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Revert "simplify #374 (determine_cutoff_radius() in dencalc.hpp)" #1389

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Revert "simplify #374 (determine_cutoff_radius() in dencalc.hpp)"

Revert "simplify #374 (determine_cutoff_radius() in dencalc.hpp)" #1389

Workflow file for this run

.github/workflows/ci.yml at 4387f5b
name: CI
on: [push, pull_request]
jobs:
macos15:
name: "macOS 15"
runs-on: macos-15
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 sphinx-inline-tabs
# 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-macos15
path: |
./gemmi-*.whl
retention-days: 14
macos13:
name: "macOS 13 (w/o python)"
runs-on: macos-13
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 -DCMAKE_CXX_STANDARD=14
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-macos13
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-inline-tabs
sphinx-build -M doctest . _build -n -E
ubuntu2404:
name: "Ubuntu 24.04 arm64"
runs-on: ubuntu-24.04-arm
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 sphinx-inline-tabs
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 DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
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 sphinx-inline-tabs
- 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
ubuntu2204_clang8:
name: "Ubuntu 22.04 with Clang 13"
runs-on: ubuntu-22.04
if: "!contains(github.event.head_commit.message, '[skip ci]')"
env:
CC: clang-13
CXX: clang++-13
SKBUILD_CMAKE_ARGS: "-DEXTRA_WARNINGS=ON;-DSTANDALONE_PYTHON_MODULE=OFF"
SKBUILD_BUILD_TARGETS: "all;check"
steps:
- name: apt-get
run: |
sudo DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
sudo apt-get update
sudo apt-get install python3-pip python3-numpy
- name: install nanobind
run: |
git clone --recursive --depth=1 https://github.com/wjakob/nanobind.git
- uses: actions/checkout@v4
- name: build from sdist
run: |
$CXX --version
echo >constraints.txt <<EOF
scikit-build-core==0.10.7
EOF
python3 -m pip install build scikit-build-core==0.10.7 nanobind
python3 -m build --sdist
python3 -m pip install -v dist/gemmi-*.tar.gz -c constraints.txt --no-build-isolation
python3 -m unittest discover -v -s tests/
- name: run doctest
run: |
python3 -m pip install -U sphinx sphinx-inline-tabs
cd docs
sphinx-build -M doctest . _build -n -E
ubuntu2004:
name: "Ubuntu 20.04"
runs-on: ubuntu-latest
container: ubuntu:20.04
if: "!contains(github.event.head_commit.message, '[skip ci]')"
steps:
- uses: actions/checkout@v4
- name: apt-get
run: |
export DEBIAN_FRONTEND=noninteractive
ln -fs /usr/share/zoneinfo/UTC /etc/localtime
apt-get update
apt-get install -y libz-dev python3-pip g++ gfortran python3-numpy valgrind cmake
- name: install nanobind
run: |
python3 -m pip install nanobind typing_extensions sphinx sphinx-inline-tabs
- 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
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/
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 sphinx-inline-tabs
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