From c1a3c244a0a87d35e93767e7092582958f4799e0 Mon Sep 17 00:00:00 2001
From: purepani <pani0028@umn.edu>
Date: Tue, 4 Mar 2025 18:28:40 -0600
Subject: [PATCH 01/14] Add scikit-build system

---
 pyproject.toml | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 24adcdac4a..c96353722d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,16 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm>=8"]
-build-backend = "setuptools.build_meta"
+requires = ["setuptools>=64", "setuptools_scm>=8",
+    	"ipp-static>=2022.0,<2022.1",
+    	"ipp-devel>=2022.0,<2022.1",
+	"nanobind",
+	"scikit-build-core>=0.11.0",
+	"intel-openmp==2025.0.5",
+]
+build-backend = "scikit_build_core.build"
+
+[tool.scikit-build.wheel.packages]
+cil = "Wrappers/Python/cil"
+"cil/cilacc" = "src/cilacc"
 
 [tool.setuptools_scm]
 version_file = "Wrappers/Python/cil/version.py"

From b7e5b0f8d4ef5af34d1afd03f05944fbc0def406 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 10:39:30 +0100
Subject: [PATCH 02/14] fixup build system

---
 pyproject.toml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index c96353722d..2e7dff67b7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,16 +1,15 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm>=8",
-    	"ipp-static>=2022.0,<2022.1",
-    	"ipp-devel>=2022.0,<2022.1",
-	"nanobind",
-	"scikit-build-core>=0.11.0",
-	"intel-openmp==2025.0.5",
+requires = [
+    "setuptools>=64",
+    "setuptools_scm>=8",
+    "scikit-build-core",
+    #"ipp-devel==2021.12.*", # PyPI conflicts with conda package
 ]
 build-backend = "scikit_build_core.build"
 
 [tool.scikit-build.wheel.packages]
 cil = "Wrappers/Python/cil"
-"cil/cilacc" = "src/cilacc"
+"cil/cilacc" = "src/Core"
 
 [tool.setuptools_scm]
 version_file = "Wrappers/Python/cil/version.py"

From f687b9d8301d8a4e5294faecbc341b7974c181da Mon Sep 17 00:00:00 2001
From: purepani <pani0028@umn.edu>
Date: Tue, 4 Mar 2025 18:28:40 -0600
Subject: [PATCH 03/14] Add CMake Build Files

---
 CMakeLists.txt                 | 19 ++++----
 Wrappers/Python/CMakeLists.txt | 30 ------------
 src/Core/CMakeLists.txt        | 86 +++++++++++++++-------------------
 3 files changed, 50 insertions(+), 85 deletions(-)
 delete mode 100644 Wrappers/Python/CMakeLists.txt

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 261c61cb66..d8441f607a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -21,20 +21,23 @@ else()
   cmake_minimum_required(VERSION 3.5)
 endif()
 
-project(cil LANGUAGES CXX)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
 
 cmake_policy(PUSH)
 
 cmake_policy(SET CMP0074 NEW)
-if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27)
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.27)
   cmake_policy(SET CMP0148 OLD)
 endif()
 
 # If APPLE don't use @rpath
-if (APPLE)
-  option(SHARED_LIBS_ABS_PATH "Force shared libraries to be installed with absolute paths (as opposed to rpaths)" ON)
-  mark_as_advanced( SHARED_LIBS_ABS_PATH )
-  if (SHARED_LIBS_ABS_PATH)
+if(APPLE)
+  option(
+    SHARED_LIBS_ABS_PATH
+    "Force shared libraries to be installed with absolute paths (as opposed to rpaths)"
+    ON)
+  mark_as_advanced(SHARED_LIBS_ABS_PATH)
+  if(SHARED_LIBS_ABS_PATH)
     # Set install_name_dir as the absolute path to install_prefix/lib
     GET_FILENAME_COMPONENT(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/lib REALPATH)
     set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
@@ -45,7 +48,7 @@ if(NOT DEFINED CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "RelWithDebInfo")
 endif()
 
-add_subdirectory(src/Core)
-add_subdirectory(Wrappers/Python)
+ 
+add_subdirectory(src/cilacc)
 
