From 86d1089be3a464287cc7aafba81646c5662869a9 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Sep 2025 12:26:43 +0200 Subject: [PATCH] Update repository URLs (again) * Update URLs and name: PEtabGUI -> PEtabGUI * Fix screenshot URL --- README.md | 22 +++++++++---------- docs/source/contributing.rst | 2 +- docs/source/index.rst | 6 ++--- docs/source/tutorial.rst | 2 +- src/petab_gui/C.py | 6 +++-- .../controllers/logger_controller.py | 6 +++-- 6 files changed, 24 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index c882cb9..56eb1e6 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ [![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) -# PEtabGUI +# PEtab-GUI -PEtabGUI provides a graphical user interface to inspect and edit parameter +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. @@ -11,13 +11,13 @@ estimation problems encoded in the ### From PyPI -To install PEtabGUI from [PyPI](https://pypi.org/project/PEtab-GUI/), run: +To install PEtab-GUI from [PyPI](https://pypi.org/project/PEtab-GUI/), run: ```bash pip install petab_gui ``` -or, to install PEtabGUI in a dedicated virtual environment using +or, to install PEtab-GUI in a dedicated virtual environment using [pipx](https://github.com/pypa/pipx) (to be installed separately), run: ```bash @@ -29,7 +29,7 @@ pipx install petab_gui To install the latest development version from GitHub, run: ```bash -pip install git+https://github.com/PEtab-dev/PEtabGUI/ +pip install git+https://github.com/PEtab-dev/PEtab-GUI/ ``` ### From a local copy @@ -37,7 +37,7 @@ pip install git+https://github.com/PEtab-dev/PEtabGUI/ 1. Clone the repository: ```bash - git clone https://github.com/PEtab-dev/PEtabGUI.git + git clone https://github.com/PEtab-dev/PEtab-GUI.git ``` 2. Install the package from the root of the working tree: @@ -48,14 +48,14 @@ pip install git+https://github.com/PEtab-dev/PEtabGUI/ ## Usage -After installation, launch PEtabGUI from the command line using the +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, PEtabGUI will look something like this: -![PEtabGUI Screenshot](https://raw.githubusercontent.com/PEtab-dev/PEtabGUI/screenshot/docs/source/_static/Application_Screenshot.png) +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 @@ -64,13 +64,13 @@ A set of real-world PEtab problems is available in the 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. +PEtab-GUI. `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 +The PEtab-GUI provides a Python-based graphical user interface that simplifies the creation, editing, and validation of PEtab parameter estimation problems. - **Unified Environment** diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst index 06106f2..4aa6362 100644 --- a/docs/source/contributing.rst +++ b/docs/source/contributing.rst @@ -42,7 +42,7 @@ Filing an Issue ---------------- If you encounter any bugs or have feature requests, please file an issue on GitHub. -`Open a new issue `__. +`Open a new issue `__. When filing an issue, provide as much detail as possible, including steps to reproduce the issue, expected behavior, and any relevant logs or screenshots. diff --git a/docs/source/index.rst b/docs/source/index.rst index f2ee706..2bd8b48 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -23,8 +23,8 @@ PEtab GUI - A graphical user interface for PEtab Quick Links ----------- -* `GitHub Repository `_ -* `Issue Tracker `_ +* `GitHub Repository `_ +* `Issue Tracker `_ * `PEtab Documentation `_ Overview @@ -54,5 +54,5 @@ To get started with PEtab GUI, check out the :doc:`installation instructions + GitHub Repository contributing diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst index b8cc796..7044566 100644 --- a/docs/source/tutorial.rst +++ b/docs/source/tutorial.rst @@ -32,7 +32,7 @@ Alternatively, you can install it from the GitHub repository by following these .. code-block:: bash - git clone https://github.com/PEtab-dev/PEtabGUI.git + git clone https://github.com/PEtab-dev/PEtab-GUI.git 2. Install using pip: diff --git a/src/petab_gui/C.py b/src/petab_gui/C.py index 466ef1d..c27860f 100644 --- a/src/petab_gui/C.py +++ b/src/petab_gui/C.py @@ -3,9 +3,11 @@ import numpy as np #: Application name -APP_NAME = "PEtabGUI" +APP_NAME = "PEtab-GUI" #: Base URL of the repository -REPO_URL = "https://github.com/PEtab-dev/PEtabGUI" +REPO_URL = "https://github.com/PEtab-dev/PEtab-GUI" +#: Base URL of the documentation +DOCS_URL = "https://petab-gui.readthedocs.io/en/latest/" COLUMNS = { "measurement": { diff --git a/src/petab_gui/controllers/logger_controller.py b/src/petab_gui/controllers/logger_controller.py index 28758c8..f5c1001 100644 --- a/src/petab_gui/controllers/logger_controller.py +++ b/src/petab_gui/controllers/logger_controller.py @@ -2,6 +2,8 @@ from datetime import datetime +from ..C import APP_NAME, DOCS_URL + class LoggerController: """Mainly responsible for handling the logger widget.""" @@ -16,11 +18,11 @@ def __init__(self, views): """ self.views = views self.logger_level = 1 - self.log_message("Welcome to PEtabGUI!", color="green") + self.log_message(f"Welcome to {APP_NAME}!", color="green") self.log_message( "If you need help, click Help in the menu," " enter the Help Mode (click question mark in toolbar) or visit " - 'the documentation.', color="green", )