fuzzy-testing.yml

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

name: Run fuzzy tests

on:
  push:
    branches: [ main ]
    paths:
      - ".github/workflows/fuzzy-testing.yml"
      - "cmake/**"
      - "src/**"
      - "test/scripts/fuzzy_test.py"
      - "test/scripts/link_h5_dataset.py"
      - "CMakeLists.txt"
      - "conanfile.txt"
    tags:
      - 'v*.*.*'

  pull_request:
    paths:
      - ".github/workflows/fuzzy-testing.yml"
      - "test/scripts/fuzzy_test.py"
      - "test/scripts/link_h5_dataset.py"

  schedule:
    # Run weekly
    - cron: '15 3 * * 0'

  workflow_dispatch:
    inputs:
      duration:
        description: 'Test duration in seconds'
        required: true
        default: '600'
        type: string

      resolution:
        description: 'Matrix resolution to use for testing'
        required: true
        default: '10000'
        type: string


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

defaults:
  run:
    shell: bash

jobs:
  build-project:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          # The .mcool file was generated by using hic2cool followed by cooler balance for all resolutions
          # We can't use the version shared by 4DNucleome because the .hic and .mcool files they publish
          # differ slightly
          - {
            title: '.cool',
            balance: 'NONE',
            url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de',
            ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de'
          }
          - {
            title: '.cool',
            balance: 'weight',
            url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de',
            ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de'
          }
          - {
            title: '.hic',
            balance: 'NONE',
            url: 'https://www.dropbox.com/s/gkzxt5ae82dvlrg/4DNFIPC7P27B.hic?dl=1',
            sha256: 'b1ba1c942693a5b6e494de7f8da097a1435598a9bb951219929b5a84cb2a6b42',
            ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de',

          }
          - {
            title: '.hic',
            balance: 'KR',
            url: 'https://www.dropbox.com/s/gkzxt5ae82dvlrg/4DNFIPC7P27B.hic?dl=1',
            sha256: 'b1ba1c942693a5b6e494de7f8da097a1435598a9bb951219929b5a84cb2a6b42',
            ref-url: 'https://www.dropbox.com/s/wq3k09rrpc8smmm/4DNFIPC7P27B.mcool?dl=1',
            ref-sha256: '7ead807936afbd02c4a0da93d86dd54de489cc07e87400a691c8e917111749de'
          }

    container:
      image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-22.04-cxx-clang-16
      options: "--user=root"

    env:
      CONAN_HOME: '/root/.conan2'

    steps:
      - name: Clone hictk
        uses: actions/checkout@v4

      - name: Clone hictkpy
        uses: actions/checkout@v4
        with:
          repository: paulsengroup/hictkpy
          ref: main
          path: hictkpy

      - name: Patch hictkpy
        working-directory: hictkpy
        if: github.event_name != 'schedule'
        run: |
          sed -i 's|URL.*\.tar\.xz"|GIT_REPOSITORY https://github.com/paulsengroup/hictk.git|' CMakeLists.txt
          sed -i 's|URL_HASH.*|GIT_TAG ${{ github.event.after }}|' CMakeLists.txt
          grep 'GIT_TAG' CMakeLists.txt

      - name: Patch hictkpy (schedule)
        working-directory: hictkpy
        if: github.event_name == 'schedule'
        run: |
          sed -i 's|URL.*\.tar\.xz"|GIT_REPOSITORY https://github.com/paulsengroup/hictk.git|' CMakeLists.txt
          sed -i 's|URL_HASH.*|GIT_TAG main|' CMakeLists.txt

      - name: Fix permissions
        run: |
          chown -R $(id -u):$(id -g) $PWD

      - name: Generate cache key
        id: cache-key
        working-directory: hictkpy
        run: |
          hash="${{ hashFiles('conanfile.txt') }}"

          echo "key=fuzzy-testing-$hash" >> $GITHUB_OUTPUT

      - name: Install Python
        run: |
          apt-get update
          apt-get install -y python3.11 python3.11-dev

      - name: Restore Conan cache
        id: cache-conan
        uses: actions/cache/restore@v3
        with:
          key: conan-${{ steps.cache-key.outputs.key }}
          path: ${{ env.CONAN_HOME }}

      - name: Clean Conan cache (pre-build)
        if: steps.cache-conan.outputs.cache-hit != 'true'
        run: |
          conan cache clean "*" --build
          conan cache clean "*" --download
          conan cache clean "*" --source
          conan remove --confirm "*"