 cmake_policy(POP)
diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
deleted file mode 100644
index 9cb60e0f60..0000000000
--- a/Wrappers/Python/CMakeLists.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-find_package(Python COMPONENTS Interpreter REQUIRED)
-
-if(PYTHON_DEST_DIR)
-  file(TO_CMAKE_PATH "${PYTHON_DEST_DIR}" PYTHON_DEST)
-endif()
-
-message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
-if(NOT DEFINED)
-  set(CMAKE_BUILD_TYPE "RelWithDebInfo")
-endif()
-
-# TODO: add to add_custom_command DEPENDS the list of python files of the project.
-# file(GLOB_RECURSE DEPS ${CMAKE_CURRENT_SOURCE_DIR}/cil/*.py )
-message("SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL: $ENV{SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL}")
-message("CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}")
-if(PYTHON_DEST_DIR)
-  message(STATUS "CIL install using ${Python_EXECUTABLE} -m pip install -t ${PYTHON_DEST}")
-  add_custom_target(pythonsetup ALL
-    COMMAND ${Python_EXECUTABLE} -m pip install ${CMAKE_SOURCE_DIR} -t ${PYTHON_DEST} --upgrade
-    DEPENDS cilacc)
-else()
-  message(STATUS "CIL install using ${Python_EXECUTABLE} -m pip install")
-  add_custom_target(pythonsetup ALL
-    COMMAND ${Python_EXECUTABLE} -m pip install ${CMAKE_SOURCE_DIR} --upgrade
-    DEPENDS cilacc)
-endif()
-# install the data if not a conda build. With conda the data is in the dependency package cil-data
-if (NOT CONDA_BUILD)
-  install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cil)
-endif()
diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index 82f0c8e0b0..1a17f94d61 100644
--- a/src/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
@@ -25,20 +25,33 @@ message ("OpenMP_CXX_FLAGS ${OpenMP_CXX_FLAGS}")
 find_package(OpenMP REQUIRED)
 add_definitions(${OpenMP_CXX_FLAGS})
 
-if (WIN32)
-	set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Ddll_EXPORTS")
+cmake_minimum_required(VERSION 3.15)
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module OPTIONAL_COMPONENTS Development.SABIModule)
+
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
 endif()
 
+find_package(nanobind CONFIG REQUIRED)
+
+
+####Needed to find IPP libraries 
+execute_process(
+	COMMAND "${Python_EXECUTABLE}" -c "import sysconfig; print(sysconfig.get_paths()[\"data\"])"
+	OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE DATA_DIR)
+list(APPEND CMAKE_PREFIX_PATH ${DATA_DIR}/cmake)
+find_package(IPP REQUIRED CONFIG)
+
+
+
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNUCC")
   # appends some flags
   add_compile_options(-ftree-vectorize -fopt-info-vec-optimized -fopt-info-vec)
   # add_compile_options(-march=native -mavx )
 endif()
 
-message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
-message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")
-message("CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS}")
-message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}")
 
 if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.9.0")
   set (OpenMP_EXE_LINKER_FLAGS OpenMP::OpenMP_CXX)
@@ -49,48 +62,27 @@ else()
   set (OpenMP_EXE_LINKER_FLAGS ${OpenMP_C_FLAGS})
 endif()
 
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
-find_package(IPP)
 
-list(APPEND cilacc_SOURCES utilities.cpp axpby.cpp FiniteDifferenceLibrary.cpp)
-list(APPEND cilacc_INCLUDES ${CMAKE_CURRENT_SOURCE_DIR}/include)
-list(APPEND cilacc_LIBRARIES ${OpenMP_EXE_LINKER_FLAGS})
 
-if(IPP_FOUND)
-  list(APPEND cilacc_SOURCES FBP_filtering.cpp Binning.cpp)
-  list(APPEND cilacc_INCLUDES ${IPP_INCLUDE_DIRS})
-  list(APPEND cilacc_LIBRARIES ${IPP_LIBRARIES})
-else()
-  message(WARNING "IPP libraries not found, FBP_filtering not in build")
-endif()
 
-add_library(cilacc SHARED ${cilacc_SOURCES})
-target_link_libraries(cilacc ${cilacc_LIBRARIES})
-include_directories(cilacc PUBLIC ${cilacc_INCLUDES})
-
-## Install
-#include(GNUInstallDirs)
-#install(TARGETS cilacc
-#	RUNTIME DESTINATION bin
-#    LIBRARY DESTINATION lib
-#    ARCHIVE DESTINATION lib
-#	CONFIGURATIONS ${CMAKE_BUILD_TYPE}
-#	)
-
-if (UNIX)
-message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
-install(TARGETS cilacc
-	LIBRARY DESTINATION lib
-	CONFIGURATIONS ${CMAKE_BUILD_TYPE}
-	)
-elseif(WIN32)
-message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
-  install(TARGETS cilacc
-	RUNTIME DESTINATION Library/bin
-	ARCHIVE DESTINATION lib
-	CONFIGURATIONS ${CMAKE_BUILD_TYPE}
-	)
-endif()
+nanobind_add_module(
+	cilacc
+	NB_STATIC
+	${CMAKE_CURRENT_SOURCE_DIR}/nanobind.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/include/axpby.h
+	${CMAKE_CURRENT_SOURCE_DIR}/include/Binning.h
+	${CMAKE_CURRENT_SOURCE_DIR}/include/FBP_filtering.h
+	${CMAKE_CURRENT_SOURCE_DIR}/include/FiniteDifferenceLibrary.h
+	${CMAKE_CURRENT_SOURCE_DIR}/include/utilities.h
+	${CMAKE_CURRENT_SOURCE_DIR}/axpby.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/Binning.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/FBP_filtering.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/FiniteDifferenceLibrary.cpp
+	${CMAKE_CURRENT_SOURCE_DIR}/utilities.cpp
+)
+target_link_libraries(cilacc PUBLIC ${OpenMP_EXE_LINKER_FLAGS} ${IPP_LIBRARIES})
+include_directories(cilacc PUBLIC 
+	${CMAKE_CURRENT_SOURCE_DIR}/include/
+)
 
