Merge pull request #297 from BASE-Laboratory/claude/issue-289-mlmg-eb… #459

Workflow file for this run

.github/workflows/build-test.yml at 733dc6f

	# .github/workflows/build-test.yml
	name: Build and Test OpenImpala

	# Define workflow triggers
	on:
	push:
	# Trigger on pushes to these specific branches
	branches:
	- master
	- working
	- build
	- 'makefile' # Include makefile branch trigger
	pull_request:
	# Trigger on Pull Requests targeting these branches
	branches: [ master, working ]
	workflow_dispatch: # Allows manual triggering

	jobs:
	format-check:
	name: C++ Format Check (clang-format)
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Install clang-format
	run: \|
	sudo apt-get update
	sudo apt-get install -y clang-format

	- name: Run clang-format check
	run: \|
	find src/ tests/ python/bindings/ -type f $ -name ".cpp" -o -name ".H" -o -name ".h" -o -name ".hpp" -o -name ".cc" -o -name ".cxx" -o -name "*.c" $ \
	-exec clang-format --dry-run --Werror {} +

	- name: Check @file/@brief documentation in headers
	run: \|
	MISSING=0
	for f in $(find src/ -type f -name ".H" -o -name ".h" \| sort); do
	if ! head -5 "$f" \| grep -q "@file"; then
	echo "::warning file=$f::Missing @file doxygen tag"
	MISSING=$((MISSING + 1))
	fi
	done
	if [ "$MISSING" -gt 0 ]; then
	echo ""
	echo "WARNING: $MISSING header(s) missing @file/@brief documentation."
	echo "Add a doxygen block before the include guard:"
	echo ' /** @file MyHeader.H'
	echo ' * @brief One-line description of the file.'
	echo ' */'
	fi

	static-analysis:
	name: Static Analysis (clang-tidy)
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Apptainer
	uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.2.5

	- name: Restore Dependency SIF Cache
	id: cache-restore-sif-tidy
	uses: actions/cache/restore@v4
	with:
	path: dependency_image.sif
	key: ${{ runner.os }}-apptainer-sif-${{ hashFiles('containers/Singularity.deps.def') }}
	restore-keys: \|
	${{ runner.os }}-apptainer-sif-

	- name: Build Dependency SIF Image (if cache miss)
	id: build_sif_tidy
	if: steps.cache-restore-sif-tidy.outputs.cache-hit != 'true'
	run: \|
	sudo apptainer build --force dependency_image.sif containers/Singularity.deps.def

	- name: Run clang-tidy
	run: \|
	sudo apptainer exec --writable-tmpfs --bind $PWD:/src ./dependency_image.sif \
	bash -c '
	set -e
	source /opt/rh/gcc-toolset-11/enable

	# Rocky 8 mirrors occasionally 404 on repodata for a few minutes
	# before AlmaLinux mirrors catch up. Retry the install with
	# backoff up to 3 times — typical transient outages recover
	# well within that window — then fail clearly with an
	# infrastructure-error message rather than silently leaving
	# clang-tidy unavailable.
	install_ok=0
	for attempt in 1 2 3; do
	if dnf install -y clang-tools-extra 2>&1 \| tail -3 && \
	command -v clang-tidy >/dev/null 2>&1; then
	install_ok=1
	break
	fi
	echo "clang-tidy install attempt $attempt failed; sleeping ${attempt}0s..."
	sleep $((attempt * 10))
	dnf clean all >/dev/null 2>&1 \|\| true
	done

	if [ $install_ok -ne 1 ] \|\| ! command -v clang-tidy >/dev/null 2>&1; then
	echo "::error::clang-tidy could not be installed (Rocky 8 mirror 404). This is an infrastructure issue, not a code issue. Re-run the job."
	exit 2
	fi

	echo "clang-tidy version: $(clang-tidy --version \| head -1)"
	cd /src
	# Fetch nlohmann/json header (used by ResultsJSON.H, normally via CMake FetchContent)
	NLOHMANN_VERSION="v3.11.3"
	mkdir -p /tmp/nlohmann_include/nlohmann
	curl -sL "https://github.com/nlohmann/json/releases/download/${NLOHMANN_VERSION}/json.hpp" \
	-o /tmp/nlohmann_include/nlohmann/json.hpp
	echo "nlohmann/json ${NLOHMANN_VERSION} downloaded for clang-tidy"
	ERRORS=0
	# Note: python/bindings/ excluded — pybind11 + Python.h not available
	# in the dependency container; those files are checked by clang-format
	for f in $(find src/ tests/ -path tests/unit -prune -o -type f -name "*.cpp" -print); do
	echo "Analyzing $f..."
	clang-tidy "$f" \
	-warnings-as-errors="*" \
	-header-filter="src/.*" \
	-- -std=c++17 -fopenmp -DOMPI_SKIP_MPICXX \
	-Isrc -Isrc/io -Isrc/props \
	-I/opt/amrex/25.03/include \
	-I/opt/hypre/v2.32.0/include \
	-I/opt/hdf5/1.12.3/include \
	-I/opt/libtiff/4.6.0/include \
	-I/tmp/nlohmann_include \|\| ERRORS=$((ERRORS+1))
	done
	if [ $ERRORS -ne 0 ]; then
	echo "::error::clang-tidy found issues in $ERRORS file(s)."
	exit 1
	fi
	echo "clang-tidy passed on all files."
	'

