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gemmi-align: option -v with --target/--query prints alignment vertically #933

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gemmi-align: option -v with --target/--query prints alignment vertically

gemmi-align: option -v with --target/--query prints alignment vertically #933

Workflow file for this run

.github/workflows/ci.yml at 937bdb0
name: CI
on: [push, pull_request]
jobs:
macos12:
name: "macOS 12"
runs-on: macos-12
if: "!contains(github.event.head_commit.message, '[skip ci]')"
env:
SKBUILD_CMAKE_ARGS: "-DEXTRA_WARNINGS=ON"
SKBUILD_CMAKE_TARGETS: "all;check"
steps:
- uses: actions/checkout@v3
- name: Build wheel and install
run: |
python3 -m pip install wheel
python3 -m pip wheel -v .
python3 -m pip install gemmi-*.whl
- name: Python Tests
run: |
python3 -m unittest discover -v -s tests/
python3 -m pip install sphinx
cd docs
sphinx-build -M doctest . _build -n -E
- uses: actions/upload-artifact@v3
with:
name: gemmi-macos12
path: |
${{runner.workspace}}/gemmi-*.whl
retention-days: 14
macos11:
name: "macOS 11 (w/o python)"
runs-on: macos-11
if: "!contains(github.event.head_commit.message, '[skip ci]')"
steps:
- uses: actions/checkout@v3
- 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=ON
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@v3
with:
name: gemmi-macos11
path: |
${{runner.workspace}}/build/gemmi
${{runner.workspace}}/build/libgemmi*
retention-days: 14
windows2022:
name: "Windows 2022"
runs-on: windows-2022
if: "!contains(github.event.head_commit.message, '[skip ci]')"
steps:
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: build and test
run: |
python -m pip install -v .
python -m pip install numpy
python -m unittest discover -v -s tests/
- name: run doctest
working-directory: ./docs
run: |
python -m pip install sphinx
sphinx-build -M doctest . _build -n -E
ubuntu2204:
name: "Ubuntu 22.04"
runs-on: ubuntu-22.04
if: "!contains(github.event.head_commit.message, '[skip ci]')"
steps:
- uses: actions/checkout@v3
- name: apt-get
run: |
sudo apt-get update
sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy
- name: install pybind11
run: |
git clone --depth=1 https://github.com/pybind/pybind11.git
#cd pybind11
#cmake . -Wno-dev -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYBIND11_TEST=OFF
#make
#sudo make install
- name: build and test
run: |
g++ --version
cmake --version
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=MinSizeRel -DUSE_FORTRAN=1 -DEXTRA_WARNINGS=1 -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3 -DBUILD_SHARED_LIBS=ON -DCMAKE_CXX_VISIBILITY_PRESET=hidden
make -j2
make -j2 check
sudo make install
python3 -m unittest discover -v -s ../tests/
strip --strip-unneeded ./gemmi ./gemmi.cpython*.so
- name: run doctest
run: |
sudo python3 -m pip install -U sphinx
export PYTHONPATH=$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@v3
- name: apt-get
run: |
sudo apt-get update
sudo apt-get install libz-dev python3-pip g++ gfortran python3-numpy valgrind
- name: install pybind11
run: |
python3 -m pip install pybind11
- name: build and test
run: |
g++ --version
cmake --version
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Debug -DUSE_PYTHON=1 -DPython_EXECUTABLE=python3
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: |
sudo pip3 install -U sphinx
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_clang6:
name: "Ubuntu 20.04 with Clang 6.0"
runs-on: ubuntu-20.04
if: "!contains(github.event.head_commit.message, '[skip ci]')"
env:
CC: clang-6.0
CXX: clang++-6.0
SKBUILD_CMAKE_ARGS: "-DCMAKE_CXX_STANDARD=11;-DEXTRA_WARNINGS=ON"
SKBUILD_CMAKE_TARGETS: "all;check"
steps:
- uses: actions/checkout@v3
- run: sudo apt-get install clang-6.0 libz-dev python3-pip python3-numpy
- name: install pybind11
run: |
sudo /usr/bin/python3 -m pip install "pybind11[global]" 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
centos:
runs-on: ubuntu-latest
name: "CentOS 7"
container: centos:7
if: "!contains(github.event.head_commit.message, '[skip ci]')"
steps:
- uses: actions/checkout@v3
- name: yum
run: |
yum update -y && yum install -y epel-release
yum install -y gcc-c++ cmake3 make git python3-devel
pip3 install -U numpy
g++ --version
python3 --version
cmake3 --version
type python3
- name: install pybind11
run: |
git clone --branch stable --depth=1 https://github.com/pybind/pybind11.git
cd pybind11
cmake3 . -Wno-dev -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPYBIND11_TEST=OFF
make
make install
- name: build and test
run: |
pwd
cmake3 . -DUSE_PYTHON=1 -DPython_EXECUTABLE=/usr/bin/python3
make -j2
make -j2 check
make install
python3 -m unittest discover -v -s ./tests/
strip --strip-unneeded ./gemmi ./gemmi.cpython*.so
- name: run doctest
run: |
pip3 install -U sphinx
cd docs
PYTHONPATH=.. sphinx-build -M doctest . _build -n -E
- uses: actions/upload-artifact@v3
with:
name: gemmi-linux
path: |
./gemmi
./gemmi.cpython*.so
retention-days: 14