-install(DIRECTORY ${PROJECT_SOURCE_DIR}/src/Core/include/
-        DESTINATION ${CMAKE_INSTALL_PREFIX}/include/cil)
+install(TARGETS cilacc LIBRARY DESTINATION cil)

From 4fc54724b4aa321845a4f8188d4f767da843c366 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 11:22:36 +0100
Subject: [PATCH 04/14] fixup & reverts

---
 CMakeLists.txt          | 19 ++++++-------
 pyproject.toml          |  4 ---
 src/Core/CMakeLists.txt | 63 ++++++++++++++++-------------------------
 3 files changed, 33 insertions(+), 53 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index d8441f607a..1054e3d78c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -21,23 +21,23 @@ else()
   cmake_minimum_required(VERSION 3.5)
 endif()
 
+if(NOT SKBUILD_PROJECT_NAME)
+  set(SKBUILD_PROJECT_NAME cil)
+endif()
 project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
 
 cmake_policy(PUSH)
 
 cmake_policy(SET CMP0074 NEW)
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.27)
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27)
   cmake_policy(SET CMP0148 OLD)
 endif()
 
 # If APPLE don't use @rpath
-if(APPLE)
-  option(
-    SHARED_LIBS_ABS_PATH
-    "Force shared libraries to be installed with absolute paths (as opposed to rpaths)"
-    ON)
-  mark_as_advanced(SHARED_LIBS_ABS_PATH)
-  if(SHARED_LIBS_ABS_PATH)
+if (APPLE)
+  option(SHARED_LIBS_ABS_PATH "Force shared libraries to be installed with absolute paths (as opposed to rpaths)" ON)
+  mark_as_advanced( SHARED_LIBS_ABS_PATH )
+  if (SHARED_LIBS_ABS_PATH)
     # Set install_name_dir as the absolute path to install_prefix/lib
     GET_FILENAME_COMPONENT(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/lib REALPATH)
     set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
@@ -48,7 +48,6 @@ if(NOT DEFINED CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "RelWithDebInfo")
 endif()
 
- 
-add_subdirectory(src/cilacc)
+add_subdirectory(src/Core)
 
 cmake_policy(POP)
diff --git a/pyproject.toml b/pyproject.toml
index 2e7dff67b7..a781f9a938 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,10 +7,6 @@ requires = [
 ]
 build-backend = "scikit_build_core.build"
 
-[tool.scikit-build.wheel.packages]
-cil = "Wrappers/Python/cil"
-"cil/cilacc" = "src/Core"
-
 [tool.setuptools_scm]
 version_file = "Wrappers/Python/cil/version.py"
 version_file_template = """
diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index 1a17f94d61..fadcafcdb7 100644
--- a/src/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
@@ -25,33 +25,20 @@ message ("OpenMP_CXX_FLAGS ${OpenMP_CXX_FLAGS}")
 find_package(OpenMP REQUIRED)
 add_definitions(${OpenMP_CXX_FLAGS})
 
-cmake_minimum_required(VERSION 3.15)
-
-find_package(Python REQUIRED COMPONENTS Interpreter Development.Module OPTIONAL_COMPONENTS Development.SABIModule)
-
-if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
-  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
-  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+if (WIN32)
+  add_definitions("/Ddll_EXPORTS")
 endif()
 
-find_package(nanobind CONFIG REQUIRED)
-
-
-####Needed to find IPP libraries 
-execute_process(
-	COMMAND "${Python_EXECUTABLE}" -c "import sysconfig; print(sysconfig.get_paths()[\"data\"])"
-	OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE DATA_DIR)
-list(APPEND CMAKE_PREFIX_PATH ${DATA_DIR}/cmake)
-find_package(IPP REQUIRED CONFIG)
-
-
-
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNUCC")
   # appends some flags
   add_compile_options(-ftree-vectorize -fopt-info-vec-optimized -fopt-info-vec)
   # add_compile_options(-march=native -mavx )
 endif()
 
+message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
+message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")
+message("CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS}")
+message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}")
 
 if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.9.0")
   set (OpenMP_EXE_LINKER_FLAGS OpenMP::OpenMP_CXX)
@@ -62,27 +49,25 @@ else()
   set (OpenMP_EXE_LINKER_FLAGS ${OpenMP_C_FLAGS})
 endif()
 
