Update repository URLs (again) (#199)

* Update URLs and name: PEtabGUI -> PEtabGUI
* Fix screenshot URL

Author: dweindl

README.md

@@ -1,23 +1,23 @@
 [![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.
 
 ## Installation
 
 ### 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
@@ -29,15 +29,15 @@ 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
 
 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**

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 <https://github.com/PEtab-dev/PEtabGUI/issues/new/choose>`__.
+`Open a new issue <https://github.com/PEtab-dev/PEtab-GUI/issues/new/choose>`__.
 
 When filing an issue, provide as much detail as possible,
 including steps to reproduce the issue, expected behavior, and any relevant logs or screenshots.

docs/source/index.rst

@@ -23,8 +23,8 @@ PEtab GUI - A graphical user interface for PEtab
 Quick Links
 -----------
 
-* `GitHub Repository <https://github.com/PEtab-dev/PEtabGUI>`_
-* `Issue Tracker <https://github.com/PEtab-dev/PEtabGUI/issues>`_
+* `GitHub Repository <https://github.com/PEtab-dev/PEtab-GUI>`_
+* `Issue Tracker <https://github.com/PEtab-dev/PEtab-GUI/issues>`_
 * `PEtab Documentation <https://petab.readthedocs.io/en/latest/>`_
 
 Overview
@@ -54,5 +54,5 @@ To get started with PEtab GUI, check out the :doc:`installation instructions <re
    :maxdepth: 1
    :caption: Development
 
-   GitHub Repository <https://github.com/PEtab-dev/PEtabGUI>
+   GitHub Repository <https://github.com/PEtab-dev/PEtab-GUI>
    contributing

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:
 

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": {

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 <b>Help</b> in the menu,"
             " enter the Help Mode (click question mark in toolbar) or visit "
-            'the <a href="https://petab-gui.readthedocs.io/en/latest/" '
+            f'the <a href="{DOCS_URL}" '
             'style="color:blue;" target="_blank">documentation</a>.',
             color="green",
         )