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10 changes: 10 additions & 0 deletions README.md
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# bioimage-cpp

[![Documentation](https://img.shields.io/badge/docs-pdoc-blue)](https://computational-cell-analytics.github.io/bioimage-cpp/)
[![Build Status](https://github.com/computational-cell-analytics/bioimage-cpp/actions/workflows/tests.yml/badge.svg)](https://github.com/computational-cell-analytics/bioimage-cpp/actions/workflows/tests.yml)
[![PyPI](https://img.shields.io/pypi/v/bioimage-cpp)](https://pypi.org/project/bioimage-cpp/)
[![conda-forge](https://img.shields.io/conda/vn/conda-forge/bioimage-cpp)](https://anaconda.org/conda-forge/bioimage-cpp)

Image processing and segmentation functionality in C++ with light-weight python bindings through nanobind and minimal dependencies to enable distribution via pip.

The `bioimage_cpp` python library can be installed via pip:
```bash
pip install bioimage-cpp
```

Or via conda-forge:
```bash
conda install -c conda-forge bioimage-cpp
```

Please refer to [the documentation](https://computational-cell-analytics.github.io/bioimage-cpp/) for details.
22 changes: 19 additions & 3 deletions src/bioimage_cpp/__init__.py
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pip install bioimage-cpp
```

Or via conda-forge:
```bash
conda install -c conda-forge bioimage-cpp
```

Additional dependencies for tests / data downloads can be installed via `pip install bioimage-cpp[test]` / `pip install bioimage-cpp[data]` respectively.

We will make it available on conda-forge as soon as possible.
You can also install this library from source. The build requires C++20 (GCC >= 10 or Clang >= 13).

You can also install this library from source as follows:
```
If your system already has a C++20-capable compiler, clone and build directly:
```bash
git clone https://github.com/computational-cell-analytics/bioimage-cpp
cd bioimage-cpp
pip install -e .
```

On systems with an older compiler (e.g. many HPC clusters ship GCC 8), install a modern one from conda-forge alongside the build dependencies, and point `CC`/`CXX` at it:
```bash
conda install gcc_linux-64 gxx_linux-64 scikit-build-core nanobind -c conda-forge -y
export CC=x86_64-conda-linux-gnu-gcc
export CXX=x86_64-conda-linux-gnu-g++
pip install --no-build-isolation -e .
```

The `--no-build-isolation` flag reuses the `scikit-build-core` and `nanobind` already installed in your environment.
Re-run the same command after any C++ source change to rebuild.

## Functionality

This library provides the following functionality:
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