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+find_package(IPP)
 
+list(APPEND cilacc_SOURCES utilities.cpp axpby.cpp FiniteDifferenceLibrary.cpp)
+list(APPEND cilacc_INCLUDES ${CMAKE_CURRENT_SOURCE_DIR}/include)
+list(APPEND cilacc_LIBRARIES ${OpenMP_EXE_LINKER_FLAGS})
 
+if(IPP_FOUND)
+  list(APPEND cilacc_SOURCES FBP_filtering.cpp Binning.cpp)
+  list(APPEND cilacc_INCLUDES ${IPP_INCLUDE_DIRS})
+  list(APPEND cilacc_LIBRARIES ${IPP_LIBRARIES})
+else()
+  message(WARNING "IPP libraries not found, FBP_filtering not in build")
+endif()
 
-nanobind_add_module(
-	cilacc
-	NB_STATIC
-	${CMAKE_CURRENT_SOURCE_DIR}/nanobind.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/include/axpby.h
-	${CMAKE_CURRENT_SOURCE_DIR}/include/Binning.h
-	${CMAKE_CURRENT_SOURCE_DIR}/include/FBP_filtering.h
-	${CMAKE_CURRENT_SOURCE_DIR}/include/FiniteDifferenceLibrary.h
-	${CMAKE_CURRENT_SOURCE_DIR}/include/utilities.h
-	${CMAKE_CURRENT_SOURCE_DIR}/axpby.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/Binning.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/FBP_filtering.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/FiniteDifferenceLibrary.cpp
-	${CMAKE_CURRENT_SOURCE_DIR}/utilities.cpp
-)
-target_link_libraries(cilacc PUBLIC ${OpenMP_EXE_LINKER_FLAGS} ${IPP_LIBRARIES})
-include_directories(cilacc PUBLIC 
-	${CMAKE_CURRENT_SOURCE_DIR}/include/
-)
+add_library(cilacc SHARED ${cilacc_SOURCES})
+target_link_libraries(cilacc ${cilacc_LIBRARIES})
+include_directories(cilacc PUBLIC ${cilacc_INCLUDES})
 
-install(TARGETS cilacc LIBRARY DESTINATION cil)
+install(TARGETS cilacc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
+        DESTINATION ${SKBUILD_PROJECT_NAME}/include/${SKBUILD_PROJECT_NAME})

From 47ec6eabe8045f8d189e8fe32cb12c022e6b7c29 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 11:47:21 +0100
Subject: [PATCH 05/14] sdist

---
 pyproject.toml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a781f9a938..846644715e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,11 +2,20 @@
 requires = [
     "setuptools>=64",
     "setuptools_scm>=8",
-    "scikit-build-core",
+    "scikit-build-core>=0.10",
     #"ipp-devel==2021.12.*", # PyPI conflicts with conda package
 ]
 build-backend = "scikit_build_core.build"
 
+[tool.scikit-build]
+minimum-version = "build-system.requires"
+cmake.version = ">=3.16"
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["Wrappers/Python/cil/version.py"]
+sdist.exclude = ["scripts", "docs", "Wrappers/Python/data", "Wrappers/Python/test", ".*"]
+[tool.scikit-build.wheel.packages]
+cil = "Wrappers/Python/cil"
+
 [tool.setuptools_scm]
 version_file = "Wrappers/Python/cil/version.py"
 version_file_template = """

From 4b56133fc10b5814cf8de4c53ea6d2dac02818c1 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 13:14:34 +0100
Subject: [PATCH 06/14] fix cilacc lib path

---
 Wrappers/Python/cil/framework/cilacc.py       | 20 +++++------------
 .../operators/GradientOperator.py             | 22 ++++---------------
 src/Core/CMakeLists.txt                       |  2 +-
 3 files changed, 11 insertions(+), 33 deletions(-)

diff --git a/Wrappers/Python/cil/framework/cilacc.py b/Wrappers/Python/cil/framework/cilacc.py
index fa96ba4c51..88e7046dc0 100644
--- a/Wrappers/Python/cil/framework/cilacc.py
+++ b/Wrappers/Python/cil/framework/cilacc.py
@@ -16,18 +16,10 @@
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 import ctypes
-import platform
-from ctypes import util
-# check for the extension
+from pathlib import Path
 
