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README: add examples, pipx #185

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@@ -1,6 +1,7 @@
[![PyPI - Version](https://badge.fury.io/py/PEtab-GUI.svg)](pypi.org/project/PEtab-GUI/)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15355753.svg)](https://doi.org/10.5281/zenodo.15355753)
# PEtabGUI

# PEtabGUI

PEtabGUI provides a graphical user interface to inspect and edit parameter
estimation problems encoded in the
Expand All @@ -16,6 +17,13 @@ To install PEtabGUI from [PyPI](https://pypi.org/project/PEtab-GUI/), run:
pip install petab_gui
```

or, to install PEtabGUI in a dedicated virtual environment using
[pipx](https://github.com/pypa/pipx) (to be installed separately), run:

```bash
pipx install petab_gui
```

### From GitHub

To install the latest development version from GitHub, run:
Expand Down Expand Up @@ -46,6 +54,17 @@ After installation, launch PEtabGUI from the command line using the
Optionally, you can provide the path to an existing PEtab YAML file
as an argument.

### Examples

A set of real-world PEtab problems is available in the
[PEtab benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).

Download and unpack the [archive](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/archive/refs/heads/master.zip),
then open one of the YAML files inside `Benchmark-Models/*/` using
PEtabGUI.
`Benchmark-Models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml`
should serve as a good starting point.

## Features

The PEtabGUI provides a Python-based graphical user interface that simplifies
Expand Down