -176,7 +176,7 @@ feature can be used to access the installed packages.
 .. _install_source:
 
 --------------------------------
-Compiling from Source with CMake
+Compiling from source with CMake
 --------------------------------
 
 .. _prerequisites:
@@ -533,7 +533,7 @@ Package Index (`PyPI <https://pypi.org/>`_). The pip command will also compile
 an executable named ``openmc`` and install it (by default in the bin folder of
 the Python package directory).
 
-Passing CMake Options to via pip
+Passing CMake arguments via pip
 --------------------------------
 
 If you need to pass CMake options to the build process, you can do so by
@@ -543,13 +543,13 @@ For example, to build OpenMC with MPI support, you can run:
 
 .. code-block:: sh
 
-    python -m pip install . --global-option="build_ext" --global-option="--" --global-option="-DOPENMC_USE_MPI=ON"
+    python -m pip install . --config-settings=cmake.args=-DOPENMC_USE_MPI=ON
 
 To build OpenMC with DAGMC support two CMake arguments are needed, you can run:
 
 .. code-block:: sh
 
-    python -m pip install . --global-option="build_ext" --global-option="--" --global-option="-DOPENMC_USE_DAGMC=ON" --global-option="-DDAGMC_ROOT=/path/to/dagmc/installation"
+    python -m pip install . --config-settings=cmake.args="-DOPENMC_USE_DAGMC=ON;DDAGMC_ROOT=/path/to/dagmc/installation"
 
 Installing in "Development" Mode
 --------------------------------

From 6850217ad5dffdcc1874c052b809c154166dfc84 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Sat, 27 Jul 2024 01:02:49 +0100
Subject: [PATCH 17/29] added diagnosis prints

---
 CMakeLists.txt          | 11 +++++++++++
 tools/ci/gha-install.py |  1 +
 2 files changed, 12 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7c86c391521..928f72c245f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,6 +41,17 @@ option(OPENMC_USE_MCPL        "Enable MCPL"
 option(OPENMC_USE_NCRYSTAL    "Enable support for NCrystal scattering"               OFF)
 option(OPENMC_USE_UWUW        "Enable UWUW"                                          OFF)
 
+message(STATUS "OPENMC_USE_OPENMP ${OPENMC_USE_OPENMP}")
+message(STATUS "OPENMC_BUILD_TESTS ${OPENMC_BUILD_TESTS}")
+message(STATUS "OPENMC_ENABLE_PROFILE ${OPENMC_ENABLE_PROFILE}")
+message(STATUS "OPENMC_ENABLE_COVERAGE ${OPENMC_ENABLE_COVERAGE}")
+message(STATUS "OPENMC_USE_DAGMC ${OPENMC_USE_DAGMC}")
+message(STATUS "OPENMC_USE_LIBMESH ${OPENMC_USE_LIBMESH}")
+message(STATUS "OPENMC_USE_MPI ${OPENMC_USE_MPI}")
+message(STATUS "OPENMC_USE_MCPL ${OPENMC_USE_MCPL}")
+message(STATUS "OPENMC_USE_NCRYSTAL ${OPENMC_USE_NCRYSTAL}")
+message(STATUS "OPENMC_USE_UWUW ${OPENMC_USE_UWUW}")
+
 # Warnings for deprecated options
 foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh")
   if(DEFINED ${OLD_OPT})
diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index dde7535e0d6..4ef2e780d3f 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -43,6 +43,7 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrys
     pip_suffix.append('-DOPENMC_ENABLE_COVERAGE=ON"')
 
     pip_command.append(';'.join(pip_suffix))
+    pip_command.append('--verbose')
     # Build and install
     print(' '.join(pip_command))
     subprocess.check_call(pip_command)

From 97a3f22bdf532315f5381310ce540a374272f7cc Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Sat, 27 Jul 2024 01:15:36 +0100
Subject: [PATCH 18/29] removed 2nd pip install which was overwritting

---
 tools/ci/gha-install.py | 2 +-
 tools/ci/gha-install.sh | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py
index 4ef2e780d3f..da94df1bc2b 100644
--- a/tools/ci/gha-install.py
+++ b/tools/ci/gha-install.py
@@ -5,7 +5,7 @@
 def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False):
 
     # Build in debug mode by default with support for MCPL
-    pip_command = ['pip', 'install', '.[test,vtk]']
+    pip_command = ['pip', 'install', '.[test,vtk,ci]']
     pip_suffix = ['--config-settings=cmake.args="-DCMAKE_BUILD_TYPE=ON;-DOPENMC_USE_MCPL=ON']
 
     # Turn off OpenMP if specified
diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh
index 87952fda9cb..e69aaaa13fb 100755
--- a/tools/ci/gha-install.sh
+++ b/tools/ci/gha-install.sh
@@ -46,6 +46,3 @@ fi
 
 # Build and install OpenMC executable
 python tools/ci/gha-install.py
-
-# Install Python API in editable mode
-pip install -e .[test,vtk,ci]

From 41d28ff3394626a467dec907deb6f68a60e904b5 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Mon, 29 Jul 2024 17:33:46 +0100
Subject: [PATCH 19/29] float_endf from endf package

---
 openmc/data/_endf.pyx |  8 ------
 openmc/data/endf.c    | 57 -------------------------------------------
 openmc/data/endf.py   | 10 +-------
 pyproject.toml        |  1 +
 4 files changed, 2 insertions(+), 74 deletions(-)
 delete mode 100644 openmc/data/_endf.pyx
 delete mode 100644 openmc/data/endf.c

diff --git a/openmc/data/_endf.pyx b/openmc/data/_endf.pyx
deleted file mode 100644
index 991ee015b29..00000000000
--- a/openmc/data/_endf.pyx
+++ /dev/null
@@ -1,8 +0,0 @@
-# cython: c_string_type=str, c_string_encoding=ascii
-
-cdef extern from "endf.c":
-    double cfloat_endf(const char* buffer, int n)
-
-def float_endf(s):
-    cdef const char* c_string = s
-    return cfloat_endf(c_string, len(s))
diff --git a/openmc/data/endf.c b/openmc/data/endf.c
deleted file mode 100644
index dd5eee54184..00000000000
--- a/openmc/data/endf.c
+++ /dev/null
@@ -1,57 +0,0 @@
-#include <stdlib.h>
-
-//! Convert string representation of a floating point number into a double
-//
-//! This function handles converting floating point numbers from an ENDF 11
-//! character field into a double, covering all the corner cases. Floating point
-//! numbers are allowed to contain whitespace (which is ignored). Also, in
-//! exponential notation, it allows the 'e' to be omitted. A field containing
-//! only whitespace is to be interpreted as a zero.
-//
-//! \param buffer character input from an ENDF file
-//! \param n Length of character input
-//! \return Floating point number
-
-double cfloat_endf(const char* buffer, int n)
-{
-  char arr[13]; // 11 characters plus e and a null terminator
-  int j = 0; // current position in arr
-  int found_significand = 0;
-  int found_exponent = 0;
-
-  // limit n to 11 characters
-  n = n > 11 ? 11 : n;
-
-  int i;
-  for (i = 0; i < n; ++i) {
-    char c = buffer[i];
-
-    // Skip whitespace characters
-    if (c == ' ') continue;
-
-    if (found_significand) {
-      if (!found_exponent) {
-        if (c == '+' || c == '-') {
-          // In the case that we encounter +/- and we haven't yet encountered
-          // e/E, we manually add it
-          arr[j++] = 'e';
-          found_exponent = 1;
-
-        } else if (c == 'e' || c == 'E' || c == 'd' || c == 'D') {
-          arr[j++] = 'e';
-          found_exponent = 1;
-          continue;
-        }
-      }
-    } else if (c == '.' || (c >= '0' && c <= '9')) {
-      found_significand = 1;
-    }
-
-    // Copy character
-    arr[j++] = c;
-  }
-
-  // Done copying. Add null terminator and convert to double
-  arr[j] = '\0';
-  return atof(arr);
-}
diff --git a/openmc/data/endf.py b/openmc/data/endf.py
index 73299723a8b..63cd092ebb1 100644
--- a/openmc/data/endf.py
+++ b/openmc/data/endf.py
@@ -14,11 +14,7 @@
 
 from .data import gnds_name
 from .function import Tabulated1D
-try:
-    from ._endf import float_endf
-    _CYTHON = True
-except ImportError:
-    _CYTHON = False
+from endf.records import float_endf
 
 
 _LIBRARY = {0: 'ENDF/B', 1: 'ENDF/A', 2: 'JEFF', 3: 'EFF',
@@ -91,10 +87,6 @@ def py_float_endf(s):
     return float(ENDF_FLOAT_RE.sub(r'\1e\2\3', s))
 
 
-if not _CYTHON:
-    float_endf = py_float_endf
-
-
 def int_endf(s):
     """Convert string of integer number in ENDF to int.
 
diff --git a/pyproject.toml b/pyproject.toml
index 2b2764cea69..98b1d152fbc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,6 +34,7 @@ dependencies = [
     "lxml",
     "uncertainties",
     "setuptools",
+    "endf",
 ]
 
 [project.optional-dependencies]

From c03a236ddda10dfcdc4c3018a046ff3ed3c2fc0e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Mon, 29 Jul 2024 17:47:23 +0100
Subject: [PATCH 20/29] removed reference to float endf

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4e24f48a123..88a45a36090 100755
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 
 kwargs = {
-    # Cython is used to add resonance reconstruction and fast float_endf
+    # Cython is used to add resonance reconstruction
     'ext_modules': cythonize('openmc/data/*.pyx'),
     'include_dirs': [np.get_include()]
 }

From 3cc88a0588ef9f23c1ea9fef6a80a884c425b79b Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Wed, 7 Aug 2024 17:22:34 +0100
Subject: [PATCH 21/29] removing resonance

---
 openmc/data/function.py               |  22 --
 openmc/data/reconstruct.pyx           | 522 --------------------------
 tests/unit_tests/test_data_neutron.py |  26 +-
 3 files changed, 4 insertions(+), 566 deletions(-)
 delete mode 100644 openmc/data/reconstruct.pyx

diff --git a/openmc/data/function.py b/openmc/data/function.py
index 23fd5e9d4fa..c5914f513d5 100644
--- a/openmc/data/function.py
+++ b/openmc/data/function.py
@@ -708,28 +708,6 @@ def __init__(self, resonances, background, mt):
         self.background = background
         self.mt = mt
 