-if platform.system() == 'Linux':
-    dll = 'libcilacc.so'
-elif platform.system() == 'Windows':
-    dll_file = 'cilacc.dll'
-    dll = util.find_library(dll_file)
-elif platform.system() == 'Darwin':
-    dll = 'libcilacc.dylib'
-else:
-    raise ValueError('Not supported platform, ', platform.system())
-
-cilacc = ctypes.cdll.LoadLibrary(dll)
+try:
+    cilacc_path = next((Path(__file__).parent.parent / 'lib').resolve().glob("*cilacc.*"))
+except StopIteration:
+    raise FileNotFoundError("cilacc library not found")
+cilacc = ctypes.cdll.LoadLibrary(str(cilacc_path))
diff --git a/Wrappers/Python/cil/optimisation/operators/GradientOperator.py b/Wrappers/Python/cil/optimisation/operators/GradientOperator.py
index ae6bbc6922..56dd9b1b1b 100644
--- a/Wrappers/Python/cil/optimisation/operators/GradientOperator.py
+++ b/Wrappers/Python/cil/optimisation/operators/GradientOperator.py
@@ -18,7 +18,7 @@
 
 from cil.optimisation.operators import LinearOperator
 from cil.optimisation.operators import FiniteDifferenceOperator
-from cil.framework import BlockGeometry, ImageGeometry
+from cil.framework import BlockGeometry, ImageGeometry, cilacc
 import logging
 from cil.utilities.multiprocessing import NUM_THREADS
 import numpy as np
@@ -258,7 +258,7 @@ def adjoint(self, x, out=None):
                     out.fill(tmp)
                 else:
                     out += tmp
-            return out 
+            return out
         else:
             tmp = self.domain_geometry().allocate()
             for i, axis_index in enumerate(self.ind):
@@ -267,20 +267,7 @@ def adjoint(self, x, out=None):
                 tmp += self.FD.adjoint(x.get_item(i))
             return tmp
 
-import ctypes, platform
-from ctypes import util
-# check for the extension
-if platform.system() == 'Linux':
-    dll = 'libcilacc.so'
-elif platform.system() == 'Windows':
-    dll_file = 'cilacc.dll'
-    dll = util.find_library(dll_file)
-elif platform.system() == 'Darwin':
-    dll = 'libcilacc.dylib'
-else:
-    raise ValueError('Not supported platform, ', platform.system())
-
-cilacc = ctypes.cdll.LoadLibrary(dll)
+import ctypes
 
 c_float_p = ctypes.POINTER(ctypes.c_float)
 
@@ -457,7 +444,7 @@ def adjoint(self, x, out=None):
         status = self.fd(out_p, *args)
         if status != 0:
             raise RuntimeError('Call to C gradient operator failed')
-    
+
         out.fill(ndout)
 
         #reset input data
@@ -466,4 +453,3 @@ def adjoint(self, x, out=None):
                 ndx[i]*= el
 
         return out
-
diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index fadcafcdb7..8c7d89e928 100644
--- a/src/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
@@ -68,6 +68,6 @@ add_library(cilacc SHARED ${cilacc_SOURCES})
 target_link_libraries(cilacc ${cilacc_LIBRARIES})
 include_directories(cilacc PUBLIC ${cilacc_INCLUDES})
 
-install(TARGETS cilacc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME})
+install(TARGETS cilacc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME}/lib)
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
         DESTINATION ${SKBUILD_PROJECT_NAME}/include/${SKBUILD_PROJECT_NAME})

From 0d65f229a6a7e1c2a99112ddff761743ac39dcac Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 14:07:42 +0100
Subject: [PATCH 07/14] conda: update build

---
 recipe/bld.bat   |  8 +-------
 recipe/build.sh  | 13 +++----------
 recipe/meta.yaml | 10 ++++++----
 3 files changed, 10 insertions(+), 21 deletions(-)

diff --git a/recipe/bld.bat b/recipe/bld.bat
index 696c6a1870..e9931541d5 100644
--- a/recipe/bld.bat
+++ b/recipe/bld.bat
@@ -4,13 +4,7 @@ set SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL=%PKG_VERSION%
 if not "%GIT_DESCRIBE_NUMBER%"=="0" (
     set SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL=%PKG_VERSION%.dev%GIT_DESCRIBE_NUMBER%+%GIT_DESCRIBE_HASH%
 )
-
 :: -G "Visual Studio 16 2019" specifies the the generator
 :: -T v142 specifies the toolset
-
-cmake -S "%RECIPE_DIR%\.." -B "%SRC_DIR%\build_framework" -G "Visual Studio 16 2019" -T "v142" -DCONDA_BUILD=ON -DCMAKE_BUILD_TYPE=RelWithDebInfo -DLIBRARY_LIB=%CONDA_PREFIX%\lib -DLIBRARY_INC=%CONDA_PREFIX% -DCMAKE_INSTALL_PREFIX=%PREFIX% -DPython_EXECUTABLE=%CONDA_PREFIX%\python
-
-if errorlevel 1 exit 1
-
-cmake --build "%SRC_DIR%\build_framework" --target install --config RelWithDebInfo
+pip install . --no-deps -Ccmake.args="-G Visual Studio 16 2019 -T v142"
 if errorlevel 1 exit 1
diff --git a/recipe/build.sh b/recipe/build.sh
index 0a1c1c629f..872bff219b 100755
--- a/recipe/build.sh
+++ b/recipe/build.sh
@@ -1,23 +1,16 @@
 #!/usr/bin/env bash
 set -euxo pipefail
 
