Major refactor #187

Workflow file for this run

.github/workflows/codecov.yml at 2d5dcab

	# Copyright (C) 2024 Roberto Rossini <[email protected]>
	#
	# SPDX-License-Identifier: GPL-3.0
	#
	# This library is free software: you can redistribute it and/or
	# modify it under the terms of the GNU Public License as published
	# by the Free Software Foundation; either version 3 of the License,
	# or (at your option) any later version.
	#
	# This library is distributed in the hope that it will be useful,
	# but WITHOUT ANY WARRANTY; without even the implied warranty of
	# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
	# Library General Public License for more details.
	#
	# You should have received a copy of the GNU Public License along
	# with this library. If not, see
	# <https://www.gnu.org/licenses/>.

	name: Run Codecov

	on:
	push:
	branches: [main]
	paths:
	- ".github/codecov.yml"
	- ".github/workflows/build-conan-deps.yml"
	- ".github/workflows/cache-test-dataset.yml"
	- ".github/workflows/codecov.yml"
	- "cmake/**"
	- "src/**"
	- "test/**"
	- "CMakeLists.txt"
	- "conanfile.py"
	- "utils/devel/collect_coverage_data.py"

	pull_request:
	paths:
	- ".github/codecov.yml"
	- ".github/workflows/build-conan-deps.yml"
	- ".github/workflows/cache-test-dataset.yml"
	- ".github/workflows/codecov.yml"
	- "cmake/**"
	- "src/**"
	- "test/**"
	- "CMakeLists.txt"
	- "conanfile.py"
	- "utils/devel/collect_coverage_data.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:
	cache-test-dataset:
	name: Cache test dataset
	uses: paulsengroup/nchg/.github/workflows/cache-test-dataset.yml@main

	build-conan-deps:
	name: Build Conan deps
	uses: paulsengroup/nchg/.github/workflows/build-conan-deps.yml@main
	with:
	os: ubuntu-24.04

	build-project:
	name: Build project
	needs: build-conan-deps
	runs-on: ubuntu-latest
	container:
	image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19
	options: "--user=root"

	env:
	CCACHE_DIR: "/opt/ccache-cache"
	CCACHE_COMPILERCHECK: "content"
	CCACHE_COMPRESSLEVEL: "1"
	CCACHE_MAXSIZE: "500M"
	CONAN_HOME: "/opt/conan/"

	steps:
	- uses: actions/checkout@v4

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

	- name: Generate cache key
	id: cache-key
	run: \|
	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')"

	ccache_key_prefix="codecov-ccache-$conanfile_hash"

	echo "ccache-key=${ccache_key_prefix}-$GITHUB_REF-${current_date}" \| tee -a "$GITHUB_OUTPUT"
	echo "ccache-restore-key-1=$ccache_key_prefix-$GITHUB_REF" \| tee -a "$GITHUB_OUTPUT"
	echo "ccache-restore-key-2=$ccache_key_prefix" \| tee -a "$GITHUB_OUTPUT"

	- 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-relwithdebinfo-key }}
	path: /tmp/cmake-prefix-rwdi.tar
	fail-on-cache-miss: true

	- name: Extract CMake configs
	run: \|
	mkdir conan-env
	tar -xf /tmp/cmake-prefix-rwdi.tar -C conan-env/ --strip-components=1

	- name: Configure project
	run: \|
	cov_flags='-fprofile-instr-generate -fcoverage-mapping -fcoverage-mcdc'

	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo \
	-DCMAKE_PREFIX_PATH="$PWD/conan-env" \
	-DENABLE_DEVELOPER_MODE=ON \
	-DOPT_ENABLE_INTERPROCEDURAL_OPTIMIZATION=OFF \
	-DOPT_ENABLE_SANITIZER_ADDRESS=OFF \
	-DOPT_ENABLE_SANITIZER_LEAK=OFF \
	-DOPT_ENABLE_SANITIZER_POINTER_COMPARE=OFF \
	-DOPT_ENABLE_SANITIZER_POINTER_SUBTRACT=OFF \
	-DOPT_ENABLE_SANITIZER_UNDEFINED_BEHAVIOR=OFF \
	-DOPT_ENABLE_CPPCHECK=OFF \
	-DOPT_ENABLE_CLANG_TIDY=OFF \
	-DNCHG_ENABLE_TESTING=ON \
	-DNCHG_DOWNLOAD_TEST_DATASET=OFF \
	-DCMAKE_C_FLAGS="$cov_flags" \
	-DCMAKE_CXX_FLAGS="$cov_flags" \
	-S . \
	-B build

