push_pr.yml

name: Run code tests on push and pull requests
on:
  push:
  pull_request:
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:
  tests:
    name: Code tests (Python ${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
        matrix:
            os: ["ubuntu-latest"]
            python-version: ["3.8", "3.9", "3.10", "3.11"]

    steps:
      - uses: actions/checkout@v3
        with:
          submodules: true
          lfs: true
      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          activate-environment: test
          environment-file: .github/requirements.yml
          auto-activate-base: false
          channels: conda-forge
      - shell: bash -l {0}
        run: |
          conda info
          conda list
      - name: Lint
        shell: bash -l {0}
        run: |
            python -m flake8 src
      - name: Run pytest
        shell: bash -l {0}
        run: |
            pip install .
            pytest -k "not with_fsl_mrs" tests
            conda install -c conda-forge -c defaults \
              -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
              fsl_mrs
            pip install .
            pytest -k "with_fsl_mrs" tests