      - name: Install build dependencies
        run: |
          conan install .                     \
          --build=missing                     \
          -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \
          -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \
          -s build_type=Release               \
          -s compiler.libcxx=libstdc++11      \
          -s compiler.cppstd=17               \
          -o '*/*:shared=True'                \
          --output-folder=build

          conan install hictkpy               \
          --build=missing                     \
          -pr:b="$CONAN_DEFAULT_PROFILE_PATH" \
          -pr:h="$CONAN_DEFAULT_PROFILE_PATH" \
          -s build_type=Release               \
          -s compiler.libcxx=libstdc++11      \
          -s compiler.cppstd=17               \
          -o '*/*:shared=True'                \
          --output-folder=build

      - name: Clean Conan cache (post-build)
        if: steps.cache-conan.outputs.cache-hit != 'true'
        run: |
          conan cache clean "*" --build
          conan cache clean "*" --download
          conan cache clean "*" --source

      - name: Install Python bindings
        working-directory: hictkpy
        run: |
          pip install --upgrade pip setuptools wheel pybind11
          env CC=clang-16 \
              CXX=clang++-16 \
              CMAKE_ARGS="-DCMAKE_PREFIX_PATH=$PWD/../build" \
              HICTKPY_SETUP_SKIP_CONAN=1 \
          pip install . -v

      - name: Save Conan cache
        uses: actions/cache/save@v3
        if: steps.cache-conan.outputs.cache-hit != 'true'
        with:
          key: conan-${{ steps.cache-key.outputs.key }}
          path: ${{ env.CONAN_HOME }}

      - name: Install test dependencies
        run: |
          apt-get update
          apt-get install -y curl zstd
          pip install --no-cache-dir 'cooler>=0.9.2'

      - name: Detect CI type
        id: ci-type
        run: |
          if git log --format=%B -n 1 ${{ github.event.after }} | grep -qF '[ci full]'; then
            echo "type=full" >> $GITHUB_OUTPUT
          else
            echo "type=short" >> $GITHUB_OUTPUT
          fi

      - name: Prepare for test
        id: test-params
        env:
          PYTHONHASHSEED: 0
        run: |
          seed="$(python3 -c 'import random; print(random.randint(0, 2**32))')"

          duration=600
          if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then
            duration='${{ inputs.duration }}'
          elif [[ ${{ steps.ci-type.outputs.type }} == 'full' ]]; then
            duration=3600
          fi

          resolution=10000
          if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then
            resolution='${{ inputs.resolution }}'
          fi

          2>&1 echo "Seed: ${seed}"
          2>&1 echo "Duration: ${duration}"
          2>&1 echo "Resolution: ${resolution}"

          echo "seed=$seed" >> $GITHUB_OUTPUT
          echo "duration=$duration" >> $GITHUB_OUTPUT
          echo "resolution=$resolution" >> $GITHUB_OUTPUT

      - name: Clone hictk
        uses: actions/checkout@v4
        with:
          path: hictk

      - name: Fix permissions
        run: |
          chown -R $(id -u):$(id -g) $PWD

      - name: Download test datasets
        working-directory: hictk
        run: |
          resolution="${{ steps.test-params.outputs.resolution }}"
          echo "${{ matrix.ref-sha256 }} reference.mcool" | tee checksums.sha256
          curl -L "${{ matrix.ref-url }}" -o reference.mcool
          sha256sum -c checksums.sha256

          cooler cp "reference.mcool::/resolutions/$resolution" reference.cool
          rm reference.mcool

          if [[ ${{ matrix.ref-sha256 }} == ${{ matrix.sha256 }} ]]; then
            ln -s reference.cool test.matrix
          else
            echo "${{ matrix.sha256 }}  test.matrix" | tee checksums.sha256
            curl -L "${{ matrix.url }}" -o test.matrix
            sha256sum -c checksums.sha256

            if [[ ${{ matrix.title }} == .cool ]]; then
              cooler cp "test.matrix::/resolutions/$resolution" test.matrix.tmp
              mv test.matrix.tmp test.matrix
            fi
          fi

      - name: Run test
        working-directory: hictk
        run: |
          test/scripts/fuzzy_test.py \
            --seed '${{ steps.test-params.outputs.seed }}' \
            --duration '${{ steps.test-params.outputs.duration }}' \
            --balance ${{ matrix.balance }} \
            test.matrix \
            reference.cool

  fuzzy-testing-status-check:
    name: Status Check (fuzzy-testing)
    if: ${{ always() }}
    runs-on: ubuntu-latest
    needs:
      - build-project

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