improve hydrogen placement #1185
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| macos14: | |
| name: "macOS 14" | |
| runs-on: macos-14 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| env: | |
| SKBUILD_CMAKE_ARGS: "-DEXTRA_WARNINGS=ON;-DFETCH_ZLIB_NG=ON" | |
| SKBUILD_BUILD_TARGETS: "all;check" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build wheel and install | |
| run: | | |
| python3 -m venv pyenv | |
| source pyenv/bin/activate | |
| python3 -m pip install wheel | |
| python3 -m pip wheel -v . | |
| python3 -m pip install gemmi-*.whl | |
| - name: Python Tests | |
| run: | | |
| source pyenv/bin/activate | |
| python3 -m pip install sphinx | |
| # run tests twice: without and with numpy | |
| python3 -m unittest discover -s tests/ | |
| (cd docs && sphinx-build -M doctest . _build -n -E) | |
| python3 -m pip install numpy | |
| python3 -m unittest discover -v -s tests/ | |
| (cd docs && sphinx-build -M doctest . _build -n -E) | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: gemmi-macos14 | |
| path: | | |
| ./gemmi-*.whl | |
| retention-days: 14 | |
| macos12: | |
| name: "macOS 12 (w/o python)" | |
| runs-on: macos-12 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: mkdir build | |
| run: cmake -E make_directory ${{runner.workspace}}/build | |
| - name: CMake Build | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: | | |
| cmake --version | |
| cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=MinSizeRel -DBUILD_SHARED_LIBS=OFF | |
| cmake --build . -j3 | |
| cmake --build . --target check -j3 | |
| - name: Install | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: sudo cmake --install . | |
| - name: Test | |
| run: | | |
| ctest --output-on-failure | |
| python3 tests/test_prog.py | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: gemmi-macos12 | |
| path: | | |
| ${{runner.workspace}}/build/gemmi | |
| ${{runner.workspace}}/build/libgemmi* | |
| retention-days: 14 | |
| windows2022: | |
| name: "Windows 2022" | |
| runs-on: windows-2022 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| env: | |
| SKBUILD_CMAKE_ARGS: "-DFETCH_ZLIB_NG=ON" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| allow-prereleases: true | |
| - name: build and test | |
| run: | | |
| python -m pip install -v . | |
| python -m pip install numpy | |
| python -m unittest discover -v -s tests/ | |
| - name: run doctest | |
| working-directory: ./docs | |
| run: | | |
| python -m pip install sphinx | |
| sphinx-build -M doctest . _build -n -E | |
| ubuntu2404: | |
| name: "Ubuntu 24.04" | |
| runs-on: ubuntu-24.04 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: apt-get | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install python3-full g++ gfortran | |
| - name: build and test | |
| run: | | |
| g++ --version | |
| python3 -m venv pyenv | |
| source pyenv/bin/activate | |
| export SKBUILD_CMAKE_ARGS='-DFETCH_ZLIB_NG=ON;-DCMAKE_BUILD_TYPE=None' | |
| python3 -m pip install -v . | |
| python3 -m pip install numpy | |
| python3 -m unittest discover -v -s tests/ | |
| - name: run doctest | |
| run: | | |
| source pyenv/bin/activate | |
| python3 -m pip install -U sphinx | |
| cd docs | |
| sphinx-build -M doctest . _build -n -E | |
| ubuntu2204: | |
| name: "Ubuntu 22.04" | |
| runs-on: ubuntu-22.04 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: apt-get | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy | |
| sudo python3 -m pip install -U typing_extensions sphinx | |
| - name: install nanobind | |
| run: | | |
| git clone --recursive --depth=1 https://github.com/wjakob/nanobind.git | |
| - name: build and test | |
| run: | | |
| g++ --version | |
| cmake --version | |
