Flake8 changes

biosimulators · Aug 24, 2023 · 3953895 · 3953895
1 parent 0b4451f
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Showing 3 changed files with 48 additions and 46 deletions.
diff --git a/biosimulators_copasi/core.py b/biosimulators_copasi/core.py
@@ -19,13 +19,12 @@
 import biosimulators_copasi.utils as utils
 
 from biosimulators_utils.config import get_config, Config  # noqa: F401
-from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, \
-    StandardOutputErrorCapturerLevel, SedDocumentLog  # noqa: F401
+from biosimulators_utils.log.data_model import TaskLog, StandardOutputErrorCapturerLevel, SedDocumentLog  # noqa: F401
 from biosimulators_utils.viz.data_model import VizFormat  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat, VariableResults, SedDocumentResults  # noqa: F401
-from biosimulators_utils.sedml.data_model import (Algorithm, AlgorithmParameterChange, Task, Model, Simulation,
-                                                  ModelLanguage, ModelChange, ModelAttributeChange,
-                                                  UniformTimeCourseSimulation, Variable, Symbol, SedDocument)  # noqa: F401
+from biosimulators_utils.sedml.data_model import \
+    Algorithm, Task, Model, Simulation, ModelLanguage, ModelChange, ModelAttributeChange, \
+    UniformTimeCourseSimulation, Variable, SedDocument  # noqa: F401
 from biosimulators_utils.sedml import validation
 from biosimulators_utils.utils.core import raise_errors_warnings
 from biosimulators_utils.warnings import warn, BioSimulatorsWarning
@@ -35,7 +34,6 @@
 import basico
 import COPASI
 import lxml
-import math
 import numpy
 import os
 import tempfile
@@ -45,6 +43,7 @@
 
 proper_args: dict = {}
 
+
 def get_simulator_version():
     """ Get the version of COPASI
 
@@ -53,6 +52,7 @@ def get_simulator_version():
     """
     return basico.__version__
 
+
 def exec_sedml_docs_in_combine_archive(archive_filename: str, out_dir: str, config: Config = None,
                                        should_fix_copasi_generated_combine_archive: bool = None) -> tuple:
     """ Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
@@ -234,7 +234,8 @@ def get_copasi_error_message(sim: Simulation, details=None):
     return error_msg
 
 
-def preprocess_sed_task(task: Task, variables: list[Variable], config: Config = None) -> data_model.BasicoInitialization:
+def preprocess_sed_task(task: Task, variables: list[Variable],
+                        config: Config = None) -> data_model.BasicoInitialization:
     """ Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
     repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
 
@@ -282,7 +283,7 @@ def preprocess_sed_task(task: Task, variables: list[Variable], config: Config =
 
     # process solution algorithm
     has_events: bool = basico_data_model.getModel().getNumEvents() >= 1
-    copasi_algorithm = utils.get_algorithm(sim.algorithm.kisao_id, has_events, config=config)
+    copasi_algorithm = utils.get_algorithm(utc_sim.algorithm.kisao_id, has_events, config=config)
 
     # Create and return preprocessed simulation settings
     preprocessed_info = data_model.BasicoInitialization(copasi_algorithm, variables, has_events)
@@ -332,9 +333,6 @@ def _apply_model_changes(sedml_model: Model, copasi_algorithm: utils.CopasiAlgor
     legal_changes: list[ModelAttributeChange] = []
     illegal_changes: list[ModelChange] = []
 
-    specs = basico.get_species()
-    comps = basico.get_compartments()
-
     # If there's no changes, get out of here
     if not sedml_model.changes:
         return legal_changes, illegal_changes
@@ -368,8 +366,8 @@ def _apply_model_changes(sedml_model: Model, copasi_algorithm: utils.CopasiAlgor
             basico.set_compartment(compart_map["name"], initial_size=model_change.new_value)
             continue
 
-        #reaction = basico.get_reactions(sbml_id=sbml_id)
-        #if reaction is not None:
+        # reaction = basico.get_reactions(sbml_id=sbml_id)
+        # if reaction is not None:
         #    basico.set_reaction(sbml_id=sbml_id, ???)
         #    continue
 
@@ -382,7 +380,6 @@ def _apply_model_changes(sedml_model: Model, copasi_algorithm: utils.CopasiAlgor
 
 def _load_algorithm_parameters(sim: Simulation, copasi_algorithm: utils.CopasiAlgorithm, config: Config = None):
     # Load the algorithm parameter changes specified by `simulation.algorithm_parameter_changes`
-    method_parameters = {}
     algorithm_substitution_policy: AlgSubPolicy = bsu_sim_utils.get_algorithm_substitution_policy(config=config)
     requested_algorithm: Algorithm = sim.algorithm
     if copasi_algorithm.KISAO_ID != requested_algorithm.kisao_id:
@@ -411,4 +408,3 @@ def _load_algorithm_parameters(sim: Simulation, copasi_algorithm: utils.CopasiAl
         warn(warning_message.format(change.new_value, change.kisao_id), BioSimulatorsWarning)
 
     return
-
diff --git a/biosimulators_copasi/data_model.py b/biosimulators_copasi/data_model.py
@@ -13,10 +13,7 @@
 
 import basico
 import pandas
-from biosimulators_utils.data_model import ValueType
-import collections
 import enum
-import math
 
