Merge branch 'develop' into screenshot

# Conflicts:
#	README.md

Author: PaulJonasJost

.readthedocs.yaml

@@ -27,5 +27,3 @@ build:
       # Avoid setuptools-scm dirty Git index issues
       - git reset --hard HEAD
       - git clean -fdx
-      # Enforce fail_on_shallow for setuptools-scm
-      - export SETUPTOOLS_SCM_OVERRIDES_FOR_${READTHEDOCS_PROJECT//-/_}='{scm.git.pre_parse="fail_on_shallow"}'

README.md

@@ -1,6 +1,7 @@
+[![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
 
+# PEtabGUI
 
 PEtabGUI provides a graphical user interface to inspect and edit parameter
 estimation problems encoded in the
@@ -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:
@@ -50,6 +58,17 @@ When launching with a problem, PEtabGUI will look like this (up to the position
 widgets):
 ![PEtabGUI Screenshot](https://raw.githubusercontent.com/PaulJonasJost/PEtab_GUI/screenshot/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
+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

docs/source/conf.py

@@ -4,10 +4,6 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 from importlib.metadata import version as get_version
 
-rst_prolog = """
-.. |petab_doc_url| replace:: https://petab.readthedocs.io/en/latest/index.html
-"""
-
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
@@ -33,6 +29,10 @@
 templates_path = ["_templates"]
 exclude_patterns = []
 
+rst_prolog = f"""
+.. |petab_doc_url| replace:: https://petab.readthedocs.io/en/latest/index.html
+.. |release| replace:: {release}
+"""
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output

docs/source/index.rst

@@ -18,7 +18,7 @@ PEtab GUI - A graphical user interface for PEtab
 **PEtab GUI** is a user-friendly graphical interface for creating and managing parameter estimation problems using the `PEtab <https://petab.readthedocs.io/en/latest/>`_ format.
 
 .. note::
-   Current version: 0.1.3
+   Current version: |release|
 
 Quick Links
 -----------

pyproject.toml

@@ -21,7 +21,8 @@ dependencies = [
     "petab[combine]>=0.6.0",
     "qtawesome",
     "copasi-basico",
-    "copasi-petab-importer"
+    "copasi-petab-importer",
+    "pyobjc; sys_platform == 'darwin'"
 ]
 license-files = ["LICENSE"]
 

src/petab_gui/C.py

@@ -2,6 +2,11 @@
 
 import numpy as np
 
+#: Application name
+APP_NAME = "PEtabGUI"
+#: Base URL of the repository
+REPO_URL = "https://github.com/PaulJonasJost/PEtab_GUI"
+
 COLUMNS = {
     "measurement": {
         "observableId": {"type": np.object_, "optional": False},

src/petab_gui/app.py

@@ -9,6 +9,7 @@
 from PySide6.QtGui import QFileOpenEvent, QIcon
 from PySide6.QtWidgets import QApplication
 
+from .C import APP_NAME
 from .controllers import MainController
 from .models import PEtabModel
 from .views import MainWindow
@@ -59,6 +60,7 @@ def __init__(self, file: str | Path = None):
         """
         super().__init__(sys.argv)
 
+        self.setApplicationName(APP_NAME)
         self.setWindowIcon(get_icon())
         self.model = PEtabModel()
         self.view = MainWindow()
@@ -120,7 +122,7 @@ def main():
     except PackageNotFoundError:
         pkg_version = "unknown"
 
-    parser = argparse.ArgumentParser(description="PEtabGUI: A PEtab editor")
+    parser = argparse.ArgumentParser(description=f"{APP_NAME}: A PEtab editor")
     parser.add_argument(
         "--version",
         action="version",
@@ -132,6 +134,13 @@ def main():
     )
     args = parser.parse_args()
 
+    if sys.platform == "darwin":
+        from Foundation import NSBundle  # type: type: ignore[import]
+
+        bundle = NSBundle.mainBundle()
+        info = bundle.localizedInfoDictionary() or bundle.infoDictionary()
+        info["CFBundleName"] = APP_NAME
+
     app = PEtabGuiApp(args.petab_yaml)
     sys.exit(app.exec())
 

src/petab_gui/controllers/mother_controller.py

@@ -4,6 +4,7 @@
 import tempfile
 import zipfile
 from functools import partial
+from importlib.metadata import version
 from io import BytesIO
 from pathlib import Path
 
@@ -32,6 +33,7 @@
     QWidget,
 )
 
+from ..C import APP_NAME, REPO_URL
 from ..models import PEtabModel, SbmlViewerModel
 from ..settings_manager import SettingsDialog, settings_manager
 from ..utils import (
@@ -164,7 +166,7 @@ def window_title(self):
         """Return the window title based on the model."""
         if isinstance(self.model.sbml, SbmlViewerModel):
             return self.model.sbml.model_id
-        return "PEtab Editor"
+        return APP_NAME
 
     def setup_context_menu(self):
         """Sets up context menus for the tables."""
@@ -438,6 +440,12 @@ def setup_actions(self):
         self._whats_this_filter = _WhatsThisClickHelp(actions["whats_this"])
         actions["whats_this"].toggled.connect(self._toggle_whats_this_mode)
 
+        # About action
+        actions["about"] = QAction(
+            qta.icon("mdi6.information"), "&About", self.view
+        )
+        actions["about"].triggered.connect(self.about)
+
         # connect actions
         actions["reset_view"] = QAction(
             qta.icon("mdi6.view-grid-plus"), "Reset View", self.view
@@ -1158,6 +1166,24 @@ def _show_help_welcome(self):
         if dont.isChecked():
             settings.setValue("help_mode/welcome_disabled", True)
 
+    def about(self):
+        """Show an about dialog."""
+        config_file = settings_manager.settings.fileName()
+        QMessageBox.about(
+            self.view,
+            f"About {APP_NAME}",
+            f"<b>{APP_NAME}</b><br>"
+            f"Version: {version('petab-gui')}<br>"
+            f"PEtab version: {version('petab')}<br><br>"
+            f"{APP_NAME} is a tool for editing and visualizing PEtab "
+            f"problems.<br><br>"
+            f"Visit the GitHub repository at "
+            f"<a href='{REPO_URL}'>{REPO_URL}</a> "
+            "for more information.<br><br>"
+            f"<small>Settings are stored in "
+            f"<a href='file://{config_file}'>{config_file}</a></small>",
+        )
+
     def get_current_problem(self):
         """Get the current PEtab problem from the model."""
         return self.model.current_petab_problem

src/petab_gui/views/main_view.py

@@ -12,6 +12,7 @@
     QWidget,
 )
 
+from ..C import APP_NAME
 from ..models.tooltips import (
     COND_TABLE_TOOLTIP,
     DATA_PLOT_TOOLTIP,
@@ -39,7 +40,7 @@ def __init__(self):
 
         self.allow_close = False
 
-        self.setWindowTitle("PEtabGUI")
+        self.setWindowTitle(APP_NAME)
         self.setGeometry(100, 100, 1200, 800)
 
         # Logger: used in both tabs

src/petab_gui/views/task_bar.py

@@ -137,6 +137,7 @@ def __init__(self, parent, actions):
         # Add actions to the menu for re-adding tables
         self.menu.addAction(actions["open_documentation"])
         self.menu.addAction(actions["whats_this"])
+        self.menu.addAction(actions["about"])
 
 
 class TaskBar: