Clean CPU examples #1340
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| name: CI | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| PYTHON_VERSION: "3.10" | |
| BART_VERSION: "0.8.00" | |
| ref_backend: "finufft" | |
| jobs: | |
| test-cpu: | |
| runs-on: cpu | |
| if: ${{ !contains(github.event.head_commit.message, '!style') || github.ref == 'refs/heads/master' }} | |
| strategy: | |
| matrix: | |
| backend: [finufft, pynfft, pynufft-cpu, bart, sigpy, torchkbnufft-cpu] | |
| exclude: | |
| - backend: bart | |
| - backend: pynufft-cpu | |
| - backend: torchkbnufft-cpu | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Install Dependencies | |
| shell: bash | |
| run: | | |
| python --version | |
| - name: Install Python Deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test] | |
| - name: Install pynfft | |
| if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }} | |
| shell: bash | |
| run: | | |
| python -m pip install "pynfft2>=1.4.3" | |
| - name: Install pynufft | |
| if: ${{ matrix.backend == 'pynufft-cpu' || env.ref_backend == 'pynufft-cpu' }} | |
| run: python -m pip install pynufft | |
| - name: Install finufft | |
| if: ${{ matrix.backend == 'finufft' || env.ref_backend == 'finufft'}} | |
| shell: bash | |
| run: python -m pip install finufft | |
| - name: Install Sigpy | |
| if: ${{ matrix.backend == 'sigpy' || env.ref_backend == 'sigpy'}} | |
| shell: bash | |
| run: python -m pip install sigpy | |
| - name: Install BART | |
| if: ${{ matrix.backend == 'bart' || env.ref_backend == 'bart'}} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| sudo apt-get install make gcc libfftw3-dev liblapacke-dev libpng-dev libopenblas-dev | |
| wget https://github.com/mrirecon/bart/archive/v${{ env.BART_VERSION }}.tar.gz | |
| tar xzvf v${{ env.BART_VERSION }}.tar.gz | |
| cd bart-${{ env.BART_VERSION }} | |
| make | |
| echo $PWD >> $GITHUB_PATH | |
| - name: Install torchkbnufft-cpu | |
| if: ${{ matrix.backend == 'torchkbnufft-cpu' || env.ref_backend == 'torchkbnufft-cpu'}} | |
| run: python -m pip install torchkbnufft | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_${{ matrix.backend }} | |
| pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_${{ matrix.backend }} | |
| path: coverage_${{ matrix.backend }} | |
| test-gpu: | |
| runs-on: gpu | |
| if: ${{ !contains(github.event.head_commit.message, '!style') || github.ref == 'refs/heads/master' }} | |
| strategy: | |
| matrix: | |
| backend: [cufinufft, gpunufft, torchkbnufft-gpu, tensorflow] | |
| exclude: | |
| # There is an issue with tensorflow and cupy. This was working. See #156 | |
| - backend: tensorflow | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install mri-nufft and finufft | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| python --version | |
| python -m venv venv | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| pip install --upgrade pip wheel | |
| pip install -e mri-nufft[test] | |
| pip install cupy-cuda12x finufft "numpy<2.0" | |
| - name: Install torch with CUDA 12.1 | |
| shell: bash | |
| if: ${{ matrix.backend != 'tensorflow'}} | |
| run: | | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| pip install torch | |
| - name: Install backend | |
| shell: bash | |
| run: | | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| export CUDA_BIN_PATH=/usr/local/cuda-12.1/ | |
| export PATH=/usr/local/cuda-12.1/bin/:${PATH} | |
| export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH} | |
| if [[ ${{ matrix.backend }} == "torchkbnufft-gpu" ]]; then | |
| pip install torchkbnufft | |
| elif [[ ${{ matrix.backend }} == "tensorflow" ]]; then | |
| pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7 | |
| elif [[ ${{ matrix.backend }} == "cufinufft" ]]; then | |
| pip install "cufinufft<2.3" | |
| else | |
| pip install ${{ matrix.backend }} | |
| fi | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE/mri-nufft | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| export COVERAGE_FILE=coverage_${{ matrix.backend }} | |
| python -m pytest -k='operators' --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_${{ matrix.backend }} | |
| path: coverage_${{ matrix.backend }} | |
| - name: Cleanup | |
| if: always() | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| ls -al | |
| rm -rf finufft | |
| rm -rf gpuNUFFT | |
| rm -rf venv | |
| get-commit-message: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| message: ${{ steps.get_commit_message.outputs.message }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Get commit message | |
| id: get_commit_message | |
| run: | | |
| COMMIT_MESSAGE=$(git log -1 --pretty=%B) | |
