diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..a5f6745 --- /dev/null +++ b/.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" + ] +} \ No newline at end of file diff --git a/README.md b/README.md index 89b8e83..ccd7b59 100644 --- a/README.md +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index 973f029..c3bd56c 100644 --- a/pyproject.toml +++ b/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" diff --git a/setup.py b/setup.py index 6652e7c..ea01af0 100644 --- a/setup.py +++ b/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") diff --git a/src/petab_gui/views/find_replace_bar.py b/src/petab_gui/views/find_replace_bar.py index 589587a..280c208 100644 --- a/src/petab_gui/views/find_replace_bar.py +++ b/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):