From 67cef0049f9ab3c8aa7ee79243757c6891c4ff1a Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 24 Sep 2025 10:13:02 +0200 Subject: [PATCH 1/3] README: add examples, pipx --- README.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/README.md b/README.md index 1865342..9a579c7 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,13 @@ 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: @@ -46,6 +53,17 @@ 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 good starting point. + ## Features The PEtabGUI provides a Python-based graphical user interface that simplifies From 6d46a0e77a226688d9129354ea2b25330a942748 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 24 Sep 2025 10:23:31 +0200 Subject: [PATCH 2/3] pypi badge --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9a579c7..31008b1 100644 --- a/README.md +++ b/README.md @@ -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 From 69c8d4de9be3bcf122a6a96cdbe69aac20699b93 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Wed, 24 Sep 2025 10:39:24 +0200 Subject: [PATCH 3/3] Update README.md Co-authored-by: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 31008b1..a182d35 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ Download and unpack the [archive](https://github.com/Benchmarking-Initiative/Ben then open one of the YAML files inside `Benchmark-Models/*/` using PEtabGUI. `Benchmark-Models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml` -should serve as good starting point. +should serve as a good starting point. ## Features