Add .pre-commit-config.yaml

.github/workflows/ci.yml

@@ -0,0 +1,24 @@
+name: CI
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  merge_group:
+
+jobs:
+  quality:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v5
+
+    - name: Prepare Python
+      uses: actions/setup-python@v6
+      with:
+          python-version: "3.11"
+
+    - name: Install dependencies
+      run: pip install pre-commit
+
+    - name: Run pre-commit hooks
+      run: pre-commit run --all-files

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+        # Optional extra validations from SchemaStore:
+        additional_dependencies: [ "validate-pyproject-schema-store[all]" ]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.1
+    hooks:
+      - id: ruff-check
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi ]

.zenodo.json

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

README.md

@@ -52,17 +52,17 @@ The PEtabGUI provides a Python-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.
@@ -71,6 +71,6 @@ the creation, editing, and validation of PEtab parameter estimation problems.
   - 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](https://combinearchive.org) 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

pyproject.toml

@@ -84,12 +84,26 @@ lint.ignore = [
     "D100",  # Ignore missing docstring in public modules
     "D101",  # Ignore missing docstring in public classes
     "F401",
+    # FIXME: those are ignored for now, should be fixed eventually
+    "E501",  # Ignore line too long
+    "ERA001", # Found commented-out code
+    "RET504",  # Unnecessary assignment before `return`
+    "T201",  # `print` found"
+    "SIM105",  # Use `contextlib.suppress`
+    "S110",  # `try`-`except`-`pass` detected, consider logging the exception
+    "A002",  # Function argument shadowing a Python builtin
+    "E701",  # Multiple statements on one line (colon)
+    "E741",  # Ambiguous variable name
 ]
 [tool.ruff.lint.per-file-ignores]
 "*/__init__.py" = [
     "F401",
     "D400",
     "D205",
 ]
+"docs/source/conf.py" = [
+    "A001", # Variable `copyright` is shadowing a Python builtin
+
+]
 [tool.ruff.lint.pydocstyle]
 convention = "pep257"

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 = {

src/petab_gui/app.py

@@ -1,8 +1,8 @@
 import argparse
 import os
 import sys
+from importlib.metadata import PackageNotFoundError, version
 from importlib.resources import files
-from importlib.metadata import version, PackageNotFoundError
 from pathlib import Path
 
 from PySide6.QtCore import QEvent
@@ -48,7 +48,7 @@ class PEtabGuiApp(QApplication):
     Inherits from QApplication and sets up the MVC components.
     """
 
-    def __init__(self, file: str|Path = None):
+    def __init__(self, file: str | Path = None):
         """Initialize the PEtab GUI application.
 
         Sets up the model, view, and controller components.
@@ -125,12 +125,10 @@ def main():
         "--version",
         action="version",
         version=f"%(prog)s {pkg_version}",
-        help="Show version number and exit"
+        help="Show version number and exit",
     )
     parser.add_argument(
-        "petab_yaml",
-        nargs="?",
-        help="Path to the PEtab YAML file"
+        "petab_yaml", nargs="?", help="Path to the PEtab YAML file"
     )
     args = parser.parse_args()
 

src/petab_gui/commands.py

@@ -141,7 +141,9 @@ def redo(self):
         df = self.model._data_frame
 
         if self.add_mode:
-            position = 0 if df.empty else df.shape[0] - 1  # insert *before* the auto-row
+            position = (
+                0 if df.empty else df.shape[0] - 1
+            )  # insert *before* the auto-row
             self.model.beginInsertRows(
                 QModelIndex(), position, position + len(self.row_indices) - 1
             )
@@ -264,12 +266,9 @@ def _apply_changes(self, use_new: bool):
             else:
                 df[col] = df[col].astype(dtype)
 
-        rows = [
-            df.index.get_loc(row_key) for (row_key, _) in self.changes
-        ]
+        rows = [df.index.get_loc(row_key) for (row_key, _) in self.changes]
         cols = [
-            df.columns.get_loc(col) + col_offset
-            for (_, col) in self.changes
+            df.columns.get_loc(col) + col_offset for (_, col) in self.changes
         ]
 
         top_left = self.model.index(min(rows), min(cols))

src/petab_gui/controllers/logger_controller.py

@@ -18,8 +18,8 @@ def __init__(self, views):
         self.logger_level = 1
         self.log_message("Welcome to PEtab-GUI!", 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 '
+            "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/" '
             'style="color:blue;" target="_blank">documentation</a>.',
             color="green",