maint: fix code style, check on gha (#252)

Follow-up to #251 

* Manual changes for compatibility with selected ruff rules
* run pre-commit hooks on GHA instead of flake8
* run tests on python3.12

Author: dweindl

.github/workflows/ci_tests.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.9", "3.12"]
     runs-on: ${{ matrix.platform }}
 
     steps:

doc/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "libpetab-python"
-copyright = "2018-2023, the PEtab developers"
+copyright = "2018-2024, the PEtab developers"
 author = "PEtab developers"
 
 # The full version, including alpha/beta/rc tags
@@ -29,7 +29,7 @@
 # -- Custom pre-build --------------------------------------------------------
 
 
-subprocess.run(["python", "md2rst.py"])
+subprocess.run([sys.executable, "md2rst.py"])  # noqa: S603
 
 # -- General configuration ---------------------------------------------------
 

petab/calculate.py

@@ -336,7 +336,7 @@ def calculate_llh_for_table(
     noise_formulas = get_symbolic_noise_formulas(observable_df)
 
     # iterate over measurements, find corresponding simulations
-    for irow, row in measurement_df.iterrows():
+    for _, row in measurement_df.iterrows():
         measurement = row[MEASUREMENT]
 
         # look up in simulation df

petab/conditions.py

@@ -47,7 +47,7 @@ def get_condition_df(
     except KeyError:
         raise KeyError(
             f"Condition table missing mandatory field {CONDITION_ID}."
-        )
+        ) from None
 
     return condition_file
 

petab/core.py

@@ -102,7 +102,8 @@ def get_visualization_df(
     except pd.errors.EmptyDataError:
         warn(
             "Visualization table is empty. Defaults will be used. "
-            "Refer to the documentation for details."
+            "Refer to the documentation for details.",
+            stacklevel=2,
         )
         vis_spec = pd.DataFrame()
     return vis_spec
@@ -226,9 +227,9 @@ def get_flattened_id_mappings(
 
         mappings[OBSERVABLE_ID][observable_replacement_id] = observable_id
 
-        for field, hyperparameter_type, target in [
-            (NOISE_PARAMETERS, "noiseParameter", NOISE_FORMULA),
-            (OBSERVABLE_PARAMETERS, "observableParameter", OBSERVABLE_FORMULA),
+        for field, hyperparameter_type in [
+            (NOISE_PARAMETERS, "noiseParameter"),
+            (OBSERVABLE_PARAMETERS, "observableParameter"),
         ]:
             if field in measurements:
                 mappings[field][
@@ -432,11 +433,11 @@ def create_combine_archive(
     # other SWIG interfaces
     try:
         import libcombine
-    except ImportError:
+    except ImportError as err:
         raise ImportError(
             "To use PEtab's COMBINE functionality, libcombine "
             "(python-libcombine) must be installed."
-        )
+        ) from err
 
     def _add_file_metadata(location: str, description: str = ""):
         """Add metadata to the added file"""

petab/measurements.py

@@ -321,7 +321,7 @@ def assert_overrides_match_parameter_count(
                     f"Mismatch of noise parameter overrides in:\n{row}\n"
                     f"Expected {expected} but got {len(replacements)}"
                 )
-        except KeyError:
+        except KeyError as err:
             # no overrides defined, but a numerical sigma can be provided
             # anyways
             if len(replacements) != 1 or not isinstance(
@@ -332,7 +332,7 @@ def assert_overrides_match_parameter_count(
                     f"for observable {row[OBSERVABLE_ID]}, but parameter ID "
                     "or multiple overrides were specified in the "
                     "noiseParameters column."
-                )
+                ) from err
 
 
 def measurement_is_at_steady_state(time: float) -> bool:

petab/models/model.py

@@ -9,6 +9,7 @@
 class Model(abc.ABC):
     """Base class for wrappers for any PEtab-supported model type"""
 
+    @abc.abstractmethod
     def __init__(self):
         ...
 

petab/observables.py

@@ -55,7 +55,7 @@ def get_observable_df(
     except KeyError:
         raise KeyError(
             f"Observable table missing mandatory field {OBSERVABLE_ID}."
-        )
+        ) from None
 
     return observable_file
 

petab/parameters.py

@@ -447,7 +447,8 @@ def get_priors_from_df(
     Arguments:
         parameter_df: PEtab parameter table
         mode: ``'initialization'`` or ``'objective'``
-        parameter_ids: A sequence of parameter IDs for which to sample starting points.
+        parameter_ids: A sequence of parameter IDs for which to sample starting
+            points.
             For subsetting or reordering the parameters.
             Defaults to all estimated parameters.
 
