Density compensation #491
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| workflow_dispatch: | |
| env: | |
| PYTHON_VERSION: "3.10" | |
| BART_VERSION: "0.8.00" | |
| ref_backend: "finufft" | |
| jobs: | |
| linter-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ env.PYTHON_VERSION }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - name: Install Python deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test,dev] | |
| - name: Black Check | |
| shell: bash | |
| run: black . --diff --color --check | |
| - name: ruff Check | |
| shell: bash | |
| run: ruff src | |
| test-cpu: | |
| runs-on: ubuntu-latest | |
| needs: linter-check | |
| strategy: | |
| matrix: | |
| backend: [finufft, pynfft, pynufft, bart, sigpy] | |
| exclude: | |
| - backend: bart | |
| - backend: pynfft | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - 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: | | |
| sudo apt install -y libnfft3-dev | |
| python -m pip install pynfft2 "cython<3.0.0" | |
| - name: Install pynufft | |
| if: ${{ matrix.backend == 'pynufft' || env.ref_backend == 'pynufft' }} | |
| 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 >> $GITHUB_PATH | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_${{ matrix.backend }} | |
| pytest --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| path: coverage_${{ matrix.backend}} | |
| test-gpu: | |
| runs-on: GPU | |
| needs: linter-check | |
| strategy: | |
| matrix: | |
| backend: [gpunufft, cufinufft] | |
| 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 finufft | |
| - name: Install Experimental cufinufft | |
| if: ${{ matrix.backend == 'cufinufft' }} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| rm -rf finufft | |
| git clone https://github.com/flatironinstitute/finufft | |
| cd finufft && mkdir build && cd build | |
| export PATH=/usr/local/cuda-11.8/bin:$PATH | |
| export CUDA_PATH=/usr/local/cuda-11.8 | |
| export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64:$LD_LIBRARY_PATH | |
| export CUDA_BIN_PATH=/usr/local/cuda-11.8 | |
| cmake -DFINUFFT_USE_CUDA=1 ../ && cmake --build . && cp libcufinufft.so ../python/cufinufft/. | |
| # enter venv | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| pip install cupy-cuda11x | |
| cd $RUNNER_WORKSPACE/finufft/python/cufinufft | |
| # HACK: copy the lib to the site package directory. | |
| cp libcufinufft.so $(python -c "import site; print(site.getsitepackages()[0])")/libcufinufft.so | |
| python setup.py install | |
| - name: Install gpuNUFFT | |
| if: ${{ matrix.backend == 'gpunufft' }} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| rm -rf gpuNUFFT | |
| git clone https://github.com/chaithyagr/gpuNUFFT | |
| cd gpuNUFFT | |
| export PATH=/usr/local/cuda-11.8/bin:$PATH | |
| export CUDA_PATH=/usr/local/cuda-11.8 | |
| export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64:$LD_LIBRARY_PATH | |
| export CUDA_BIN_PATH=/usr/local/cuda-11.8 | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| python setup.py install | |
| - 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 --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| path: coverage_${{ matrix.backend }} | |
| - name: Cleanup | |
| if: always() | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| ls -al | |
| rm -rf finufft | |
| rm -rf gpuNUFFT | |
| rm -rf venv | |
| test-examples: | |
| runs-on: ubuntu-latest | |
| needs: linter-check | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - 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 | |
| - name: Run examples | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_plots | |
| pytest examples --cov --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| 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@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - 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: coverage combine -a coverage_data/* | |
| - name: Reports | |
| run: | | |
| coverage xml | |
| coverage report |