autofix

Author: dweindl

.zenodo.json

@@ -20,4 +20,4 @@
     "Biological Modeling",
     "Parameter Estimation"
   ]
-}
+}

MANIFEST.in

@@ -1,3 +1,3 @@
 include  example/*.csv
 include  example/*.tsv
-include  example/*.xml
+include  example/*.xml

README.md

@@ -2,7 +2,7 @@
 # PEtabGUI
 
 
-This is a graphical user interface to create parameter estimation problems. It is 
+This is a graphical user interface to create parameter estimation problems. It is
 based on the [PEtab](https://petab.readthedocs.io/en/latest/#) format.
 
 ## Installation
@@ -32,32 +32,32 @@ To start the PEtab GUI, you can run the following command line:
 ```bash
 petab_gui $PATH_TO_YOUR_MODEL
 ```
-where `$PATH_TO_YOUR_MODEL` is an optional argument with a file path of your 
-yaml-model file in case you want to work on an existing model. You can also leave this 
+where `$PATH_TO_YOUR_MODEL` is an optional argument with a file path of your
+yaml-model file in case you want to work on an existing model. You can also leave this
 argument out to start from scratch.
 
 ## Features
 
-The PEtabGUI is a Pythin based graphical user interface that simplifies the creation, 
+The PEtabGUI is a Pythin based graphical user interface that simplifies the creation,
 editing, and validation of PEtab parameter estimation problems.
 - **Unified Environment**
-  - Integrates all PEtab components (SBML/PySB 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 
+  - Integrates all PEtab components (SBML/PySB 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. 
+  - 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 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. 
+  - Export individual tables, the SBML model, or complete PEtab problems.
   - Save as directory structures or COMBINE archives for reproducibility

docs/source/conf.py

@@ -10,30 +10,29 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'PEtab GUI'
-copyright = '2025, Paul Jonas Jost, Frank T. Bergmann'
-author = 'Paul Jonas Jost, Frank T. Bergmann'
-release = '0.1.3'
+project = "PEtab GUI"
+copyright = "2025, Paul Jonas Jost, Frank T. Bergmann"
+author = "Paul Jonas Jost, Frank T. Bergmann"
+release = "0.1.3"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    'sphinx.ext.napoleon',      # For Google/Numpy style docstrings
-    'sphinx.ext.viewcode',      # Add links to highlighted source code
-    'sphinx.ext.githubpages',   # For publishing on GitHub Pages
-    'sphinx.ext.todo',          # Support todo items
-    'sphinx.ext.mathjax',       # For LaTeX math rendering
-    'myst_parser',              # For Markdown support
-    'sphinx_copybutton',        # To allow copying code snippets
-    'sphinx_design',            # For better design elements
+    "sphinx.ext.napoleon",  # For Google/Numpy style docstrings
+    "sphinx.ext.viewcode",  # Add links to highlighted source code
+    "sphinx.ext.githubpages",  # For publishing on GitHub Pages
+    "sphinx.ext.todo",  # Support todo items
+    "sphinx.ext.mathjax",  # For LaTeX math rendering
+    "myst_parser",  # For Markdown support
+    "sphinx_copybutton",  # To allow copying code snippets
+    "sphinx_design",  # For better design elements
 ]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
 exclude_patterns = []
 
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 

example/data_matrix.csv

@@ -1,4 +1,4 @@
 Time,obsA,obsB,obsC
 3, 1, 2, 3
 5, 4, 5, 6
-7, 7, 8, 9
+7, 7, 8, 9

example/dose_response.csv

@@ -1,4 +1,4 @@
 pApB,obsA,obsB,obsC
 3, 1, 2, 3
 5, 4, 5, 6
-7, 7, 8, 9
+7, 7, 8, 9

example/meas.tsv

@@ -46,4 +46,4 @@ rSTAT5A_rel		model1_data1	41.0627332148332	100.0		sd_rSTAT5A_rel	model1_data1_rS
 rSTAT5A_rel		model1_data1	39.2358300289377	120.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
 rSTAT5A_rel		model1_data1	36.6194605442418	160.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
 rSTAT5A_rel		model1_data1	34.8937144010561	200.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
-rSTAT5A_rel		model1_data1	32.2110771608676	240.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel
+rSTAT5A_rel		model1_data1	32.2110771608676	240.0		sd_rSTAT5A_rel	model1_data1_rSTAT5A_rel

example/problem.yaml

@@ -8,4 +8,4 @@ problems:
   observable_files:
   - obs.tsv
   sbml_files:
-  - sbml_model.xml
+  - sbml_model.xml

setup.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """Setup script for petab-gui."""
+
 from setuptools import setup  # type: ignore
 
 if __name__ == "__main__":

src/petab_gui/C.py

@@ -71,7 +71,7 @@
         "yLabel": {"type": np.object_, "optional": True},
         "yScale": {"type": np.object_, "optional": True},
         "legendEntry": {"type": np.object_, "optional": True},
-    }
+    },
 }
 
 CONFIG = {