python-package.yml

# Workflow is based on the Astropy GitHub actions workflow, ci_workflows.yml
name: CI

on:
    push:
        branches:
            - '*'
        tags:
            - '*'
    pull_request:

jobs:
    tests:
        name: Unit tests
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: true
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.9', '3.10']  # fuji+guadalupe, not ready for 3.11 yet?
                astropy-version: ['==5.0', '<6']  # fuji+guadalupe, latest
                fitsio-version: ['==1.1.6', '<2']  # fuji+guadalupe, latest
                numpy-version: ['<1.23']  # to keep asscalar, used by astropy
        env:
            DESIUTIL_VERSION: 3.4.2
            DESIMODEL_DATA: branches/test-0.18

        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install pytest
                python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
                python -m pip install -r requirements.txt
                python -m pip install -U 'numpy${{ matrix.numpy-version }}'
                python -m pip install -U 'astropy${{ matrix.astropy-version }}'
                python -m pip cache remove fitsio
                python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}'
                svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data
            - name: Run the test
              run: DESIMODEL=$(pwd) pytest

    coverage:
        name: Test coverage
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: true
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.10'] # latest
                astropy-version: ['<6']  # latest
                fitsio-version: ['<2']  # latest
                numpy-version: ['<1.23']  # to keep asscalar, used by astropy
        env:
            DESIUTIL_VERSION: 3.4.2
            DESIMODEL_DATA: branches/test-0.18

        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install pytest pytest-cov coveralls
                python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
                python -m pip install -r requirements.txt
                python -m pip install specutils
                python -m pip install -U 'numpy${{ matrix.numpy-version }}'
                python -m pip install -U 'astropy${{ matrix.astropy-version }}'
                python -m pip cache remove fitsio
                python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}'
                svn export https://desi.lbl.gov/svn/code/desimodel/${DESIMODEL_DATA}/data
            - name: Run the test with coverage
              run: DESIMODEL=$(pwd) pytest --cov
            - name: Coveralls
              env:
                COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
              run: coveralls

    desilite:
        name: Test minimal env
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: true
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.10']
        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install astropy scipy numba "numpy<2.0"
                python -m pip install pytest
                python -m pip cache remove fitsio
                python -m pip install --no-deps --force-reinstall --ignore-installed fitsio
                python -m pip install git+https://github.com/desihub/desiutil.git
                python -m pip install git+https://github.com/desihub/desitarget.git
            - name: Run just the lite env test
              run: pytest py/desispec/test/test_lite.py

    docs:
        name: Doc test
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.9']

        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: python -m pip install --upgrade pip setuptools wheel Sphinx
              # run: python -m pip install --upgrade pip wheel docutils\<0.18 Sphinx==3.1.2
            - name: Test the documentation
              run: sphinx-build -W --keep-going -b html doc doc/_build/html

    api:
        name: API doc completeness test
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.9']
        env:
            DESIUTIL_VERSION: 3.3.0

        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install git+https://github.com/desihub/desiutil.git@${DESIUTIL_VERSION}#egg=desiutil
            - name: Generate api.rst
              run: desi_api_file --api ./api.rst desispec
            - name: Compare generated api.rst to checked-in version
              run: diff --ignore-space-change --ignore-blank-lines ./api.rst ./doc/api.rst

    style:
        name: Style check
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.9']

        steps:
            - name: Checkout code
              uses: actions/checkout@v2
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v2
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: python -m pip install --upgrade pip setuptools wheel pycodestyle
            - name: Test the style; failures are allowed
              # This is equivalent to an allowed falure.
              continue-on-error: true
              run: pycodestyle --count py/desispec


# SAVE