-    def __call__(self, x):
-        # Get background cross section
-        xs = self.background(x)
-
-        for r in self.resonances:
-            if not isinstance(r, openmc.data.resonance._RESOLVED):
-                continue
-
-            if isinstance(x, Iterable):
-                # Determine which energies are within resolved resonance range
-                within = (r.energy_min <= x) & (x <= r.energy_max)
-
-                # Get resonance cross sections and add to background
-                resonant_xs = r.reconstruct(x[within])
-                xs[within] += resonant_xs[self.mt]
-            else:
-                if r.energy_min <= x <= r.energy_max:
-                    resonant_xs = r.reconstruct(x)
-                    xs += resonant_xs[self.mt]
-
-        return xs
-
     @property
     def background(self):
         return self._background
diff --git a/openmc/data/reconstruct.pyx b/openmc/data/reconstruct.pyx
deleted file mode 100644
index cd0bbc38b95..00000000000
--- a/openmc/data/reconstruct.pyx
+++ /dev/null
@@ -1,522 +0,0 @@
-from libc.stdlib cimport malloc, calloc, free
-from libc.math cimport cos, sin, sqrt, atan, M_PI
-
-cimport numpy as np
-import numpy as np
-from numpy.linalg import inv
-cimport cython
-
-
-cdef extern from "complex.h":
-    double cabs(double complex)
-    double complex conj(double complex)
-    double creal(complex double)
-    double cimag(complex double)
-    double complex cexp(double complex)
-
-# Physical constants are from CODATA 2014
-cdef double NEUTRON_MASS_ENERGY = 939.5654133e6  # eV/c^2
-cdef double HBAR_C = 197.3269788e5  # eV-b^0.5
-
-
-@cython.cdivision(True)
-def wave_number(double A, double E):
-    r"""Neutron wave number in center-of-mass system.
-
-    ENDF-102 defines the neutron wave number in the center-of-mass system in
-    Equation D.10 as
-
-    .. math::
-        k = \frac{2m_n}{\hbar} \frac{A}{A + 1} \sqrt{|E|}
-
-    Parameters
-    ----------
-    A : double
-        Ratio of target mass to neutron mass
-    E : double
-        Energy in eV
-
-    Returns
-    -------
-    double
-        Neutron wave number in b^-0.5
-
-    """
-    return A/(A + 1)*sqrt(2*NEUTRON_MASS_ENERGY*abs(E))/HBAR_C
-
-@cython.cdivision(True)
-cdef double _wave_number(double A, double E):
-    return A/(A + 1)*sqrt(2*NEUTRON_MASS_ENERGY*abs(E))/HBAR_C
-
-
-@cython.cdivision(True)
-cdef double phaseshift(int l, double rho):
-    """Calculate hardsphere phase shift as given in ENDF-102, Equation D.13
-
-    Parameters
-    ----------
-    l : int
-        Angular momentum quantum number
-    rho : float
-        Product of the wave number and the channel radius
-
-    Returns
-    -------
-    double
-        Hardsphere phase shift
-
-    """
-    if l == 0:
-        return rho
-    elif l == 1:
-        return rho - atan(rho)
-    elif l == 2:
-        return rho - atan(3*rho/(3 - rho**2))
-    elif l == 3:
-        return rho - atan((15*rho - rho**3)/(15 - 6*rho**2))
-    elif l == 4:
-        return rho - atan((105*rho - 10*rho**3)/(105 - 45*rho**2 + rho**4))
-
-
-@cython.cdivision(True)
-def penetration_shift(int l, double rho):
-    r"""Calculate shift and penetration factors as given in ENDF-102, Equations D.11
-    and D.12.
-
-    Parameters
-    ----------
-    l : int
-        Angular momentum quantum number
-    rho : float
-        Product of the wave number and the channel radius
-
-    Returns
-    -------
-    double
-        Penetration factor for given :math:`l`
-    double
-        Shift factor for given :math:`l`
-
-    """
-    cdef double den
-
-    if l == 0:
-        return rho, 0.
-    elif l == 1:
-        den = 1 + rho**2
-        return rho**3/den, -1/den
-    elif l == 2:
-        den = 9 + 3*rho**2 + rho**4
-        return rho**5/den, -(18 + 3*rho**2)/den
-    elif l == 3:
-        den = 225 + 45*rho**2 + 6*rho**4 + rho**6
-        return rho**7/den, -(675 + 90*rho**2 + 6*rho**4)/den
-    elif l == 4:
-        den = 11025 + 1575*rho**2 + 135*rho**4 + 10*rho**6 + rho**8
-        return rho**9/den, -(44100 + 4725*rho**2 + 270*rho**4 + 10*rho**6)/den
-
-
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
-def reconstruct_mlbw(mlbw, double E):
-    """Evaluate cross section using MLBW data.
-
-    Parameters
-    ----------
-    mlbw : openmc.data.MultiLevelBreitWigner
-        Multi-level Breit-Wigner resonance parameters
-    E : double
-        Energy in eV at which to evaluate the cross section
-
-    Returns
-    -------
-    elastic : double
-        Elastic scattering cross section in barns
-    capture : double
-        Radiative capture cross section in barns
-    fission : double
-        Fission cross section in barns
-
-    """
-    cdef int i, nJ, ij, l, n_res, i_res
-    cdef double elastic, capture, fission
-    cdef double A, k, rho, rhohat, I
-    cdef double P, S, phi, cos2phi, sin2phi
-    cdef double Ex, Q, rhoc, rhochat, P_c, S_c
-    cdef double jmin, jmax, j, Dl
-    cdef double E_r, gt, gn, gg, gf, gx, P_r, S_r, P_rx
-    cdef double gnE, gtE, Eprime, x, f
-    cdef double *g
-    cdef double (*s)[2]
-    cdef double [:,:] params
-
-    I = mlbw.target_spin
-    A = mlbw.atomic_weight_ratio
-    k = _wave_number(A, E)
-
-    elastic = 0.
-    capture = 0.
-    fission = 0.
-
-    for i, l in enumerate(mlbw._l_values):
-        params = mlbw._parameter_matrix[l]
-
-        rho = k*mlbw.channel_radius[l](E)
-        rhohat = k*mlbw.scattering_radius[l](E)
-        P, S = penetration_shift(l, rho)
-        phi = phaseshift(l, rhohat)
-        cos2phi = cos(2*phi)
-        sin2phi = sin(2*phi)
-
-        # Determine shift and penetration at modified energy
-        if mlbw._competitive[i]:
-            Ex = E + mlbw.q_value[l]*(A + 1)/A
-            rhoc = mlbw.channel_radius[l](Ex)
-            rhochat = mlbw.scattering_radius[l](Ex)
-            P_c, S_c = penetration_shift(l, rhoc)
-            if Ex < 0:
-                P_c = 0
-
-        # Determine range of total angular momentum values based on equation
-        # 41 in LA-UR-12-27079
-        jmin = abs(abs(I - l) - 0.5)
-        jmax = I + l + 0.5
-        nJ = int(jmax - jmin + 1)
-
-        # Determine Dl factor using Equation 43 in LA-UR-12-27079
-        Dl = 2*l + 1
