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Merge pull request #353 from 3dgeo-heidelberg/pre-commit-ci-update-co… #998

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Merge pull request #353 from 3dgeo-heidelberg/pre-commit-ci-update-co…

Merge pull request #353 from 3dgeo-heidelberg/pre-commit-ci-update-co… #998

Workflow file for this run

.github/workflows/ci.yml at b54a599
name: CI
on:
# We run CI on pushes to the main branch
push:
branches:
- main
# and on all pull requests to the main branch
pull_request:
branches:
- main
# as well as upon manual triggers through the 'Actions' tab of the Github UI
workflow_dispatch:
jobs:
build-and-test:
name: Testing on ${{matrix.os}} Py${{matrix.python-version}}- OpenMP ${{matrix.openmp}}
runs-on: ${{matrix.os}}
strategy:
matrix:
os: [ubuntu-22.04, macos-13, macos-14, windows-2019]
python-version: ["3.9", "3.12"]
openmp: ['ON', 'OFF']
steps:
- uses: actions/checkout@v4
with:
submodules: 'recursive'
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install OpenMP
if: runner.os == 'macOS' && matrix.openmp == 'ON'
run: brew install libomp
- name: make build directory
run: cmake -E make_directory ${{runner.workspace}}/build
- name: configure cmake
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCS=OFF -DBUILD_BENCHMARKS=ON -DPY4DGEO_WITH_OPENMP=${{matrix.openmp}}
- name: build
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake --build .
- name: Install Python package and development requirements
run: |
python -m pip install -r requirements-dev.txt
python -m pip install -v .
- name: Install py4dgeo test data
shell: bash
run: |
mkdir -p $GITHUB_WORKSPACE/tests/data
copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
- name: run tests
shell: bash
working-directory: ${{runner.workspace}}/build
run: ctest --output-on-failure -C Debug
- name: Run Python tests
run: |
python -m pytest --nbval
coverage-test:
name: Coverage Testing
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v4
with:
submodules: 'recursive'
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.9"
- name: Install LCov
run: |
sudo apt-get install -y lcov
- name: Install Python package and development requirements
run: |
python -m pip install -r requirements-dev.txt
python -m pip install -v --editable .
- name: Install py4dgeo test data
shell: bash
run: |
mkdir -p $GITHUB_WORKSPACE/tests/data
copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
- name: make build directory
run: cmake -E make_directory ${{runner.workspace}}/build
- name: configure cmake
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="--coverage" -DBUILD_DOCS=OFF
- name: build
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake --build .
- name: run tests
shell: bash
working-directory: ${{runner.workspace}}/build
run: ctest -C Debug
- name: collect coverage report
shell: bash
working-directory: ${{runner.workspace}}
run: |
lcov --directory ./build --capture --output-file coverage.info
lcov_cobertura coverage.info -o coverage2.xml
- name: Run coverage tests
run: |
python -m pytest --cov=src --cov-report=xml
- name: Upload coverage to Codecov.io
working-directory: ${{runner.workspace}}
run: |
curl --connect-timeout 10 --retry 5 -Os https://uploader.codecov.io/latest/linux/codecov
chmod +x codecov
./codecov -f py4dgeo/coverage.xml -F python
./codecov -f coverage2.xml -F cxx
address-sanitizer:
name: Address sanitizer run
runs-on: ubuntu-20.04
env:
ASAN_OPTIONS: "detect_stack_use_after_return=1:check_initialization_order=1:strict_init_order=1"
steps:
- uses: actions/checkout@v4
with:
submodules: 'recursive'
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: "3.9"
- name: Install Python development requirements
run: |
python -m pip install -r requirements-dev.txt
python -m pip install -v .
- name: Install py4dgeo test data
shell: bash
run: |
mkdir -p $GITHUB_WORKSPACE/tests/data
copy_py4dgeo_test_data $GITHUB_WORKSPACE/tests/data
- name: make build directory
run: cmake -E make_directory ${{runner.workspace}}/build
- name: configure cmake
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-fsanitize=address -fsanitize-address-use-after-scope -fno-omit-frame-pointer" -DCMAKE_EXE_LINKER_FLAGS="-fsanitize=address -fsanitize-address-use-after-scope -fno-omit-frame-pointer" -DBUILD_DOCS=OFF
- name: build
shell: bash
working-directory: ${{runner.workspace}}/build
run: cmake --build .
- name: run c++ tests
shell: bash
working-directory: ${{runner.workspace}}/build
run: ctest --rerun-failed --output-on-failure -C Debug
- name: run python tests
shell: bash
working-directory: ${{runner.workspace}}/py4dgeo
# for LD_PRELOAD see https://github.com/google/sanitizers/issues/934#issuecomment-649516500
run: |
mv ../build/_py4dgeo.*.so src/py4dgeo/.
echo "leak:/usr/bin/bash" > supp.txt
echo "leak:_PyObject_New" >> supp.txt
echo "leak:_PyObject_GC" >> supp.txt
echo "leak:_PyUnicodeWriter_Finish">> supp.txt
echo "leak:insert_to_emptydict" >> supp.txt
echo "leak:new_keys_object" >> supp.txt
echo "leak:PyArrayMethod_FromSpec_int" >> supp.txt
echo "leak:PyDict_Copy" >> supp.txt
echo "leak:PyUnicode_New" >> supp.txt
echo "leak:pyo3::types::function::PyCFunction::internal_new_from_pointers" >> supp.txt
echo "leak:pyo3::types::function::PyCFunction::internal_new::" >> supp.txt
# hack to prevent external libs from dlclosing libraries,
# which otherwise results in <module not found> LSAN leaks that cannot be suppressed
# https://github.com/google/sanitizers/issues/89#issuecomment-406316683
echo "#include <stdio.h>" > dlclose.c
echo "int dlclose(void *handle) { return 0; }" >> dlclose.c
clang -shared dlclose.c -o libdlclose.so
LSAN_OPTIONS=suppressions="$(pwd)/supp.txt" PYTHONPATH=src LD_PRELOAD="$(gcc -print-file-name=libasan.so) /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $(pwd)/libdlclose.so" PYTHONMALLOC=malloc pytest -s