test_and_deploy.yml

name: tests

on:
  push:
    branches:
      - "main"
    tags:
      - "*"
  pull_request:
  workflow_dispatch:

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}

jobs:
  linting:
    name: Linting
    runs-on: ubuntu-latest
    steps:
      - uses: neuroinformatics-unit/actions/lint@v2

  manifest:
    name: Check manifest
    runs-on: ubuntu-latest
    steps:
      - uses: neuroinformatics-unit/actions/check_manifest@v2

  test:
    needs: [linting, manifest]
    name: ${{ matrix.os }} py${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    env:
      KERAS_BACKEND: torch
    strategy:
      fail-fast: false
      matrix:
        # Run tests on ubuntu across all supported versions
        python-version: ["3.10", "3.11", "3.12"]
        os: [ubuntu-latest]
        # Include a Windows test and new Mac runs
        include:
          - os: macos-latest
            python-version: "3.12"
          - os: windows-latest
            python-version: "3.12"
    steps:
      # Cache atlases
      - name: Cache brainglobe directory
        uses: actions/cache@v3
        with:
          path: | # ensure we don't cache any interrupted atlas download and extraction, if e.g. we cancel the workflow manually
            ~/.brainglobe
            !~/.brainglobe/atlas.tar.gz
          key: atlases-models
          fail-on-cache-miss: true
          enableCrossOsArchive: true
      # install additional Macos dependencies
      - name: install HDF5 libraries (needed on M1 Macs only)
        if: matrix.os == 'macos-latest'
        run: |
          brew install hdf5
      # Cache cellfinder workflow data
      - name: Cache data for cellfinder workflow tests
        uses: actions/cache@v3
        with:
          path: "~/.brainglobe-tests"
          key: cellfinder-test-data
          fail-on-cache-miss: true
          enableCrossOsArchive: true
      # Run tests
      - uses: neuroinformatics-unit/actions/test@v2
        with:
          python-version: ${{ matrix.python-version }}
          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}

  benchmarks:
    name: Check benchmarks
    runs-on: ubuntu-latest

    # Set shell in login mode as global setting for the job
    defaults:
      run:
        shell: bash -l {0}

    strategy:
      matrix:
        python-version: ["3.12"]

    steps:
      - name: Checkout brainglobe-workflows repository
        uses: actions/checkout@v4

      - name: Create and activate conda environment  # we need conda for asv management of environments
        uses: conda-incubator/setup-miniconda@v2.1.1 # see https://github.com/conda-incubator/setup-miniconda/issues/261
        with:
          miniconda-version: py310_24.1.2-0  # we need conda<24.3, see https://github.com/airspeed-velocity/asv/pull/1397
          python-version: ${{ matrix.python-version }}
          activate-environment: asv-only

      - name: Install asv
        run: |
          pip install --upgrade pip
          pip install asv

      - name: Run asv check with pip dependencies
        working-directory: ${{ github.workspace }}/benchmarks
        run: |

          # check benchmarks with pip dependencies
          asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.pip.conf.json

      - name: Run asv check with latest-github dependencies
        working-directory: ${{ github.workspace }}/benchmarks
        run: |

          # check benchmarks with latest-github dependencies
          asv check -v --config $GITHUB_WORKSPACE/benchmarks/asv.latest-github.conf.json


  build_sdist_wheels:
    name: Build source distribution
    needs: [test]
    if: github.event_name == 'push' && github.ref_type == 'tag'
    runs-on: ubuntu-latest
    steps:
      - uses: neuroinformatics-unit/actions/build_sdist_wheels@v2

  upload_all:
    name: Publish build distributions
    needs: [build_sdist_wheels]
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && github.ref_type == 'tag'
    steps:
    - uses: neuroinformatics-unit/actions/upload_pypi@v2
      with:
        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}