Update to use the latest C++ libraries via pybind11.

.github/workflows/build-docs.yml

@@ -2,28 +2,23 @@ name: Build documentation
 
 on:
   push:
-    branches:
-      - master
+    tags:
+      - "*"
 
 jobs:
-  test:
-    name: Build docs
+  build_docs:
+    name: Build docs 
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
           cache: 'pip'
 
-      - name: Set up ccache
-        uses: hendrikmuhs/[email protected]
-
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip setuptools
@@ -32,17 +27,16 @@ jobs:
           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}
 
-      # Note that doc building requires the inplace shared library.
       - name: Build docs
         run: |
-          CC="ccache gcc" python setup.py build_ext --inplace
+          touch src/singler/lib_singler.py
           sphinx-build --color -b html -d docs/doctrees docs docs/_build/html
           touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
         if: github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/tags/')
-        uses: JamesIves/github-pages-deploy-action@4.1.3
+        uses: JamesIves/github-pages-deploy-action@v4
         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
+          clean: true # Automatically remove deleted files from the deploy branch

.github/workflows/pypi-publish.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@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: x86_64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          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@v4
+        with:
+          name: cibw-wheels-ubuntu-x86_64
+          path: ./wheelhouse/*.whl
+
+  build_macosx_x86_64:
+    name: Build wheels for macosx x86_64
+    runs-on: macos-13
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - 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: ">=3.9"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=x86_64\""
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_SKIP: pp*
+          MACOSX_DEPLOYMENT_TARGET: 11.7
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-macos-x86_64
+          path: ./wheelhouse/*.whl
+
+  build_macosx_arm64:
+    name: Build wheels for macosx arm64
+    runs-on: macos-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Grab prebuilt dependencies
+        run: |
+            curl -L https://github.com/ArtifactDB/prebuilt-hdf5/releases/download/0.0.4-manual/macosx_arm64.tar.gz > bundle.tar.gz
+            tar -xvf bundle.tar.gz
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_ARCHS: arm64
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=$(pwd)/installed -DCMAKE_OSX_ARCHITECTURES=arm64\""
+          CIBW_BUILD_VERBOSITY: 3
+          MACOSX_DEPLOYMENT_TARGET: 13.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-maxos_arm64
+          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@v4
+#
+#      - 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" >> $env:GITHUB_ENV
+#        shell: powershell
+#
+#      - name: Build wheels
+#        uses: pypa/[email protected]
+#        env:
+#          CIBW_ARCHS: AMD64
+#          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
+#          CIBW_ENVIRONMENT: "MORE_CMAKE_OPTIONS=\"-DCMAKE_INSTALL_PREFIX=${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@v4
+        with:
+          submodules: true
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_linux_x86_64, build_macosx_x86_64, build_macosx_arm64, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -1,111 +1,44 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Test the library
 
 on:
   push:
     branches:
       - master
-    tags:
-      - "*"
   pull_request:
 
 jobs:
   test:
-    name: Running tests
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
+    name: Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
         with:
-          submodules: true
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Specify gypsum cache
+        run: |
+          LOCATION=$(pwd)/.gypsum_cache
+          mkdir -p ${LOCATION} # TODO: move to gypsum_client
+          echo "GYPSUM_CACHE_DIR=${LOCATION}" >> $GITHUB_ENV
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Cache gypsum assets
+        uses: actions/cache@v4
         with:
-          python-version: 3.9
-          cache: 'pip'
+          path: ${{ env.GYPSUM_CACHE_DIR }}
+          key: gypsum-cache
 
-      - 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}
+      - name: Get latest CMake
+        uses: lukka/get-cmake@latest
 
-      # 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, in a PR, we don't need the full clean test.
-      - 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
-
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-20.04, macos-11] # at some point get this to work on windows-2019
-
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS_MACOS: x86_64 arm64
-          CIBW_ARCHS_LINUX: x86_64 # remove this later so we build for all linux archs
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
-          CIBW_SKIP: pp*
-      - 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: [test, build_wheels, 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/')
-    # alternatively, to publish when a GitHub Release is created, use the following rule:
-    # if: github.event_name == 'release' && github.event.action == 'published'
-    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 }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 23.9.1
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.0.287
+  rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs