Build project with Scikit-build-core

.github/workflows/build.yml

@@ -32,12 +32,15 @@ jobs:
     steps:
     - uses: actions/checkout@v4
       with: {fetch-depth: 0, submodules: recursive}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        version: "0.6.9"
     - id: reqs
       name: set requirements
       run: |
         envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}"
         echo "envname=$envname" >> $GITHUB_OUTPUT
-        sed -ri -e 's/^(name: ).*/\1$envname/' -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' scripts/requirements-test.yml
     - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
@@ -48,12 +51,13 @@ jobs:
       name: build
       run: |
         conda activate "${{ steps.reqs.outputs.envname }}"
+        UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --inexact --all-extras
         cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
         cmake --build ./build --target install
     - name: test
       run: |
         conda activate "${{ steps.reqs.outputs.envname }}"
-        TESTS_FORCE_GPU=1 python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test
+        TESTS_FORCE_GPU=1 UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv run --no-sync python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test
     - if: always()
       name: Post Run conda-incubator/setup-miniconda@v3
       shell: bash
@@ -74,6 +78,11 @@ jobs:
     steps:
     - uses: actions/checkout@v4
       with: {fetch-depth: 0, submodules: recursive}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        version: "0.6.9"
+        enable-cache: true
     - name: set requirements
       run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml
     - uses: conda-incubator/setup-miniconda@v3
@@ -83,10 +92,11 @@ jobs:
         activate-environment: cil_dev
     - name: build
       run: |
+        UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --inexact
         cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
         cmake --build ./build --target install
     - name: test
-      run: python -m unittest discover -v ./Wrappers/Python/test
+      run: UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX  uv run --no-sync python -m unittest discover -v ./Wrappers/Python/test
   conda-matrix:
     runs-on: ubuntu-22.04
     outputs:
@@ -175,22 +185,32 @@ jobs:
         fetch-depth: 0
         submodules: recursive
         ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
-    - uses: conda-incubator/setup-miniconda@v3
-      with: {python-version: 3.11}
+    - name: Set up uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        version: "0.6.9"
+        enable-cache: true
+    - name: set requirements
+      working-directory: .
+      run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml
+    - name: Set conda environment
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: scripts/requirements-test.yml
+        activate-environment: cil_dev
     - uses: ruby/setup-ruby@v1
       with:
         ruby-version: '3.2'
         bundler-cache: true
         cache-version: 0
     - name: install dependencies
       run: |
-        conda install -c conda-forge -yq conda-merge
-        conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml
-        conda env update -n test
-        conda list
+        conda install -c conda-forge -yq pandoc
     - name: build cil
       working-directory: .
       run: |
+        UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --group docs --inexact
         cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
         cmake --build ./build --target install
     - name: checkout docs
@@ -208,7 +228,7 @@ jobs:
         docs_dir="${{ github.ref_name }}"
         docs_dir="${docs_dir//\//_}"
         if test "$docs_dir" = master; then docs_dir=nightly; fi
-        make BUILDSUBDIR="$docs_dir" dirhtml
+        UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv run --dev --group docs --no-sync make BUILDSUBDIR="$docs_dir" dirhtml
     - uses: actions/upload-artifact@v4
       with:
         name: DocumentationHTML
@@ -263,7 +283,7 @@ jobs:
     - name: test
       run: >
         docker run --rm -v .:/CIL tomographicimaging/cil:test /bin/bash -c
-        'python -m unittest discover -v /CIL/Wrappers/Python/test'
+        'uv run --dev --inexact python -m unittest discover -v /CIL/Wrappers/Python/test'
     - uses: docker/build-push-action@v6
       with:
         cache-from: type=gha

