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Add Python pybind11 bindings + Upgrade ci/cd
This PR adds python bindings as well as updates the backend build process of the mmtf-cpp library significantly. These improvements are mainly from a convenience perspective and include: - Removing all build-based submodules - Moving to cmake fetchcontent build - Simplify CMakeLists with better linking procedures - Upgrade msgpack-c - Upgrade catch2 - Move to github actions for ci/cd - Use cibuildwheel for wheel cd Pybind11 library: The pybind11 library utilizes the c++ code of mmtf-cpp in order to build an extremely fast cpp layer underneath the python interface. You have to keep in mind that moving between c++ and python is slow, but this is still much faster than the previously existing python library. see this example: time to load a single mmtf file 1000x cpp bare 0.29s this library 0.44s python og 4.34s
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‎.github/workflows/cpp.yml‎

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---
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name: cpp
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'on':
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workflow_dispatch: null
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pull_request: null
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push:
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branches:
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- master
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concurrency:
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group: '${{ github.workflow }}-${{ github.ref }}'
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cancel-in-progress: true
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jobs:
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build:
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name: Build and test cpp
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strategy:
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fail-fast: false
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matrix:
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include:
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- os: ubuntu-22.04
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cc: gcc
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cxx: g++
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- os: ubuntu-22.04
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cc: gcc
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cxx: g++
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env_list: EMSCRIPTEN=ON
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- os: ubuntu-22.04
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cc: clang
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cxx: clang++
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- os: ubuntu-22.04
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cc: gcc
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cxx: g++
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cmake_args: "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS='-march=native'"
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- os: macos-latest
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cc: clang
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cxx: clang++
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- os: windows-latest
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cc: ''
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cxx: ''
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runs-on: '${{ matrix.os }}'
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env:
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CC: '${{ matrix.cc }}'
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CXX: '${{ matrix.cxx }}'
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CMAKE_ARGS: '${{ matrix.cmake_args }}'
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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fetch-depth: 0
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- name: Set environment list variables
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run: |
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env_vars="${{ matrix.env_list }}"
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for var in $env_vars; do
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echo "$var" >> $GITHUB_ENV
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done
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if: matrix.os != 'windows-latest'
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- name: Setup cmake
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uses: jwlawson/actions-setup-cmake@v1.13
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with:
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cmake-version: 3.16.x
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- uses: seanmiddleditch/gha-setup-ninja@master
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- name: build and test
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run: ./ci/build_and_run_tests.sh

‎.github/workflows/emscripten.yml‎

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---
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name: WASM
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'on':
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workflow_dispatch: null
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push:
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branches:
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- master
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concurrency:
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group: '${{ github.workflow }}-${{ github.ref }}'
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cancel-in-progress: true
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jobs:
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build-wasm-emscripten:
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name: Pyodide
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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- name: Install pyodide-build
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run: pip install pyodide-build==0.23.4
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- name: Compute emsdk version
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id: compute-emsdk-version
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run: |
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pyodide xbuildenv install --download
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EMSCRIPTEN_VERSION=$(pyodide config get emscripten_version)
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echo "emsdk-version=$EMSCRIPTEN_VERSION" >> $GITHUB_OUTPUT
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- uses: mymindstorm/setup-emsdk@v12
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with:
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version: '${{ steps.compute-emsdk-version.outputs.emsdk-version }}'
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actions-cache-folder: emsdk-cache
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- name: Build
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run: CFLAGS=-fexceptions LDFLAGS=-fexceptions pyodide build
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.whl
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- uses: actions/setup-node@v4
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with:
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node-version: 18
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- name: Set up Pyodide virtual environment
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run: |
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pyodide venv .venv-pyodide
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.venv-pyodide/bin/pip install $(echo -n dist/*.whl)
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- name: Test
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run: .venv-pyodide/bin/python -m unittest src/python/tests/tests.py

‎.github/workflows/pip.yml‎

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---
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name: Pip
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'on':
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workflow_dispatch: null
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pull_request: null
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push:
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branches:
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- master
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concurrency:
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group: '${{ github.workflow }}-${{ github.ref }}'
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cancel-in-progress: true
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jobs:
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build:
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name: Build with Pip
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runs-on: '${{ matrix.platform }}'
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strategy:
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fail-fast: false
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matrix:
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platform:
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- windows-latest
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- macos-latest
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- ubuntu-latest
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python-version:
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- '3.8'
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- '3.11'
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- '3.12'
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- pypy-3.8
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: '${{ matrix.python-version }}'
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- name: Build and install
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run: pip install --verbose .
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- name: Test
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run: python src/python/tests/tests.py

‎.github/workflows/wheels.yml‎

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---
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name: Wheels
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'on':
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workflow_dispatch: null
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pull_request: null
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push:
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branches:
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- master
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release:
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types:
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- published
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env:
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FORCE_COLOR: 3
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concurrency:
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group: '${{ github.workflow }}-${{ github.ref }}'
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cancel-in-progress: true
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jobs:
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build_sdist:
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name: Build SDist
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Build SDist
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run: pipx run build --sdist
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- name: Check metadata
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run: pipx run twine check dist/*
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- uses: actions/upload-artifact@v3
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with:
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path: dist/*.tar.gz
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build_wheels:
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name: 'Wheels on ${{ matrix.os }}'
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runs-on: '${{ matrix.os }}'
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strategy:
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fail-fast: false
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matrix:
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os:
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- ubuntu-latest
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- macos-latest
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- windows-latest
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steps:
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- uses: actions/checkout@v4
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with:
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submodules: true
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- uses: pypa/cibuildwheel@v2.16.2
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env:
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CIBW_ARCHS_MACOS: universal2
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CIBW_ARCHS_WINDOWS: auto ARM64
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CMAKE_GENERATOR: '${{ env.CMAKE_GENERATOR }}'
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- name: Verify clean directory
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run: git diff --exit-code
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shell: bash
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- uses: actions/upload-artifact@v3
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with:
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path: wheelhouse/*.whl
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upload_all:
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name: Upload if release
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needs:
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- build_wheels
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- build_sdist
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runs-on: ubuntu-latest
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/setup-python@v4
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with:
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python-version: 3.x
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- uses: actions/download-artifact@v3
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with:
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name: artifact
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: '${{ secrets.pypi_password }}'

‎.gitignore‎

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docs/html/*
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examples/out/*
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examples/out_json_ref/*
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# python eggs
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src/python/*.egg-info
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**/__pycache__
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**/*.pyc
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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**/_version.py
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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