	- name: Restore Ccache folder
	id: cache-ccache
	uses: actions/cache/restore@v4
	with:
	key: ${{ steps.cache-key.outputs.ccache-restore-key-1 }}
	restore-keys: ${{ steps.cache-key.outputs.ccache-restore-key-2 }}
	path: ${{ env.CCACHE_DIR }}

	- name: Reset Ccache stats
	run: ccache --zero-stats

	- name: Build project
	run: cmake --build build -j $(nproc)

	- name: Package build folder
	run: tar --exclude='*.o' -cf - build/ \| zstd -T0 -13 -o build.tar.zst

	- name: Upload build folder
	uses: actions/upload-artifact@v4
	with:
	name: "build-codecov"
	path: build.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

	- name: Generate list of stale cache entries
	id: stale-cache
	if: steps.cache-ccache.outputs.cache-matched-key != ''
	run: \|
	fname='stale-cache-codecov.txt'
	echo '${{ steps.cache-ccache.outputs.cache-matched-key }}' > "$fname"

	echo "name=$fname" \| tee -a "$GITHUB_OUTPUT"

	- name: Upload stale cache entries
	if: steps.cache-ccache.outputs.cache-matched-key != ''
	uses: actions/upload-artifact@v4
	with:
	name: ${{ steps.stale-cache.outputs.name }}
	path: "${{ steps.stale-cache.outputs.name }}"
	if-no-files-found: error
	retention-days: 1

	clean-stale-cache:
	needs: [build-project]
	name: Evict stale cache entries
	runs-on: ubuntu-latest
	permissions:
	actions: write

	steps:
	- name: Download artifacts
	uses: actions/download-artifact@v4
	continue-on-error: true
	with:
	pattern: stale-cache-*
	merge-multiple: true

	- name: Evict cache entries
	continue-on-error: true
	run: \|
	set -x
	while read entry; do
	if ! grep -q '/heads/main' <(echo "$entry"); then
	gh cache delete --repo '${{ github.repository }}' "$entry"
	fi
	done < <(cat stale-cache*.txt \| grep -v '^$')
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	run-unit-tests:
	name: Run unit tests
	needs: [cache-test-dataset, build-project]
	runs-on: ubuntu-latest
	container:
	image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19
	options: "--user=root"

	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/nchg_test_data.tar.zst
	fail-on-cache-miss: true

	- name: Download unit tests artifact
	uses: actions/download-artifact@v4
	with:
	name: "build-codecov"

	- name: Extract binaries and test dataset
	run: \|
	tar -xf build.tar.zst
	tar -xf test/data/nchg_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 \
	gpg \
	gpg-agent \
	sudo \
	tar

	- name: Run unit tests
	run: \|
	readarray -t -d '' binaries < <(find build/test/units/ -type f -executable \| xargs printf '%q\0')

	mkdir profiles
	chown devel:devel profiles

	for bin in "${binaries[@]}"; do
	hash="$(sha256sum "$bin" \| cut -f1 -d ' ')"
	LLVM_PROFILE_FILE="$PWD/profiles/$hash.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	"$bin"

	if [ $? -ne 0 ]; then
	exit 1
	fi

	done

	- name: Collect coverage data
	run: \|
	readarray -t -d '' binaries < <(find build/test/units/ -type f -executable \| xargs printf '%q\0')

	utils/devel/collect_coverage_data.py \
	--output-dir coverage/ \
	--prefix=profiles/ \
	--format lcov \
	--llvm-cov-bin llvm-cov-19 \
	--llvm-profdata-bin llvm-profdata-19 \
	"${binaries[@]}"

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	flags: "tests \| unittests"
	fail_ci_if_error: true
	handle_no_reports_found: true
	directory: coverage
	os: linux
	token: ${{ secrets.CODECOV_TOKEN }}
	verbose: true

	run-integration-tests:
	name: Run integration tests
	needs: [cache-test-dataset, build-project]
	runs-on: ubuntu-latest
	container:
	image: ghcr.io/paulsengroup/ci-docker-images/ubuntu-24.04-cxx-clang-19
	options: "--user=root"

	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/nchg_test_data.tar.zst
	fail-on-cache-miss: true

	- name: Download binaries artifact
	uses: actions/download-artifact@v4
	with:
	name: "build-codecov"

	- name: Extract binaries and test dataset
	run: \|
	tar -xf build.tar.zst
	tar -xf test/data/nchg_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 \
	gpg \
	gpg-agent \
	sudo \
	tar

	pip install -r test/requirements.txt

	- name: Setup test environment
	run: \|
	echo "DATA_DIR=$PWD/test/data/integration_tests" \| tee -a "$GITHUB_ENV"
	echo "OUT_PREFIX=ENCFF447ERX.1000000" \| tee -a "$GITHUB_ENV"

