Add missing dep in conanfile.py #1167
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# Copyright (C) 2022 Roberto Rossini (roberros@uio.no) | |
# SPDX-License-Identifier: MIT | |
name: Ubuntu CI | |
on: | |
push: | |
branches: [main] | |
paths: | |
- ".github/workflows/ubuntu-ci.yml" | |
- "cmake/**" | |
- "examples/**" | |
- "src/**" | |
- "test/integration/**" | |
- "test/units/**" | |
- "CMakeLists.txt" | |
- "conanfile.py" | |
tags: | |
- "v*.*.*" | |
pull_request: | |
paths: | |
- ".github/workflows/ubuntu-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 | |
defaults: | |
run: | |
shell: bash | |
jobs: | |
matrix-factory: | |
runs-on: ubuntu-latest | |
outputs: | |
matrix: ${{ steps.set-result.outputs.result }} | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
ref: ${{ github.event.after }} | |
- 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 "$GITHUB_OUTPUT" | |
fi | |
- name: Generate matrix | |
uses: actions/github-script@v7 | |
id: set-result | |
with: | |
script: | | |
// Documentation | |
// https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
// https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
var ci_short = "${{ steps.ci-type.outputs.type }}" === "short" | |
var includes = [] | |
// Debug builds (short CI) | |
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' }) | |
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' }) | |
// Release builds (short CI) | |
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' }) | |
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' }) | |
if (ci_short) { | |
return { include: includes } | |
} | |
// Debug builds (long CI) | |
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' }) | |
// Release builds (long CI) | |
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
// Make sure project builds with CMake 3.25 | |
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.25.2', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' }) | |
// Make sure project builds with make | |
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Unix Makefiles', cmake: '3.29.*', conan: '2.4.*', 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-project: | |
name: Build project | |
needs: matrix-factory | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
container: | |
image: ghcr.io/paulsengroup/ci-docker-images/${{ matrix.os }}-cxx-${{ matrix.compiler }}:latest | |
options: "--user=root" | |
env: | |
CCACHE_DIR: "/opt/ccache-cache" | |
CCACHE_COMPILERCHECK: "content" | |
CCACHE_COMPRESSLEVEL: "1" | |
CCACHE_MAXSIZE: "500M" | |
CONAN_HOME: "/opt/conan/" | |
outputs: | |
ccache-old-cache-key: ${{ steps.cache-ccache.outputs.cache-matched-key }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Fix permissions | |
run: | | |
chown -R $(id -u):$(id -g) $PWD | |
- name: Check build deps are up-to-date | |
id: build-deps-outdated | |
run: | | |
pattern='[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+$' | |
flag=false | |
if [[ $(cmake --version | grep -o "$pattern") != ${{ matrix.cmake }} || | |
$(conan --version | grep -o "$pattern") != ${{ matrix.conan }} ]]; then | |
flag=true | |
fi | |
echo "outdated=$flag" | tee -a "$GITHUB_OUTPUT" | |
- name: Update build deps | |
if: ${{ steps.buld-deps-outdated.outputs.outdated }} | |
run: | | |
apt-get update | |
apt-get install -y --no-install-recommends python3-pip | |
python3 -m pip install \ | |
"cmake==${{ matrix.cmake }}" \ | |
"conan==${{ matrix.conan }}" | |
- name: Generate cache keys | |
id: cache-key | |
run: | | |
set -u | |
os="${{ matrix.os }}" | |
compiler="${{ matrix.compiler }}" | |
generator="${{ matrix.generator }}" | |
build_type="${{ matrix.build_type }}" | |
dev_mode="${{ matrix.developer_mode }}" | |
conanfile_hash="${{ hashFiles('conanfile.py') }}" | |
# This can be used by to always update a cache entry (useful e.g. for ccache) | |
current_date="$(date '+%s')" | |
conan_key_prefix="conan-$os-$compiler-$conanfile_hash-$build_type-$generator-$dev_mode" | |
ccache_key_prefix="ccache-$os-$compiler-$GITHUB_REF-$conanfile_hash-$build_type-$generator-$dev_mode" | |
echo "conan-key=$conan_key_prefix" | tee -a $GITHUB_OUTPUT | |
echo "ccache-key=${ccache_key_prefix}-${current_date}" | tee -a $GITHUB_OUTPUT | |
echo "ccache-restore-key=$ccache_key_prefix" | tee -a $GITHUB_OUTPUT | |
- name: Restore Conan cache | |
id: cache-conan | |
