test-ci.yml

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@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        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@v4

      - 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@v4
         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@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        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 .[extra,test,dev]
          python -m pip install finufft pooch brainweb-dl torch fastmri
        
      - 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 fastmri

      - 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@v4

      - 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@v5
        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]') || github.ref == 'refs/heads/master' }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      
      - 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@v5
        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