| echo "Commit message $COMMIT_MESSAGE" | |
| echo "::set-output name=message::$COMMIT_MESSAGE" | |
| test-examples: | |
| runs-on: gpu | |
| needs: get-commit-message | |
| if: ${{ !contains(needs.get-commit-message.outputs.message, '!style') || github.ref == 'refs/heads/master' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: Restore cached brainweb-dl directory | |
| uses: actions/cache/restore@v4 | |
| id: cache-restore | |
| with: | |
| path: ~/.cache/brainweb | |
| key: ${{ runner.os }}-Brainweb | |
| - name: Install Python deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test,dev] | |
| python -m pip install finufft pooch brainweb-dl torch | |
| - name: Install GPU related interfaces | |
| run: | | |
| export CUDA_BIN_PATH=/usr/local/cuda-12.1/ | |
| export PATH=/usr/local/cuda-12.1/bin/:${PATH} | |
| export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH} | |
| pip install cupy-cuda12x torch | |
| python -m pip install gpuNUFFT "cufinufft<2.3" sigpy scikit-image | |
| - name: Run examples | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_plots | |
| pytest examples tests -k="not operators" --cov --cov-branch --cov-report=term | |
| - name: Cache brainweb-dl directory | |
| uses: actions/cache/save@v4 | |
| if: ${{ steps.cache-restore.outputs.cache-hit != 'true' }} | |
| with: | |
| path: ~/.cache/brainweb | |
| key: ${{ runner.os }}-Brainweb | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_plots | |
| path: coverage_plots | |
| coverage: | |
| runs-on: ubuntu-latest | |
| needs: [test-cpu, test-gpu, test-examples] | |
| if: ${{ always() }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Collect Coverages | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: coverage_data | |
| pattern: coverage_* | |
| merge-multiple: true | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - name: add the coverage tool | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install coverage[toml] | |
| python -m pip install -e . | |
| - name: Combine coverage | |
| run: | | |
| export COVERAGE_FILE=coverage_combined | |
| coverage combine -a coverage_data/* | |
| - name: Upload Combined coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_combined | |
| path: coverage_combined | |
| - name: Reports | |
| run: | | |
| export COVERAGE_FILE=coverage_combined | |
| coverage xml | |
| coverage report | |
| echo COVERAGE_PERC=$(coverage report | tail -n 1 | grep -oE [0-9\.]*?% | cut -d '%' -f1) >> $GITHUB_ENV | |
| - name: Create a Coverage Badge | |
| if: ${{github.event_name == 'push'}} | |
| run: | | |
| wget https://img.shields.io/badge/coverage-${{env.COVERAGE_PERC}}%25-green -O coverage_badge.svg | |
| - name: Upload badge as artifact | |
| if: ${{github.event_name == 'push'}} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_badge | |
| path: coverage_badge.svg | |
| BuildDocs: | |
| name: Build API Documentation | |
| runs-on: gpu | |
| needs: get-commit-message | |
| if: ${{ contains(needs.get-commit-message.outputs.message, '!docs_build') || github.ref == 'refs/heads/master' }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Get history and tags for SCM versioning to work | |
| run: | | |
| git fetch --prune --unshallow | |
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install .[doc] | |
| python -m pip install finufft | |
| - name: Install GPU related interfaces | |
| run: | | |
| export CUDA_BIN_PATH=/usr/local/cuda-12.1/ | |
| export PATH=/usr/local/cuda-12.1/bin/:${PATH} | |
| export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH} | |
| pip install cupy-cuda12x torch | |
| python -m pip install gpuNUFFT "cufinufft<2.3" | |
| - name: Build API documentation | |
| run: | | |
| python -m sphinx docs docs_build | |
| - name: Display data | |
| run: ls -R | |
| working-directory: docs_build/_static | |
| - name: Upload artifact | |
| id: artifact-upload-step | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| # Upload the docs | |
| name: docs | |
| path: 'docs_build' | |
| retention-days: 5 | |
| CompileDocs: | |
| name: Compile the coverage badge in docs | |
| runs-on: ubuntu-latest | |
| if: ${{ github.ref == 'refs/heads/master' }} | |
| needs: [BuildDocs, coverage] | |
| steps: | |
| - name: Get the docs_build artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docs | |
| path: docs_build | |
| overwrite: true | |
| - name: Get the badge from CI | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: coverage_badge | |
| path: docs_build/_static | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: ReUpload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docs_final | |
| retention-days: 20 | |
| path: docs_build |