Zenodo Integration

.zenodo.json

@@ -0,0 +1,23 @@
+{
+  "title": "PEtab GUI",
+  "description": "Graphical user interface for the PEtab format",
+  "creators": [
+    {
+      "name": "Paul Jonas Jost",
+      "affiliation": "University Bonn",
+      "orcid": "0000-0001-7613-6244"
+    },
+    {
+      "name": "Frank T. Bergman",
+      "affiliation": "University Heidelberg",
+      "orcid": "0000-0001-5553-4702"
+    }
+  ],
+  "keywords": [
+    "PEtab",
+    "GUI",
+    "Python",
+    "Biological Modeling",
+    "Parameter Estimation"
+  ]
+}

README.md

@@ -23,7 +23,7 @@ pip install .
 
 To start the PEtab GUI, you can run the following command line:
 ```bash
-PEtab_gui $PATH_TO_YOUR_MODEL
+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 

pyproject.toml

@@ -70,7 +70,25 @@ lint.select = [
     "W",  # pycodestyle Warnings
     "E",  # pycodestyle Errors
     "UP",  # pyupgrade
-    # "ANN",  # flakes-annotations TODO: currently produces ~1500 errors to manual fix
+    "ERA",
+    "A",  # flake8-builtins
+    "RET",  # flake8-return
+    "SIM",  # flake8-simplify
+]
+lint.ignore = [
+    "D107",  # Ignore missing docstring in __init__.py files
+    "D102",  # Ignore missing docstring in public methods
+    "D103",  # Ignore missing docstring in public functions
+    "D401",  # Ignore imperative mood in docstrings
+    "D100",  # Ignore missing docstring in public modules
+    "D101",  # Ignore missing docstring in public classes
+    "F401",
+]
+[tool.ruff.lint.per-file-ignores]
+"*/__init__.py" = [
+    "F401",
+    "D400",
+    "D205",
 ]
 [tool.ruff.lint.pydocstyle]
 convention = "pep257"

setup.py

@@ -3,4 +3,4 @@
 from setuptools import setup  # type: ignore
 
 if __name__ == "__main__":
-    setup(version="0.1.1")
+    setup(version="0.1.2")

src/petab_gui/views/find_replace_bar.py

@@ -267,6 +267,7 @@ def update_selected_controllers(self):
                 self.controller_map[table_name]
                 for table_name, action in self.filter_actions.items()
                 if action.isChecked() and (table_name != "All")
+            }
         self.run_find()
 
     def keyPressEvent(self, event):