Revert "Implement WsiAnnotations in C++ (#252)"

This reverts commit a497eab.

.clang-format

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

.github/workflows/codecov.yml

@@ -8,22 +8,16 @@ on:
 jobs:
  build:
  runs-on: ubuntu-latest
+ env:
+ CODECOV_CI: true
  steps:
  - name: Install build dependencies
  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 libboost-all-dev libopencv-dev
- - name: Install Rust for pyhaloxml
- run: |
- curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
- echo "Rust and Cargo installed in:"
- echo $HOME/.cargo/bin
- ls $HOME/.cargo/bin
- export PATH="$HOME/.cargo/bin:$PATH"
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
  - name: Build and install OpenSlide
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/openslide/openslide.git
  cd openslide
  meson setup builddir
@@ -32,7 +26,6 @@ jobs:
  cd ..
  - name: Build and install libvips
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/libvips/libvips.git
  cd libvips
  meson setup builddir --prefix=/usr/local
@@ -41,24 +34,35 @@ jobs:
  sudo ldconfig
  cd ..
  - uses: actions/checkout@v4
- - name: Set up Python 3.11
+ - name: Set up Python 3.10
  uses: actions/setup-python@v5
  with:
- python-version: "3.11"
+ python-version: "3.10"
+ - name: Clean up any existing installations
+ run: |
+ sudo rm -rf /usr/local/lib/python3.10/site-packages/dlup*
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/dlup*
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/_dlup_editable_loader.py
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/easy-install.pth
+ sudo rm -rf dlup/build
+ sudo rm -rf /tmp/*
  - name: Install environment
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  python -m pip install --upgrade pip
  python -m pip install ninja meson meson-python>=0.15.0 numpy==1.26.4 Cython>=0.29 spin pybind11
- python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1 spin
- python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock tox
- spin build
- cp build/dlup/_*.so dlup/
- cp build/src/_*.so dlup/
- python -m pip install .
+ python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1
+ python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock
+ echo "Python executable: $(which python)"
+ echo "Python version: $(python --version)"
+ echo "Current directory: $PWD"
+ meson setup builddir
+ meson compile -C builddir
+ meson install -C builddir
  - name: Run coverage
  run: |
- coverage run -m pytest || true
+ mv dlup _dlup # This is needed because otherwise it won't find the compiled libraries
+ export PYTHONPATH=$(python -c "import site; print(site.getsitepackages()[0])")
+ coverage run -m pytest
  - name: Upload Coverage to Codecov
  uses: codecov/codecov-action@v4
  with:

.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 libboost-all-dev libopencv-dev
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
  - name: Build and install OpenSlide
  run: |
  git clone https:/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 libboost-all-dev libopencv-dev
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
  - name: Build and install OpenSlide
  run: |
  git clone https:/openslide/openslide.git

.github/workflows/tox.yml

@@ -8,22 +8,16 @@ on:
 jobs:
  build:
  runs-on: ubuntu-latest
+ env:
+ CODECOV_CI: true
  steps:
  - name: Install build dependencies
  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 libboost-all-dev libopencv-dev
- - name: Install Rust for pyhaloxml
- run: |
- curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
- echo "Rust and Cargo installed in:"
- echo $HOME/.cargo/bin
- ls $HOME/.cargo/bin
- export PATH="$HOME/.cargo/bin:$PATH"
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
  - name: Build and install OpenSlide
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/openslide/openslide.git
  cd openslide
  meson setup builddir
@@ -32,7 +26,6 @@ jobs:
  cd ..
  - name: Build and install libvips
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/libvips/libvips.git
  cd libvips
  meson setup builddir --prefix=/usr/local
@@ -41,23 +34,28 @@ jobs:
  sudo ldconfig
  cd ..
  - uses: actions/checkout@v4
- - name: Set up Python 3.11
+ - name: Set up Python 3.10
  uses: actions/setup-python@v5
  with:
- python-version: "3.11"
+ python-version: "3.10"
+ - name: Clean up any existing installations
+ run: |
+ sudo rm -rf /usr/local/lib/python3.10/site-packages/dlup*
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/dlup*
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/_dlup_editable_loader.py
+ sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/easy-install.pth
+ sudo rm -rf dlup/build
+ sudo rm -rf /tmp/*
  - name: Install environment
  run: |
- export PATH="$HOME/.cargo/bin:$PATH"
  python -m pip install --upgrade pip
  python -m pip install ninja meson meson-python>=0.15.0 numpy==1.26.4 Cython>=0.29 spin pybind11
- python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1 spin
- python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock tox
- spin build
- cp build/dlup/_*.so dlup/
- cp build/src/_*.so dlup/
- python -m pip install .
+ python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1
+ python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock
+ echo "Python executable: $(which python)"
+ echo "Python version: $(python --version)"
+ echo "Current directory: $PWD"
  - name: Run tox
  run: |
- export GITHUB_ACTIONS=1
- export PATH="$HOME/.cargo/bin:$PATH"
- tox || true
+ python -m pip install tox
+ tox