+extra_args="-G Ninja"
 if test $(python -c "from __future__ import print_function; import platform; print(platform.system())") = Darwin ; then
   echo "Darwin"
-  extra_args="-DOPENMP_LIBRARIES=${CONDA_PREFIX}/lib -DOPENMP_INCLUDES=${CONDA_PREFIX}/include"
+  extra_args="$extra_args -DOPENMP_LIBRARIES=${CONDA_PREFIX}/lib -DOPENMP_INCLUDES=${CONDA_PREFIX}/include"
 else
   echo "something else"
-  extra_args=""
 fi
 
 export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL="${PKG_VERSION}"
 if test "${GIT_DESCRIBE_NUMBER}" != "0"; then
   export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL="${PKG_VERSION}.dev${GIT_DESCRIBE_NUMBER}+${GIT_DESCRIBE_HASH}"
 fi
-cmake ${RECIPE_DIR}/../ ${extra_args} \
-                        -DCONDA_BUILD=ON \
-                        -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-                        -DLIBRARY_LIB=${CONDA_PREFIX}/lib \
-                        -DLIBRARY_INC=${CONDA_PREFIX}/include \
-                        -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-                        -DPython_EXECUTABLE=${CONDA_PREFIX}/bin/python
-cmake --build . --target install
+pip install . --no-deps -Ccmake.args="${extra_args}"
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
index a84600143d..7f2bb87005 100644
--- a/recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -34,7 +34,7 @@ test:
     - pip install unittest-parametrize
     - python -m unittest discover -v -s Wrappers/Python/test  # [win]
     - python -m unittest discover -s Wrappers/Python/test -v  # [not win]
-    
+
 
 requirements:
   build:
@@ -50,9 +50,11 @@ requirements:
     - _openmp_mutex # [linux]
     - openmp        # [osx]
     - vc 14         # [win]
-    - ipp-include {{ ipp_version }} 
-    - ipp-devel {{ ipp_version }} 
-    - ipp {{ ipp_version }} 
+    - ninja         # [not win]
+    - ipp-include {{ ipp_version }}
+    - ipp-devel {{ ipp_version }}
+    - ipp {{ ipp_version }}
+    - scikit-build-core >=0.10
 
   run:
     - python

From 77c0c2598b7b5576b03a5b3d710d1318bccec921 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 14:16:01 +0100
Subject: [PATCH 08/14] CI: update build

---
 .github/workflows/build.yml | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 98f1428808..7c7f327e2e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -48,8 +48,7 @@ jobs:
       name: build
       run: |
         conda activate "${{ steps.reqs.outputs.envname }}"
-        cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
-        cmake --build ./build --target install
+        pip install .
     - name: test
       run: |
         conda activate "${{ steps.reqs.outputs.envname }}"
@@ -81,10 +80,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         environment-file: scripts/requirements-test.yml
         activate-environment: cil_dev
-    - name: build
-      run: |
-        cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
-        cmake --build ./build --target install
+    - run: pip install .
     - name: test
       run: python -m unittest discover -v ./Wrappers/Python/test
   conda-matrix:
@@ -179,11 +175,7 @@ jobs:
         conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml
         conda env update -n test
         conda list
-    - name: build cil
-      working-directory: .
-      run: |
-        cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
-        cmake --build ./build --target install
+    - run: pip install ..
     - name: checkout docs
       uses: actions/checkout@v4
       with:

From 3a3bc6dde56769d19a95f328692569fd047b8e75 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 23 Apr 2025 14:28:49 +0100
Subject: [PATCH 09/14] docker: update build

---
 Dockerfile | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 5dc5f25bca..5c508e0d71 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -29,7 +29,5 @@ ENV TENSORBOARD_PROXY_URL=/user-redirect/proxy/6006/
 
 # build & install CIL
 COPY --chown="${NB_USER}" . src
-RUN cmake -S ./src -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="${CONDA_DIR}" \
-  && cmake --build ./build --target install \
-  && rm -rf src build \
+RUN pip install ./src && rm -rf src \
   && fix-permissions "${CONDA_DIR}" /home/${NB_USER}

From f703f069bb2186a2126cde3a3a953432c2f4185b Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Mon, 5 May 2025 07:24:19 +0100
Subject: [PATCH 10/14] cilacc: fix windows paths

---
 src/Core/CMakeLists.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index 8c7d89e928..51aaa92851 100644
--- a/src/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
@@ -68,6 +68,8 @@ add_library(cilacc SHARED ${cilacc_SOURCES})
 target_link_libraries(cilacc ${cilacc_LIBRARIES})
 include_directories(cilacc PUBLIC ${cilacc_INCLUDES})
 