uses: actions/cache/restore@v4 | |
with: | |
key: ${{ steps.cache-key.outputs.conan-key }} | |
path: ${{ env.CONAN_HOME }}/p | |
- name: Clean Conan cache (pre-build) | |
if: steps.cache-conan.outputs.cache-hit != 'true' | |
run: | | |
conan cache clean "*" --build | |
conan cache clean "*" --download | |
conan cache clean "*" --source | |
conan remove --confirm "*" | |
- name: Copy Conan settings | |
run: | | |
if [ ! -f "$CONAN_HOME/settings.yml" ]; then | |
cp "/root/.conan2/settings.yml" "$CONAN_HOME" | |
fi | |
- name: Install build dependencies | |
run: | | |
conan install . \ | |
--build=missing \ | |
-pr:b="$CONAN_DEFAULT_PROFILE_PATH" \ | |
-pr:h="$CONAN_DEFAULT_PROFILE_PATH" \ | |
-s build_type="${{ matrix.build_type }}" \ | |
-s compiler.libcxx=libstdc++11 \ | |
-s compiler.cppstd=17 \ | |
--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: Save Conan cache | |
uses: actions/cache/save@v4 | |
if: steps.cache-conan.outputs.cache-hit != 'true' | |
with: | |
key: ${{ steps.cache-key.outputs.conan-key }} | |
path: ${{ env.CONAN_HOME }}/p | |
env: | |
ZSTD_CLEVEL: 19 | |
- name: Restore Ccache folder | |
id: cache-ccache | |
uses: actions/cache/restore@v4 | |
with: | |
key: ${{ steps.cache-key.outputs.ccache-restore-key }} | |
path: ${{ env.CCACHE_DIR }} | |
- name: Reset Ccache stats | |
run: ccache --zero-stats | |
- name: Configure project | |
run: | | |
cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
-DCMAKE_PREFIX_PATH="$PWD/build" \ | |
-DENABLE_DEVELOPER_MODE=${{ matrix.developer_mode }} \ | |
-DOPT_ENABLE_CLANG_TIDY=OFF \ | |
-DOPT_ENABLE_CPPCHECK=OFF \ | |
-DHICTK_ENABLE_TESTING=ON \ | |
-DHICTK_BUILD_EXAMPLES=ON \ | |
-DHICTK_DOWNLOAD_TEST_DATASET=OFF \ | |
-DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF \ | |
-DCMAKE_INSTALL_PREFIX=dest \ | |
-S . \ | |
-B build | |
- name: Build project | |
run: cmake --build build -j $(nproc) | |
- name: Package binaries | |
run: | | |
cmake --install build | |
tar -cf - -C dest/ bin | zstd -T0 -13 -o binaries.tar.zst | |
- name: Package unit tests | |
run: | | |
rm -r build/src | |
tar -cf - build/ | zstd -T0 -13 -o unit-tests.tar.zst | |
- name: Upload unit tests | |
uses: actions/upload-artifact@v4 | |
with: | |
name: "unit-tests-${{ matrix.os }}-\ | |
${{ matrix.compiler }}-\ | |
${{ matrix.generator }}-\ | |
${{ 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 }}-\ | |
${{ matrix.generator }}-\ | |
${{ matrix.build_type }}-\ | |
${{ matrix.developer_mode }}" | |
path: binaries.tar.zst | |
if-no-files-found: error | |
retention-days: 1 | |
- name: Print Ccache statistics (pre-cleanup) | |
run: | | |
ccache --show-stats \ | |
--show-compression \ | |
--verbose | |
- name: Cleanup Ccache folder | |
run: | | |
ccache --evict-older-than=14400s # 4h | |
ccache --recompress=19 --recompress-threads="$(nproc)" | |
ccache --cleanup | |
- name: Print Ccache statistics (post-cleanup) | |
run: | | |
ccache --show-stats \ | |
--show-compression \ | |
--verbose | |
- name: Save Ccache folder | |
uses: actions/cache/save@v4 | |
with: | |
key: ${{ steps.cache-key.outputs.ccache-key }} | |
path: ${{ env.CCACHE_DIR }} | |
env: | |
ZSTD_CLEVEL: 1 | |
clean-stale-cache: | |
needs: [build-project] | |
uses: paulsengroup/hictk/.github/workflows/evict-gha-cache.yml@main | |
name: Clean stale Ccache cache | |
permissions: | |
actions: write | |
if: needs.build-project.outputs.ccache-old-cache-key != '' | |
with: | |
cache-key: "${{ needs.build-project.outputs.ccache-old-cache-key }}" | |
run-unit-tests: | |
name: Run unit tests | |
needs: [matrix-factory, cache-test-dataset, build-project] | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
container: | |
image: ghcr.io/paulsengroup/ci-docker-images/${{ matrix.os }}-cxx-${{ matrix.compiler }}:latest | |
options: "--user=root" | |
env: | |
HICTK_CI: "1" | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
- name: Restore test dataset | |
uses: actions/cache/restore@v4 | |
with: | |
key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
path: test/data/hictk_test_data.tar.zst | |
fail-on-cache-miss: true | |
- name: Download unit tests artifact | |
uses: actions/download-artifact@v4 | |
with: | |
name: "unit-tests-${{ matrix.os }}-\ | |
${{ matrix.compiler }}-\ | |
${{ matrix.generator }}-\ | |
${{ matrix.build_type }}-\ | |
${{ matrix.developer_mode }}" | |
- name: Extract binaries and test dataset | |
