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

.github/workflows/cpp.yml

@@ -0,0 +1,62 @@
+---
+name: cpp
+'on':
+  workflow_dispatch: null
+  pull_request: null
+  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: 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: ./ci/build_and_run_tests.sh

.github/workflows/emscripten.yml

@@ -0,0 +1,48 @@
+---
+name: WASM
+'on':
+  workflow_dispatch: null
+  push:
+    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
+      - 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

@@ -0,0 +1,39 @@
+---
+name: Pip
+'on':
+  workflow_dispatch: null
+  pull_request: null
+  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: Build and install
+        run: pip install --verbose .
+      - name: Test
+        run: python src/python/tests/tests.py

.github/workflows/wheels.yml

@@ -0,0 +1,79 @@
+---
+name: Wheels
+'on':
+  workflow_dispatch: null
+  pull_request: null
+  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
+      - uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS_MACOS: universal2
+          CIBW_ARCHS_WINDOWS: auto ARM64
+          CMAKE_GENERATOR: '${{ env.CMAKE_GENERATOR }}'
+      - name: Verify clean directory
+        run: git diff --exit-code
+        shell: bash
+      - uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+  upload_all:
+    name: Upload if release
+    needs:
+      - build_wheels
+      - build_sdist
+    permissions:
+      id-token: write
+    environment:
+      name: publishing
+      url: https://pypi.org/p/mmtf-cppy
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: '${{ secrets.pypi_password }}'