-        g = <double *> malloc(nJ*sizeof(double))
-        for ij in range(nJ):
-            j = jmin + ij
-            g[ij] = (2*j + 1)/(4*I + 2)
-            Dl -= g[ij]
-
-        s = <double (*)[2]> calloc(2*nJ, sizeof(double))
-        for i_res in range(params.shape[0]):
-            # Copy resonance parameters
-            E_r = params[i_res, 0]
-            j = params[i_res, 2]
-            ij = int(j - jmin)
-            gt = params[i_res, 3]
-            gn = params[i_res, 4]
-            gg = params[i_res, 5]
-            gf = params[i_res, 6]
-            gx = params[i_res, 7]
-            P_r = params[i_res, 8]
-            S_r = params[i_res, 9]
-            P_rx = params[i_res, 10]
-
-            # Calculate neutron and total width at energy E
-            gnE = P*gn/P_r  # ENDF-102, Equation D.7
-            gtE = gnE + gg + gf
-            if gx > 0:
-                gtE += gx*P_c/P_rx
-
-            Eprime = E_r + (S_r - S)/(2*P_r)*gn  # ENDF-102, Equation D.9
-            x = 2*(E - Eprime)/gtE    # LA-UR-12-27079, Equation 26
-            f = 2*gnE/(gtE*(1 + x*x)) # Common factor in Equation 40
-            s[ij][0] += f             # First sum in Equation 40
-            s[ij][1] += f*x           # Second sum in Equation 40
-            capture += f*g[ij]*gg/gtE
-            if gf > 0:
-                fission += f*g[ij]*gf/gtE
-
-        for ij in range(nJ):
-            # Add all but last term of LA-UR-12-27079, Equation 40
-            elastic += g[ij]*((1 - cos2phi - s[ij][0])**2 +
-                              (sin2phi + s[ij][1])**2)
-
-        # Add final term with Dl from Equation 40
-        elastic += 2*Dl*(1 - cos2phi)
-
-        # Free memory
-        free(g)
-        free(s)
-
-    capture *= 2*M_PI/(k*k)
-    fission *= 2*M_PI/(k*k)
-    elastic *= M_PI/(k*k)
-
-    return (elastic, capture, fission)
-
-
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
-def reconstruct_slbw(slbw, double E):
-    """Evaluate cross section using SLBW data.
-
-    Parameters
-    ----------
-    slbw : openmc.data.SingleLevelBreitWigner
-        Single-level Breit-Wigner resonance parameters
-    E : double
-        Energy in eV at which to evaluate the cross section
-
-    Returns
-    -------
-    elastic : double
-        Elastic scattering cross section in barns
-    capture : double
-        Radiative capture cross section in barns
-    fission : double
-        Fission cross section in barns
-
-    """
-    cdef int i, l, i_res
-    cdef double elastic, capture, fission
-    cdef double A, k, rho, rhohat, I
-    cdef double P, S, phi, cos2phi, sin2phi, sinphi2
-    cdef double Ex, rhoc, rhochat, P_c, S_c
-    cdef double E_r, J, gt, gn, gg, gf, gx, P_r, S_r, P_rx
-    cdef double gnE, gtE, Eprime, f
-    cdef double x, theta, psi, chi
-    cdef double [:,:] params
-
-    I = slbw.target_spin
-    A = slbw.atomic_weight_ratio
-    k = _wave_number(A, E)
-
-    elastic = 0.
-    capture = 0.
-    fission = 0.
-
-    for i, l in enumerate(slbw._l_values):
-        params = slbw._parameter_matrix[l]
-
-        rho = k*slbw.channel_radius[l](E)
-        rhohat = k*slbw.scattering_radius[l](E)
-        P, S = penetration_shift(l, rho)
-        phi = phaseshift(l, rhohat)
-        cos2phi = cos(2*phi)
-        sin2phi = sin(2*phi)
-        sinphi2 = sin(phi)**2
-
-        # Add potential scattering -- first term in ENDF-102, Equation D.2
-        elastic += 4*M_PI/(k*k)*(2*l + 1)*sinphi2
-
-        # Determine shift and penetration at modified energy
-        if slbw._competitive[i]:
-            Ex = E + slbw.q_value[l]*(A + 1)/A
-            rhoc = k*slbw.channel_radius[l](Ex)
-            rhochat = k*slbw.scattering_radius[l](Ex)
-            P_c, S_c = penetration_shift(l, rhoc)
-            if Ex < 0:
-                P_c = 0
-
-        for i_res in range(params.shape[0]):
-            # Copy resonance parameters
-            E_r = params[i_res, 0]
-            J = params[i_res, 2]
-            gt = params[i_res, 3]
-            gn = params[i_res, 4]
-            gg = params[i_res, 5]
-            gf = params[i_res, 6]
-            gx = params[i_res, 7]
-            P_r = params[i_res, 8]
-            S_r = params[i_res, 9]
-            P_rx = params[i_res, 10]
-
-            # Calculate neutron and total width at energy E
-            gnE = P*gn/P_r  # Equation D.7
-            gtE = gnE + gg + gf
-            if gx > 0:
-                gtE += gx*P_c/P_rx
-
-            Eprime = E_r + (S_r - S)/(2*P_r)*gn  # Equation D.9
-            gJ = (2*J + 1)/(4*I + 2)  # Mentioned in section D.1.1.4
-
-            # Calculate common factor for elastic, capture, and fission
-            # cross sections
-            f = M_PI/(k*k)*gJ*gnE/((E - Eprime)**2 + gtE**2/4)
-
-            # Add contribution to elastic per Equation D.2
-            elastic += f*(gnE*cos2phi - 2*(gg + gf)*sinphi2
-                          + 2*(E - Eprime)*sin2phi)
-
-            # Add contribution to capture per Equation D.3
-            capture += f*gg
-
-            # Add contribution to fission per Equation D.6
-            if gf > 0:
-                fission += f*gf
-
-    return (elastic, capture, fission)
-
-
-@cython.boundscheck(False)
-@cython.wraparound(False)
-@cython.cdivision(True)
-def reconstruct_rm(rm, double E):
-    """Evaluate cross section using Reich-Moore data.
-
-    Parameters
-    ----------
-    rm : openmc.data.ReichMoore
-        Reich-Moore resonance parameters
-    E : double
-        Energy in eV at which to evaluate the cross section
-
-    Returns
-    -------
-    elastic : double
-        Elastic scattering cross section in barns
-    capture : double
-        Radiative capture cross section in barns
-    fission : double
-        Fission cross section in barns
-
-    """
-    cdef int i, l, m, n, i_res
-    cdef int i_s, num_s, i_J, num_J
-    cdef double elastic, capture, fission, total
-    cdef double A, k, rho, rhohat, I
-    cdef double P, S, phi
-    cdef double smin, smax, s, Jmin, Jmax, J, j
-    cdef double E_r, gn, gg, gfa, gfb, P_r
-    cdef double E_diff, abs_value, gJ
-    cdef double Kr, Ki, x
-    cdef double complex Ubar, U_, factor
-    cdef bint hasfission
-    cdef np.ndarray[double, ndim=2] one
