extensive_ci.yml

# This file is based on examples in
# https://docs.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions

# Note that all the "sudo" commands here appear to cause a warning message
# "sudo: setrlimit(RLIMIT_CORE): operation not permitted"
# This appears to be a known harmless annoyance:
# https://gitlab.alpinelinux.org/alpine/aports/-/issues/11122

name: Extensive CI

on:
  push: 
    branches: [master]
    tags: [v*]
  pull_request:
    branches: [master]
  workflow_dispatch: 

jobs:
  test:
    runs-on: ubuntu-latest

    env:
      OMPI_ALLOW_RUN_AS_ROOT: 1
      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1

    strategy:
      fail-fast: false
      matrix:
        test-type: [unit, integrated]
        packages: [all, vmec, spec, none]
        python-version: [3.7.15, 3.8.15, 3.9.16] # , 3.10.0] # To sync with coveragerc use 3 levels with python version
        include:
            - python-version: 3.9.16
              test-type: unit
              packages: none
            - python-version: 3.9.16
              test-type: integrated
              packages: none

    steps:
    # First print out lots of information. We do this in separate 
    # "name" blocks because otherwise the output gets mixed together
    # in the github actions log.
    
    - name: Print user and group id
      run: |
        set -ex
        id

    - name: PWD
      run: |
        set -ex
        pwd

    - name: ls -l
      run: |
        set -ex
        ls -l

    - name: apt-get stuff needed for libstell and vmec
      run: |
        sudo apt-get update
        sudo apt-get install -y build-essential gfortran openmpi-bin libopenmpi-dev libnetcdf-dev libnetcdff-dev liblapack-dev libscalapack-mpi-dev libhdf5-dev libhdf5-serial-dev git m4 libfftw3-dev libopenblas-dev libboost-all-dev
    
    - uses: actions/checkout@v3
      # If we want submodules downloaded, uncomment the next 2 lines:
      #with:
      #  submodules: true

    # We must run actions/checkout@v3 before downloading and building VMEC, since checkout deletes the contents of the directory.
    - name: Download the VMEC2000 standalone repository
      if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
      run: git clone https://github.com/hiddensymmetries/VMEC2000.git

    - name: ls -l again
      run: |
        set -ex
        ls -l
        pwd

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: which python3 after python setup
      run: which python3

    - name: which pip after python setup
      run: |
        python -m pip install --upgrade pip
        pip --version

    - name: env after adding python
      run: env

    - name: Install python dependencies
      run: |
           sudo apt-get install graphviz graphviz-dev
           pip install wheel numpy scipy f90nml h5py scikit-build cmake qsc sympy pyevtk matplotlib ninja plotly networkx pygraphviz

    - name: Install booz_xform
      if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
      run: pip install -v git+https://github.com/hiddenSymmetries/booz_xform

    - name: Install virtual_casing
      run: pip install -v git+https://github.com/hiddenSymmetries/virtual-casing

    # See https://github.community/t/best-way-to-clone-a-private-repo-during-script-run-of-private-github-action/16116/7
    # https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions
    # https://docs.github.com/en/free-pro-team@latest/github/authenticating-to-github/creating-a-personal-access-token
    - name: Check out SPEC
      if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
      uses: actions/checkout@v3
      with:
        repository: PrincetonUniversity/SPEC
        path: SPEC

    # For some reason, installing py_spec does not install the dependencies f90nml and h5py. Therefore I installed these manually above.
    - name: Install py_spec
      if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
      run: |
        pip install -r SPEC/Utilities/pythontools/requirements.txt
        pip install -e SPEC/Utilities/pythontools
        python -c "import py_spec; print('success')"

    - name: Install f90wrap
      run: pip install -U git+https://github.com/zhucaoxiang/f90wrap

    - name: Build SPEC python wrapper.
      if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
      run: |
         cd SPEC
         pip install .

    - name: Try import spec
      if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
      run: python -c "import spec.spec_f90wrapped as spec; print(spec.constants.version)"

    - name: ls in /usr/lib/x86_64-linux-gnu
      run: ls -l /usr/lib/x86_64-linux-gnu

    - name: Add to LD_LIBRARY_PATH so scalapack etc can be found
      run: echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" >> $GITHUB_ENV

    - name: env after adding to LD_LIBRARY_PATH
      run: env

    - name: ls in VMEC2000/python 1
      if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
      run: ls -l VMEC2000/python

    - name: Configure VMEC2000 module
      if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
      run: |
        cd VMEC2000
        cp cmake/machines/ubuntu.json cmake_config_file.json
        cat cmake_config_file.json
        pip install .

