Switch to pybind11 (#47)

Moving from cython to pybind11 for implementing the bindings to rds2cpp. 
Update workflows, actions, documentation and tests.

.github/workflows/build-docs.yml

@@ -0,0 +1,43 @@
+name: Build documentation
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  test:
+    name: Build docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+          cache: 'pip'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          DEPENDENCIES=$(python -c 'from setuptools.config.setupcfg import read_configuration as c; a = c("setup.cfg"); print(" ".join(a["options"]["install_requires"][1:]))')
+          pip install ${DEPENDENCIES}
+          DOCDEPENDENCIES=$(python -c 'with open("docs/requirements.txt") as a: available = list(a); print(" ".join(map(lambda x : x.strip(), filter(lambda x : not x.startswith("#"), available))))')
+          pip install ${DOCDEPENDENCIES}
+
+      - name: Build docs
+        run: |
+          touch src/dolomite_base/lib_dolomite_base.py
+          sphinx-build --color -b html -d docs/doctrees docs docs/_build/html
+          touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/[email protected]
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch

.github/workflows/publish-pypi.yml

@@ -0,0 +1,146 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "*"
+
+jobs:
+  build_linux_x86_64:
+    name: Build wheels for linux x86_64
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: x86_64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/artifactdb/prebuilt-hdf5/manylinux_x86_64:0.0.4
+          CIBW_MUSLLINUX_X86_64_IMAGE: ghcr.io/artifactdb/prebuilt-hdf5/musllinux_x86_64:0.0.4
+          CIBW_SKIP: pp*
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_macosx_x86_64:
+    name: Build wheels for macosx x86_64
+    runs-on: macos-11
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Grab prebuilt dependencies
+        run: |
+            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4/macosx_x86_64.tar.gz > bundle.tar.gz
+            tar -xvf bundle.tar.gz
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: x86_64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=x86_64\""
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_SKIP: pp*
+          MACOSX_DEPLOYMENT_TARGET: 11.7
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_macosx_arm64:
+    name: Build wheels for macosx arm64
+    runs-on: macos-13
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Grab prebuilt dependencies
+        run: |
+            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4-manual/macosx_arm64.tar.gz > bundle.tar.gz
+            tar -xvf bundle.tar.gz
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: arm64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=arm64\""
+          CIBW_BUILD_VERBOSITY: 3
+          MACOSX_DEPLOYMENT_TARGET: 13.0
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+#  build_windows_x86_64:
+#    name: Build wheels for windows x86_64
+#    runs-on: windows-2019
+#    steps:
+#      - name: Check out repository
+#        uses: actions/checkout@v3
+#
+#      - name: Grab prebuilt dependencies
+#        run: |
+#            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4/windows_x86_64.tar.gz > bundle.tar.gz
+#            tar -xvf bundle.tar.gz
+#        shell: bash
+#
+#      - name: Store path
+#        run: |
+#            $wd = pwd
+#            echo "INSTALL_DIR=$wd\\installed" >> $env:GITHUB_ENV
+#        shell: powershell
+#
+#      - name: Build wheels
+#        uses: pypa/[email protected]
+#        env:
+#          CIBW_ARCHS: AMD64
+#          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
+#          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=${INSTALL_DIR}\" VERBOSE=1"
+#          CIBW_BEFORE_BUILD_WINDOWS: "pip install delvewheel"
+#          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: "delvewheel repair -w {dest_dir} {wheel}"
+#          CIBW_TEST_EXTRAS: "testing"
+#          CIBW_TEST_COMMAND: "pytest {package}/tests"
+#          CIBW_BUILD_VERBOSITY: 3
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_linux_x86_64, build_macosx_x86_64, build_macosx_arm64, build_sdist]
+    runs-on: ubuntu-latest
+    # upload to PyPI on every tag starting with 'v'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          # unpacks default artifact into dist/
+          # if `name: artifact` is omitted, the action will create extra parent dir
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/run-tests.yml

@@ -0,0 +1,51 @@
+name: Run unit tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          DEPENDENCIES=$(python -c 'from setuptools.config.setupcfg import read_configuration as c; a = c("setup.cfg"); print(" ".join(a["options"]["install_requires"][1:] + a["options"]["extras_require"]["testing"][1:]))')
+          pip install ${DEPENDENCIES} pybind11
+
+      # We do proper tests if we're on the master branch, or if we're creating a new release.
+      - name: Test with tox
+        if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
+        run: |
+          pip install tox
+          tox
+
+      # Otherwise we do some cached builds and tests for faster merging of PRs.
+      - name: Set up ccache
+        if: github.ref != 'refs/heads/master' && !startsWith(github.ref, 'refs/tags')
+        uses: hendrikmuhs/[email protected]
+
+      - name: Quickly build and test
+        if: github.ref != 'refs/heads/master' && !startsWith(github.ref, 'refs/tags')
+        run: |
+          CC="ccache gcc" python setup.py install
+          pytest