python-tests.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: build

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  test:
    name: ${{ matrix.os }}, python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}

    strategy:
      matrix:
        os: ["ubuntu-latest", "macos-latest"]
        python-version: ["3.10", "3.11", "3.12"]

    # Run all shells using bash (including Windows)
    defaults:
      run:
        shell: bash -l {0}

    steps:
    - uses: actions/checkout@v4

    # We initiate the environment empty, and check if a key for this environment doesn't already exist in the cache
    - name: Initiate empty environment
      uses: conda-incubator/setup-miniconda@v3
      with:
        miniforge-version: latest
        auto-update-conda: true
        use-mamba: true
        channel-priority: strict
        activate-environment: xdem-dev
        python-version:

    - name: Get month for resetting cache
      id: get-date
      run: echo "cache_date=$(/bin/date -u '+%Y%m')" >> $GITHUB_ENV
      shell: bash

    - name: Cache conda env
      uses: actions/cache@v4
      with:
        path: ${{ env.CONDA }}/envs
        key: conda-${{ matrix.os }}-${{ matrix.python-version }}-${{ env.cache_date }}-${{ hashFiles('dev-environment.yml') }}-${{ env.CACHE_NUMBER }}
      env:
        CACHE_NUMBER: 0 # Increase this value to reset cache if environment.yml has not changed
      id: cache

    # The trick below is necessary because the generic environment file does not specify a Python version, and ONLY
    # "conda env update" CAN BE USED WITH CACHING, which upgrades the Python version when using the base environment
    # (we add "graphviz" from dev-environment to solve all dependencies at once, at graphviz relies on image
    # processing packages very much like geo-packages; not a problem for docs, dev installs where all is done at once)
    - name: Install base environment with a fixed Python version
      if: steps.cache.outputs.cache-hit != 'true'
      run: |
        mamba install pyyaml python=${{ matrix.python-version }}
        python .github/scripts/generate_yml_env_fixed_py.py --pyv ${{ matrix.python-version }} --add "graphviz,pytransform3d" "environment.yml"
        mamba env update -n xdem-dev -f environment-ci-py${{ matrix.python-version }}.yml

    - name: Install project
      run: pip install -e . --no-dependencies

    # This steps allows us to check the "import xdem" with the base environment provided to users, before adding
    # development-specific dependencies by differencing the env and dev-env yml files
    - name: Check import works with base environment
      run: |
        # We unset the PROJ_DATA environment variable to make PROJ work on Windows
        unset PROJ_DATA
        python -c "import xdem"

    # This time, the trick below is necessary because: 1/ "conda update" does not support a file -f as argument
    # and also 2/ "conda env update" does not support --freeze-installed or --no-update-deps
    - name: Update environment with development packages if cache does not exist
      if: steps.cache.outputs.cache-hit != 'true'
      run: |
        # We unset the PROJ_DATA environment variable to make PROJ work on Windows
        unset PROJ_DATA
        pkgs_conda_dev=`python -c "import xdem.misc; xdem.misc.diff_environment_yml('environment.yml', 'dev-environment.yml', 'conda')"`
        pkgs_pip_dev=`python -c "import xdem.misc; xdem.misc.diff_environment_yml('environment.yml', 'dev-environment.yml', 'pip')"`
        mamba install $pkgs_conda_dev --freeze-installed
        if [[ "$pkgs_pip_dev" != "None" ]]; then
          pip install $pkgs_pip_dev
        fi

    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Setup pip dependencies
      run: pip install pytest-cov coveralls coveragepy-lcov 'coverage<7'

    - name: Print conda environment (for debugging)
      run: |
        conda info
        conda list

    - name: Test with pytest
      run: |
        # We unset the PROJ_DATA environment variable to make PROJ work on Windows
        unset PROJ_DATA
        pytest -ra --cov=xdem/

    # We can skip the conversion step once this PR of pytest is merged: https://github.com/pytest-dev/pytest-cov/pull/536
    # and replace pytest argument by --cov-report=lcov
    - name: Converting coverage to LCOV format
      run: coveragepy-lcov --data_file_path .coverage --output_file_path coverage.info

    - name: Upload coverage to Coveralls
      uses: coverallsapp/github-action@master
      with:
        github-token: ${{ secrets.github_token }}
        flag-name: run-${{ matrix.test_number }}
        path-to-lcov: coverage.info
        parallel: true

  finish:
    needs: test
    runs-on: ubuntu-latest
    steps:
    - name: Upload to Coveralls finished
      uses: coverallsapp/github-action@master
      with:
        github-token: ${{ secrets.github_token }}
        parallel-finished: true