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Add missing include #672

Add missing include

Add missing include #672

Workflow file for this run

# 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