CI: test macos (M1) arm64

.github/workflows/build.yml

@@ -22,60 +22,27 @@ on:
     - 'NOTICE.txt'
     - 'README.md'
 jobs:
-  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}
-    - 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 }}
-        environment-file: scripts/requirements-test.yml
-        activate-environment: ${{ steps.reqs.outputs.envname }}
-        run-post: false
-    - id: build
-      name: build
-      run: |
-        conda activate "${{ steps.reqs.outputs.envname }}"
-        cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
-        cmake --build ./build --target install
-    - name: test
-      run: |
-        conda activate "${{ 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
-    - 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 }}"
   test:
     defaults: {run: {shell: 'bash -el {0}'}}
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
         include:
-        - python-version: '3.10'
-          numpy-version: 1.23
         - python-version: 3.12
           numpy-version: 1.26
+          os: macos
     steps:
     - uses: actions/checkout@v4
       with: {fetch-depth: 0, submodules: recursive}
     - name: set requirements
-      run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml
+      run: |
+        case ${{ matrix.os }} in
+        ubuntu)
+          sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml ;;
+        macos)
+          sed -ri '' -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e '/not arm64/d' -e '/linux/d' scripts/requirements-test.yml ;
+          echo -e "  - astra-toolbox=2.2.0\n  - llvm-openmp" >> scripts/requirements-test.yml ;;
+        esac
     - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
@@ -87,182 +54,3 @@ jobs:
         cmake --build ./build --target install
     - name: test
       run: python -m unittest discover -v ./Wrappers/Python/test
-  conda-matrix:
-    runs-on: ubuntu-latest
-    outputs:
-      python-version: ${{ steps.matrix.outputs.python-version }}
-      numpy-version: ${{ steps.matrix.outputs.numpy-version }}
-    steps:
-    - id: matrix
-      run: |
-        if ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }}; then
-          echo "python-version=['3.10', 3.11]" >> $GITHUB_OUTPUT
-          echo "numpy-version=[1.23, 1.24, 1.25, 1.26]" >> $GITHUB_OUTPUT
-        else
-          echo "python-version=['3.10']" >> $GITHUB_OUTPUT
-          echo "numpy-version=[1.23]" >> $GITHUB_OUTPUT
-        fi
-  conda:
-    defaults: {run: {shell: 'bash -el {0}'}}
-    runs-on: ubuntu-latest
-    needs: conda-matrix
-    strategy:
-      matrix:
-        python-version: ${{ fromJson(needs.conda-matrix.outputs.python-version) }}
-        numpy-version: ${{ fromJson(needs.conda-matrix.outputs.numpy-version) }}
-        include:
-        - python-version: 3.12
-          numpy-version: 1.26
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        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: ${{ matrix.python-version }}
-        mamba-version: "1.5"
-        channels: conda-forge
-    - name: conda build & test
-      working-directory: recipe
-      run: |
-        conda install boa
-        conda mambabuild . -c conda-forge -c https://tomography.stfc.ac.uk/conda --override-channels --python=${{ matrix.python-version }} --numpy=${{ matrix.numpy-version }} --output-folder .
-    - uses: actions/upload-artifact@v4
-      with:
-        name: cil-package-py${{ matrix.python-version }}-np${{ matrix.numpy-version }}
-        path: recipe/linux-64/cil*
-    - name: anaconda upload -c ccpi
-      if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
-      run: |
-        conda install anaconda-client
-        anaconda -v -t ${{ secrets.CCPI_CONDA_TOKEN }} upload --force --label ${{ startsWith(github.ref, 'refs/tags') && 'main' || 'dev' }} recipe/linux-64/cil*
-    - name: conda upload -c tomography.stfc.ac.uk/conda
-      if: startsWith(github.ref, 'refs/tags')
-      run: |
-        echo '${{ secrets.STFC_SSH_KEY }}' > ./key
-        chmod 600 ./key
-        rsync -e 'ssh -o StrictHostKeyChecking=no -i ./key' -P recipe/linux-64/cil* \
-          '${{ secrets.STFC_SSH_HOST }}:${{ secrets.STFC_SSH_CONDA_DIR }}/linux-64/'
-  conda-reindex:
-    if: startsWith(github.ref, 'refs/tags')
-    needs: conda
-    runs-on: ubuntu-latest
-    steps:
-    - name: conda index tomography.stfc.ac.uk/conda
-      run: |
-        echo '${{ secrets.STFC_SSH_KEY }}' > ./key
-        chmod 600 ./key
-        ssh -o StrictHostKeyChecking=no -i ./key ${{ secrets.STFC_SSH_HOST }} \
-          'bash -lic "conda index --bz2 --zst --run-exports --channeldata --rss -n ccpi ${{ secrets.STFC_SSH_CONDA_DIR }}"'
-  docs:
-    defaults: {run: {shell: 'bash -el {0}', working-directory: docs}}
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        submodules: recursive
-        ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
-    - uses: conda-incubator/setup-miniconda@v3
-      with: {python-version: 3.11}
-    - uses: ruby/setup-ruby@v1
-      with:
-        ruby-version: '3.2'
-        bundler-cache: true
-        cache-version: 0
-    - name: install dependencies
-      run: |
-        conda install -c conda-forge -yq conda-merge
-        conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml
-        conda env update -n test
-        conda list
-    - name: build cil
-      working-directory: .
-      run: |
-        cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX"
-        cmake --build ./build --target install
-    - name: checkout docs
-      uses: actions/checkout@v4
-      with:
-        path: docs/build
-        ref: gh-pages
-    - id: pages
-      uses: actions/configure-pages@v5
-    - name: update web pages (jekyll)
-      run: make JEKYLLOPTS="--baseurl ${{ steps.pages.outputs.base_path }}" web-deps web
-      env: {JEKYLL_ENV: production}
-    - name: update docs pages (sphinx)
-      run: |
-        docs_dir="${{ github.ref_name }}"
-        docs_dir="${docs_dir//\//_}"
-        if test "$docs_dir" = master; then docs_dir=nightly; fi
-        make BUILDSUBDIR="$docs_dir" dirhtml
-    - uses: actions/upload-artifact@v4
-      with:
-        name: DocumentationHTML
-        path: docs/build
-    - name: Push changes
-      if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
-      uses: casperdcl/push-dir@v1
-      with:
-        message: Update documentation
-        branch: gh-pages
-        dir: docs/build
-        nojekyll: true
-  docker:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        submodules: recursive
-        ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA
-    - uses: jlumbroso/[email protected]
-      with:
-        docker-images: false
-        large-packages: false
-    - uses: docker/setup-buildx-action@v3
-    - uses: docker/metadata-action@v5
-      id: meta
-      with:
-        images: ghcr.io/${{ github.repository }}
-        tags: |
-          type=ref,event=branch
-          type=semver,pattern={{version}}
-          type=semver,pattern={{major}}.{{minor}}
-        labels: |
-          org.opencontainers.image.licenses=Apache-2.0 AND BSD-3-Clause AND GPL-3.0
-    - uses: docker/login-action@v3
-      if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags')
-      with:
-        registry: ghcr.io
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-    - uses: docker/build-push-action@v6
-      with:
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
-        context: .
-        load: true
-        tags: tomographicimaging/cil:test
-    - name: test
-      run: >
-        docker run --rm -v .:/CIL tomographicimaging/cil:test /bin/bash -c
-        'python -m unittest discover -v /CIL/Wrappers/Python/test'
-    - uses: docker/build-push-action@v6
-      with:
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
-        context: .
-        push: ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags') }}
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
-  pass:
-    needs: [test-cuda, test, conda, docs, docker]
-    runs-on: ubuntu-latest
-    steps: [{run: echo success}]

