tests.yml

name: Tests

on:
  pull_request:
  push:
    branches: [main]

jobs:
  pre-commit:
    name: Lint
    runs-on: ubuntu-latest
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
      - name: install clang-format
        run: |
          pip install clang-format==6.0.1
      - uses: pre-commit/action@v3.0.1

  test:
    name: Python
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python: [ 3.9, 3.12 ]
        os:  [ macos-latest, ubuntu-latest, windows-latest ]
    defaults:
      run:
        shell: bash
    steps:
      - name: Cancel Previous Runs
        uses: styfle/cancel-workflow-action@0.12.1
        with:
          access_token: ${{ github.token }}

      - name: Checkout
        uses: actions/checkout@v4
        with:
          submodules: true

      - name: Cache conda and dependencies
        id: cache
        uses: actions/cache@v3
        with:
          path: ${{ env.CONDA }}/envs
          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v2-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}

      - name: Install Conda
        uses: conda-incubator/setup-miniconda@v3
        if: steps.cache.outputs.cache-hit != 'true'
        with:
          activate-environment: anaconda-client-env
          python-version: ${{ matrix.python }}
          channels: conda-forge, anaconda
          channel-priority: strict
          auto-update-conda: true

      - name: Fix windows symlinks
        # This is horrible, but the "git config core.symlinks true" didn't work.
        if: matrix.os == 'windows-latest'
        run: |
          rm lwt_interface
          cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface

      - name: Fix windows .profile
        if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
        run: |
          cp ~/.bash_profile ~/.profile

      - name: Install conda deps
        if: steps.cache.outputs.cache-hit != 'true'
        shell: bash -l {0} #We need a login shell to get conda
        run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt

      - name: Install pip deps
        if: steps.cache.outputs.cache-hit != 'true'
        shell: bash -l {0}
        run: | 
          pip install -r requirements/CI-tests-pip/requirements.txt
          pip uninstall -y msprime

      - name: Build module
        env:
          MSP_CONDA_PREFIX: c:\Miniconda\envs\anaconda-client-env
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          python setup.py build_ext --inplace

      - name: Run tests
        run: |
          source ~/.profile
          conda activate anaconda-client-env
          pytest -xvs -n0