Metadata-Version: 2.1
Name: paquo
Version: 0.6.0
Summary: library for interacting with QuPath
Home-page: https://github.com/bayer-science-for-a-better-life/paquo
Download-URL: https://github.com/bayer-science-for-a-better-life/paquo
Author: Santiago Villalba, Andreas Poehlmann
Author-email: santiago.villalba@bayer.com, andreas.poehlmann@bayer.com
License: GPLv3
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Java
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: ome
Provides-Extra: dev
Provides-Extra: docs
License-File: LICENSE

# PAQUO: PAthological QUpath Obsession

[![PyPI Version](https://img.shields.io/pypi/v/paquo)](https://pypi.org/project/paquo/)
[![Read the Docs](https://img.shields.io/readthedocs/paquo)](https://paquo.readthedocs.io)
[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/bayer-science-for-a-better-life/paquo/paquo%20ci?label=tests)](https://github.com/bayer-science-for-a-better-life/paquo/actions)
[![Codecov](https://img.shields.io/codecov/c/github/bayer-science-for-a-better-life/paquo)](https://codecov.io/gh/bayer-science-for-a-better-life/paquo)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/paquo)](https://github.com/bayer-science-for-a-better-life/paquo)
[![GitHub issues](https://img.shields.io/github/issues/bayer-science-for-a-better-life/paquo)](https://github.com/bayer-science-for-a-better-life/paquo/issues)

Welcome to `paquo` :wave:, a library for interacting with [QuPath](https://qupath.github.io/)
from [Python](https://www.python.org/).

`paquo`'s goal is to provide a pythonic interface to important features of
QuPath, and to make creating and working with QuPath projects intuitive for
Python programmers.

We strive to make your lives as easy as possible: If `paquo` is not pythonic,
unintuitive, slow or if its documentation is confusing, it's a bug in
`paquo`. Feel free to report any issues or feature requests in the issue
tracker!

Development
[happens on github](https://github.com/bayer-science-for-a-better-life/paquo)
:octocat:

## Documentation

You can find `paquo`'s documentation at
[paquo.readthedocs.io](https://paquo.readthedocs.io) :heart:

## Installation

paquo's stable releases can be installed via `pip`:
```bash
pip install paquo
```

or via `conda`:
```bash
conda install -c conda-forge paquo
```


## Getting QuPath

After installing, paquo requires a QuPath installation to run. To get QuPath follow the
[installation instructions](https://qupath.readthedocs.io/en/stable/docs/intro/installation.html).
If you choose the default installation paths paquo should autodetect your QuPath.

Or you can run the following command to download a specific version of QuPath
to a location on your machine. Follow the printed instructions to configure
paquo to use that version. Currently, paquo supports every version of QuPath from
`0.2.0` to the most recent. _(We even support older `0.2.0-mX` versions but no guarantees)._

```shell
> paquo get_qupath --install-path "/some/path/on/your/machine" 0.3.2
# downloading: https://github.com/qupath/qupath/releases/download/v0.3.2/QuPath-0.3.2-Linux.tar.xz
# progress ................... OK
# extracting: [...]/QuPath-0.3.2-Linux.tar.xz
# available at: /some/path/on/your/machine/QuPath-0.3.2
#
# use via environment variable:
#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.3.2
#
# use via .paquo.toml config file:
#   qupath_dir="/some/path/on/your/machine/QuPath-0.3.2"
/some/path/on/your/machine/QuPath-0.3.2
```


## Development Installation

1. Install conda and git
2. Clone paquo `git clone https://github.com/bayer-science-for-a-better-life/paquo.git`
3. Run `conda env create -f environment.devenv.yaml`
4. Activate the environment `conda activate paquo`

Note that in this environment `paquo` is already installed in development mode,
so go ahead and hack.


## Contributing Guidelines

- Please follow [pep-8 conventions](https://www.python.org/dev/peps/pep-0008/) but:
  - We allow 120 character long lines (try anyway to keep them short)
- Please use [numpy docstrings](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard).
- When contributing code, please try to use Pull Requests.
- tests go hand in hand with modules on ```tests``` packages at the same level. We use ```pytest```.

You can setup your IDE to help you adhering to these guidelines.
<br>
_([Santi](https://github.com/sdvillal) is happy to help you setting up pycharm in 5 minutes)_


## Acknowledgements

Build with love by Andreas Poehlmann and Santi Villalba from the _Machine
Learning Research_ group at Bayer. In collaboration with the _Pathology Lab 2_
and the _Mechanistic and Toxicologic Pathology_ group.

`paquo`: copyright 2020-2022 Bayer AG, licensed under [GPL-3.0](https://github.com/bayer-science-for-a-better-life/paquo/blob/master/LICENSE)