-    cdef np.ndarray[double complex, ndim=2] K, Imat, U
-    cdef double [:,:] params
-
-    # Get nuclear spin
-    I = rm.target_spin
-
-    elastic = 0.
-    fission = 0.
-    total = 0.
-    A = rm.atomic_weight_ratio
-    k = _wave_number(A, E)
-    one = np.eye(3)
-    K = np.zeros((3,3), dtype=complex)
-
-    for i, l in enumerate(rm._l_values):
-        # Check for l-dependent scattering radius
-        rho = k*rm.channel_radius[l](E)
-        rhohat = k*rm.scattering_radius[l](E)
-
-        # Calculate shift and penetrability
-        P, S = penetration_shift(l, rho)
-
-        # Calculate phase shift
-        phi = phaseshift(l, rhohat)
-
-        # Calculate common factor on collision matrix terms (term outside curly
-        # braces in ENDF-102, Eq. D.27)
-        Ubar = cexp(-2j*phi)
-
-        # The channel spin is the vector sum of the target spin, I, and the
-        # neutron spin, 1/2, so can take on values of |I - 1/2| < s < I + 1/2
-        smin = abs(I - 0.5)
-        smax = I + 0.5
-        num_s = int(smax - smin + 1)
-
-        for i_s in range(num_s):
-            s = i_s + smin
-
-            # Total angular momentum is the vector sum of l and s and can assume
-            # values between |l - s| < J < l + s
-            Jmin = abs(l - s)
-            Jmax = l + s
-            num_J = int(Jmax - Jmin + 1)
-
-            for i_J in range(num_J):
-                J = i_J + Jmin
-
-                # Initialize K matrix
-                for m in range(3):
-                    for n in range(3):
-                        K[m,n] = 0.0
-
-                hasfission = False
-                if (l, J) in rm._parameter_matrix:
-                    params = rm._parameter_matrix[l, J]
-
-                    for i_res in range(params.shape[0]):
-                        # Sometimes, the same (l, J) quantum numbers can occur
-                        # for different values of the channel spin, s. In this
-                        # case, the sign of the channel spin indicates which
-                        # spin is to be used. If the spin is negative assume
-                        # this resonance comes from the I - 1/2 channel and vice
-                        # versa.
-                        j = params[i_res, 2]
-                        if l > 0:
-                            if (j < 0 and s != smin) or (j > 0 and s != smax):
-                                continue
-
-                        # Copy resonance parameters
-                        E_r = params[i_res, 0]
-                        gn = params[i_res, 3]
-                        gg = params[i_res, 4]
-                        gfa = params[i_res, 5]
-                        gfb = params[i_res, 6]
-                        P_r = params[i_res, 7]
-
-                        # Calculate neutron width at energy E
-                        gn = sqrt(P*gn/P_r)
-
-                        # Calculate j/2 * inverse of denominator of K matrix terms
-                        factor = 0.5j/(E_r - E - 0.5j*gg)
-
-                        # Upper triangular portion of K matrix -- see ENDF-102,
-                        # Equation D.28
-                        K[0,0] = K[0,0] + gn*gn*factor
-                        if gfa != 0.0 or gfb != 0.0:
-                            # Negate fission widths if necessary
-                            gfa = (-1 if gfa < 0 else 1)*sqrt(abs(gfa))
-                            gfb = (-1 if gfb < 0 else 1)*sqrt(abs(gfb))
-
-                            K[0,1] = K[0,1] + gn*gfa*factor
-                            K[0,2] = K[0,2] + gn*gfb*factor
-                            K[1,1] = K[1,1] + gfa*gfa*factor
-                            K[1,2] = K[1,2] + gfa*gfb*factor
-                            K[2,2] = K[2,2] + gfb*gfb*factor
-                            hasfission = True
-
-                # Get collision matrix
-                gJ = (2*J + 1)/(4*I + 2)
-                if hasfission:
-                    # Copy upper triangular portion of K to lower triangular
-                    K[1,0] = K[0,1]
-                    K[2,0] = K[0,2]
-                    K[2,1] = K[1,2]
-
-                    Imat = inv(one - K)
-                    U = Ubar*(2*Imat - one)  # ENDF-102, Eq. D.27
-                    elastic += gJ*cabs(1 - U[0,0])**2  # ENDF-102, Eq. D.24
-                    total += 2*gJ*(1 - creal(U[0,0]))  # ENDF-102, Eq. D.23
-
-                    # Calculate fission from ENDF-102, Eq. D.26
-                    fission += 4*gJ*(cabs(Imat[1,0])**2 + cabs(Imat[2,0])**2)
-                else:
-                    U_ = Ubar*(2/(1 - K[0,0]) - 1)
-                    if abs(creal(K[0,0])) < 3e-4 and abs(phi) < 3e-4:
-                        # If K and phi are both very small, the calculated cross
-                        # sections can lose precision because the real part of U
-                        # ends up very close to unity. To get around this, we
-                        # use Euler's formula to express Ubar by real and
-                        # imaginary parts, expand cos(2phi) = 1 - 2phi^2 +
-                        # O(phi^4), and then simplify
-                        Kr = creal(K[0,0])
-                        Ki = cimag(K[0,0])
-                        x = 2*(-Kr + (Kr*Kr + Ki*Ki)*(1 - phi*phi) + phi*phi -
-                               sin(2*phi)*Ki)/((1 - Kr)*(1 - Kr) + Ki*Ki)
-                        total += 2*gJ*x
-                        elastic += gJ*(x*x + cimag(U_)**2)
-                    else:
-                        total += 2*gJ*(1 - creal(U_))   # ENDF-102, Eq. D.23
-                        elastic += gJ*cabs(1 - U_)**2   # ENDF-102, Eq. D.24
-
-    # Calculate capture as difference of other cross sections as per ENDF-102,
-    # Equation D.25
-    capture = total - elastic - fission
-
-    elastic *= M_PI/(k*k)
-    capture *= M_PI/(k*k)
-    fission *= M_PI/(k*k)
-
-    return (elastic, capture, fission)
diff --git a/tests/unit_tests/test_data_neutron.py b/tests/unit_tests/test_data_neutron.py
index c0d6a1f1547..5e685854367 100644
--- a/tests/unit_tests/test_data_neutron.py
+++ b/tests/unit_tests/test_data_neutron.py
@@ -282,10 +282,6 @@ def test_slbw(xe135):
     s = resolved.parameters.iloc[0]
     assert s['energy'] == pytest.approx(0.084)
 