	build-and-test-openimpala:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Apptainer
	uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.2.5

	- name: Restore Dependency SIF Cache
	id: cache-restore-sif
	uses: actions/cache/restore@v4
	with:
	path: dependency_image.sif
	key: ${{ runner.os }}-apptainer-sif-${{ hashFiles('containers/Singularity.deps.def') }}

	- name: Build Dependency SIF Image (if cache miss)
	if: steps.cache-restore-sif.outputs.cache-hit != 'true'
	run: sudo apptainer build --force dependency_image.sif containers/Singularity.deps.def

	- name: Save Dependency SIF Image Cache
	if: steps.cache-restore-sif.outputs.cache-hit != 'true'
	uses: actions/cache/save@v4
	with:
	path: dependency_image.sif
	key: ${{ runner.os }}-apptainer-sif-${{ hashFiles('containers/Singularity.deps.def') }}

	- name: Build and Test OpenImpala C++
	run: \|
	sudo apptainer exec \
	--bind $PWD:/src \
	./dependency_image.sif \
	bash -c '
	source /opt/rh/gcc-toolset-11/enable
	cd /src
	rm -rf cmake_build && mkdir cmake_build && cd cmake_build

	# Notice we can use standard cmake now!
	cmake .. \
	-DCMAKE_BUILD_TYPE=Release \
	-DCMAKE_C_COMPILER=$(which mpicc) \
	-DCMAKE_CXX_COMPILER=$(which mpicxx) \
	-DCMAKE_PREFIX_PATH="/opt/amrex/25.03;/opt/hypre/v2.32.0;/opt/hdf5/1.12.3;/opt/libtiff/4.6.0" \
	-DBUILD_TESTING=ON

	make -j$(nproc)
	ctest --output-on-failure --timeout 300
	'

	python-bindings-test:
	name: Python Bindings Test
	runs-on: ubuntu-latest
	needs: build-and-test-openimpala

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Apptainer
	uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.2.5

	- name: Restore Dependency SIF Cache
	uses: actions/cache/restore@v4
	with:
	path: dependency_image.sif
	key: ${{ runner.os }}-apptainer-sif-${{ hashFiles('containers/Singularity.deps.def') }}

	- name: Build and Test Python Bindings
	run: \|
	sudo apptainer exec \
	--bind $PWD:/src \
	./dependency_image.sif \
	bash -c '
	source /opt/rh/gcc-toolset-11/enable
	cd /src
	rm -rf cmake_build_py && mkdir cmake_build_py && cd cmake_build_py

	# 1. Ask Python exactly where the pybind11 CMake files are
	PYBIND11_DIR=$(python3.11 -m pybind11 --cmakedir)
	echo "Found pybind11 CMake dir at: $PYBIND11_DIR"

	# 2. Pass it to CMake using -Dpybind11_DIR
	cmake .. \
	-DCMAKE_BUILD_TYPE=Release \
	-DCMAKE_C_COMPILER=$(which mpicc) \
	-DCMAKE_CXX_COMPILER=$(which mpicxx) \
	-DPython_EXECUTABLE=/usr/bin/python3.11 \
	-Dpybind11_DIR=${PYBIND11_DIR} \
	-DCMAKE_PREFIX_PATH="/opt/amrex/25.03;/opt/hypre/v2.32.0;/opt/hdf5/1.12.3;/opt/libtiff/4.6.0" \
	-DBUILD_TESTING=ON \
	-DOPENIMPALA_PYTHON=ON

	make -j$(nproc)

	# pytest and pyAMReX are native to the container now!
	ctest --output-on-failure --timeout 120 -L python
	'

	coverage:
	name: Code Coverage
	runs-on: ubuntu-latest
	if: github.event_name == 'pull_request'
	permissions:
	pull-requests: write

