pip build

.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:

.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*

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)

CMakeLists.txt

@@ -21,7 +21,10 @@ else()
   cmake_minimum_required(VERSION 3.5)
 endif()
 
-project(cil LANGUAGES CXX)
+if(NOT SKBUILD_PROJECT_NAME)
+  set(SKBUILD_PROJECT_NAME cil)
+endif()
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
 
 cmake_policy(PUSH)
 
@@ -46,6 +49,5 @@ if(NOT DEFINED CMAKE_BUILD_TYPE)
 endif()
 
 add_subdirectory(src/Core)
-add_subdirectory(Wrappers/Python)
 
 cmake_policy(POP)

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}

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:
@@ -189,18 +175,15 @@ 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>
 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>

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))

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
-

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

pyproject.toml

@@ -1,6 +1,20 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm>=8"]
-build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools>=64",
+    "setuptools_scm>=8",
+    "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"

recipe/bld.bat

@@ -4,13 +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
-
-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
 if errorlevel 1 exit 1

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}"