From 8ea19bdf71cdcd5a5f0aaf32d2c321166ce8b678 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Tue, 12 Nov 2024 11:14:55 +0100
Subject: [PATCH] ..

---
 petab_select/candidate_space.py | 27 ++++++++++++---------------
 petab_select/ui.py              |  1 -
 pyproject.toml                  |  2 +-
 setup.py                        |  1 -
 4 files changed, 13 insertions(+), 18 deletions(-)

diff --git a/petab_select/candidate_space.py b/petab_select/candidate_space.py
index 733faced..35aa90f5 100644
--- a/petab_select/candidate_space.py
+++ b/petab_select/candidate_space.py
@@ -1035,7 +1035,6 @@ def update_after_calibration(
         **kwargs,
     ) -> None:
         """See `CandidateSpace.update_after_calibration`."""
-
         super().update_after_calibration(
             *args,
             iteration_calibrated_models=iteration_calibrated_models,
@@ -1073,8 +1072,8 @@ def update_from_iteration_calibrated_models(
     ) -> bool:
         """Update ``self.best_models`` with the latest ``iteration_calibrated_models``
         and determine if there was a new best model. If so, return
-        ``False``. ``True`` otherwise."""
-
+        ``False``. ``True`` otherwise.
+        """
         go_into_switch_method = True
         for model in iteration_calibrated_models.values():
             if (
@@ -1112,7 +1111,8 @@ def update_from_iteration_calibrated_models(
 
     def insert_model_into_best_models(self, model_to_insert: Model) -> None:
         """Inserts a model into the list of best_models which are sorted
-        w.r.t. the criterion specified."""
+        w.r.t. the criterion specified.
+        """
         insert_index = bisect.bisect_left(
             [
                 model.get_criterion(self.criterion)
@@ -1125,8 +1125,8 @@ def insert_model_into_best_models(self, model_to_insert: Model) -> None:
     def consider(self, model: Union[Model, None]) -> bool:
         """Re-define ``consider`` of FAMoS to be the ``consider`` method
         of the ``inner_candidate_space``. Update all the attributes
-        changed in the ``consider`` method."""
-
+        changed in the ``consider`` method.
+        """
         if self.limit.reached():
             return False
 
@@ -1157,7 +1157,8 @@ def is_plausible(self, model: Model) -> bool:
 
     def check_swap(self, model: Model) -> bool:
         """Check if parameters that are swapped are contained in the
-        same swap parameter set."""
+        same swap parameter set.
+        """
         if self.method != Method.LATERAL:
             return True
 
@@ -1177,7 +1178,6 @@ def check_swap(self, model: Model) -> bool:
 
     def check_critical(self, model: Model) -> bool:
         """Check if the model contains all necessary critical parameters"""
-
         estimated_parameters_ids = set(model.get_estimated_parameter_ids_all())
         for critical_set in self.critical_parameter_sets:
             if not estimated_parameters_ids.intersection(set(critical_set)):
@@ -1188,8 +1188,8 @@ def switch_method(
         self,
     ) -> None:
         """Switch to the next method with respect to the history
-        of methods used and the switching scheme in ``self.method_scheme``."""
-
+        of methods used and the switching scheme in ``self.method_scheme``.
+        """
         previous_method = self.method
         next_method = previous_method
         logging.info("SWITCHING", self.method_history)
@@ -1248,7 +1248,6 @@ def switch_method(
 
     def update_method(self, method: Method):
         """Update ``self.method`` to ``method``."""
-
         self.method = method
 
     def switch_inner_candidate_space(
@@ -1261,7 +1260,6 @@ def switch_inner_candidate_space(
             excluded_hashes:
                 Hashes of excluded models.
         """
-
         # if self.method != Method.MOST_DISTANT:
         self.inner_candidate_space = self.inner_candidate_spaces[self.method]
         # reset the next inner candidate space with the current history of all
@@ -1275,8 +1273,8 @@ def jump_to_most_distant(
         self,
     ):
         """Jump to most distant model with respect to the history of all
-        calibrated models."""
-
+        calibrated models.
+        """
         predecessor_model = self.get_most_distant()
 
         logging.info("JUMPING: ", predecessor_model.parameters)
@@ -1319,7 +1317,6 @@ def get_most_distant(
         If not we choose the model in a subspace that has least distance to this
         complement model.
         """
-
         most_distance = 0
         most_distant_indices = []
 
diff --git a/petab_select/ui.py b/petab_select/ui.py
index 3a0d11d6..db183e7c 100644
--- a/petab_select/ui.py
+++ b/petab_select/ui.py
@@ -92,7 +92,6 @@ def start_iteration(
             :const:`petab_select.constants.MODELS`:
                 The uncalibrated models of the current iteration.
     """
-
     """
     FIXME(dilpath)
     - currently takes predecessor model from
diff --git a/pyproject.toml b/pyproject.toml
index 7bef2696..2de8f22b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,7 @@ line-length = 79
 exclude = ["amici_models"]
 extend-include = ["*.ipynb"]
 lint.ignore = [
-    # FIXME: we should be able to remive move of those
+    # FIXME: we should be able to remove move of those
     "D103", # Missing docstring in public function
     "S101", # Use of assert detected
     "E501", # Line too long
diff --git a/setup.py b/setup.py
index 13c51919..174cdbf1 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,6 @@ def read(fname):
 
 def absolute_links(txt):
     """Replace relative petab github links by absolute links."""
-
     raw_base = f"(https://raw.githubusercontent.com/{org}/{repo}/main/"
     embedded_base = f"(https://github.com/{org}/{repo}/tree/main/"
     # iterate over links