@@ -463,7 +464,8 @@ def get_priors_from_df(
         except KeyError as e:
             missing_ids = set(parameter_ids) - set(par_to_estimate.index)
             raise KeyError(
-                f"Parameter table does not contain estimated parameter(s) {missing_ids}."
+                "Parameter table does not contain estimated parameter(s) "
+                f"{missing_ids}."
             ) from e
 
     prior_list = []
@@ -567,7 +569,10 @@ def map_scale(
     """
     if isinstance(scale_strs, str):
         scale_strs = [scale_strs] * len(parameters)
-    return map(lambda x: scale(x[0], x[1]), zip(parameters, scale_strs))
+    return (
+        scale(par_val, scale_str)
+        for par_val, scale_str in zip(parameters, scale_strs)
+    )
 
 
 def map_unscale(
@@ -588,7 +593,10 @@ def map_unscale(
     """
     if isinstance(scale_strs, str):
         scale_strs = [scale_strs] * len(parameters)
-    return map(lambda x: unscale(x[0], x[1]), zip(parameters, scale_strs))
+    return (
+        unscale(par_val, scale_str)
+        for par_val, scale_str in zip(parameters, scale_strs)
+    )
 
 
 def normalize_parameter_df(parameter_df: pd.DataFrame) -> pd.DataFrame:

petab/problem.py

@@ -5,7 +5,7 @@
 import tempfile
 from math import nan
 from pathlib import Path, PurePosixPath
-from typing import TYPE_CHECKING, Iterable, Optional, Union
+from typing import TYPE_CHECKING, Iterable
 from urllib.parse import unquote, urlparse, urlunparse
 from warnings import warn
 
@@ -78,12 +78,12 @@ def __init__(
         mapping_df: pd.DataFrame = None,
         extensions_config: dict = None,
     ):
-        self.condition_df: Optional[pd.DataFrame] = condition_df
-        self.measurement_df: Optional[pd.DataFrame] = measurement_df
-        self.parameter_df: Optional[pd.DataFrame] = parameter_df
-        self.visualization_df: Optional[pd.DataFrame] = visualization_df
-        self.observable_df: Optional[pd.DataFrame] = observable_df
-        self.mapping_df: Optional[pd.DataFrame] = mapping_df
+        self.condition_df: pd.DataFrame | None = condition_df
+        self.measurement_df: pd.DataFrame | None = measurement_df
+        self.parameter_df: pd.DataFrame | None = parameter_df
+        self.visualization_df: pd.DataFrame | None = visualization_df
+        self.observable_df: pd.DataFrame | None = observable_df
+        self.mapping_df: pd.DataFrame | None = mapping_df
 
         if any(
             (sbml_model, sbml_document, sbml_reader),
@@ -109,7 +109,7 @@ def __init__(
                 model_id=model_id,
             )
 
-        self.model: Optional[Model] = model
+        self.model: Model | None = model
         self.extensions_config = extensions_config or {}
 
     def __getattr__(self, name):
@@ -169,14 +169,12 @@ def __str__(self):
 
     @staticmethod
     def from_files(
-        sbml_file: Union[str, Path] = None,
-        condition_file: Union[str, Path, Iterable[Union[str, Path]]] = None,
-        measurement_file: Union[str, Path, Iterable[Union[str, Path]]] = None,
-        parameter_file: Union[str, Path, Iterable[Union[str, Path]]] = None,
-        visualization_files: Union[
-            str, Path, Iterable[Union[str, Path]]
-        ] = None,
-        observable_files: Union[str, Path, Iterable[Union[str, Path]]] = None,
+        sbml_file: str | Path = None,
+        condition_file: str | Path | Iterable[str | Path] = None,
+        measurement_file: str | Path | Iterable[str | Path] = None,
+        parameter_file: str | Path | Iterable[str | Path] = None,
+        visualization_files: str | Path | Iterable[str | Path] = None,
+        observable_files: str | Path | Iterable[str | Path] = None,
         model_id: str = None,
         extensions_config: dict = None,
     ) -> Problem:
@@ -252,7 +250,7 @@ def from_files(
         )
 
     @staticmethod
-    def from_yaml(yaml_config: Union[dict, Path, str]) -> Problem:
+    def from_yaml(yaml_config: dict | Path | str) -> Problem:
         """
         Factory method to load model and tables as specified by YAML file.
 
