ruff config + make compatible

.pre-commit-config.yaml

@@ -16,15 +16,21 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - python/sdist/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - python/sdist/pyproject.toml
 
 exclude: '^(ThirdParty|models)/'

documentation/conf.py

@@ -5,7 +5,6 @@
 # This file does only contain a selection of the most common options. For a
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/stable/config
-
 import os
 import re
 import subprocess
@@ -18,6 +17,7 @@
 import exhale_multiproject_monkeypatch
 import mock
 import pandas as pd
+import sphinx
 import sympy as sp
 from exhale import configs as exhale_configs
 from sphinx.transforms.post_transforms import ReferencesResolver

python/sdist/amici/__init__.py

@@ -107,18 +107,21 @@ def _imported_from_setup() -> bool:
         #  from .swig_wrappers
         hdf5_enabled = "readSolverSettingsFromHDF5" in dir()
         # These modules require the swig interface and other dependencies
-        from .numpy import ExpDataView, ReturnDataView
+        from .numpy import ExpDataView, ReturnDataView  # noqa: F401
         from .pandas import *
         from .swig_wrappers import *
 
     # These modules don't require the swig interface
     from typing import Protocol, runtime_checkable
 
-    from .de_export import DEExporter, DEModel
-    from .sbml_import import SbmlImporter, assignmentRules2observables
+    from .de_export import DEExporter, DEModel  # noqa: F401
+    from .sbml_import import (  # noqa: F401
+        SbmlImporter,
+        assignmentRules2observables,
+    )
 
     @runtime_checkable
-    class ModelModule(Protocol):
+    class ModelModule(Protocol):  # noqa: F811
         """Type of AMICI-generated model modules.
 
         To enable static type checking."""

python/sdist/amici/__init__.template.py

@@ -15,7 +15,7 @@
         "version currently installed."
     )
 
-from .TPL_MODELNAME import *
-from .TPL_MODELNAME import getModel as get_model
+from .TPL_MODELNAME import *  # noqa: F403, F401
+from .TPL_MODELNAME import getModel as get_model # noqa: F401
 
 __version__ = "TPL_PACKAGE_VERSION"

python/sdist/amici/gradient_check.py

@@ -331,7 +331,7 @@ def _check_results(
     """
 
     result = rdata[field]
-    if type(result) is float:
+    if type(result) is float:  # noqa E721
         result = np.array(result)
 
     _check_close(

python/sdist/amici/petab/util.py

@@ -1,6 +1,6 @@
 """Various helper functions for working with PEtab problems."""
 import re
-from typing import Dict, Tuple, Union
+from typing import TYPE_CHECKING, Dict, Tuple, Union
 
 import libsbml
 import pandas as pd
@@ -9,6 +9,9 @@
 from petab.mapping import resolve_mapping
 from petab.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
 
+if TYPE_CHECKING:
+    pysb = None
+
 
 def get_states_in_condition_table(
     petab_problem: petab.Problem,

python/sdist/pyproject.toml

@@ -15,3 +15,8 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 79
+
+[tool.ruff]
+line-length = 79
+ignore = ["E402", "F403", "F405", "E741"]
+extend-include = ["*.ipynb"]

python/tests/test_pysb.py

@@ -1,4 +1,5 @@
 """PYSB model tests"""
+# flake8: noqa: F821
 
 import importlib
 import logging

tests/conftest.py

@@ -3,10 +3,13 @@
 import re
 import sys
 from pathlib import Path
-from typing import List, Set, Tuple
+from typing import TYPE_CHECKING, List, Set, Tuple
 
 import pytest
 
+if TYPE_CHECKING:
+    from _pytest.reports import TestReport
+
 # stores passed SBML semantic test suite IDs
 passed_ids = []