windows-ci.yml

# Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
# SPDX-License-Identifier: MIT

name: Windows CI

on:
  push:
    branches: [main]
    paths:
      - ".github/workflows/build-conan-deps.yml"
      - ".github/workflows/cache-test-dataset.yml"
      - ".github/workflows/windows-ci.yml"
      - "cmake/**"
      - "examples/**"
      - "src/**"
      - "test/integration/**"
      - "test/units/**"
      - "CMakeLists.txt"
      - "conanfile.py"

  pull_request:
    paths:
      - ".github/workflows/build-conan-deps.yml"
      - ".github/workflows/cache-test-dataset.yml"
      - ".github/workflows/windows-ci.yml"
      - "cmake/**"
      - "examples/**"
      - "src/**"
      - "test/integration/**"
      - "test/units/**"
      - "CMakeLists.txt"
      - "conanfile.py"

# https://stackoverflow.com/a/72408109
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  CONAN_HOME: "${{ github.workspace }}\\.conan2"
  HICTK_CI: "1"

defaults:
  run:
    shell: bash

jobs:
  matrix-factory:
    name: Generate job matrix
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.set-result.outputs.result }}
    steps:
      - uses: actions/github-script@v7
        id: set-result
        with:
          script: |
            // Documentation
            // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson
            // https://github.com/actions/runner/issues/982#issuecomment-809360765

            var includes = []

            includes.push({ compiler_name: 'msvc', os: 'windows-2022', cmake: '3.29.*', build_type: 'Debug', developer_mode: 'OFF' })
            includes.push({ compiler_name: 'msvc', os: 'windows-2022', cmake: '3.29.*', build_type: 'Release', developer_mode: 'OFF' })

            return { include: includes }

  cache-test-dataset:
    uses: paulsengroup/hictk/.github/workflows/cache-test-dataset.yml@main
    name: Cache test dataset

  build-conan-deps:
    name: Build Conan deps
    uses: robomics/gha-devel/.github/workflows/build-conan-deps.yml@main
    with:
      os: windows-2019

  build-project:
    needs:
      - matrix-factory
      - build-conan-deps
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }}

    steps:
      - uses: actions/checkout@v4

      - name: Generate requirements.txt for pip
        run: echo 'cmake==${{ matrix.cmake }}' > requirements.txt

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"

      - name: Detect number available CPUs
        run: |
          ncpus=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())')

          echo "CMAKE_BUILD_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV
          echo "CTEST_PARALLEL_LEVEL=$ncpus" >> $GITHUB_ENV

      - name: Install deps
        run: pip install -r requirements.txt

      - name: Restore Conan cache
        uses: actions/cache/restore@v4
        with:
          key: ${{ needs.build-conan-deps.outputs.conan-key }}
          path: ${{ env.CONAN_HOME }}\p
          fail-on-cache-miss: true

      - name: Restore CMake configs (Debug)
        if: matrix.build_type == 'Debug'
        uses: actions/cache/restore@v4
        with:
          key: ${{ needs.build-conan-deps.outputs.cmake-prefix-debug-key }}
          path: ${{ github.workspace }}\cmake-prefix-dbg.tar
          fail-on-cache-miss: true

      - name: Restore CMake configs (Release)
        if: matrix.build_type == 'Release'
        uses: actions/cache/restore@v4
        with:
          key: ${{ needs.build-conan-deps.outputs.cmake-prefix-release-key }}
          path: ${{ github.workspace }}\cmake-prefix-rel.tar
          fail-on-cache-miss: true

      - name: Extract CMake configs
        run: |
          mkdir conan-env
          srcdir="$(cygpath '${{ github.workspace }}')"
          tar -xf "$srcdir/"cmake-prefix-*.tar -C conan-env/ --strip-components=1

      - name: Configure project
        run: |
          cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}          \
                -DCMAKE_PREFIX_PATH="$PWD/conan-env"                 \
                -DENABLE_DEVELOPER_MODE=${{ matrix.developer_mode }} \
                -DHICTK_ENABLE_TESTING=ON                            \
                -DHICTK_BUILD_EXAMPLES=ON                            \
                -DHICTK_DOWNLOAD_TEST_DATASET=OFF                    \
                -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF              \
                -DOPT_ENABLE_CLANG_TIDY=OFF                          \
                -DOPT_ENABLE_CPPCHECK=OFF                            \
                -DCMAKE_INSTALL_PREFIX=dest                          \
                -S "${{ github.workspace }}"                         \
                -B "${{ github.workspace }}/build"

      - name: Build project
        run: cmake --build build --config ${{ matrix.build_type }}

      - name: Package binaries
        run: |
          cmake --install build

          tar -cf - -C dest/ bin | zstd -T0 -13 -o binaries.tar.zst

      - name: Package unit tests
        run: |
          rm -r build/src
          tar --exclude='*.obj' -cf - build/ | zstd -T0 -13 -o unit-tests.tar.zst

      - name: Upload unit tests
        uses: actions/upload-artifact@v4
        with:
          name: "unit-tests-${{ matrix.os }}-\
            ${{ matrix.compiler_name }}-\
            ${{ matrix.build_type }}-\
            ${{ matrix.developer_mode }}"
          path: unit-tests.tar.zst
          if-no-files-found: error
          retention-days: 1