| mkdir build | |
| cd build | |
| cmake .. -DCMAKE_BUILD_TYPE=MinSizeRel -DUSE_FORTRAN=1 -DEXTRA_WARNINGS=1 -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3 -DBUILD_SHARED_LIBS=ON -DCMAKE_CXX_VISIBILITY_PRESET=hidden | |
| make -j2 | |
| make -j2 check | |
| sudo make install | |
| python3 -m unittest discover -v -s ../tests/ | |
| strip --strip-unneeded ./gemmi ./py/gemmi/gemmi_ext.cpython*.so | |
| - name: run doctest | |
| run: | | |
| export PYTHONPATH=$PWD/build | |
| cd docs | |
| sphinx-build -M doctest . _build -n -E | |
| ubuntu2004: | |
| name: "Ubuntu 20.04" | |
| runs-on: ubuntu-20.04 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: apt-get | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy valgrind | |
| - name: install nanobind | |
| run: | | |
| python3 -m pip install nanobind typing_extensions sphinx | |
| - name: build and test | |
| run: | | |
| g++ --version | |
| cmake --version | |
| mkdir build | |
| cd build | |
| cmake .. -DCMAKE_BUILD_TYPE=Debug -DUSE_PYTHON=1 -DPython_EXECUTABLE=python3 -DBUILD_SHARED_LIBS=OFF | |
| cmake --build . --config Debug -j2 | |
| cmake --build . --config Debug --target check -j2 | |
| sudo cmake --install . --config Debug | |
| cd .. | |
| python3 -m unittest discover -v -s tests/ | |
| - name: run doctest | |
| run: | | |
| cd docs | |
| sphinx-build -M doctest . _build -n -E | |
| - name: run tests under valgrind | |
| run: PYTHONMALLOC=malloc valgrind python3 -m unittest discover -v -s tests/ | |
| ubuntu2004_clang8: | |
| name: "Ubuntu 20.04 with Clang 8" | |
| runs-on: ubuntu-20.04 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| env: | |
| CC: clang-8 | |
| CXX: clang++-8 | |
| SKBUILD_CMAKE_ARGS: "-DEXTRA_WARNINGS=ON;-DSTANDALONE_PYTHON_MODULE=OFF" | |
| SKBUILD_BUILD_TARGETS: "all;check" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - run: sudo apt-get install clang-8 libz-dev python3-pip python3-numpy | |
| - name: install nanobind | |
| run: | | |
| sudo /usr/bin/python3 -m pip install nanobind build | |
| - name: build and test | |
| run: | | |
| $CXX --version | |
| python3 -m build --sdist | |
| python3 -m pip install -v dist/gemmi-*.tar.gz | |
| python3 -m unittest discover -v -s tests/ | |
| - name: run doctest | |
| run: | | |
| python3 -m pip install -U sphinx | |
| cd docs | |
| sphinx-build -M doctest . _build -n -E | |
| almalinux: | |
| runs-on: ubuntu-latest | |
| name: "AlmaLinux 8" | |
| container: almalinux:8 | |
| if: "!contains(github.event.head_commit.message, '[skip ci]')" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: yum | |
| run: | | |
| dnf update -y | |
| dnf install -y gcc-c++ cmake make git python38-devel python38-pip | |
| python3.8 -m pip install -U numpy typing_extensions sphinx | |
| g++ --version | |
| python3.8 --version | |
| cmake --version | |
| type python3.8 | |
| - name: install nanobind | |
| run: | | |
| git clone --recursive --depth=1 https://github.com/wjakob/nanobind.git | |
| cd nanobind | |
| cmake . -Wno-dev -DPYTHON_EXECUTABLE=/usr/bin/python3.8 -DNB_TEST=OFF | |
| make | |
| make install | |
| - name: build and test | |
| run: | | |
| pwd | |
| cmake . -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3.8 -DFETCH_ZLIB_NG=ON | |
| make -j2 | |
| make -j2 check | |
| make install | |
| python3.8 -m unittest discover -v -s ./tests/ | |
| strip --strip-unneeded ./gemmi ./py/gemmi/gemmi_ext.cpython*.so | |
| - name: run doctest | |
| run: | | |
| cd docs | |
| PYTHONPATH=.. sphinx-build -M doctest . _build -n -E | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: gemmi-linux | |
| path: | | |
| ./gemmi | |
| ./libgemmi_cpp.so | |
| ./py | |
| retention-days: 14 |