Implement WsiAnnotations in C++

.clang-format

@@ -1,4 +1,6 @@
 ---
+BasedOnStyle: Google
+IndentWidth: 2
 Language: Cpp
 ColumnLimit: 120
 AccessModifierOffset: -4
@@ -69,7 +71,6 @@ IncludeCategories:
 IncludeIsMainRegex: '(Test)?$'
 IndentCaseLabels: false
 IndentPPDirectives: None
-IndentWidth: 4
 IndentWrappedFunctionNames: false
 JavaScriptQuotes: Leave
 JavaScriptWrapImports: true

.github/workflows/codecov.yml

@@ -15,7 +15,7 @@ jobs:
       run: |
         sudo apt update
         sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
-        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
+        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build libboost-all-dev libopencv-dev
     - name: Build and install OpenSlide
       run: |
         git clone https://github.com/openslide/openslide.git
@@ -57,7 +57,7 @@ jobs:
         echo "Current directory: $PWD"
         meson setup builddir
         meson compile -C builddir
-        meson install -C builddir
+        sudo meson install -C builddir
     - name: Run coverage
       run: |
         mv dlup _dlup # This is needed because otherwise it won't find the compiled libraries

.github/workflows/mypy.yml

@@ -13,7 +13,7 @@ jobs:
       run: |
         sudo apt update
         sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
-        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
+        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev libboost-all-dev libopencv-dev
     - name: Build and install OpenSlide
       run: |
         git clone https://github.com/openslide/openslide.git

.github/workflows/pylint.yml

@@ -13,7 +13,7 @@ jobs:
       run: |
         sudo apt update
         sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
-        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
+        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev libboost-all-dev libopencv-dev
     - name: Build and install OpenSlide
       run: |
         git clone https://github.com/openslide/openslide.git

.github/workflows/tox.yml

@@ -15,7 +15,7 @@ jobs:
       run: |
         sudo apt update
         sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
-        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
+        sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build libboost-all-dev libopencv-dev
     - name: Build and install OpenSlide
       run: |
         git clone https://github.com/openslide/openslide.git

.gitignore

@@ -2,8 +2,9 @@
 _background.c
 _background.cpp
 _background.html
-_background.cpython-*-darwin.so
+_background.cpython-*.so
 _libtiff_tiff_writer.cpython-*.so
+_geometry.cython-*.so
 
 # Output files
 *.tif

.spin/cmds.py

@@ -27,11 +27,28 @@ def test(verbose, tests):
     cmd = ["pytest"]
     if verbose:
         cmd.append("-v")
+    if coverage:
+        cmd.extend(["--cov=dlup --cov=tests --cov-report=html --cov-report=term"])
     if tests:
         cmd.extend(tests)
     subprocess.run(cmd, check=True)
 
 
+@cli.command()
+@click.option("-v", "--verbose", is_flag=True, help="Verbose output")
+@click.argument("tests", nargs=-1)
+def coverage(verbose, tests):
+    """🧪 Run tests and generate coverage report"""
+    cmd = ["pytest", "--cov=dlup", "--cov=tests", "--cov-report=html", "--cov-report=term"]
+    if verbose:
+        cmd.append("-v")
+    if tests:
+        cmd.extend(tests)
+    subprocess.run(cmd, check=True)
+    coverage_path = Path.cwd() / "htmlcov" / "index.html"
+    webbrowser.open(f"file://{coverage_path.resolve()}")
+
+
 @cli.command()
 def mypy():
     """🦆 Run mypy for type checking"""
@@ -133,16 +150,6 @@ def clean():
             path.unlink()
 
 
-@cli.command()
-def coverage():
-    """🧪 Run tests and generate coverage report"""
-    subprocess.run(["coverage", "run", "--source", "dlup", "-m", "pytest"], check=True)
-    subprocess.run(["coverage", "report", "-m"], check=True)
-    subprocess.run(["coverage", "html"], check=True)
-    coverage_path = Path.cwd() / "htmlcov" / "index.html"
-    webbrowser.open(f"file://{coverage_path.resolve()}")
-
-
 @cli.command()
 def release():
     """📦 Package and upload a release"""

dlup/_geometry.pyi

@@ -0,0 +1,66 @@
+from typing import Callable, overload
+
+from dlup._types import GenericNumber
+from dlup.geometry import Point as Point_
+from dlup.geometry import Polygon as Polygon_
+
+class Polygon:
+    @property
+    def fields(self) -> list[str]: ...
+    def get_exterior(self) -> list[tuple[float, float]]: ...
+    def get_interiors(self) -> list[list[tuple[float, float]]]: ...
+    def contains(self, other: Polygon_) -> bool: ...
+    def correct_orientation(self) -> None: ...
+    @property
+    def area(self) -> float: ...
+
+def set_polygon_factory(factory: Callable[[Polygon_], Polygon_]) -> None: ...
+
+class Point:
+    @property
+    def fields(self) -> list[str]: ...
+    def scale(self, scaling: float) -> None: ...
+    def get_coordinates(self) -> tuple[float, float]: ...
+    @property
+    def x(self) -> float: ...
+    @property
+    def y(self) -> float: ...
+
+def set_point_factory(factory: Callable[[Point_], Point_]) -> None: ...
+
+class AnnotationRegion:
+    @property
+    def polygons(self) -> list[Polygon_]: ...
+    @property
+    def points(self) -> list[Point_]: ...
+
+class GeometryCollection:
+    def add_polygon(self, polygon: Polygon) -> None: ...
+    def add_point(self, point: Point_) -> None: ...
+    @property
+    def polygons(self) -> list[Polygon_]: ...
+    @property
+    def points(self) -> list[Point_]: ...
+    def set_offset(self, offset: tuple[float, float]) -> None: ...
+    def rebuild_rtree(self) -> None: ...
+    def reindex_polygons(self, index_map: dict[str, int]) -> None: ...
+    @overload
+    def remove_point(self, index: int) -> None: ...
+    @overload
+    def remove_point(self, point: Point_) -> None: ...
+    @overload
+    def remove_polygon(self, index: int) -> None: ...
+    @overload
+    def remove_polygon(self, polygon: Polygon_) -> None: ...
+    def sort_polygons(self, key: Callable[[Polygon_], int | float | str | None], reverse: bool) -> None: ...
+    @property
+    def bounding_box(self) -> tuple[tuple[float, float], tuple[float, float]]: ...
+    def size(self) -> int: ...
+    def simplify(self, tolerance: float) -> None: ...
+    def scale(self, scaling: float) -> None: ...
+    def read_region(
+        self,
+        coordinates: tuple[GenericNumber, GenericNumber],
+        scaling: float,
+        size: tuple[GenericNumber, GenericNumber],
+    ) -> AnnotationRegion: ...