CI.yml

# This workflow will set up GitHub-hosted runners and install the required dependencies for elephant tests.
# On a pull requests and on pushes to master it will run different tests for elephant.

name: tests
# define events that trigger workflow 'tests'
on:
  workflow_dispatch: # enables manual triggering of workflow
    inputs:
      logLevel:
        description: 'Log level'
        required: true
        default: 'warning'
        type: choice
        options:
          - info
          - warning
          - debug

  pull_request:
    branches:
      - master
    types:
      #- assigned
      #- unassigned
      #- labeled
      #- unlabeled
      - opened
      #- edited
      #- closed
      - reopened
      - synchronize
      #- converted_to_draft
      #- ready_for_review
      #- locked
      #- unlocked
      #- review_requested
      #- review_request_removed
      #- auto_merge_enabled
      #- auto_merge_disabled

  push:
    branches:
      - master

# Cancel previous workflows on the same pull request
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

# jobs define the steps that will be executed on the runner
jobs:

  #        _
  #  _ __ (_)_ __
  #  | '_ \| | '_ \
  #  | |_) | | |_) |
  #  | .__/|_| .__/
  #  |_|     |_|

  # install dependencies and elephant with pip and run tests with pytest
  build-and-test-pip:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.8, 3.9, "3.10", 3.11, 3.12]
        python-version: [3.9, "3.10", 3.11, 3.12]
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [ubuntu-latest]
      # do not cancel all in-progress jobs if any matrix job fails
      fail-fast: false

    steps:
      # used to reset cache every month
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
      
      - name: Get pip cache dir
        id: pip-cache
        run: |
          echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

      - uses: actions/checkout@v3

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
          cache-dependency-path: '**/requirements.txt'

      - name: Cache test_env
        uses: actions/cache@v3
        with:
          path: ${{ steps.pip-cache.outputs.dir }}
          # Look to see if there is a cache hit for the corresponding requirements files
          # cache will be reset on changes to any requirements or every month
          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('**/CI.yml') }}-${{ hashFiles('setup.py') }}
            -${{ steps.date.outputs.date }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install coveralls
          pip install -e .[extras,tests]

      - name: List packages
        run: |
          pip list
          python --version

      - name: Test with pytest
        run: |
          coverage run --source=elephant -m pytest
          coveralls --service=github || echo "Coveralls submission failed"
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

  #                        ___  ____
  #  _ __ ___   __ _  ___ / _ \/ ___|
  # | '_ ` _ \ / _` |/ __| | | \___ \
  # | | | | | | (_| | (__| |_| |___) |
  # |_| |_| |_|\__,_|\___|\___/|____/

  test-macOS:
    name: conda (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      # do not cancel all in-progress jobs if any matrix job fails
      fail-fast: false
      matrix:
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [macos-12,macos-13]
        python-version: [3.11]
    steps:
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

      - uses: actions/checkout@v4.1.6

      - name: Cache conda
        uses: actions/cache@v3
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

      - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # corresponds to v3.0.4
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          channels: conda-forge,defaults
          channel-priority: true
          activate-environment: elephant
          environment-file: requirements/environment-tests.yml

      - name: Install dependencies
        shell: bash -l {0}
        run: |
          python --version
          mamba install pytest pytest-cov coveralls
          pip install -e .[extras]

      - name: List packages
        shell: bash -l {0}
        run: |
          pip list
          mamba list
          python --version

      - name: Test with pytest
        shell: bash -l {0}
        run: |
          pytest --cov=elephant

  # __        ___           _
  # \ \      / (_)_ __   __| | _____      _____
  #  \ \ /\ / /| | '_ \ / _` |/ _ \ \ /\ / / __|
  #   \ V  V / | | | | | (_| | (_) \ V  V /\__ \
  #    \_/\_/  |_|_| |_|\__,_|\___/ \_/\_/ |___/

  # install dependencies with pip and run tests with pytest
  test-pip:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
        python-version: [3.11,]
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [windows-latest]

    steps:
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

      - uses: actions/checkout@v3

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

      - name: Cache pip
        uses: actions/cache@v3
        with:
          path: ~\AppData\Local\pip\Cache
          # Look to see if there is a cache hit for the corresponding requirements files
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pytest-cov coveralls
          pip install -e .[extras,tests]

      - name: List packages
        run: |
          pip list
          python --version

      - name: Test with pytest
        run: |
          pytest --cov=elephant

  #  __  __ ____ ___
  # |  \/  |  _ \_ _|
  # | |\/| | |_) | |
  # | |  | |  __/| |
  # |_|  |_|_|  |___|

  # install dependencies and elephant with pip and run MPI
  test-pip-MPI:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
        python-version: [3.9]
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [ubuntu-latest]

      # do not cancel all in-progress jobs if any matrix job fails
      fail-fast: false

    steps:
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
      - uses: actions/checkout@v3

