Metadata-Version: 2.4
Name: ndevio
Version: 0.4.0
Summary: Read, write, and manage images in napari
Project-URL: Bug Tracker, https://github.com/ndev-kit/ndevio/issues
Project-URL: Documentation, https://github.com/ndev-kit/ndevio#README.md
Project-URL: Source Code, https://github.com/ndev-kit/ndevio
Project-URL: User Support, https://github.com/ndev-kit/ndevio/issues
Author: Tim Monko
Author-email: timmonko@gmail.com
License: 
        Copyright (c) 2025, Tim Monko
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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License-File: LICENSE
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.11
Requires-Dist: bioio-base
Requires-Dist: bioio-imageio
Requires-Dist: bioio-ome-tiff>=1.2.0
Requires-Dist: bioio-ome-zarr>=3
Requires-Dist: bioio-tifffile
Requires-Dist: bioio>=2
Requires-Dist: napari-plugin-manager>=0.1.7
Requires-Dist: ndev-settings
Requires-Dist: xarray
Requires-Dist: zarr>=3.1.3
Provides-Extra: all
Requires-Dist: napari[all]; extra == 'all'
Description-Content-Type: text/markdown

# ndevio

[![License BSD-3](https://img.shields.io/pypi/l/ndevio.svg?color=green)](https://github.com/ndev-kit/ndevio/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/ndevio.svg?color=green)](https://pypi.org/project/ndevio)
[![Python Version](https://img.shields.io/pypi/pyversions/ndevio.svg?color=green)](https://python.org)
[![tests](https://github.com/ndev-kit/ndevio/workflows/tests/badge.svg)](https://github.com/ndev-kit/ndevio/actions)
[![codecov](https://codecov.io/gh/ndev-kit/ndevio/branch/main/graph/badge.svg)](https://codecov.io/gh/ndev-kit/ndevio)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/ndevio)](https://napari-hub.org/plugins/ndevio)
[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)

Read, write, and manage images in napari

----------------------------------

This [napari] plugin was generated with [copier] using the [napari-plugin-template].

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/napari-plugin-template#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

## Installation

You can install `ndevio` via [pip]:

```bash
pip install ndevio
```

If napari is not already installed, you can install `ndevio` with napari and Qt via:

```bash
pip install "ndevio[all]"
```

To install the latest development version:

```bash
pip install git+https://github.com/ndev-kit/ndevio.git
```

### Additional Image Format Support

**ndevio** uses [bioio](https://github.com/bioio-devs/bioio) for flexible image reading. Basic formats (TIFF, OME-TIFF, OME-Zarr, PNG, etc.) are supported out of the box via:

- `bioio-ome-tiff` - OME-TIFF files
- `bioio-ome-zarr` - OME-Zarr files
- `bioio-tifffile` - General TIFF files
- `bioio-imageio` - PNG, JPEG, and other common formats

If your image format is not supported by the default readers, then you will get a warning and (by default in napari) a widget to install the suggested reader.
If you know of your additional proprietary formats, install the appropriate bioio reader.

```bash
# CZI files (GPL-3 licensed)
pip install bioio-czi

# LIF files (GPL-3 licensed)
pip install bioio-lif

# Bio-Formats for many formats (behavior not guaranteed)
pip install bioio-bioformats
```

See the [bioio documentation](https://bioio-devs.github.io/bioio/) for the full list of available readers.

### Pixi Usage

You can use [Pixi](https://pixi.sh) for reproducible development environments:

```bash
git clone https://github.com/ndev-kit/ndevio.git
cd ndevio
pixi install -e dev
pixi run -e dev test
```

Or activate the environment and run commands directly:

```bash
pixi shell -e dev
pytest -v
```

### Development

For development, clone the repository and install with the dev dependency group:

```bash
git clone https://github.com/ndev-kit/ndevio.git
cd ndevio
pip install -e . --group dev
```

This includes pytest, pytest-cov, pytest-qt, tox-uv, napari, and pyqt6.

Run tests with:

```bash
pytest -v --cov=ndevio --cov-report=html
```

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [BSD-3] license,
"ndevio" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[file an issue]: https://github.com/ndev-kit/ndevio/issues

[napari]: https://github.com/napari/napari
[copier]: https://copier.readthedocs.io/en/stable/
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[napari-plugin-template]: https://github.com/napari/napari-plugin-template
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