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Apptainer
	uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.2.5

	- name: Restore Dependency SIF Cache
	id: cache-restore-sif-cov
	uses: actions/cache/restore@v4
	with:
	path: dependency_image.sif
	key: ${{ runner.os }}-apptainer-sif-${{ hashFiles('containers/Singularity.deps.def') }}
	restore-keys: \|
	${{ runner.os }}-apptainer-sif-

	- name: Build Dependency SIF Image (if cache miss)
	if: steps.cache-restore-sif-cov.outputs.cache-hit != 'true'
	run: \|
	sudo apptainer build --force dependency_image.sif containers/Singularity.deps.def

	- name: Build with coverage and run tests
	run: \|
	sudo apptainer exec \
	--writable-tmpfs \
	--bind $PWD:/src \
	./dependency_image.sif \
	bash -c '
	source /opt/rh/gcc-toolset-11/enable
	cd /src
	rm -rf cmake_build_cov && mkdir cmake_build_cov && cd cmake_build_cov

	# Changed cmake3 to cmake
	cmake .. \
	-DCMAKE_BUILD_TYPE=Debug \
	-DCMAKE_C_COMPILER=$(which mpicc) \
	-DCMAKE_CXX_COMPILER=$(which mpicxx) \
	-DCMAKE_PREFIX_PATH="/opt/amrex/25.03;/opt/hypre/v2.32.0;/opt/hdf5/1.12.3;/opt/libtiff/4.6.0" \
	-DBUILD_TESTING=ON \
	-DENABLE_COVERAGE=ON

	make -j$(nproc)
	ctest --output-on-failure --timeout 300 \|\| true
	'

	- name: Generate coverage report
	run: \|
	sudo apptainer exec \
	--writable-tmpfs \
	--bind $PWD:/src \
	./dependency_image.sif \
	bash -c '
	source /opt/rh/gcc-toolset-11/enable

	# Dropped the dnf install and used native python3.11 pip!
	python3.11 -m pip install gcovr

	cd /src
	gcovr --root . \
	--filter "src/" \
	--print-summary \
	--gcov-ignore-parse-errors=suspicious_hits.warn_once_per_file \
	--xml coverage.xml \
	--txt coverage.txt \
	cmake_build_cov/
	'

	- name: Generate summary
	if: always()
	run: \|
	if [ -f coverage.txt ]; then
	echo "## Code Coverage Report" >> $GITHUB_STEP_SUMMARY
	echo "" >> $GITHUB_STEP_SUMMARY
	echo '```' >> $GITHUB_STEP_SUMMARY
	cat coverage.txt >> $GITHUB_STEP_SUMMARY
	echo '```' >> $GITHUB_STEP_SUMMARY
	fi

	- name: Upload coverage artifacts
	if: always()
	uses: actions/upload-artifact@v4
	with:
	name: coverage-report-${{ github.run_id }}
	path: \|
	coverage.xml
	coverage.txt
	retention-days: 30
	if-no-files-found: warn

	- name: Upload to Codecov
	if: always()
	uses: codecov/codecov-action@v5
	with:
	files: coverage.xml
	fail_ci_if_error: false
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

	- name: Post coverage summary to PR
	if: github.event_name == 'pull_request'
	uses: actions/github-script@v7
	with:
	script: \|
	const fs = require('fs');
	let coverageText = '';
	try {
	coverageText = fs.readFileSync('coverage.txt', 'utf8');
	} catch (e) {
	coverageText = 'Coverage report not available.';
	}

	const marker = '<!-- coverage-report -->';
	const body = [
	marker,
	'## Code Coverage Report',
	'',
	'```',
	coverageText,
	'```',
	'',
	'---',
	'Generated by CI — coverage data from [gcovr](https://gcovr.com/)',
	].join('\n');

	const { data: comments } = await github.rest.issues.listComments({
	owner: context.repo.owner,
	repo: context.repo.repo,
	issue_number: context.issue.number,
	});

	const existing = comments.find(c => c.body.includes(marker));

	if (existing) {
	await github.rest.issues.updateComment({
	owner: context.repo.owner,
	repo: context.repo.repo,
	comment_id: existing.id,
	body: body,
	});
	} else {
	await github.rest.issues.createComment({
	owner: context.repo.owner,
	repo: context.repo.repo,
	issue_number: context.issue.number,
	body: body,
	});
	}

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Merge pull request #297 from BASE-Laboratory/claude/issue-289-mlmg-eb… #459

Workflow file

Merge pull request #297 from BASE-Laboratory/claude/issue-289-mlmg-eb… #459

Uh oh!

Workflow file for this run