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:
                include:
                  - os: ubuntu-latest
                    python-version: '3.13'
                    numpy-version: '<2.3' # Numba does not yet support NumPy 2.3!
                    scipy-version: ''
                    astropy-version: '<8.0'
                    matplotlib-version: ''
                    fitsio-version: ''
                    numba-version: ''
                  - os: ubuntu-latest
                    python-version: '3.12'
                    numpy-version: '<2.2'
                    scipy-version: '<1.16'
                    astropy-version: '<7.0'
                    matplotlib-version: '<3.12'
                    fitsio-version: ''
                    numba-version: ''
                  - os: ubuntu-latest
                    python-version: '3.11'
                    numpy-version: '<2.1'
                    scipy-version: '<1.14'
                    astropy-version: '<6.1'
                    matplotlib-version: '<3.11'
                    fitsio-version: ''
                    numba-version: '<0.70'
                  - os: ubuntu-latest
                    python-version: '3.10'
                    numpy-version: '<2.0'
                    scipy-version: '<1.14'
                    astropy-version: '<6.1'
                    matplotlib-version: '<3.10'
                    fitsio-version: ''
                    numba-version: '<0.70'
                # 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
                # numba-version: ['<0.61.0'] # for compatibility with old numpy

        steps:
            - name: Install System Packages
              run: sudo apt install libbz2-dev subversion
            - name: Checkout code
              uses: actions/checkout@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install pytz healpy llvmlite speclite
                python -m pip install 'numpy${{ matrix.numpy-version }}' 'scipy${{ matrix.scipy-version }}' 'astropy${{ matrix.astropy-version }}' 'matplotlib${{ matrix.matplotlib-version }}' specutils
                python -m pip cache remove fitsio
                python -m pip cache remove numba
                python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}' 'numba${{ matrix.numba-version }}'
                python -m pip install pytest
            - name: Install DESI dependencies
              env:
                DESIUTIL_VERSION: 3.6.0   # required for astropy 7.x
                SPECTER_VERSION: 0.11.0
                GPU_SPECTER_VERSION: main
                DESIMODEL_VERSION: 0.19.3
                DESITARGET_VERSION: main
                REDROCK_VERSION: 0.20.4
              run: |
                # --no-build-isolation needed for older code tags with latest pip/setuputils
                python -m pip install --no-build-isolation desiutil==${DESIUTIL_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/specter.git@${SPECTER_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/gpu_specter.git@${GPU_SPECTER_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/redrock.git@${REDROCK_VERSION}
            - name: Install desimodel data
              env:
                DESIMODEL_DATA: branches/test-0.19
              run: install_desimodel_data --desimodel-version ${DESIMODEL_DATA}
            - name: Run the test
              run: pytest

    coverage:
        name: Test coverage
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: true
            matrix:
                # matches python 3.10 environment above, approximately matching NERSC
                os: [ubuntu-latest]
                python-version: ['3.10']
                numpy-version: ['<2.0']
                scipy-version: ['<1.14']
                astropy-version: ['<6.1']
                matplotlib-version: ['<3.10']
                fitsio-version: ['']
                numba-version: ['<0.70']

        steps:
            - name: Install System Packages
              run: sudo apt install libbz2-dev subversion
            - name: Checkout code
              uses: actions/checkout@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install pytz healpy llvmlite speclite
                python -m pip install 'numpy${{ matrix.numpy-version }}' 'scipy${{ matrix.scipy-version }}' 'astropy${{ matrix.astropy-version }}' 'matplotlib${{ matrix.matplotlib-version }}'
                python -m pip cache remove fitsio
                python -m pip cache remove numba
                python -m pip install --no-deps --force-reinstall --ignore-installed 'fitsio${{ matrix.fitsio-version }}' 'numba${{ matrix.numba-version }}'
                python -m pip install pytest pytest-cov coveralls
            - name: Install DESI dependencies
              env:
                DESIUTIL_VERSION: 3.6.0   # required for astropy 7.x
                SPECTER_VERSION: 0.11.0
                GPU_SPECTER_VERSION: main
                DESIMODEL_VERSION: 0.19.3
                DESITARGET_VERSION: main
                REDROCK_VERSION: 0.20.4
              run: |
                # --no-build-isolation needed for older code tags with latest pip/setuputils
                python -m pip install --no-build-isolation desiutil==${DESIUTIL_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/desimodel.git@${DESIMODEL_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/specter.git@${SPECTER_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/gpu_specter.git@${GPU_SPECTER_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/desitarget.git@${DESITARGET_VERSION}
                python -m pip install --no-build-isolation git+https://github.com/desihub/redrock.git@${REDROCK_VERSION}
            - name: Install desimodel data
              env:
                DESIMODEL_DATA: branches/test-0.19
              run: install_desimodel_data --desimodel-version ${DESIMODEL_DATA}
            - name: Run the test
              run: pytest --cov

# 2026-02-27 : Coveralls is having a major outage; skip the coverage upload
###            - 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@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel pytest
                ### 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 desiutil
                ### python -m pip install git+https://github.com/desihub/desitarget.git
                python -m pip install .
            - 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: ['3.10']

        steps:
            - name: Checkout code
              uses: actions/checkout@v4
              with:
                fetch-depth: 0
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: python -m pip install --upgrade pip setuptools wheel Sphinx sphinx-rtd-theme
              # 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: ['3.10']
        steps:
            - name: Checkout code
              uses: actions/checkout@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              with:
                python-version: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install 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: ['3.10']

        steps:
            - name: Checkout code
              uses: actions/checkout@v4
            - name: Set up Python ${{ matrix.python-version }}
              uses: actions/setup-python@v5
              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