..

doc/conf.py

@@ -2,9 +2,12 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
+from __future__ import annotations
 
 import inspect
 
+import sphinx
+
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
@@ -73,5 +76,5 @@ def autodoc_skip_member(app, what, name, obj, skip, options):
     return None
 
 
-def setup(app: "sphinx.application.Sphinx"):
+def setup(app: sphinx.application.Sphinx):
     app.connect("autodoc-skip-member", autodoc_skip_member, priority=0)

petab_select/candidate_space.py

@@ -690,8 +690,8 @@ def __init__(
         if predecessor_model is None:
             predecessor_model = VIRTUAL_INITIAL_MODEL
         super().__init__(
-            method=Method.FORWARD if self.direction == 1 else Method.BACKWARD,
             *args,
+            method=Method.FORWARD if self.direction == 1 else Method.BACKWARD,
             predecessor_model=predecessor_model,
             **kwargs,
         )
@@ -976,8 +976,8 @@ def __init__(
         ]
 
         super().__init__(
-            method=self.method,
             *args,
+            method=self.method,
             predecessor_model=predecessor_model,
             **kwargs,
         )
@@ -990,7 +990,8 @@ def __init__(
             and (Method.LATERAL,) not in self.method_scheme
         ):
             raise ValueError(
-                "Please provide a method to switch to after a lateral search, if not enabling the `consecutive_laterals` option."
+                "Please provide a method to switch to after a lateral search, "
+                "if not enabling the `consecutive_laterals` option."
             )
 
         if self.n_reattempts:
@@ -1401,8 +1402,8 @@ def __init__(
                 Maximal allowed number of swap moves. If 0 then there is no maximum.
         """
         super().__init__(
-            method=Method.LATERAL,
             *args,
+            method=Method.LATERAL,
             predecessor_model=predecessor_model,
             **kwargs,
         )
@@ -1453,8 +1454,8 @@ def __init__(self, *args, **kwargs):
         #        'brute force candidate space.'
         #    )
         super().__init__(
-            method=Method.BRUTE_FORCE,
             *args,
+            method=Method.BRUTE_FORCE,
             **kwargs,
         )
 

petab_select/model.py

@@ -1001,7 +1001,7 @@ def hash_model_subspace_indices(model_subspace_indices: list[int]) -> str:
                 for index in model_subspace_indices
             )
         except KeyError:
-            return MODEL_SUBSPACE_INDICES_HAS_HASH_DELIMITER.join(
+            return MODEL_SUBSPACE_INDICES_HASH_DELIMITER.join(
                 str(i) for i in model_subspace_indices
             )
 

petab_select/model_subspace.py

@@ -923,41 +923,42 @@ def get_estimated(
             The parameter IDs.
         """
         raise NotImplementedError
-        parameters = []
-        for parameter_id, parameter_value in self.parameters_all.items():
-            if additional_parameters.get(parameter_id, None) == ESTIMATE:
-                parameters.append(parameter_id)
-                continue
-
-            if parameter_id in additional_parameters:
-                # Presumably not estimated.
-                continue
 
-        old_estimated_all = {
-            parameter_id
-            for parameter_id, parameter_values in self.parameters_all.items()
-            if
-            (
-                # Predecessor model sets the parameter to be estimated
-                (
-                    candidate_space.predecessor_model.parameters.get(
-                        parameter_id, None
-                    )
-                    == ESTIMATE
-                )
-                or (
-                    # Predecessor model takes the default PEtab parameter
-                    parameter_id
-                    not in candidate_space.predecessor_model.parameters
-                    and
-                    # And the default PEtab parameter is estimated
-                    # The PEtab problem of this subspace and the
-                    # `candidate_space` is the same, as verified earlier with
-                    # `self.check_compatibility_stepwise_method`.
-                    self.petab_parameters[parameter_id] == [ESTIMATE]
-                )
-            )
-        }
+        # parameters = []
+        # for parameter_id, parameter_value in self.parameters_all.items():
+        #     if additional_parameters.get(parameter_id, None) == ESTIMATE:
+        #         parameters.append(parameter_id)
+        #         continue
+        #
+        #     if parameter_id in additional_parameters:
+        #         # Presumably not estimated.
+        #         continue
+        #
+        # old_estimated_all = {
+        #     parameter_id
+        #     for parameter_id, parameter_values in self.parameters_all.items()
+        #     if
+        #     (
+        #         # Predecessor model sets the parameter to be estimated
+        #         (
+        #             candidate_space.predecessor_model.parameters.get(
+        #                 parameter_id, None
+        #             )
+        #             == ESTIMATE
+        #         )
+        #         or (
+        #             # Predecessor model takes the default PEtab parameter
+        #             parameter_id
+        #             not in candidate_space.predecessor_model.parameters
+        #             and
+        #             # And the default PEtab parameter is estimated
+        #             # The PEtab problem of this subspace and the
+        #             # `candidate_space` is the same, as verified earlier with
+        #             # `self.check_compatibility_stepwise_method`.
+        #             self.petab_parameters[parameter_id] == [ESTIMATE]
+        #         )
+        #     )
+        # }
 
     def __len__(self) -> int:
         """Get the number of models in this subspace."""

pyproject.toml

@@ -20,7 +20,6 @@ lint.ignore = [
     "S301", # pickle module used
     "S102", # Use of exec detected
     "S307", # Use of possibly insecure function
-    "B026", # Star-arg unpacking after a keyword argument
     "B006",
     "E722",
     "B904",