pre-commit ruff (#2257)

Replace black&isort by [ruff](https://docs.astral.sh/ruff/) (faster, additional functionality).

* Enable (99%) black-compatible formatting 
* Enable linting with autofixing
* Fix some linting issues
* `pre-commit run --all-files`

.pre-commit-config.yaml

@@ -1,12 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,15 +10,21 @@ 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/de_export.py

@@ -587,7 +587,7 @@ def smart_multiply(
 
 
 def smart_is_zero_matrix(
-    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix]
+    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix],
 ) -> bool:
     """A faster implementation of sympy's is_zero_matrix
 

python/sdist/amici/gradient_check.py

@@ -6,7 +6,7 @@
 """
 
 import copy
-from typing import Callable, List, Optional, Sequence
+from typing import List, Optional, Sequence
 
 import numpy as np
 
@@ -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/import_utils.py

@@ -72,7 +72,7 @@ class ObservableTransformation(str, enum.Enum):
 
 
 def noise_distribution_to_observable_transformation(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> ObservableTransformation:
     """
     Parse noise distribution string and extract observable transformation
@@ -93,7 +93,7 @@ def noise_distribution_to_observable_transformation(
 
 
 def noise_distribution_to_cost_function(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> Callable[[str], str]:
     """
     Parse noise distribution string to a cost function definition amici can
@@ -423,7 +423,7 @@ def _parse_special_functions(sym: sp.Expr, toplevel: bool = True) -> sp.Expr:
 
 
 def _denest_piecewise(
-    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]
+    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]],
 ) -> Tuple[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]:
     """
     Denest piecewise functions that contain piecewise as condition

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,
@@ -63,7 +66,7 @@ def get_states_in_condition_table(
             spm = pysb.pattern.SpeciesPatternMatcher(
                 model=petab_problem.model.model
             )
-        except NotImplementedError as e:
+        except NotImplementedError:
             raise NotImplementedError(
                 "Requires https://github.com/pysb/pysb/pull/570. "
                 "To use this functionality, update pysb via "

python/sdist/amici/plotting.py

@@ -56,8 +56,7 @@ def plot_state_trajectories(
     elif model is not None and prefer_names:
         labels = np.asarray(model.getStateNames())[list(state_indices)]
         labels = [
-            l if l else model.getStateIds()[ix]
-            for ix, l in enumerate(labels)
+            l if l else model.getStateIds()[ix] for ix, l in enumerate(labels)
         ]
     elif model is not None:
         labels = np.asarray(model.getStateIds())[list(state_indices)]

python/sdist/amici/pysb_import.py

@@ -410,7 +410,7 @@ def _process_pysb_species(pysb_model: pysb.Model, ode_model: DEModel) -> None:
                 sp.Symbol(f"__s{ix}"), f"{specie}", init, xdot[ix]
             )
         )
-    logger.debug(f"Finished Processing PySB species ")
+    logger.debug("Finished Processing PySB species ")
 
 
 @log_execution_time("processing PySB parameters", logger)
@@ -1353,7 +1353,7 @@ def has_fixed_parameter_ic(
 
 
 def extract_monomers(
-    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]]
+    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]],
 ) -> List[str]:
     """
     Constructs a list of monomer names contained in complex patterns.

python/sdist/amici/sbml_import.py

@@ -21,7 +21,6 @@
     List,
     Optional,
     Sequence,
-    Set,
     Tuple,
     Union,
 )
@@ -1165,7 +1164,7 @@ def _process_reactions(self):
                     # accounts for possibly variable compartments.
                     self.stoichiometric_matrix[
                         species["index"], reaction_index
-                    ] += (sign * stoichiometry * species["conversion_factor"])
+                    ] += sign * stoichiometry * species["conversion_factor"]
             if reaction.isSetId():
                 sym_math = self._local_symbols[reaction.getId()]
             else:
@@ -2360,9 +2359,9 @@ def _replace_in_all_expressions(
         # rule (at the end of the _process_species method), hence needs to be
         # processed here too.
         self.compartments = {
-            smart_subs(c, old, new)
-            if replace_identifiers
-            else c: smart_subs(v, old, self._make_initial(new))
+            smart_subs(c, old, new) if replace_identifiers else c: smart_subs(
+                v, old, self._make_initial(new)
+            )
             for c, v in self.compartments.items()
         }
 

python/sdist/amici/sbml_utils.py

@@ -519,7 +519,7 @@ def mathml2sympy(
 
 
 def _parse_logical_operators(
-    math_str: Union[str, float, None]
+    math_str: Union[str, float, None],
 ) -> Union[str, float, None]:
     """
     Parses a math string in order to replace logical operators by a form

python/sdist/amici/splines.py

@@ -1510,7 +1510,10 @@ def spline_user_functions(
         "AmiciSplineSensitivity": [
             (
                 lambda *args: True,
-                lambda spline_id, x, param_id, *p: f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}",
+                lambda spline_id,
+                x,
+                param_id,
+                *p: f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}",
             )
         ],
     }

python/sdist/amici/swig_wrappers.py

@@ -54,7 +54,7 @@ def _capture_cstdout():
 
 
 def _get_ptr(
-    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData]
+    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData],
 ) -> Union[
     "amici_swig.Model",
     "amici_swig.ExpData",

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/conftest.py

@@ -2,7 +2,6 @@
 import copy
 import importlib
 import os
-import shutil
 import sys
 
 import amici

python/tests/petab_test_problems/lotka_volterra/model/writer.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import petab
 import yaml2sbml
 
 yaml2sbml_yaml = "lotka_volterra.yaml"

python/tests/test_edata.py

@@ -2,11 +2,11 @@
 import amici
 import numpy as np
 from amici.testing import skip_on_valgrind
-from test_sbml_import import model_units_module
+from test_sbml_import import model_units_module  # noqa: F401
 
 
 @skip_on_valgrind
-def test_edata_sensi_unscaling(model_units_module):
+def test_edata_sensi_unscaling(model_units_module):  # noqa: F811
     """
     ExpData parameters should be used for unscaling initial state
     sensitivities.

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 = []
 

tests/generateTestConfig/example_steadystate.py

@@ -2,7 +2,7 @@
 import sys
 
 import numpy as np
-from example import AmiciExample, dict2attrs
+from example import AmiciExample
 
 
 class ExampleSteadystate(AmiciExample):