CI.yml

name: Linux

on:
  push:
    branches:
      - '**'
    paths:
      - '**'
    tags:
      - 'v*.*.*'
  pull_request:
    branches:
      - 'master'
    paths:
      - '**'

jobs:
  test:
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60
    env:
      COVERAGE_PROCESS_START: "${{ github.workspace }}/.coveragerc"
    defaults:
      run:
        shell: bash
    strategy:
      matrix:
        julia-version: ['1']
        python-version: ['3.12']
        os: [ubuntu-latest]
        test-id: [main]
        include:
          - julia-version: '1.6'
            python-version: '3.8'
            os: ubuntu-latest
            test-id: include
          - julia-version: '1'
            python-version: '3.12'
            os: ubuntu-latest
            test-id: include

    steps:
      - uses: actions/checkout@v4
      - name: "Set up Julia"
        uses: julia-actions/setup-julia@v2
        with:
          version: ${{ matrix.julia-version }}
      - name: "Cache Julia"
        uses: julia-actions/cache@v2
        with:
          cache-name: ${{ matrix.os }}-test-${{ matrix.julia-version }}-${{ matrix.python-version }}
          cache-packages: false
      - name: "Set up Python"
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip
      - name: "Install PySR"
        run: |
            python -m pip install --upgrade pip
            pip install .
            python -c 'import pysr'
      - name: "Assert Julia version"
        if: ${{ matrix.julia-version != '1'}}
        run: python3 -c "from pysr import jl; assert jl.VERSION.major == jl.seval('v\"${{ matrix.julia-version }}\"').major; assert jl.VERSION.minor == jl.seval('v\"${{ matrix.julia-version }}\"').minor"
      - name: "Install test dependencies"
        run: pip install coverage coveralls pytest nbval
      - name: "Set up coverage for subprocesses"
        run: echo 'import coverage; coverage.process_startup()' > "${{ github.workspace }}/sitecustomize.py"
      - name: "Run tests"
        run: coverage run -m pysr test main,cli,startup
      - name: "Install JAX"
        run: pip install jax jaxlib # (optional import)
        if: ${{ matrix.test-id == 'main' }}
      - name: "Run JAX tests"
        run: coverage run --append -m pysr test jax
        if: ${{ matrix.test-id == 'main' }}
      - name: "Install Torch"
        run: pip install torch # (optional import)
        if: ${{ matrix.test-id == 'main' }}
      - name: "Run Torch tests"
        run: coverage run --append -m pysr test torch
        if: ${{ matrix.test-id == 'main' }}
      - name: "Coveralls"
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          COVERALLS_FLAG_NAME: test-${{ matrix.julia-version }}-${{ matrix.python-version }}-${{ matrix.test-id }}
          COVERALLS_PARALLEL: true
        run: coveralls --service=github

  dev_install:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ['ubuntu-latest']
        python-version: ['3.12']
        julia-version: ['1']
        include:
          - os: ubuntu-latest
            python-version: '3.8'
            julia-version: '1.6'
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
      - name: "Install PySR"
        run: |
            python -m pip install --upgrade pip
            pip install .
      - name: "Run development test"
        run: PYSR_TEST_JULIA_VERSION=${{ matrix.julia-version }} PYSR_TEST_PYTHON_VERSION=${{ matrix.python-version }} python -m pysr test dev

  conda_test:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      matrix:
        python-version: ['3.12']
        os: ['ubuntu-latest']

    steps:
      - uses: actions/checkout@v4
      - name: "Cache conda"
        uses: actions/cache@v4
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
      - name: "Set up Conda"
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          miniforge-version: latest
          auto-activate-base: true
          python-version: ${{ matrix.python-version }}
          activate-environment: pysr-test
          environment-file: environment.yml
      - name: "Cache Julia"
        uses: julia-actions/cache@v2
        with:
          cache-name: ${{ matrix.os }}-conda-${{ matrix.python-version }}
          cache-packages: false
      - name: "Install PySR"
        run: |
            python3 -m pip install .
            python3 -c 'import pysr'
      - name: "Run tests"
        run: cd /tmp && python -m pysr test main

  coveralls:
    name: Indicate completion to coveralls.io
    needs:
      - test
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    container: python:3-slim
    steps:
      - name: Finished
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
            pip install coveralls
            coveralls --finish

  types:
    name: Check types
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      matrix:
        python-version:
          - '3.12'
          - '3.8'
        os: ['ubuntu-latest']

    steps:
      - uses: actions/checkout@v4
      - name: "Set up Python"
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: pip
      - name: "Install PySR and all dependencies"
        run: |
            python -m pip install --upgrade pip
            pip install .
            pip install mypy
      - name: "Install additional dependencies"
        run: python -m pip install jax jaxlib torch
        if: ${{ matrix.python-version != '3.8' }}
      - name: "Run mypy"
        run: python -m mypy --install-types --non-interactive pysr
        if: ${{ matrix.python-version != '3.8' }}
      - name: "Run compatible mypy"
        run: python -m mypy --ignore-missing-imports pysr
        if: ${{ matrix.python-version == '3.8' }}