 __all__ = [
     'Units',
@@ -107,7 +104,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -125,7 +123,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -143,7 +142,8 @@ def get_value(self) -> bool:
         return self._value
 
     def set_value(self, new_value: bool):
-        if new_value is not None and not (type(new_value) == bool):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == bool):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -161,7 +161,8 @@ def get_value(self) -> int:
         return self._value
 
     def set_value(self, new_value: int):
-        if new_value is not None and not (type(new_value) == int):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == int):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -179,7 +180,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -197,7 +199,8 @@ def get_value(self) -> int:
         return self._value
 
     def set_value(self, new_value: int):
-        if new_value is not None and not (type(new_value) == int):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == int):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -224,7 +227,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -242,7 +246,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -260,7 +265,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -278,7 +284,8 @@ def get_value(self) -> int:
         return self._value
 
     def set_value(self, new_value: int):
-        if new_value is not None and not (type(new_value) == int):  # can't use isinstance because PEP 285:
+        # can't use isinstance because PEP 285:
+        if new_value is not None and not (type(new_value) == int):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -296,7 +303,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285:
+        # can't use isinstance because PEP 285:
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -325,7 +333,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -342,7 +351,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -360,7 +370,8 @@ def get_value(self) -> float:
         return self._value
 
     def set_value(self, new_value: float):
-        if new_value is not None and not (type(new_value) == float):  # can't use isinstance because PEP 285
+        # can't use isinstance because PEP 285
+        if new_value is not None and not (type(new_value) == float):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -378,7 +389,8 @@ def get_value(self) -> bool:
         return self._value
 
     def set_value(self, new_value: bool):
-        if new_value is not None and not (type(new_value) == bool):  # can't use isinstance because PEP 285:
+        # can't use isinstance because PEP 285:
+        if new_value is not None and not (type(new_value) == bool):  # noqa: E721
             raise ValueError
         self._value = new_value
 
@@ -432,12 +444,11 @@ def get_method_settings(self) -> dict[str, str]:
     def __eq__(self, other):
         if not isinstance(other, type(self)):
             return False
-        return (True if (
-            self.KISAO_ID == other.KISAO_ID,
-            self.ID == other.ID,
-            self.NAME == other.NAME,
+        equality = self.KISAO_ID == other.KISAO_ID and \
+            self.ID == other.ID and \
+            self.NAME == other.NAME and \
             self.CAN_SUPPORT_EVENTS == other.CAN_SUPPORT_EVENTS
-        ) else False)
+        return True if equality else False
 
 
 class GibsonBruckAlgorithm(CopasiAlgorithm):
@@ -757,6 +768,7 @@ class CopasiAlgorithmType(enum.Enum):
     HYBRID_RK45 = HybridRK45Algorithm
     SDE_SOLVE_RI5 = SDESolveRI5Algorithm
 
+
 class CopasiMappings:
     @staticmethod
     def format_to_copasi_reaction_name(sbml_name: str):
@@ -821,7 +833,7 @@ def _map_sbml_id_to_copasi_name(for_output: bool) -> dict[str, str]:
             compartment_mapping = {compartments.at[row, "sbml_id"]: str(row) for row in compartments.index}
             metabolites_mapping = {metabolites.at[row, "sbml_id"]: str(row) for row in metabolites.index}
             reactions_mapping = {reactions.at[row, "sbml_id"]: str(row) for row in reactions.index}
-            parameters_mapping = {parameters.at[row, "sbml_id"] : str(row) for row in parameters.index}
+            parameters_mapping = {parameters.at[row, "sbml_id"]: str(row) for row in parameters.index}
 
         # Combine mappings
         sbml_id_to_sbml_name_map = {"Time": "Time"}

diff --git a/biosimulators_copasi/utils.py b/biosimulators_copasi/utils.py
@@ -14,15 +14,14 @@
 from biosimulators_utils.combine.io import CombineArchiveReader, CombineArchiveWriter
 from biosimulators_utils.config import get_config, Config  # noqa: F401
 from biosimulators_utils.simulator.utils import get_algorithm_substitution_policy
-from biosimulators_utils.sedml.data_model import Variable, UniformTimeCourseSimulation, AlgorithmParameterChange
+from biosimulators_utils.sedml.data_model import AlgorithmParameterChange
 from kisao.data_model import AlgorithmSubstitutionPolicy, ALGORITHM_SUBSTITUTION_POLICY_LEVELS
 from kisao.utils import get_preferred_substitute_algorithm_by_ids
 import libsedml
 import lxml
 import os
 import shutil
 import tempfile
-import pandas
 
 __all__ = [
     'get_algorithm',
@@ -178,8 +177,3 @@ def fix_copasi_generated_combine_archive(in_filename, out_filename, config=None)
         CombineArchiveWriter().run(archive, archive_directory_name, out_filename)
     finally:
         shutil.rmtree(archive_directory_name)
-
-
-
-
-