test.yml

name: Unit and integration tests

on:
  push:
    branches:
      - main
      - maint/*
  pull_request:
    branches:
      - main
      - maint/*
  # Allow job to be triggered manually from GitHub interface
  workflow_dispatch:

defaults:
  run:
    shell: bash

# Force tox and pytest to use color
env:
  FORCE_COLOR: true
  TEST_DATA_HOME: /home/runner/nifreeze-tests/
  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4
  ANTSPATH: /usr/share/miniconda/bin/

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

permissions:
  contents: read

jobs:
  stable:
    # Unit tests only on Linux/Python 3.12
    runs-on: 'ubuntu-latest'
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive
          fetch-depth: 0
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'
      - name: Install ANTs
        run: |
          conda install -c conda-forge ants=2.5
      - name: Install datalad
        run: |
          python -m pip install datalad-installer
          datalad-installer --sudo ok git-annex
          python -m pip install datalad datalad-osf
          datalad wtf
      - uses: actions/cache/restore@v4
        with:
          path: /home/runner/nifreeze-tests/
          key: data-v0
      - name: Get test data with DataLad
        run: |
          if [[ ! -d "${TEST_DATA_HOME}" ]]; then
            datalad install -rg --source=https://gin.g-node.org/nipreps-data/tests-nifreeze.git ${TEST_DATA_HOME}
          else
            cd ${TEST_DATA_HOME}
            datalad update --merge -r .
            datalad get -r -J4 *
          fi
      - uses: actions/cache/save@v4
        with:
          path: /home/runner/nifreeze-tests/
          key: data-v0
      - name: Install tox
        run: |
          python -m pip install --upgrade pip
          python -m pip install tox tox-gh-actions
      - name: Show tox config
        run: tox c
      - name: Run tox
        run: |
          export PATH=$ANTSPATH:$PATH
          tox -v --exit-and-dump-after 1200
      - uses: codecov/codecov-action@v4
        if: ${{ always() }}
        with:
          files: cov.xml
          token: ${{ secrets.CODECOV_TOKEN }}