Dockerfile

@@ -9,13 +9,14 @@ LABEL org.opencontainers.image.source=https://github.com/TomographicImaging/CIL
 LABEL org.opencontainers.image.licenses="Apache-2.0 AND BSD-3-Clause AND GPL-3.0"
 
 # CUDA-specific packages
+ARG CIL_EXCLUDE_PACKAGES="cuda"
 ARG CIL_EXTRA_PACKAGES="tigre=2.6 astra-toolbox=2.1.0=cuda*"
 # build & runtime dependencies
 # TODO: sync scripts/create_local_env_for_cil_development.sh, scripts/requirements-test.yml, recipe/meta.yaml (e.g. missing libstdcxx-ng _openmp_mutex pip)?
 # vis. https://github.com/TomographicImaging/CIL/pull/1590
 COPY --chown="${NB_USER}" scripts/requirements-test.yml environment.yml
 # channel_priority: https://stackoverflow.com/q/58555389
-RUN sed -ri '/tigre|astra-toolbox| python /d' environment.yml \
+RUN sed -ri "/$CIL_EXCLUDE_PACKAGES| python /d" environment.yml \
   && 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 \

Wrappers/Python/test/test_DataContainer.py

@@ -1037,13 +1037,12 @@ def test_sapyb_datacontainer_f(self):
         # equals to 1 + -1 = 0
         out = d1.sapyb(a,d2,b)
         res = np.zeros_like(d1.as_array())
-        np.testing.assert_array_equal(res, out.as_array())
+        np.testing.assert_array_almost_equal(res, out.as_array(), decimal=7)
 
         out.fill(0)
         d1.sapyb(a,d2,b, out)
         res = np.zeros_like(d1.as_array())
-        np.testing.assert_array_equal(res, out.as_array())
-
+        np.testing.assert_array_almost_equal(res, out.as_array(), decimal=7)
 
     def test_sapyb_scalar_f(self):
         # a,b scalar