ci.yml

name: CI

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  pre_commit_check:
    name: Pre-Commit Check
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          auto-activate-base: false
          activate-environment: tiktorch-server-env
          environment-file: environment.yml
          channel-priority: strict
          miniforge-variant: Miniforge3
      - name: Get the latest commit hash and target ref
        run: |
          echo "COMMIT_HASH=$(git log -1 --format='%H')" >> $GITHUB_ENV
          echo "REF=${{ github.event.pull_request.base.ref || github.ref_name }}" >> $GITHUB_ENV
      - name: Run Pre-Commit
        run: |
          echo $REF
          echo $COMMIT_HASH
          git fetch origin
          pre-commit run --from-ref origin/$REF --to-ref $COMMIT_HASH

  test-dev:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout code
        uses: actions/checkout@v4
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          auto-activate-base: false
          activate-environment: tiktorch-server-env
          environment-file: environment.yml
          channel-priority: strict
          miniforge-variant: Miniforge3
      - name: conda diagnostics
        run: |
          conda list
          conda info
      - name: install submodules
        run: |
          git submodule init
          git submodule update
          make install_submodules
      - name: Run tests
        run: |
          pytest -v -s --cov=tiktorch --cov-report=xml
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          fail_ci_if_error: true
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}


  conda-noarch-build:
    runs-on: ubuntu-latest
    outputs:
      version: ${{ steps.version.outputs.version }}
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          auto-activate-base: true
          channel-priority: strict
          miniforge-variant: Miniforge3
      - name: install common conda dependencies
        run: conda install -n base -c conda-forge conda-build setuptools_scm -y
      - name: Cache Conda Packages
        uses: actions/cache@v4
        with:
          path: |
            pkgs/noarch
            pkgs/channeldata.json
          key: ${{ github.sha }}-packages
      - id: version
        run: |
          vers=$( python setup.py --version )
          echo "version=${vers}" >> $GITHUB_OUTPUT
      - name: Linux Conda Build
        run: |
          mkdir -p ./pkgs/noarch
          conda build -c ilastik-forge -c pytorch -c conda-forge \
          conda-recipe --no-test --output-folder ./pkgs

  test-build-conda-packages:
    needs: [conda-noarch-build]
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, windows-latest, ubuntu-latest]
    runs-on: ${{ matrix.os }}
    env:
      TIKTORCH_PACKAGE_NAME: tiktorch-${{ needs.conda-noarch-build.outputs.version }}-py_0.tar.bz2
    steps:
      # Use GNU tar instead of BSD tar on Windows
      - name: "Use GNU tar instead of BSD tar"
        if: matrix.os == 'windows-latest'
        shell: cmd
        run: echo C:\Program Files\Git\usr\bin>>"%GITHUB_PATH%"
      - name: Checkout code
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          auto-activate-base: true
          channel-priority: strict
          miniforge-variant: Miniforge3
      - name: install common conda dependencies
        run: conda install -n base -c conda-forge conda-build setuptools_scm -y
      - name: Cache Conda Packages
        uses: actions/cache@v4
        with:
          path: |
            pkgs/noarch
            pkgs/channeldata.json
          key: ${{ github.sha }}-packages
          enableCrossOsArchive: true
      - name: Linux Test
        if: matrix.os == 'ubuntu-latest'
        shell: bash -l {0}
        run: |
          conda build --test --override-channels \
            -c ./pkgs -c ilastik-forge -c pytorch -c conda-forge \
            ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
      - name: macOS Test
        if: matrix.os == 'macos-latest'
        shell: bash -l {0}
        run: |
          conda build --test --override-channels \
            -c ./pkgs -c ilastik-forge -c pytorch -c conda-forge \
            ./pkgs/noarch/${TIKTORCH_PACKAGE_NAME}
      - name: Windows Test
        if: matrix.os == 'windows-latest'
        # HACK: due to a bug in conda-build need to point to
        # libarchive explicitly.
        # https://github.com/conda/conda/issues/12563#issuecomment-1494264704
        env:
          LIBARCHIVE: C:\Miniconda\Library\bin\archive.dll
        shell: cmd /C CALL {0}
        run: |
          conda build --test --override-channels ^
            -c %CD%\pkgs -c ilastik-forge -c pytorch -c conda-forge ^
            .\pkgs\noarch\%TIKTORCH_PACKAGE_NAME%