test-ci.yml

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:
  test-cpu:
    runs-on: ubuntu-latest
    if: ${{ !contains(github.event.head_commit.message, 'style')}}
    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
    if: ${{ !contains(github.event.head_commit.message, 'style')}}
    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 cupy-cuda11x
          pip install finufft

      - name: Install backend
        shell: bash
        run: |
          source $RUNNER_WORKSPACE/venv/bin/activate
          export CUDA_BIN_PATH=/usr/local/cuda-11.8/
          export PATH=/usr/local/cuda-11.8/bin/${PATH:+:${PATH}}
          export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib/{LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
          pip install ${{ matrix.backend }}

      - 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
    if: ${{ !contains(github.event.head_commit.message, 'style')}}

    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: |
          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