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:
  schedule:
    - cron: '0 22 * * 0' # At 22:00 UTC every Sunday

defaults:
  run:
    shell: bash

# Force tox and pytest to use color
env:
  FORCE_COLOR: true
  TEST_DATA_HOME: /home/runner/nifreeze-tests/
  TEST_OUTPUT_DIR: /home/runner/nifreeze-tests/test-output
  DIPY_HOME: /home/runner/nifreeze-tests/dipy
  ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 4
  ANTSPATH: /usr/share/miniconda/bin/
  NIFREEZE_WERRORS: 1
  TEST_DATA_REPO: https://gin.g-node.org/nipreps-data/tests-nifreeze

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

permissions:
  contents: read

jobs:
  cache-test-data:
    runs-on: 'ubuntu-latest'
    outputs:
      SHA: ${{ steps.test-head.outputs.SHA }}
    steps:
      - name: Check remote HEAD
        id: test-head
        run: |
          SHA=$( git ls-remote $TEST_DATA_REPO HEAD | cut -f 1 )
          echo SHA=$SHA >> $GITHUB_OUTPUT
          echo SHA7=${SHA:0:7} >> $GITHUB_OUTPUT
      - name: Check for data-v2-${{ steps.test-head.outputs.SHA }}
        uses: actions/cache@v5
        id: test-data
        with:
          path: ${{ env.TEST_DATA_HOME }}
          key: data-v2-${{ steps.test-head.outputs.SHA }}
          lookup-only: true
      - name: Create data-v2-${{ steps.test-head.outputs.SHA }}
        uses: actions/cache@v5
        if: steps.test-data.outputs.cache-hit != 'true'
        with:
          path: ${{ env.TEST_DATA_HOME }}
          key: data-v2-${{ steps.test-head.outputs.SHA }}
          restore-keys: |
            data-v2
            data-v1
            data-v0
      - name: Install the latest version of uv
        uses: astral-sh/setup-uv@v7
        if: steps.test-data.outputs.cache-hit != 'true'
      - name: Install datalad
        if: steps.test-data.outputs.cache-hit != 'true'
        run: |
          uvx datalad-installer --sudo ok git-annex
          uv tool install --with=datalad-osf --with=datalad-next datalad
          uv tool install --with=datalad-next datalad-osf
          datalad wtf
      - name: Checkout commit ${{ steps.test-head.outputs.SHA7 }}
        if: steps.test-data.outputs.cache-hit != 'true'
        run: |
          if [[ ! -d "${TEST_DATA_HOME}" ]]; then
            datalad install -rg --source=${TEST_DATA_REPO} ${TEST_DATA_HOME}
          else
            cd ${TEST_DATA_HOME}
            datalad update --merge -r .
            datalad get -r -J4 *
          fi
      - name: Install DIPY and fetch stanford_hardi dataset
        if: steps.test-data.outputs.cache-hit != 'true'
        run: |
          echo "from dipy.data import fetch_stanford_hardi; fetch_stanford_hardi()" > fetch.py
          uv tool install dipy
          uv add --script fetch.py dipy
          uv run fetch.py

  stable:
    # Unit tests only on Linux/Python 3.12
    runs-on: 'ubuntu-latest'
    needs: ['cache-test-data']
    strategy:
      matrix:
        python-version: ${{ github.event_name == 'schedule' && fromJson('["3.10", "3.11", "3.12", "3.13"]') || fromJson('["3.12"]') }}
    steps:
      - uses: actions/checkout@v5
        with:
          submodules: recursive
          fetch-depth: 0
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install the latest version of uv
        uses: astral-sh/setup-uv@v7
      - name: Install ANTs
        run: |
          # Override libiconv pre-installed from anaconda channel
          # See https://github.com/conda-forge/libitk-feedstock/issues/98
          # Since we're not creating a new environment, we must be explicit
          conda install -c conda-forge ants=2.4 libitk=5.3 libiconv
      - name: Verify antsRegistration path
        run: |
          export PATH=$ANTSPATH:$PATH
          which antsRegistration
          antsRegistration --version
      - uses: actions/cache/restore@v5
        with:
          path: ${{ env.TEST_DATA_HOME }}
          key: data-v2-${{ needs.cache-test-data.outputs.SHA }}
      - name: Install TeX Live
        run: |
          sudo apt-get update
          sudo apt install texlive texlive-latex-extra texlive-fonts-recommended cm-super dvipng
      - name: Install tox
        run: |
          uv tool install --with=tox-uv --with=tox-gh-actions tox
      - name: Show tox config
        run: tox c
      - name: Prepare test output directory
        run: mkdir -p "${TEST_OUTPUT_DIR}"
      - name: Run tox
        run: |
          export PATH=$ANTSPATH:$PATH
          tox -v --exit-and-dump-after 1200
      - name: Upload test artifacts
        if: ${{ always() }}
        uses: actions/upload-artifact@v7
        with:
          name: test-output-py${{ matrix.python-version }}
          path: ${{ env.TEST_OUTPUT_DIR }}
          if-no-files-found: warn
      - uses: codecov/codecov-action@v5
        if: ${{ always() }}
        with:
          files: cov.xml
          token: ${{ secrets.CODECOV_TOKEN }}

  checks:
    runs-on: 'ubuntu-latest'
    continue-on-error: true
    strategy:
      matrix:
        check: ['spellcheck', 'typecheck']
    steps:
      - uses: actions/checkout@v5
      - name: Install the latest version of uv
        uses: astral-sh/setup-uv@v7
      # Can remove this once there is a traits release that supports 3.13
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: 3.12
      - name: Install tox
        run: uv tool install tox --with=tox-uv
      - name: Show tox config
        run: tox c
      - name: Show tox config (this call)
        run: tox c -e ${{ matrix.check }}
      - name: Run check
        run: tox -e ${{ matrix.check }}