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 +1,74 @@
+---
+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: '${{ env.CMAKE_GENERATOR }}'
+      - name: Verify clean directory
+        run: git diff --exit-code
+        shell: bash
+      - uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse/*.whl
+  upload_all:
+    name: Upload if release
+    needs:
+      - build_wheels
+      - build_sdist
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: '${{ secrets.pypi_password }}'

.gitignore

@@ -39,3 +39,172 @@ build/*
 docs/html/*
 examples/out/*
 examples/out_json_ref/*
+
+# python eggs
+src/python/*.egg-info
+**/__pycache__
+**/*.pyc
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+**/_version.py
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+