Add missing include #672
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# Copyright (C) 2023 Roberto Rossini <roberros@uio.no> | |
# SPDX-License-Identifier: MIT | |
name: Run fuzzy tests | |
on: | |
push: | |
branches: [main] | |
paths: | |
- ".github/workflows/build-conan-deps.yml" | |
- ".github/workflows/fuzzy-testing.yml" | |
- "cmake/**" | |
- "src/**" | |
- "test/fuzzer/**" | |
- "CMakeLists.txt" | |
- "conanfile.py" | |
pull_request: | |
paths: | |
- ".github/workflows/build-conan-deps.yml" | |
- ".github/workflows/fuzzy-testing.yml" | |
- "cmake/**" | |
- "src/**" | |
- "test/fuzzer/**" | |
- "CMakeLists.txt" | |
- "conanfile.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: "random" | |
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-conan-deps: | |
name: Build Conan deps | |
uses: paulsengroup/hictk/.github/workflows/build-conan-deps.yml@main | |
with: | |
os: ubuntu-20.04 | |
build-project: | |
name: Build project | |
needs: build-conan-deps | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
include: | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "weight", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "VC", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "cool", | |
normalization: "NONE", | |
bin-type: "variable", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic8", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic8", | |
normalization: "KR", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic9", | |
normalization: "NONE", | |
bin-type: "fixed", | |
} | |
- { | |
dataset: "4DNFIYECESRC", | |
format: "hic9", | |
normalization: "VC", | |
bin-type: "fixed", | |
} | |
container: | |
image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19 | |
options: "--user=root" | |
env: | |
CCACHE_DISABLE: "1" | |
CONAN_HOME: "/opt/conan/" | |
HICTK_CI: "1" | |
steps: | |
- name: Clone hictk | |
uses: actions/checkout@v4 | |
- name: Fix permissions | |
run: | | |
chown -R $(id -u):$(id -g) $PWD | |
- name: Install Python | |
run: | | |
apt-get update | |
apt-get install -y python3.12 python3.12-dev | |
- 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 | |
uses: actions/cache/restore@v4 | |
with: | |
key: ${{ needs.build-conan-deps.outputs.cmake-prefix-release-key }} | |
path: /tmp/cmake-prefix-rel.tar | |
fail-on-cache-miss: true | |
- name: Extract CMake configs | |
run: | | |
mkdir conan-env | |
tar -xf /tmp/cmake-prefix-rel.tar -C conan-env/ --strip-components=1 | |
- name: Configure project | |
run: | | |
cmake -DCMAKE_BUILD_TYPE=Release \ | |
-DCMAKE_PREFIX_PATH="$PWD/conan-env" \ | |
-DENABLE_DEVELOPER_MODE=ON \ | |
-DOPT_ENABLE_CLANG_TIDY=OFF \ | |
-DOPT_ENABLE_CPPCHECK=OFF \ | |
-DHICTK_ENABLE_TESTING=ON \ | |
-DHICTK_ENABLE_FUZZY_TESTING=ON \ | |
-DHICTK_BUILD_EXAMPLES=OFF \ | |
-DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
-S . \ | |
-B build | |
- name: Build hictk_fuzzer | |
run: cmake --build build -j $(nproc) -t hictk_fuzzer | |
- name: Install test dependencies | |
run: | | |
pip install --no-cache-dir 'cooler==0.10.*' 'numpy<2' | |
- name: Detect CI type | |
id: ci-type | |
run: | | |
if git log --format=%B -n 1 ${{ github.event.after }} | grep -qF '[ci full]'; then | |
echo "type=full" | tee -a "$GITHUB_OUTPUT" | |
else | |
echo "type=short" | tee -a "$GITHUB_OUTPUT" | |
fi | |
- name: Prepare for test | |
id: test-params | |
run: | | |
duration=120 | |
if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
duration='${{ inputs.duration }}' | |
elif [[ '${{ steps.ci-type.outputs.type }}' == 'full' ]]; then | |
duration=3600 | |
fi | |
resolution=50000 | |
if [[ ${{ github.event_name }} == 'workflow_dispatch' ]]; then | |
if [[ '${{ inputs.resolution }}' == 'random' ]]; then | |
resolution="$( | |
python3 -c 'import random; import sys; print(random.choice([int(x) for x in sys.argv[1:]]))' \ | |
1000 5000 10000 50000 100000 500000 | |
)" | |
else | |
resolution='${{ inputs.resolution }}' | |
fi | |
fi | |
if [[ '${{ matrix.bin-type }}' == variable ]]; then | |
resolution=0 | |
fi | |
2>&1 echo "Duration: ${duration}" | |
2>&1 echo "Resolution: ${resolution}" | |
echo "duration=$duration" | tee -a "$GITHUB_OUTPUT" | |
echo "resolution=$resolution" | tee -a "$GITHUB_OUTPUT" | |
- name: Download test datasets | |
run: | | |
test/fuzzer/scripts/download_test_datasets.py \ | |
test/fuzzer/test_files.json \ | |
. \ | |
--format cool "${{ matrix.format }}" \ | |
--resolution "${{ steps.test-params.outputs.resolution }}" \ | |
--dataset "${{ matrix.dataset }}" \ | |
--nproc 2 | |
- name: Run test (df) | |
run: | | |
build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format df \ | |
*".${{ matrix.format }}" \ | |
*.cool | |
- name: Run test (dense) | |
run: | | |
build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format dense \ | |
*".${{ matrix.format }}" \ | |
*.cool | |
- name: Run test (sparse) | |
run: | | |
build/test/fuzzer/src/hictk_fuzzer fuzz \ | |
--resolution ${{ steps.test-params.outputs.resolution }} \ | |
--duration '${{ steps.test-params.outputs.duration }}' \ | |
--normalization ${{ matrix.normalization }} \ | |
--nproc $(nproc) \ | |
--format sparse \ | |
*".${{ matrix.format }}" \ | |
*.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 |