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Add missing dep in conanfile.py #1167

Add missing dep in conanfile.py

Add missing dep in conanfile.py #1167

Workflow file for this run

# 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