.github/workflows/build_uv.yml

@@ -0,0 +1,95 @@
+name: build_uv
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master]
+    tags: ['**']
+    paths-ignore:
+    - 'CHANGELOG.md'
+    - 'CITATION.cff'
+    - 'LICENSE'
+    - 'scripts/**'
+    - 'NOTICE.txt'
+    - 'README.md'
+  pull_request:
+    branches: [master]
+    paths-ignore:
+    - 'CHANGELOG.md'
+    - 'CITATION.cff'
+    - 'LICENSE'
+    - 'scripts/**'
+    - 'NOTICE.txt'
+    - 'README.md'
+jobs:
+  uv-test-cuda:
+    defaults: {run: {shell: 'bash -el {0}'}}
+    runs-on: [self-hosted, python, cuda]
+    strategy:
+      matrix:
+        python-version: [3.11]
+        numpy-version: [1.25]
+    steps:
+    - uses: actions/checkout@v4
+      with: {fetch-depth: 0, submodules: recursive}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5 
+      with:
+        version: "0.6.5"
+    - id: reqs
+      name: set requirements
+      run: |
+        envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}"
+        echo "envname=$envname" >> $GITHUB_OUTPUT
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+        environment-file: scripts/requirements-cuda.yml
+        activate-environment: ${{ steps.reqs.outputs.envname }}
+        run-post: false
+    - name: "Set up Python" 
+      uses: actions/setup-python@v5 
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: "Install Project"
+      run: | 
+        conda activate "${{ steps.reqs.outputs.envname }}"
+        conda install conda-forge::cudatoolkit-dev=11.7.0
+        uv sync --dev --all-extras
+    - name: test
+      run: CIL_DATA_DIR=./Wrappers/Python/data uv run --dev python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test
+    - if: always()
+      name: Post Run conda-incubator/setup-miniconda@v3
+      shell: bash
+      run: |
+        sed -i '/${{ steps.reqs.outputs.envname }}/d' ~/.profile
+        source ~/.profile
+        conda env remove -n "${{ steps.reqs.outputs.envname }}"
+  uv-test:
+    defaults: {run: {shell: 'bash -el {0}'}}
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        include:
+          - python-version: '3.10'
+          - python-version: 3.12
+    steps:
+    - uses: actions/checkout@v4
+      with: {fetch-depth: 0, submodules: recursive}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5 
+      with:
+        version: "0.6.5"
+        enable-cache: true
+    - name: "Set up Python" 
+      uses: actions/setup-python@v5 
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: "Install Project"
+      run: uv sync --dev
+    - name: test
+      run: CIL_DATA_DIR=./Wrappers/Python/data uv run --dev python -m unittest discover -v ./Wrappers/Python/test
+  pass:
+    needs: [uv-test-cuda, uv-test]
+    runs-on: ubuntu-22.04
+    steps: [{run: echo success}]

.gitignore

@@ -5,3 +5,4 @@ __pycache__/
 /build*
 *.vscode*
 *.egg*
+.ropeproject/

CMakeLists.txt

@@ -23,17 +23,21 @@ else()
   cmake_minimum_required(VERSION 3.4)
 endif()
 
-project(cil LANGUAGES CXX)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
 
-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)
@@ -44,5 +48,5 @@ if(NOT DEFINED CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE "RelWithDebInfo")
 endif()
 
-add_subdirectory(src/Core)
-add_subdirectory(Wrappers/Python)
+ 
+add_subdirectory(src/cilacc)

Dockerfile

@@ -16,13 +16,15 @@ ARG CIL_EXTRA_PACKAGES="tigre=2.6 astra-toolbox=2.1.0=cuda*"
 COPY --chown="${NB_USER}" scripts/requirements-test.yml environment.yml
 # channel_priority: https://stackoverflow.com/q/58555389
 RUN sed -ri '/tigre|astra-toolbox| python /d' environment.yml \
+  && curl -LsSf https://astral.sh/uv/0.6.9/install.sh | sh \
   && for pkg in 'jupyter-server-proxy>4.1.0' $CIL_EXTRA_PACKAGES; do echo "  - $pkg" >> environment.yml; done \
   && conda config --env --set channel_priority strict \
   && for ch in defaults nvidia ccpi https://software.repos.intel.com/python/conda conda-forge; do conda config --env --add channels $ch; done \
   && mamba env update -n base \
   && mamba clean -a -y -f \
   && rm environment.yml \
-  && fix-permissions "${CONDA_DIR}" /home/${NB_USER}
+  && fix-permissions "${CONDA_DIR}" /home/${NB_USER} \
+  && UV_PROJECT_ENVIRONMENT=$CONDA_DIR uv sync --all-extras --dev --inexact
 
 # NB: trailing `/` is required
 ENV TENSORBOARD_PROXY_URL=/user-redirect/proxy/6006/

Wrappers/Python/cil/__init__.py

@@ -15,5 +15,4 @@
 #
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
-
 from .version import version as __version__

Wrappers/Python/cil/framework/__init__.py

@@ -16,7 +16,7 @@
 # Authors:
 # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
-from .cilacc import cilacc
+from cil import cilacc
 from .acquisition_data import AcquisitionData
 from .acquisition_geometry import AcquisitionGeometry, SystemConfiguration
 from .data_container import DataContainer