      - name: Upload binaries
        uses: actions/upload-artifact@v4
        with:
          name: "binaries-${{ matrix.os }}-\
            ${{ matrix.compiler_name }}-\
            ${{ matrix.build_type }}-\
            ${{ matrix.developer_mode }}"
          path: binaries.tar.zst
          if-no-files-found: error
          retention-days: 1

  run-unit-tests:
    name: Run unit tests
    needs: [matrix-factory, cache-test-dataset, build-project]
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }}

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Restore test dataset
        uses: actions/cache/restore@v4
        with:
          key: ${{ needs.cache-test-dataset.outputs.cache-key }}
          path: test/data/hictk_test_data.tar.zst
          fail-on-cache-miss: true
          enableCrossOsArchive: true

      - name: Download unit tests artifact
        uses: actions/download-artifact@v4
        with:
          name: "unit-tests-${{ matrix.os }}-\
            ${{ matrix.compiler_name }}-\
            ${{ matrix.build_type }}-\
            ${{ matrix.developer_mode }}"

      - name: Extract binaries test dataset
        run: |
          tar -xf unit-tests.tar.zst
          tar -xf test/data/hictk_test_data.tar.zst

      - name: Generate requirements.txt for pip
        run: |
          echo 'cmake==${{ matrix.cmake }}' > requirements.txt

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache: "pip"

      - name: Install test dependencies
        run: pip install -r requirements.txt

      - name: Run unit tests (Debug)
        if: matrix.build_type == 'Debug'
        run: |
          skip_labels=(
            '.*dataset large read\/write.*'
            '.*HiCFileWriter.*'
            '.*VectorOfAtomicDecimals.*'
          )

          pattern="$(IFS='|' ; echo "${skip_labels[*]}")"

          ctest --test-dir build    \
                --schedule-random   \
                --output-on-failure \
                --no-tests=error    \
                --timeout 360       \
                --exclude-regex "$pattern" |&
          tail -n 1000

      - name: Run unit tests (Release)
        if: matrix.build_type == 'Release'
        run: |
          ctest --test-dir build    \
                --schedule-random   \
                --output-on-failure \
                --no-tests=error    \
                --timeout 120       |&
          tail -n 1000

  run-integration-tests:
    name: Run integration tests
    needs: [matrix-factory, cache-test-dataset, build-project]
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }}

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: "3.12"
          cache-dependency-path: "test/integration/pyproject.toml"
          cache: "pip"

      - name: Restore test dataset
        uses: actions/cache/restore@v4
        with:
          key: ${{ needs.cache-test-dataset.outputs.cache-key }}
          path: test/data/hictk_test_data.tar.zst
          fail-on-cache-miss: true
          enableCrossOsArchive: true

      - name: Download binaries artifact
        uses: actions/download-artifact@v4
        with:
          name: "binaries-${{ matrix.os }}-\
            ${{ matrix.compiler_name }}-\
            ${{ matrix.build_type }}-\
            ${{ matrix.developer_mode }}"

      - name: Extract binaries test dataset
        run: |
          tar -xf binaries.tar.zst
          tar -xf test/data/hictk_test_data.tar.zst

      - name: Install test suite
        run: |
          python.exe -m venv venv --upgrade
          venv/Scripts/pip.exe install test/integration

      - name: Detect number available CPUs
        run: |
          ncpus=$(python -c 'import multiprocessing as mp; print(mp.cpu_count())')

          echo "NPROC=$ncpus" | tee -a $GITHUB_ENV

      - name: Test hictk balance
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.balance.json \
            --suites=balance

      - name: Test hictk convert
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.convert.json \
            --suites=convert

      - name: Test hictk dump
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.dump.json \
            --suites=dump

      - name: Test hictk fix-mcool
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.fix-mcool.json \
            --suites=fix-mcool

      - name: Test hictk load
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.load.json \
            --suites=load

      - name: Test hictk merge
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.merge.json \
            --suites=merge

      - name: Test hictk metadata
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.metadata.json \
            --suites=metadata

      - name: Test hictk rename-chromosomes
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.rename-chromosomes.json \
            --suites=rename-chromosomes

      - name: Test hictk validate
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.validate.json \
            --suites=validate

      - name: Test hictk zoomify
        run: |
          venv/Scripts/hictk_integration_suite.exe \
            bin/hictk.exe \
            test/integration/config.toml \
            --data-dir test/data \
            --threads "$NPROC" \
            --result-file integration-test-report.zoomify.json \
            --suites=zoomify

  windows-ci-status-check:
    name: Status Check (Windows CI)
    if: ${{ always() }}
    runs-on: ubuntu-latest
    needs:
      - matrix-factory
      - cache-test-dataset
      - build-project
      - run-unit-tests
      - run-integration-tests

    steps:
      - name: Collect job results
        if: |
          needs.build-project.result != 'success'      ||
          needs.run-unit-tests.result != 'success'     ||
          needs.run-integration-tests.result != 'success'
        run: exit 1