    - name: Try importing vmec module
      if: contains(matrix.packages, 'vmec') || contains(matrix.packages, 'all')
      run: python -c "print(dir()); import vmec; print(dir()); print(dir(vmec)); print('package:', vmec.__package__); print('spec:', vmec.__spec__); print('doc:', vmec.__doc__); print('file:', vmec.__file__); print('path:', vmec.__path__)"

    - name: Install simsopt package
      if: contains(matrix.packages, 'spec') || contains(matrix.packages, 'all')
      run: pip install -v .[MPI,SPEC]

    - name: Install simsopt package
      if: contains(matrix.packages, 'none')
      run: pip install -v .

    - name: Install simsopt package
      if: contains(matrix.packages, 'vmec')
      run: pip install -v .[MPI]

    - name: Run serial examples as part of integrated tests
      if: contains(matrix.test-type, 'integrated') && (contains(matrix.packages, 'none') || contains(matrix.packages, 'all'))
      run: |
        cd examples
        ./run_serial_examples

    - name: Run simple parallel examples as part of integrated tests
      if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'all')
      run: |
        cd examples
        ./run_parallel_examples

    - name: Run spec examples as part of integrated tests
      if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'spec')
      run: |
        cd examples
        ./run_spec_examples

    - name: Run vmec examples as part of integrated tests
      if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'vmec')
      run: |
        cd examples
        ./run_vmec_examples

    - name: Run vmec and spec examples as part of integrated tests
      if: contains(matrix.test-type, 'integrated') && contains(matrix.packages, 'all')
      run: |
        cd examples
        ./run_spec_vmec_examples

    - name: Install coverage dependencies
      if: contains(matrix.test-type, 'unit')
      run: pip install coverage 

    - name: Run expensive tests on 1 MPI process using coverage
      if: contains(matrix.test-type, 'unit') && (contains(matrix.packages, 'none') || contains(matrix.packages, 'all'))
      run: |
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/geo
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/field

    - name: Run remaining tests on 1 MPI process using coverage
      if: contains(matrix.test-type, 'unit')
      run: | 
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/core
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/mhd
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/objectives
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/solve
        coverage run --source=simsopt -m unittest discover -t tests -v -s tests/util

    - name: Run MPI tests using coverage
      if: contains(matrix.test-type, 'unit') && (contains(matrix.packages, 'all') || contains(matrix.packages, 'vmec') || contains(matrix.packages, 'spec'))
      run: |
        mpiexec -n 1 coverage run -m unittest discover -k "mpi" -s tests -v
        mpiexec -n 2 coverage run -m unittest discover -k "mpi" -s tests -v
        mpiexec -n 3 --oversubscribe coverage run -m unittest discover -k "mpi" -s tests -v

    - name: Upload uncombined coverage to github
      if: contains(matrix.test-type, 'unit')
      uses: actions/upload-artifact@v3
      with:
        name: gh-actions-parallel-coverage
        path: .coverage.*
        if-no-files-found: error

  coverage:
    runs-on: ubuntu-latest
    needs: [ test ]
    steps:

    - name: Set up Python 
      uses: actions/setup-python@v4
      with:
        python-version: 3.8.15

    - name: Install coverage
      run: pip install coverage

    - name: Checkout simsopt 
      uses: actions/checkout@v3

    - name: Install simsopt before running coverage
      run: pip install .

    - name: Download artifact
      uses: actions/download-artifact@v3
      with:
        name: gh-actions-parallel-coverage
        path: ./

    - name: Display coverage files before combine 
      run: ls -a

    - name: Combine coverage reports
      run: | 
        coverage combine
        coverage report
        coverage xml

    - name: Upload coverage to github
      uses: actions/upload-artifact@v3
      with:
        name: tox-gh-actions-coverage
        path: coverage.xml
        if-no-files-found: error

    - name: Upload coverage to Codecov
      # The next line prevents github from trying to upload to Codecov on forks of the repository, avoiding a permissions error
      if: github.repository_owner == 'hiddenSymmetries'
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        flags: unittests
        env_vars: PYTHON
        name: codecov-umbrella
        fail_ci_if_error: true
        verbose: true