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

      - name: Get pip cache dir
        id: pip-cache
        run: |
          echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

      - name: Cache test_env
        uses: actions/cache@v3
        with:
          path: ${{ steps.pip-cache.outputs.dir }}
          # look to see if there is a cache hit for the corresponding requirements files
          # cache will be reset on changes to any requirements or every month
          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

      - name: Setup environment
        run: |
          sudo apt-get update
          sudo apt install -y libopenmpi-dev openmpi-bin

          python -m pip install --upgrade pip
          pip install mpi4py
          pip install pytest-cov coveralls
          pip install -e .[extras,tests]

      - name: List packages
        run: |
          pip list
          python --version

      - name: Test with pytest
        run: |
          mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest
          coveralls --service=github || echo "Coveralls submission failed"
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

  #   ____                _
  #  / ___|___  _ __   __| | __ _
  # | |   / _ \| '_ \ / _` |/ _` |
  # | |__| (_) | | | | (_| | (_| |
  #  \____\___/|_| |_|\__,_|\__,_|

  # install dependencies with conda and run tests with pytest
  test-conda:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
        python-version: [3.11]
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [ubuntu-latest]

      # do not cancel all in-progress jobs if any matrix job fails
      fail-fast: false

    steps:
      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

      - uses: actions/checkout@v3

      - name: Get pip cache dir
        id: pip-cache
        run: |
          echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

      - name: Cache pip
        uses: actions/cache@v3
        with:
          path: ${{ steps.pip-cache.outputs.dir }}

          key: ${{ runner.os }}-pip-${{hashFiles('requirements/environment-tests.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          channels: conda-forge,defaults
          channel-priority: true
          activate-environment: elephant
          environment-file: requirements/environment-tests.yml

      - name: Install dependencies
        shell: bash -el {0}
        run: |
          python --version
          conda install mpi4py openmpi
          mamba install pytest pytest-cov coveralls
          pip install -e .

      - name: List packages
        shell: bash -el {0}
        run: |
          pip list
          mamba list
          python --version

      - name: Test with pytest
        shell: bash -el {0}
        run: |
          pytest --cov=elephant

  #  ____
  # |  _ \  ___   ___ ___
  # | | | |/ _ \ / __/ __|
  # | |_| | (_) | (__\__ \
  # |____/ \___/ \___|___/

  # install dependencies for the documentation and build .html
  docs:
    name: docs (${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.8, 3.9, 3.10, 3.11, 3.12]
        python-version: [3.12]
        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [ubuntu-latest]

    steps:

      - name: Get current year-month
        id: date
        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

      - uses: actions/checkout@v3

      - name: Get pip cache dir
        id: pip-cache
        run: |
          echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

      - name: Cache pip
        uses: actions/cache@v3
        with:
          path: ${{ steps.pip-cache.outputs.dir }}
          # Look to see if there is a cache hit for the corresponding requirements files
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements-docs.txt') }}-${{ hashFiles('**/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
           -${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

      - uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          activate-environment: elephant
          environment-file: requirements/environment.yml

      - name: Install dependencies
        shell: bash -el {0} # enables conda incubator to activate environment
        run: |
          sudo apt-get update
          sudo apt install -y libopenmpi-dev openmpi-bin
          
          conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
          mamba env update --file requirements/environment-docs.yml --name elephant
          python -m pip install --upgrade pip
          pip install -e .[extras,tutorials,docs]
          # run notebooks
          sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py

      - name: List packages
        shell: bash -el {0}
        run: |
          pip list
          mamba list
          python --version

      - name: make html
        shell: bash -el {0}
        run: |
          cd doc
          make html

  # install dependencies and elephant with pip and run tests with pytest
  doctests:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
        python-version: ["3.10"]

        # OS [ubuntu-latest, macos-latest, windows-latest]
        os: [ubuntu-latest]

    steps:
      # used to reset cache every month
      - name: Get current year-month
        id: date
        run: echo "::set-output name=date::$(date +'%Y-%m')"
      - uses: actions/checkout@v3

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

      - name: Cache test_env
        uses: actions/cache@v3
        with:
          path: ~/test_env
          # Look to see if there is a cache hit for the corresponding requirements files
          # cache will be reset on changes to any requirements or every month
          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('**/CI.yml') }}-${{ hashFiles('setup.py') }}
            -${{ steps.date.outputs.date }}

      - name: Install dependencies
        run: |
          # create an environment and install everything
          python -m venv ~/test_env
          source ~/test_env/bin/activate
          sudo apt install -y libopenmpi-dev openmpi-bin

          python -m pip install --upgrade pip
          pip install mpi4py
          pip install pytest-cov coveralls
          pip install -e .[extras,tests]

      - name: List packages
        run: |
          source ~/test_env/bin/activate
          pip list
          python --version

      - name: Run doctests
        run: |
          source ~/test_env/bin/activate
          pytest elephant --doctest-modules --ignore=elephant/test/