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.github/workflows/cpp.yml

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+name: "cpp"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build and test cpp
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-22.04
+            cc: gcc
+            cxx: g++
+          - os: ubuntu-22.04
+            cc: gcc
+            cxx: g++
+            env_list: EMSCRIPTEN=ON
+          - os: ubuntu-22.04
+            cc: clang
+            cxx: clang++
+          - os: ubuntu-22.04
+            cc: gcc
+            cxx: g++
+            cmake_args: "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS='-march=native'"
+          - os: macos-latest
+            cc: clang
+            cxx: clang++
+          - os: windows-latest
+            cc: ''
+            cxx: ''
+    runs-on: ${{ matrix.os }}
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+      CMAKE_ARGS: ${{ matrix.cmake_args }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+        fetch-depth: 0
+
+    # - name: install mingw & deps
+    #   uses: msys2/setup-msys2@v2
+    #   with:
+    #     update: true
+    #     install: >-
+    #       git
+    #       make
+    #     pacboy: >-
+    #       toolchain:p
+    #       cmake:p
+    #       ninja:p
+    #   if: matrix.os == 'windows-latest'
+
+    - name: Set environment list variables
+      run: |
+        env_vars="${{ matrix.env_list }}"
+        for var in $env_vars; do
+          echo "$var" >> $GITHUB_ENV
+        done
+      if: matrix.os != 'windows-latest'
+
+    - name: Setup cmake
+      uses: jwlawson/[email protected]
+      with:
+        cmake-version: '3.16.x'
+
+    - uses: seanmiddleditch/gha-setup-ninja@master
+
+    - name: build and test
+      run: |
+        mkdir build && cd build
+        cmake $CMAKE_ARGS -G Ninja -Dmmtf_build_examples=ON -DBUILD_TESTS=ON -DCMAKE_BUILD_TYPE=debug ..
+        ninja
+        ./tests/mmtf_tests
+        ./tests/multi_cpp_test
+        ./examples/mmtf_demo ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf
+        ./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf
+        ./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf json
+        ./examples/traverse ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf print
+        ./examples/print_as_pdb ../submodules/mmtf_spec/test-suite/mmtf/173D.mmtf

.github/workflows/emscripten.yml

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

.github/workflows/pip.yml

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+name: "Pip"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build with Pip
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python-version: ["3.8", "3.11", "3.12", "pypy-3.8"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # - name: Setup cmake
+    #   uses: jwlawson/[email protected]
+    #   with:
+    #     cmake-version: '3.16.x'
+
+      # - uses: seanmiddleditch/gha-setup-ninja@master
+
+    - name: Build and install
+      run: pip install --verbose .
+
+    - name: Test
+      run: python src/python/tests/tests.py
+

.github/workflows/wheels.yml

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