maint: black -> ruff (#251)

Instead of black and isort, run ruff as pre-commit hook. Enable pyupgrade and additional rules.

Applied safe auto-fixes, but validation currently fails. Will be addressed in a follow-up PR (#252).

Relevant changes: `.pre-commit-config.yaml`, `pyproject.toml`

Author: dweindl

.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:
@@ -16,13 +10,19 @@ 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
+        - pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - pyproject.toml

petab/calculate.py

@@ -322,7 +322,8 @@ def calculate_llh_for_table(
     parameter_df: pd.DataFrame,
 ) -> float:
     """Calculate log-likelihood for one set of tables. For the arguments, see
-    `calculate_llh`."""
+    `calculate_llh`.
+    """
     llhs = []
 
     # matching columns

petab/composite_problem.py

@@ -46,7 +46,6 @@ def from_yaml(yaml_config: Union[Dict, str]) -> "CompositeProblem":
         Arguments:
             yaml_config: PEtab configuration as dictionary or YAML file name
         """
-
         if isinstance(yaml_config, str):
             path_prefix = os.path.dirname(yaml_config)
             yaml_config = yaml.load_yaml(yaml_config)

petab/conditions.py

@@ -18,7 +18,7 @@
 
 
 def get_condition_df(
-    condition_file: Union[str, pd.DataFrame, Path, None]
+    condition_file: Union[str, pd.DataFrame, Path, None],
 ) -> pd.DataFrame:
     """Read the provided condition file into a ``pandas.Dataframe``
 
@@ -75,7 +75,6 @@ def create_condition_df(
         A :py:class:`pandas.DataFrame` with empty given rows and columns and
         all nan values
     """
-
     condition_ids = [] if condition_ids is None else list(condition_ids)
 
     data = {CONDITION_ID: condition_ids}

petab/core.py

@@ -72,7 +72,7 @@ def write_simulation_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
 
 
 def get_visualization_df(
-    visualization_file: Union[str, Path, pd.DataFrame, None]
+    visualization_file: Union[str, Path, pd.DataFrame, None],
 ) -> Union[pd.DataFrame, None]:
     """Read PEtab visualization table
 
@@ -357,7 +357,6 @@ def concat_tables(
     Returns:
         The concatenated DataFrames
     """
-
     if isinstance(tables, pd.DataFrame):
         return tables
 
@@ -389,7 +388,6 @@ def to_float_if_float(x: Any) -> Any:
     Returns:
         ``x`` as float if possible, otherwise ``x``
     """
-
     try:
         return float(x)
     except (ValueError, TypeError):
@@ -427,7 +425,6 @@ def create_combine_archive(
         email: E-mail address of archive creator
         organization: Organization of archive creator
     """
-
     path_prefix = os.path.dirname(str(yaml_file))
     yaml_config = yaml.load_yaml(yaml_file)
 

petab/lint.py

@@ -105,7 +105,6 @@ def check_condition_df(
     Raises:
         AssertionError: in case of problems
     """
-
     # Check required columns are present
     req_cols = []
     _check_df(df, req_cols, "condition")
@@ -167,7 +166,6 @@ def check_measurement_df(
     Raises:
         AssertionError, ValueError: in case of problems
     """
-
     _check_df(df, MEASUREMENT_DF_REQUIRED_COLS, "measurement")
 
     for column_name in MEASUREMENT_DF_REQUIRED_COLS:
@@ -432,7 +430,6 @@ def assert_measured_observables_defined(
     Raises:
         AssertionError: in case of problems
     """
-
     used_observables = set(measurement_df[OBSERVABLE_ID].values)
     defined_observables = set(observable_df.index.values)
     if undefined_observables := (used_observables - defined_observables):
@@ -453,7 +450,6 @@ def condition_table_is_parameter_free(condition_df: pd.DataFrame) -> bool:
         ``True`` if there are no parameter overrides in the condition table,
         ``False`` otherwise.
     """
-
     return len(petab.get_parametric_overrides(condition_df)) == 0
 
 
@@ -468,7 +464,6 @@ def assert_parameter_id_is_string(parameter_df: pd.DataFrame) -> None:
     Raises:
         AssertionError: in case of problems
     """
-
     for parameter_id in parameter_df:
         if isinstance(parameter_id, str):
             if parameter_id[0].isdigit():
@@ -1088,7 +1083,6 @@ def assert_measurement_conditions_present_in_condition_table(
     Raises:
         AssertionError: in case of problems
     """
-
     used_conditions = set(measurement_df[SIMULATION_CONDITION_ID].values)
     if PREEQUILIBRATION_CONDITION_ID in measurement_df:
         used_conditions |= set(

petab/mapping.py

@@ -16,7 +16,7 @@
 
 
 def get_mapping_df(
-    mapping_file: Union[None, str, Path, pd.DataFrame]
+    mapping_file: Union[None, str, Path, pd.DataFrame],
 ) -> pd.DataFrame:
     """
     Read the provided mapping file into a ``pandas.Dataframe``.

petab/measurements.py

@@ -28,7 +28,7 @@
 
 
 def get_measurement_df(
-    measurement_file: Union[None, str, Path, pd.DataFrame]
+    measurement_file: Union[None, str, Path, pd.DataFrame],
 ) -> pd.DataFrame:
     """
     Read the provided measurement file into a ``pandas.Dataframe``.
@@ -217,7 +217,6 @@ def create_measurement_df() -> pd.DataFrame:
     Returns:
         Created DataFrame
     """
-
     return pd.DataFrame(
         data={
             OBSERVABLE_ID: [],

petab/models/model.py

@@ -3,7 +3,7 @@
 
 import abc
 from pathlib import Path
-from typing import Any, Iterable, Tuple
+from typing import Any, Iterable
 
 
 class Model(abc.ABC):
@@ -55,7 +55,7 @@ def get_parameter_value(self, id_: str) -> float:
     @abc.abstractmethod
     def get_free_parameter_ids_with_values(
         self,
-    ) -> Iterable[Tuple[str, float]]:
+    ) -> Iterable[tuple[str, float]]:
         """Get free model parameters along with their values
 
         Returns:
@@ -106,7 +106,6 @@ def symbol_allowed_in_observable_formula(self, id_: str) -> bool:
 
         :returns: ``True``, if allowed, ``False`` otherwise
         """
-
         ...
 
     @abc.abstractmethod

petab/observables.py

@@ -24,7 +24,7 @@
 
 
 def get_observable_df(
-    observable_file: Union[str, pd.DataFrame, Path, None]
+    observable_file: Union[str, pd.DataFrame, Path, None],
 ) -> Union[pd.DataFrame, None]:
     """
     Read the provided observable file into a ``pandas.Dataframe``.
@@ -191,7 +191,6 @@ def get_placeholders(
         List of placeholder parameters from observable table observableFormulas
         and noiseFormulas.
     """
-
     # collect placeholder parameters overwritten by
     # {observable,noise}Parameters
     placeholder_types = []
@@ -224,5 +223,4 @@ def create_observable_df() -> pd.DataFrame:
     Returns:
         Created DataFrame
     """
-
     return pd.DataFrame(data={col: [] for col in OBSERVABLE_DF_COLS})