-    xs = resolved.reconstruct([10., 30., 100.])
-    assert sorted(xs.keys()) == [2, 18, 102]
-    assert np.all(xs[18] == 0.0)
-
 
 def test_mlbw(sm150):
     resolved = sm150.resonances.resolved
@@ -294,10 +290,6 @@ def test_mlbw(sm150):
     assert resolved.energy_max == pytest.approx(1570.)
     assert resolved.target_spin == 0.0
 
-    xs = resolved.reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
-    assert np.all(xs[18] == 0.0)
-
 
 def test_reichmoore(gd154):
     res = gd154.resonances
@@ -347,8 +339,6 @@ def test_mlbw_cov_lcomp0(cf252):
     assert not subset.parameters.empty
     assert (subset.file2res.parameters['energy'] < 100).all()
     samples = cov.sample(1)
-    xs = samples[0].reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
 
 
 def test_mlbw_cov_lcomp1(ti50):
@@ -365,9 +355,7 @@ def test_mlbw_cov_lcomp1(ti50):
     subset = cov.subset('L', [1, 1])
     assert not subset.parameters.empty
     assert (subset.file2res.parameters['L'] == 1).all()
-    samples = cov.sample(1)
-    xs = samples[0].reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
+    cov.sample(1)
 
 
 def test_mlbw_cov_lcomp2(na23):
@@ -384,9 +372,7 @@ def test_mlbw_cov_lcomp2(na23):
     subset = cov.subset('L', [1, 1])
     assert not subset.parameters.empty
     assert (subset.file2res.parameters['L'] == 1).all()
-    samples = cov.sample(1)
-    xs = samples[0].reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
+    cov.sample(1)
 
 
 def test_rmcov_lcomp1(gd154):
@@ -403,9 +389,7 @@ def test_rmcov_lcomp1(gd154):
     subset = cov.subset('energy', [0, 100])
     assert not subset.parameters.empty
     assert (subset.file2res.parameters['energy'] < 100).all()
-    samples = cov.sample(1)
-    xs = samples[0].reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
+    cov.sample(1)
 
 
 def test_rmcov_lcomp2(th232):
@@ -422,9 +406,7 @@ def test_rmcov_lcomp2(th232):
     subset = cov.subset('energy', [0, 100])
     assert not subset.parameters.empty
     assert (subset.file2res.parameters['energy'] < 100).all()
-    samples = cov.sample(1)
-    xs = samples[0].reconstruct([10., 100., 1000.])
-    assert sorted(xs.keys()) == [2, 18, 102]
+    cov.sample(1)
 
 
 def test_madland_nix(am241):

From f8f9ac4277f02bf285896fb1c9e831f55e5a9c55 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Thu, 8 Aug 2024 08:13:01 +0100
Subject: [PATCH 22/29] no longer calling ResonancesWithBackground

---
 tests/unit_tests/test_data_neutron.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/unit_tests/test_data_neutron.py b/tests/unit_tests/test_data_neutron.py
index 5e685854367..db6ae1eb850 100644
--- a/tests/unit_tests/test_data_neutron.py
+++ b/tests/unit_tests/test_data_neutron.py
@@ -311,7 +311,6 @@ def test_reichmoore(gd154):
 
     elastic = gd154.reactions[2].xs['0K']
     assert isinstance(elastic, openmc.data.ResonancesWithBackground)
-    assert elastic(0.0253) == pytest.approx(5.7228949796394524)
 
 
 def test_rml(cl35):

From a2bc5552dda4d803ed40fd102ab42cc5d5e09620 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <drshimwell@gmail.com>
Date: Tue, 13 Aug 2024 15:56:58 +0100
Subject: [PATCH 23/29] [skip ci] removed prints

---
 CMakeLists.txt | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 928f72c245f..14047e171d6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,16 +41,6 @@ option(OPENMC_USE_MCPL        "Enable MCPL"
 option(OPENMC_USE_NCRYSTAL    "Enable support for NCrystal scattering"               OFF)
 option(OPENMC_USE_UWUW        "Enable UWUW"                                          OFF)
 
-message(STATUS "OPENMC_USE_OPENMP ${OPENMC_USE_OPENMP}")
-message(STATUS "OPENMC_BUILD_TESTS ${OPENMC_BUILD_TESTS}")
-message(STATUS "OPENMC_ENABLE_PROFILE ${OPENMC_ENABLE_PROFILE}")
-message(STATUS "OPENMC_ENABLE_COVERAGE ${OPENMC_ENABLE_COVERAGE}")
-message(STATUS "OPENMC_USE_DAGMC ${OPENMC_USE_DAGMC}")
-message(STATUS "OPENMC_USE_LIBMESH ${OPENMC_USE_LIBMESH}")
-message(STATUS "OPENMC_USE_MPI ${OPENMC_USE_MPI}")
-message(STATUS "OPENMC_USE_MCPL ${OPENMC_USE_MCPL}")
-message(STATUS "OPENMC_USE_NCRYSTAL ${OPENMC_USE_NCRYSTAL}")
-message(STATUS "OPENMC_USE_UWUW ${OPENMC_USE_UWUW}")
 
 # Warnings for deprecated options
 foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh")

From f994293108cfcbcb46eec4e43453028eff117f25 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Tue, 13 Aug 2024 22:37:04 +0100
Subject: [PATCH 24/29] added action

---
 .github/workflows/build_wheels.yml | 23 +++++++++++++++++++++++
 pyproject.toml                     | 10 +++++++++-
 2 files changed, 32 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/build_wheels.yml

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
new file mode 100644
index 00000000000..d3e8606e96d
--- /dev/null
+++ b/.github/workflows/build_wheels.yml
@@ -0,0 +1,23 @@
+name: Build
+
+on: [push, pull_request]
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.20.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index a77149c8a48..c24026300b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -78,6 +78,14 @@ openmc-voxel-to-vtk = "scripts.openmc_voxel_to_vtk:main"
 openmc = "openmc.openmc_exec:main"
 
 [tool.scikit-build]
-cmake.verbose = true
+build.verbose = true
 # cmake args can be passed in here or in the command line via exports or inline with the pip install
 cmake.args = ["-DCMAKE_BUILD_TYPE=RELEASE"]
+
+[tool.cibuildwheel]
+skip = "*-win_*"
+before-all = """
+    yum install -y epel-release
+    yum install -y hdf5 hdf5-devel libpng-devel cmake eigen3-devel gcc gcc-c++ wget
+"""
+manylinux-x86_64-image = "manylinux_2_28"

From 0b7975764bb736c19418b27dbc856343a6c1de24 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 27 Aug 2024 22:31:36 +0100
Subject: [PATCH 25/29] added source dir include

---
 CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 14047e171d6..c2b39903a94 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -581,6 +581,7 @@ add_executable(openmc src/main.cpp)
 add_executable(OpenMC::openmc ALIAS openmc)
 target_compile_options(openmc PRIVATE ${cxxflags})
 target_include_directories(openmc PRIVATE ${CMAKE_BINARY_DIR}/include)
+target_include_directories(openmc PRIVATE ${CMAKE_SOURCE_DIR}/include)
 target_link_libraries(openmc libopenmc)
 
 # Ensure C++17 standard is used and turn off GNU extensions

From 22df26a99adce7d436a3c349409cacd54151f9fe Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 27 Aug 2024 22:43:05 +0100
Subject: [PATCH 26/29] trying to get libopenmc.so found

---
 CMakeLists.txt | 1 +
 pyproject.toml | 8 ++++++++
 setup.py       | 7 ++++++-
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c2b39903a94..77ce2e7e264 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -336,6 +336,7 @@ endif()
 if(SKBUILD)
   set(CMAKE_INSTALL_RPATH "$ORIGIN")
   set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/openmc/lib)
 endif()
 
 #===============================================================================
diff --git a/pyproject.toml b/pyproject.toml
index c24026300b1..e4556d4106d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,9 @@
 requires = ["setuptools", "wheel", "numpy", "cython", "scikit-build-core"]
 build-backend = "scikit_build_core.build"
 
+[tool.scikit-build-core]
+generator = "Ninja"
+
 [project]
 name = "openmc"
 authors = [
@@ -61,11 +64,13 @@ Issues = "https://github.com/openmc-dev/openmc/issues"
 [tool.setuptools.packages.find]
 include = ['openmc*', 'scripts*']
 exclude = ['tests*']
+packages = ["find:"]
 
 [tool.setuptools.package-data]
 "openmc.data.effective_dose" = ["*.txt"]
 "openmc.data" = ["*.txt", "*.DAT", "*.json", "*.h5"]
 "openmc.lib" = ["libopenmc.dylib", "libopenmc.so"]
+"lib" = ["libopenmc.so"]
 
 [project.scripts]
 openmc-ace-to-hdf5 = "scripts.openmc_ace_to_hdf5:main"
@@ -89,3 +94,6 @@ before-all = """
     yum install -y hdf5 hdf5-devel libpng-devel cmake eigen3-devel gcc gcc-c++ wget
 """
 manylinux-x86_64-image = "manylinux_2_28"
+
+[tool.setuptools.extension]
+libopenmc = {sources = [], libraries = ["openmc"], library-dirs = ["lib"], runtime-library-dirs = ["lib"]}
\ No newline at end of file
diff --git a/setup.py b/setup.py
index f26b3138274..eec492647b9 100755
--- a/setup.py
+++ b/setup.py
@@ -10,10 +10,15 @@ def __init__(self, name, cmake_lists_dir=".", sources=[], **kwa):
         Extension.__init__(self, name, sources=sources, **kwa)
         self.cmake_lists_dir = os.path.abspath(cmake_lists_dir)
 
+lib_dir = os.path.join('openmc', 'lib')
+libopenmc_path = os.path.join(lib_dir, 'libopenmc.so')
 
 kwargs = {
     'ext_modules': [OpenMCExtension('libopenmc')],
-    'include_dirs': [np.get_include()]
+    'include_dirs': [np.get_include()],
+    'package_data': {
+        'openmc': [os.path.join('lib', 'libopenmc.so')],
+    },
 }
 
 setup(**kwargs)

From a7bde522c2ed8450fec07539b59daba82f0695db Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 27 Aug 2024 22:49:16 +0100
Subject: [PATCH 27/29] correcting dir for lib

---
 pyproject.toml |  3 +--
 setup.py       | 11 +++++++++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e4556d4106d..686cf8fde72 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,7 +70,6 @@ packages = ["find:"]
 "openmc.data.effective_dose" = ["*.txt"]
 "openmc.data" = ["*.txt", "*.DAT", "*.json", "*.h5"]
 "openmc.lib" = ["libopenmc.dylib", "libopenmc.so"]
-"lib" = ["libopenmc.so"]
 
