python-package.yml

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

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


# 2025-01-07
# NERSC has Python 3.10, Numpy 1.22.4, Scipy 1.8.1, matplotlib 3.8.4, astropy 6.0.1, healpy 1.16.6, PyYAML 6.0.1
# PyPI has Python 3.13, Numpy 2.2.1, Scipy 1.15.0, matplotlib 3.10.0, astropy 7.0.0, healpy 1.18.0, PyYAML 6.0.2
# Numpy 1.26.4 was the last pre-2.0 Numpy.
#
jobs:
    tests:
        name: Unit tests
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: true
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.11', '3.12']
                numpy-version: ['<2.0', '<2.1', '<2.2', '<3']
                astropy-version: ['<6.1', '<7.0']  # , '<7.1'] 7 has an IERS issue
                include:
                    # Close to current NERSC configuration.
                    - os: ubuntu-latest
                      python-version: '3.10'
                      numpy-version: '<1.23'
                      astropy-version: '<6.1'
                    # Stable, yet close to bleeding-edge.
                    - os: ubuntu-latest
                      python-version: '3.13'
                      numpy-version: '<3'
                      astropy-version: '<7.0'  # not <7.1 yet, see above

        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: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install --upgrade --upgrade-strategy only-if-needed "numpy${{ matrix.numpy-version }}"
                python -m pip install --upgrade --upgrade-strategy only-if-needed "astropy${{ matrix.astropy-version }}"
                python -m pip install --editable .[test]
            - name: Run the test
              run: pytest

    coverage:
        name: Test coverage
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os: [ubuntu-latest]
                python-version: ['3.10']
                numpy-version: ['<1.23']
                astropy-version: ['<6.1']

        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: ${{ matrix.python-version }}
            - name: Install Python dependencies
              run: |
                python -m pip install --upgrade pip setuptools wheel
                python -m pip install --upgrade --upgrade-strategy only-if-needed "numpy${{ matrix.numpy-version }}"
                python -m pip install --upgrade --upgrade-strategy only-if-needed "astropy${{ matrix.astropy-version }}"
                python -m pip install --editable .[coverage]
            - name: Run the test with coverage
              run: pytest --cov
            - name: Coveralls
              env:
                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
                COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
              run: coveralls

    docs:
        name: Doc test
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os:
                    - ubuntu-latest
                python-version:
                    - '3.13'

        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
                python -m pip install --editable .[doc]
            - 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:
                    - '3.13'

        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
                python -m pip install --editable .
            - name: Generate api.rst
              run: ./bin/desi_api_file --api ./api.rst desiutil
            - name: Compare generated api.rst to checked-in version
              run: diff --ignore-space-change --ignore-blank-lines ./api.rst ./doc/api.rst

    scripts:
        name: Script definition completeness test
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os:
                    - ubuntu-latest
                python-version:
                    - '3.13'

        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: Compare contents of bin/ to options.scripts in setup.cfg
              run: python -c 'import os; import sys; from configparser import ConfigParser; conf = ConfigParser(); foo = conf.read(["setup.cfg"]); scripts = [os.path.basename(s) for s in conf["options"]["scripts"].strip().split("\n")]; sys.exit(int(set(os.listdir("bin")) != set(scripts)))'

    style:
        name: Style check
        runs-on: ${{ matrix.os }}
        strategy:
            fail-fast: false
            matrix:
                os:
                    - ubuntu-latest
                python-version:
                    - '3.13'

        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 pycodestyle
            - name: Test the style; failures are allowed
              # This is equivalent to an allowed falure.
              # continue-on-error: true
              run: pycodestyle --count py/desiutil