.gitignore

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

.spin/cmds.py

@@ -1,10 +1,8 @@
-import os
 import subprocess
 import webbrowser
 from pathlib import Path
 
 import click
-from spin.cmds import meson
 
 
 @click.group()
@@ -14,32 +12,11 @@ def cli():
 
 
 @cli.command()
-@click.option("-j", "--jobs", help="Number of parallel tasks to launch", type=int)
-@click.option("--clean", is_flag=True, help="Clean build directory before build")
-@click.option("-v", "--verbose", is_flag=True, help="Print all build output, even installation")
-@click.argument("meson_args", nargs=-1)
-@click.pass_context
-def build(ctx, meson_args, jobs=None, clean=False, verbose=False, quiet=False, *args, **kwargs):
+def build():
  """🔧 Build the project"""
- build_dir = Path("build")
- build_dir.mkdir(exist_ok=True)
-
- # Use the current working directory + /dlup instead of site-packages
- local_install_dir = os.path.join(os.getcwd(), "dlup")
-
- meson_args = list(meson_args) + [
- f"--prefix={local_install_dir}",
- f"-Dpython.platlibdir={local_install_dir}",
- f"-Dpython.purelibdir={local_install_dir}",
- ]
-
- ctx.params["meson_args"] = meson_args
- ctx.params["jobs"] = jobs
- ctx.params["clean"] = clean
- ctx.params["verbose"] = verbose
- ctx.params["quiet"] = quiet
-
- ctx.forward(meson.build)
+ subprocess.run(["meson", "setup", "builddir", "--prefix", str(Path.cwd())], check=True)
+ subprocess.run(["meson", "compile", "-C", "builddir"], check=True)
+ subprocess.run(["meson", "install", "-C", "builddir"], check=True)
 
 
 @cli.command()
@@ -48,28 +25,11 @@ def build(ctx, meson_args, jobs=None, clean=False, verbose=False, quiet=False, *
 def test(verbose, tests):
  """🔍 Run 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()
@@ -173,6 +133,16 @@ 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"""
@@ -193,25 +163,5 @@ def dist():
  subprocess.run(["ls", "-l", "dist"], check=True)
 
 
-@cli.command()
-def precommit():
- """🛠️ Run pre-commit hooks"""
- subprocess.run(["pre-commit", "run", "--all-files"], check=True)
-
-
-@cli.command()
-def format():
- """🛠️ Run clang-format and black"""
- # Run clang-format
- subprocess.run(
- "find src -name '*.cpp' -o -name '*.h' -o -name '*.hpp' | xargs clang-format -i",
- shell=True,
- check=True,
- )
-
- # Run black
- subprocess.run(["black", "."], check=True)
-
-
 if __name__ == "__main__":
  cli()

README.md

@@ -45,15 +45,3 @@ or the following plain bibliography:
 ```
 Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus E. (2024). DLUP: Deep Learning Utilities for Pathology (Version 0.7.0) [Computer software]. https:/NKI-AI/dlup
 ```
-
-## Contributors
-In alphabetic order:
-
-## Contributors
-In alphabetic order:
-
-## Contributors
-In alphabetic order:
-
-| [<img src="https:/AjeyPaiK.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Ajey Pai Karkala</b></sub>](https:/AjeyPaiK) | [<img src="https:/EricMarcus-ai.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Eric Marcus</b></sub>](https:/EricMarcus-ai) | [<img src="https:/jonasteuwen.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Jonas Teuwen</b></sub>](https:/jonasteuwen) | [<img src="https:/lromor.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Leonardo Romor</b></sub>](https:/lromor) | [<img src="https:/rharkes.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Rolf Harkes</b></sub>](https:/rharkes) | [<img src="https:/YoniSchirris.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Yoni Schirris</b></sub>](https:/YoniSchirris) |
-| :---: | :---: | :---: | :---: | :---: | :---: |