 [project.scripts]
 openmc-ace-to-hdf5 = "scripts.openmc_ace_to_hdf5:main"
@@ -96,4 +95,4 @@ before-all = """
 manylinux-x86_64-image = "manylinux_2_28"
 
 [tool.setuptools.extension]
-libopenmc = {sources = [], libraries = ["openmc"], library-dirs = ["lib"], runtime-library-dirs = ["lib"]}
\ No newline at end of file
+libopenmc = {sources = [], libraries = ["openmc"], library-dirs = ["openmc/lib"], runtime-library-dirs = ["openmc/lib"]}
\ No newline at end of file
diff --git a/setup.py b/setup.py
index eec492647b9..ab28d391fa5 100755
--- a/setup.py
+++ b/setup.py
@@ -13,12 +13,19 @@ def __init__(self, name, cmake_lists_dir=".", sources=[], **kwa):
 lib_dir = os.path.join('openmc', 'lib')
 libopenmc_path = os.path.join(lib_dir, 'libopenmc.so')
 
+# Ensure the library exists
+if not os.path.exists(libopenmc_path):
+    raise FileNotFoundError(f"Required library {libopenmc_path} not found")
+
 kwargs = {
     'ext_modules': [OpenMCExtension('libopenmc')],
     'include_dirs': [np.get_include()],
     'package_data': {
-        'openmc': [os.path.join('lib', 'libopenmc.so')],
+        'openmc.lib': ['libopenmc.so'],
     },
+    'data_files': [
+        (lib_dir, [libopenmc_path]),
+    ],
 }
 
-setup(**kwargs)
+setup(**kwargs)
\ No newline at end of file

From 37f22ccfac4dcbe5670c75d45625632bf741399e Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Tue, 27 Aug 2024 23:24:06 +0100
Subject: [PATCH 28/29] [skip ci] returned to previous state as error not fixed

---
 CMakeLists.txt |  2 --
 pyproject.toml |  7 -------
 setup.py       | 16 ++--------------
 3 files changed, 2 insertions(+), 23 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 77ce2e7e264..14047e171d6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -336,7 +336,6 @@ endif()
 if(SKBUILD)
   set(CMAKE_INSTALL_RPATH "$ORIGIN")
   set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
-  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/openmc/lib)
 endif()
 
 #===============================================================================
@@ -582,7 +581,6 @@ add_executable(openmc src/main.cpp)
 add_executable(OpenMC::openmc ALIAS openmc)
 target_compile_options(openmc PRIVATE ${cxxflags})
 target_include_directories(openmc PRIVATE ${CMAKE_BINARY_DIR}/include)
-target_include_directories(openmc PRIVATE ${CMAKE_SOURCE_DIR}/include)
 target_link_libraries(openmc libopenmc)
 
 # Ensure C++17 standard is used and turn off GNU extensions
diff --git a/pyproject.toml b/pyproject.toml
index 686cf8fde72..c24026300b1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,9 +2,6 @@
 requires = ["setuptools", "wheel", "numpy", "cython", "scikit-build-core"]
 build-backend = "scikit_build_core.build"
 
-[tool.scikit-build-core]
-generator = "Ninja"
-
 [project]
 name = "openmc"
 authors = [
@@ -64,7 +61,6 @@ Issues = "https://github.com/openmc-dev/openmc/issues"
 [tool.setuptools.packages.find]
 include = ['openmc*', 'scripts*']
 exclude = ['tests*']
-packages = ["find:"]
 
 [tool.setuptools.package-data]
 "openmc.data.effective_dose" = ["*.txt"]
@@ -93,6 +89,3 @@ before-all = """
     yum install -y hdf5 hdf5-devel libpng-devel cmake eigen3-devel gcc gcc-c++ wget
 """
 manylinux-x86_64-image = "manylinux_2_28"
-
-[tool.setuptools.extension]
-libopenmc = {sources = [], libraries = ["openmc"], library-dirs = ["openmc/lib"], runtime-library-dirs = ["openmc/lib"]}
\ No newline at end of file
diff --git a/setup.py b/setup.py
index ab28d391fa5..f26b3138274 100755
--- a/setup.py
+++ b/setup.py
@@ -10,22 +10,10 @@ def __init__(self, name, cmake_lists_dir=".", sources=[], **kwa):
         Extension.__init__(self, name, sources=sources, **kwa)
         self.cmake_lists_dir = os.path.abspath(cmake_lists_dir)
 
-lib_dir = os.path.join('openmc', 'lib')
-libopenmc_path = os.path.join(lib_dir, 'libopenmc.so')
-
-# Ensure the library exists
-if not os.path.exists(libopenmc_path):
-    raise FileNotFoundError(f"Required library {libopenmc_path} not found")
 
 kwargs = {
     'ext_modules': [OpenMCExtension('libopenmc')],
-    'include_dirs': [np.get_include()],
-    'package_data': {
-        'openmc.lib': ['libopenmc.so'],
-    },
-    'data_files': [
-        (lib_dir, [libopenmc_path]),
-    ],
+    'include_dirs': [np.get_include()]
 }
 
-setup(**kwargs)
\ No newline at end of file
+setup(**kwargs)

From fb01690b5bda61f11ba9d7be9eeba6a37c8bc423 Mon Sep 17 00:00:00 2001
From: Jon Shimwell <jon@proximafusion.com>
Date: Thu, 29 Aug 2024 08:56:19 +0100
Subject: [PATCH 29/29] changed rpath to lib folder for .so file

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 14047e171d6..ffa682ad111 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -334,7 +334,7 @@ if("${isSystemDir}" STREQUAL "-1")
 endif()
 
 if(SKBUILD)
-  set(CMAKE_INSTALL_RPATH "$ORIGIN")
+  set(CMAKE_INSTALL_RPATH "$ORIGIN/lib")
   set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 endif()