@@ -308,7 +306,7 @@ def from_yaml(yaml_config: Union[dict, Path, str]) -> Problem:
                 f"{format_version.__format_version__}."
             )
         if yaml_config[FORMAT_VERSION] == "2.0.0":
-            warn("Support for PEtab2.0 is experimental!")
+            warn("Support for PEtab2.0 is experimental!", stacklevel=2)
 
         problem0 = yaml_config["problems"][0]
 
@@ -421,7 +419,7 @@ def from_yaml(yaml_config: Union[dict, Path, str]) -> Problem:
         )
 
     @staticmethod
-    def from_combine(filename: Union[Path, str]) -> Problem:
+    def from_combine(filename: Path | str) -> Problem:
         """Read PEtab COMBINE archive (http://co.mbine.org/documents/archive).
 
         See also :py:func:`petab.create_combine_archive`.
@@ -444,8 +442,7 @@ def from_combine(filename: Union[Path, str]) -> Problem:
 
         archive = libcombine.CombineArchive()
         if archive.initializeFromArchive(str(filename)) is None:
-            print(f"Invalid Combine Archive: {filename}")
-            return None
+            raise ValueError(f"Invalid Combine Archive: {filename}")
 
         with tempfile.TemporaryDirectory() as tmpdirname:
             archive.extractTo(tmpdirname)
@@ -458,7 +455,7 @@ def from_combine(filename: Union[Path, str]) -> Problem:
 
     def to_files_generic(
         self,
-        prefix_path: Union[str, Path],
+        prefix_path: str | Path,
     ) -> str:
         """Save a PEtab problem to generic file names.
 
@@ -510,17 +507,17 @@ def to_files_generic(
 
     def to_files(
         self,
-        sbml_file: Union[None, str, Path] = None,
-        condition_file: Union[None, str, Path] = None,
-        measurement_file: Union[None, str, Path] = None,
-        parameter_file: Union[None, str, Path] = None,
-        visualization_file: Union[None, str, Path] = None,
-        observable_file: Union[None, str, Path] = None,
-        yaml_file: Union[None, str, Path] = None,
-        prefix_path: Union[None, str, Path] = None,
+        sbml_file: None | str | Path = None,
+        condition_file: None | str | Path = None,
+        measurement_file: None | str | Path = None,
+        parameter_file: None | str | Path = None,
+        visualization_file: None | str | Path = None,
+        observable_file: None | str | Path = None,
+        yaml_file: None | str | Path = None,
+        prefix_path: None | str | Path = None,
         relative_paths: bool = True,
-        model_file: Union[None, str, Path] = None,
-        mapping_file: Union[None, str, Path] = None,
+        model_file: None | str | Path = None,
+        mapping_file: None | str | Path = None,
     ) -> None:
         """
         Write PEtab tables to files for this problem
@@ -573,7 +570,7 @@ def to_files(
         if prefix_path is not None:
             prefix_path = Path(prefix_path)
 
-            def add_prefix(path0: Union[None, str, Path]) -> str:
+            def add_prefix(path0: None | str | Path) -> str:
                 return path0 if path0 is None else str(prefix_path / path0)
 
             model_file = add_prefix(model_file)
@@ -913,7 +910,7 @@ def get_optimization_to_simulation_parameter_mapping(self, **kwargs):
             )
         )
 
-    def create_parameter_df(self, *args, **kwargs):
+    def create_parameter_df(self, **kwargs):
         """Create a new PEtab parameter table
 
         See :py:func:`create_parameter_df`.
@@ -924,7 +921,6 @@ def create_parameter_df(self, *args, **kwargs):
             observable_df=self.observable_df,
             measurement_df=self.measurement_df,
             mapping_df=self.mapping_df,
-            *args,
             **kwargs,
         )