-install(TARGETS cilacc LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME}/lib)
+install(TARGETS cilacc
+        LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME}/lib
+        RUNTIME DESTINATION ${SKBUILD_PROJECT_NAME}/lib)
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
         DESTINATION ${SKBUILD_PROJECT_NAME}/include/${SKBUILD_PROJECT_NAME})

From c9bd7391dbf10a8e71fb226917ad1043605e094b Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 8 May 2025 15:44:27 +0100
Subject: [PATCH 11/14] docs: pip install

---
 README.md                       | 47 +++++++++++----------------------
 docs/source/developer_guide.rst |  3 +--
 2 files changed, 16 insertions(+), 34 deletions(-)

diff --git a/README.md b/README.md
index 5cdd6b3dea..75e80d2e23 100644
--- a/README.md
+++ b/README.md
@@ -31,6 +31,7 @@ conda create --name cil -c conda-forge -c https://software.repos.intel.com/pytho
 ```
 
 where:
+
 - `astra-toolbox=*=py*` enables CIL support for [ASTRA toolbox](http://www.astra-toolbox.com) CPU projector (2D Parallel beam only) (GPLv3 license)
 - `astra-toolbox=*=cuda*` (requires an NVIDIA GPU) enables CIL support for [ASTRA toolbox](http://www.astra-toolbox.com) GPU projectors (GPLv3 license)
 - `tigre` (requires an NVIDIA GPU) enables support for [TIGRE](https://github.com/CERN/TIGRE) toolbox projectors (BSD license)
@@ -86,7 +87,8 @@ docker run --rm --gpus all -p 8888:8888 -it ghcr.io/tomographicimaging/cil:lates
 ## Getting Started with CIL
 
 ### CIL Training
-We typically run training courses at least twice a year - check https://ccpi.ac.uk/training/ for our upcoming events!
+
+We typically run training courses at least twice a year - check <https://ccpi.ac.uk/training/> for our upcoming events!
 
 ### CIL on binder
 
@@ -116,60 +118,45 @@ The use of `--recurse-submodule` is necessary if the user wants the examples dat
 git submodule update --init --recursive
 ```
 
-### Build dependencies
+### Building with `pip`
+
+#### Install Dependencies
 
 To create a conda environment with all the dependencies for building CIL run the following shell script:
 
 ```sh
-bash scripts/create_local_env_for_cil_development.sh
+bash ./scripts/create_local_env_for_cil_development.sh
 ```
 
 Or with the CIL build and test dependencies:
 
 ```sh
-bash scripts/create_local_env_for_cil_development.sh -t
+bash ./scripts/create_local_env_for_cil_development.sh -t
 ```
 
-And then install CIL in to this environment using CMake.
+And then install CIL in to this environment using `pip`.
 
 Alternatively, one can use the `scripts/requirements-test.yml` to create a conda environment with all the
 appropriate dependencies on any OS, using the following command:
 
 ```sh
-conda env create -f scripts/requirements-test.yml
+conda env create -f ./scripts/requirements-test.yml
 ```
 
-### Build with CMake
-
-CMake and a C++ compiler are required to build the source code. Let's suppose that the user is in the source directory, then the following commands should work:
+#### Build CIL
 
-```sh
-cmake -S . -B ./build -DCMAKE_INSTALL_PREFIX=<install_directory> -DPython_EXECUTABLE=<path_to_python_executable>
-cmake --build ./build --target install
-```
+A C++ compiler is required to build the source code. Let's suppose that the user is in the source directory, then the following commands should work:
 
-If targeting an active conda environment then the `<install_directory>` can be set to the `CONDA_PREFIX` environment variable (e.g. `${CONDA_PREFIX}` in Bash, or `%CONDA_PREFIX%` in the Anaconda Prompt on Windows). Similarly, `<path_to_python_executable>` can be set to the active conda environment by passing `${CONDA_PREFIX}/bin/python` on linux or `%CONDA_PREFIX%\python` in windows.
-
-#### Linux
-```sh
-cmake -S . -B ./build -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} -DPython_EXECUTABLE=${CONDA_PREFIX}/bin/python
-```
-#### Windows
 ```sh
-cmake -S . -B .\build -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX% -DPython_EXECUTABLE=%CONDA_PREFIX%\python
+pip install --no-deps .
 ```
 
-If not installing to a conda environment then the user will also need to set the locations of the IPP library and includes, and the path to CIL.
-
-By default the location of the IPP library and includes is `${CMAKE_INSTALL_PREFIX}/lib` and `${CMAKE_INSTALL_PREFIX}/include` respectively. To pass the location of the IPP library and headers please pass the following parameters:
+If not installing inside a conda environment, then the user might need to set the locations of optional libraries:
 
 ```sh
-cmake -S . -B ./build -DCMAKE_INSTALL_PREFIX=<install_directory> -DPython_EXECUTABLE=<path_to_python_executable> -DIPP_ROOT=<path_to_ipp>
+pip install . -Ccmake.define.IPP_ROOT="<path_to_ipp>" -Ccmake.define.OpenMP_ROOT="<path_to_openmp>"
 ```
 
