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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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permissions:
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id-token: write
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environment:
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name: publishing
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url: https://pypi.org/p/mmtf-cppy
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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 }}'

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