Metadata-Version: 2.4
Name: PEtab-GUI
Version: 0.1.4
Summary: Graphical user interface for the PEtab format
Author-email: Paul Jonas Jost <jost.pauljonas@gmail.com>, "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Maintainer-email: Paul Jonas Jost <jost.pauljonas@gmail.com>, "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Project-URL: Repository, https://github.com/PEtab-dev/PEtabGUI
Project-URL: Issues, https://github.com/PEtab-dev/PEtabGUI/issues
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pyside6
Requires-Dist: pandas
Requires-Dist: antimony
Requires-Dist: python-libsbml
Requires-Dist: matplotlib
Requires-Dist: petab[combine]>=0.6.0
Requires-Dist: qtawesome
Requires-Dist: copasi-basico
Requires-Dist: copasi-petab-importer
Requires-Dist: pyobjc; sys_platform == "darwin"
Provides-Extra: doc
Requires-Dist: sphinx; extra == "doc"
Requires-Dist: sphinx-rtd-theme; extra == "doc"
Requires-Dist: myst-parser; extra == "doc"
Requires-Dist: sphinx_copybutton; extra == "doc"
Requires-Dist: sphinx-design; extra == "doc"
Dynamic: license-file

[![PyPI - Version](https://badge.fury.io/py/PEtab-GUI.svg)](https://pypi.org/project/PEtab-GUI/)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15355753.svg)](https://doi.org/10.5281/zenodo.15355753)

# PEtab-GUI

PEtab-GUI provides a graphical user interface to inspect and edit parameter
estimation problems encoded in the
[PEtab](https://petab.readthedocs.io/en/latest/#) format.

## Installation

### From PyPI

To install PEtab-GUI from [PyPI](https://pypi.org/project/PEtab-GUI/), run:

```bash
pip install petab_gui
```

or, to install PEtab-GUI 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:

```bash
pip install git+https://github.com/PEtab-dev/PEtab-GUI/
```

### From a local copy

1. Clone the repository:

   ```bash
   git clone https://github.com/PEtab-dev/PEtab-GUI.git
   ```

2. Install the package from the root of the working tree:

   ```bash
   pip install .
   ```

## Usage

After installation, launch PEtab-GUI from the command line using the
`petab_gui` command.

Optionally, you can provide the path to an existing PEtab YAML file
as an argument.

After loading a PEtab problem, PEtab-GUI will look something like this:
![PEtab-GUI Screenshot](https://raw.githubusercontent.com/PEtab-dev/PEtab-GUI/main/docs/source/_static/Application_Screenshot.png)

### 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
PEtab-GUI.
`Benchmark-Models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml`
should serve as a good starting point.

## Features

The PEtab-GUI provides a Python-based graphical user interface that simplifies
the creation, editing, and validation of PEtab parameter estimation problems.

- **Unified Environment**
  - Integrates all PEtab components (SBML models, conditions, observables,
    measurements, parameters, and visualization files).
  - Supports drag-and-drop import of YAML or individual component files.
  - Automatically resolves mismatches and converts matrix-format experimental data
    into valid PEtab format.
- **Interactive and Intuitive Editing**
  - Dockable, resizable, and movable table widgets for each PEtab file.
  - Context-aware editing with combo-boxes, drop-downs, and multi-cell editing.
  - Automatic generation of missing observables/conditions with customizable defaults.
  - Real-time validation and plausibility checks with PEtab linting tools.
  - SBML view in both XML and human-readable Antimony syntax.
- **Visualization and Simulation**
  - Interactive plots linking measurement data with model simulations.
  - Bidirectional highlighting between plots and tables.
  - Built-in simulation via [BasiCO](https://github.com/copasi/basico)
    with one-click parameter testing.
  - Intelligent defaults for visualization with optional user customization.
  - Ability to disable plotting for large models to maintain responsiveness.
- **Archiving and Export**
  - Export individual tables, the SBML model, or complete PEtab problems.
  - Save as directory structures or
    [COMBINE archives](https://combinearchive.org) for reproducibility