-The user will then need to add the path `<install_directory>/lib` to the environment variable `PATH` or `LD_LIBRARY_PATH`, depending on system OS.
-
-
 ### Building with Docker
 
 In the repository root, simply update submodules and run `docker build`:
@@ -179,7 +166,6 @@ git submodule update --init --recursive
 docker build . -t ghcr.io/tomographicimaging/cil
 ```
 
-
 ### Testing
 
 One installed, CIL functionality can be tested using the following command:
@@ -189,10 +175,8 @@ export TESTS_FORCE_GPU=1  # optional, makes GPU test failures noisy
 python -m unittest discover -v ./Wrappers/Python/test
 ```
 
-
 ## Citing CIL
 
-
 If you use CIL in your research, please include citations to **both** the software on Zenodo, and a CIL paper:
 
 E. Pasca, J. S. Jørgensen, E. Papoutsellis, E. Ametova, G. Fardell, K. Thielemans, L. Murgatroyd, M. Duff and H. Robarts (2023) <br>
@@ -200,7 +184,6 @@ Core Imaging Library (CIL) <br>
 Zenodo [software archive] <br>
 **DOI:** https://doi.org/10.5281/zenodo.4746198 <br>
 
-
 In most cases, the first CIL paper will be the appropriate choice:
 
 J. S. Jørgensen, E. Ametova, G. Burca, G. Fardell, E. Papoutsellis, E. Pasca, K. Thielemans, M. Turner, R. Warr, W. R. B. Lionheart and P. J. Withers (2021) <br>
diff --git a/docs/source/developer_guide.rst b/docs/source/developer_guide.rst
index ea78b8bb7e..f1472925f9 100644
--- a/docs/source/developer_guide.rst
+++ b/docs/source/developer_guide.rst
@@ -137,8 +137,7 @@ Example:
   cd CIL
   sh scripts/create_local_env_for_cil_development_tests.sh -n NUMPY_VERSION -p PYTHON_VERSION -e ENVIRONMENT_NAME
   conda activate ENVIRONMENT_NAME
-  cmake -S . -B ./build -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX}
-  cmake --build ./build --target install
+  pip install .
   cd docs
   conda update -n base -c defaults conda
   conda env update -f docs_environment.yml # with the name field set to ENVIRONMENT_NAME

From 2c226288bcbc5ccc64bc2bff930ba356770c52d9 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Thu, 15 May 2025 14:31:51 +0100
Subject: [PATCH 12/14] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ffad4c4127..93488ba57d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,7 @@
     - Added tests for Normaliser processor
     - Update minimum cmake version to 3.5
   - Dependencies:
+    - Move from CMake to `pip install` (#2145)
     - matplotlib-base is an optional dependency, instead of required (#2093)
     - `unittest-parametrize has been added as a dependency for tests (#1990)
     - olefile and dxchange are an optional dependency, instead of required (#2149)

From b57a779088f3c04e62ba2e79db6f11ff2accb498 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Fri, 16 May 2025 11:37:34 +0100
Subject: [PATCH 13/14] update .gitignore for in-place install

---
 .gitignore | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index db3970f85a..81b4942ab4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,8 @@
-/build/
+/build*
 __pycache__/
-/Wrappers/Python/build/
 /Wrappers/Python/cil/version.py
-/build*
+/Wrappers/Python/cil-*.dist-info/
+/Wrappers/Python/cil/include/
+/Wrappers/Python/cil/lib/
 *.vscode*
 *.egg*

From 417329313ae3fe564baee50f744e6c8b6f456af8 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Tue, 10 Jun 2025 10:25:23 +0100
Subject: [PATCH 14/14] windows: auto-generator

---
 recipe/bld.bat | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/recipe/bld.bat b/recipe/bld.bat
index e9931541d5..97fb90517d 100644
--- a/recipe/bld.bat
+++ b/recipe/bld.bat
@@ -4,7 +4,5 @@ set SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL=%PKG_VERSION%
 if not "%GIT_DESCRIBE_NUMBER%"=="0" (
     set SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL=%PKG_VERSION%.dev%GIT_DESCRIBE_NUMBER%+%GIT_DESCRIBE_HASH%
 )
-:: -G "Visual Studio 16 2019" specifies the the generator
-:: -T v142 specifies the toolset
-pip install . --no-deps -Ccmake.args="-G Visual Studio 16 2019 -T v142"
+pip install . --no-deps
 if errorlevel 1 exit 1