run: | | |
zstd -dcf unit-tests.tar.zst | tar -xf - | |
tar -xf test/data/hictk_test_data.tar.zst | |
- name: Add test user | |
run: useradd devel | |
- name: Fix permissions | |
run: | | |
chown -R devel:devel build/ | |
- name: Setup dependencies | |
run: | | |
apt-get update | |
apt-get install -q -y --no-install-recommends \ | |
python3-pip \ | |
sudo | |
python3 -m pip install "cmake==${{ matrix.cmake }}" | |
- name: Run unit tests | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
ctest --test-dir build/ \ | |
--schedule-random \ | |
--output-on-failure \ | |
--no-tests=error \ | |
--timeout 360 \ | |
-j $(nproc) |& | |
head -n 1000 | |
run-integration-tests: | |
name: Run integration tests | |
needs: [matrix-factory, cache-test-dataset, build-project] | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: ${{ fromJSON(needs.matrix-factory.outputs.matrix) }} | |
container: | |
image: ubuntu:24.04 | |
options: "--user=root" | |
env: | |
HICTK_CI: "1" | |
DEBIAN_FRONTEND: "noninteractive" | |
TZ: "Etc/UTC" | |
steps: | |
- name: Install dependencies | |
run: | | |
apt-get update | |
apt-get install -q -y --no-install-recommends \ | |
curl \ | |
git \ | |
python3.12 \ | |
python3.12-venv \ | |
python3-pip \ | |
sudo \ | |
tar \ | |
zip \ | |
zstd | |
if [ "${{ matrix.developer_mode }}" = ON ]; then | |
apt-get install -q -y --no-install-recommends \ | |
libasan8 \ | |
libubsan1 | |
fi | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
- name: Restore test dataset | |
uses: actions/cache/restore@v4 | |
with: | |
key: ${{ needs.cache-test-dataset.outputs.cache-key }} | |
path: test/data/hictk_test_data.tar.zst | |
fail-on-cache-miss: true | |
- name: Download binaries artifact | |
uses: actions/download-artifact@v4 | |
with: | |
name: "binaries-${{ matrix.os }}-\ | |
${{ matrix.compiler }}-\ | |
${{ matrix.generator }}-\ | |
${{ matrix.build_type }}-\ | |
${{ matrix.developer_mode }}" | |
- name: Extract binaries and test dataset | |
run: | | |
tar -xf binaries.tar.zst | |
tar -xf test/data/hictk_test_data.tar.zst | |
- name: Install test suite | |
run: | | |
python3.12 -m venv venv --upgrade | |
venv/bin/pip install test/integration | |
- name: Add test user | |
run: useradd devel | |
- name: Test hictk balance | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.balance.json \ | |
--suites=balance | |
- name: Test hictk convert | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.convert.json \ | |
--suites=convert | |
- name: Test hictk dump | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.dump.json \ | |
--suites=dump | |
- name: Test hictk fix-mcool | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.fix-mcool.json \ | |
--suites=fix-mcool | |
- name: Test hictk load | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.load.json \ | |
--suites=load | |
- name: Test hictk merge | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.merge.json \ | |
--suites=merge | |
- name: Test hictk metadata | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.metadata.json \ | |
--suites=metadata | |
- name: Test hictk rename-chromosomes | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.rename-chromosomes.json \ | |
--suites=rename-chromosomes | |
- name: Test hictk validate | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.validate.json \ | |
--suites=validate | |
- name: Test hictk zoomify | |
run: | | |
sudo -u devel -E env "PATH=$PATH" \ | |
venv/bin/hictk_integration_suite \ | |
bin/hictk \ | |
test/integration/config.toml \ | |
--data-dir test/data \ | |
--threads "$(nproc)" \ | |
--result-file integration-test-report.zoomify.json \ | |
--suites=zoomify | |
- name: Upload integration test results | |
if: ${{ always() }} | |
uses: actions/upload-artifact@v4 | |
with: | |
name: "integration-test-reports-\ | |
${{ matrix.os }}-\ | |
${{ matrix.compiler }}-\ | |
${{ matrix.generator }}-\ | |
${{ matrix.build_type }}-\ | |
${{ matrix.developer_mode }}" | |
path: integration-test-report*.json | |
retention-days: 7 | |
ubuntu-ci-status-check: | |
name: Status Check (Ubuntu 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.matrix-factory.result != 'success' || | |
needs.cache-test-dataset.result != 'success' || | |
needs.build-project.result != 'success' || | |
needs.run-unit-tests.result != 'success' || | |
needs.run-integration-tests.result != 'success' | |
run: exit 1 |