	- name: Test NCHG compute (mt)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.compute-mt.%$(nproc)m.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG compute \
	test/data/ENCFF447ERX.1000000.cool \
	"$OUT_PREFIX" \
	--threads "$(nproc)"

	test/scripts/validate_nchg_output.py compute \
	"$OUT_PREFIX" \
	"$DATA_DIR/compute/$OUT_PREFIX"

	rm "$OUT_PREFIX"*

	- name: Test NCHG compute (st)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.compute-st.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG compute \
	test/data/ENCFF447ERX.1000000.cool \
	"$OUT_PREFIX" \
	--cis-only \
	--threads 1

	rm "$OUT_PREFIX"*

	- name: Test NCHG compute (mt; w/ domain list)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.compute-mt-with-domains.%$(nproc)m.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG compute \
	test/data/ENCFF447ERX.1000000.cool \
	"$OUT_PREFIX" \
	--threads "$(nproc)" \
	--domains test/data/ENCFF447ERX.1000000.compartments.bed

	test/scripts/validate_nchg_output.py compute \
	"$OUT_PREFIX" \
	"$DATA_DIR/compute_with_domains/$OUT_PREFIX"

	rm "$OUT_PREFIX"*

	- name: Test NCHG merge
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.merge.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG merge \
	"$DATA_DIR/compute/$OUT_PREFIX" \
	"$OUT_PREFIX.parquet" \
	--threads "$(nproc)"

	test/scripts/validate_nchg_output.py merge \
	"$OUT_PREFIX.parquet" \
	"$DATA_DIR/merge/$OUT_PREFIX.parquet"

	rm "$OUT_PREFIX"*

	- name: Test NCHG filter
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.filter.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG filter \
	"$DATA_DIR/merge/$OUT_PREFIX.parquet" \
	"$OUT_PREFIX.filtered.parquet" \
	--threads "$(nproc)"

	test/scripts/validate_nchg_output.py filter \
	"$OUT_PREFIX.filtered.parquet" \
	"$DATA_DIR/filter/$OUT_PREFIX.parquet"

	rm "$OUT_PREFIX"*

	- name: Test NCHG view (compute)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.view.compute.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG view \
	"$DATA_DIR/merge/$OUT_PREFIX.parquet" > /dev/null

	- name: Test NCHG view (filter)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.view.filter.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG view \
	"$DATA_DIR/filter/$OUT_PREFIX.parquet" \
	> "$OUT_PREFIX.tsv"

	test/scripts/validate_nchg_output.py view \
	"$OUT_PREFIX.tsv" \
	"$DATA_DIR/view/$OUT_PREFIX.tsv"

	rm "$OUT_PREFIX"*

	- name: Test NCHG expected (w/ mask)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.expected.mask.profraw"

	printf 'chr1\t0\t248956422' > mask.bed

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG expected \
	test/data/ENCFF447ERX.1000000.cool \
	--output "$OUT_PREFIX.h5" \
	--bin-mask mask.bed

	rm "$OUT_PREFIX"* mask.bed

	- name: Test NCHG expected (wo/ mask)
	run: \|
	LLVM_PROFILE_FILE="$PWD/nchg.expected.no-mask.profraw"

	sudo -u devel \
	-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
	build/src/nchg/NCHG expected \
	test/data/ENCFF447ERX.1000000.cool \
	--output "$OUT_PREFIX.h5"

	test/scripts/validate_nchg_output.py expected \
	"$OUT_PREFIX.h5" \
	"$DATA_DIR/expected/$OUT_PREFIX.h5"

	rm "$OUT_PREFIX"*

	- name: Collect coverage data
	run: \|
	utils/devel/collect_coverage_data.py \
	--output-dir coverage/ \
	--prefix="$PWD/nchg" \
	--format lcov \
	--llvm-cov-bin llvm-cov-19 \
	--llvm-profdata-bin llvm-profdata-19 \
	build/src/nchg/NCHG

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v4
	with:
	flags: "tests \| integration"
	fail_ci_if_error: true
	handle_no_reports_found: true
	directory: coverage
	os: linux
	token: ${{ secrets.CODECOV_TOKEN }}
	verbose: true

	codecov-status-check:
	name: Status Check (Codecov)
	if: ${{ always() }}
	runs-on: ubuntu-latest
	needs:
	- build-project
	- run-unit-tests
	- run-integration-tests

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

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Major refactor #187

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Major refactor #187

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Workflow file for this run