Remove instances of trailing whitespace + whitespace on new lines

src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_combined.py

@@ -86,7 +86,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -105,7 +105,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth fHE growth case 1":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -124,7 +124,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                                
+
             "GDP growth fHE growth case 3":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -143,7 +143,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                                                
+
             "GDP growth fHE growth case 4":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -162,7 +162,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                                                
+
             "GDP growth fHE growth case 6":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -181,7 +181,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth FL case 1 const i":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -200,7 +200,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth FL case 2 const i":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -219,7 +219,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth FL case 1 vary i":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -238,7 +238,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                                
+
             "GDP growth FL case 2 vary i":
                 mix_scenarios(
                     get_parameters_for_status_quo(),

src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_scaling.py

@@ -70,11 +70,11 @@ def draw_parameters(self, draw_number, rng):
     def _get_scenarios(self) -> Dict[str, Dict]:
         """Return the Dict with values for the parameters that are changed, keyed by a name for the scenario.
         """
-        
+
         self.YEAR_OF_CHANGE = 2019
 
         return {
-   
+
             # =========== STATUS QUO ============
             "No growth status quo":
                 mix_scenarios(
@@ -85,7 +85,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth status quo":
                 mix_scenarios(
                     self._baseline(),
@@ -95,7 +95,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth fHE growth case 1 status quo":
                 mix_scenarios(
                     self._baseline(),
@@ -105,7 +105,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
- 
+
             "GDP growth fHE growth case 3 status quo":
                 mix_scenarios(
                     self._baseline(),
@@ -116,7 +116,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                     }
                 ),
 
- 
+
             "GDP growth fHE growth case 4 status quo":
                 mix_scenarios(
                     self._baseline(),
@@ -136,7 +136,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-   
+
             # =========== PERFECT CONSUMABLES AVAILABILITY ============
             "No growth perfect consumables":
                 mix_scenarios(
@@ -149,7 +149,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth perfect consumables":
                 mix_scenarios(
                     self._baseline(),
@@ -161,7 +161,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth fHE growth case 1 perfect consumables":
                 mix_scenarios(
                     self._baseline(),
@@ -173,7 +173,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
- 
+
             "GDP growth fHE growth case 3 perfect consumables":
                 mix_scenarios(
                     self._baseline(),
@@ -186,7 +186,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                     }
                 ),
 
- 
+
             "GDP growth fHE growth case 4 perfect consumables":
                 mix_scenarios(
                     self._baseline(),
@@ -227,7 +227,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                           },
                     }
                 ),
-                
+
             "GDP growth perfect healthsystem":
                 mix_scenarios(
                     self._baseline(),
@@ -243,7 +243,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                           },
                     }
                 ),
-                
+
             "GDP growth fHE growth case 1 perfect healthsystem":
                 mix_scenarios(
                     self._baseline(),
@@ -259,7 +259,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                           },
                     }
                 ),
- 
+
             "GDP growth fHE growth case 3 perfect healthsystem":
                 mix_scenarios(
                     self._baseline(),
@@ -276,7 +276,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                     }
                 ),
 
- 
+
             "GDP growth fHE growth case 4 perfect healthsystem":
                 mix_scenarios(
                     self._baseline(),
@@ -310,7 +310,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                 ),
 
         }
-        
+
     def _baseline(self) -> Dict:
         """Return the Dict with values for the parameter changes that define the baseline scenario. """
         return mix_scenarios(

src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_test_scaling.py

@@ -86,7 +86,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -105,7 +105,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                
+
             "GDP growth fHE growth case 1":
                 mix_scenarios(
                     get_parameters_for_status_quo(),
@@ -124,7 +124,7 @@ def _get_scenarios(self) -> Dict[str, Dict]:
                       },
                     }
                 ),
-                    
+
             "GDP growth fHE growth case 6":
                 mix_scenarios(
                     get_parameters_for_status_quo(),

src/scripts/profiling/run_profiling.py

@@ -295,7 +295,7 @@ def run_profiling(
         print(f"Writing {output_ipysession_file}", end="...", flush=True)
         scale_run_session.save(output_ipysession_file)
         print("done")
-        
+
     if write_flat_html:
         output_html_file = output_dir / f"{output_name}.flat.html"
         console_renderer = ConsoleRenderer(

src/scripts/profiling/scale_run.py

@@ -26,10 +26,10 @@ def save_arguments_to_json(arguments_dict: dict, output_path: Path):
     with open(output_path, "w") as f:
         json.dump(
             {
-                k: str(v) if isinstance(v, Path) else v 
+                k: str(v) if isinstance(v, Path) else v
                 for k, v in arguments_dict.items()
-            }, 
-            f, 
+            },
+            f,
             indent=4
         )
 

src/scripts/task_runner/generate_html.py

@@ -101,8 +101,8 @@ def get_html_for_commit(commit_dir: Path) -> str:
 <body>
 <h1>$title</h1>
 <p style="font-size: small;">
-    This page was generated on $generated_time. The 
-    <a href="https://github.com/UCL/TLOmodel/actions/workflows/calibration.yaml">calibration workflow</a> runs every 
+    This page was generated on $generated_time. The
+    <a href="https://github.com/UCL/TLOmodel/actions/workflows/calibration.yaml">calibration workflow</a> runs every
     night on the latest new commit on the master branch. <a href="#" id="toggleIncomplete">toggle incomplete</a>
 </p>
 $body

src/tlo/analysis/utils.py

@@ -1131,7 +1131,7 @@ def get_parameters_for_status_quo() -> Dict:
             "equip_availability": "all",  # <--- NB. Existing calibration is assuming all equipment is available
         },
     }
-    
+
 def get_parameters_for_standard_mode2_runs() -> Dict:
     """
     Returns a dictionary of parameters and their updated values to indicate

src/tlo/core.py

@@ -170,7 +170,7 @@ def _default_value(self) -> Any:
         """
         Default value for this property, which will be used to fill the respective columns
         of the population dataframe, for example.
-        
+
         If not explicitly set, it will fall back on the ``PANDAS_TYPE_DEFAULT_TYPE_MAP``.
         If a value is provided, it must:
 
@@ -386,8 +386,8 @@ def initialise_population(self, population: Population) -> None:
 
         Modules that wish to implement this behaviour do not need to implement this method,
         it will be inherited automatically. Modules that wish to perform additional steps
-        during the initialise_population stage should reimplement this method and call 
-        
+        during the initialise_population stage should reimplement this method and call
+
         ```python
         super().initialise_population(population=population)
         ```

src/tlo/logging/helpers.py

@@ -59,11 +59,11 @@ def get_dataframe_row_as_dict_for_logging(
     columns: Optional[Iterable[str]] = None,
 ) -> dict:
     """Get row of a pandas dataframe in a format suitable for logging.
-    
+
     Retrieves entries for all or a subset of columns for a particular row in a dataframe
     and returns a dict keyed by column name, with values NumPy or pandas extension types
     which should be the same for all rows in dataframe.
-    
+
     :param dataframe: Population properties dataframe to get properties from.
     :param row_label: Unique index label identifying row in dataframe.
     :param columns: Set of column names to extract - if ``None``, the default, all

src/tlo/methods/alri.py

@@ -3040,7 +3040,7 @@ def apply(self, person_id):
 
         assert 'fast_breathing_pneumonia' == \
                self.module.get_imci_classification_based_on_symptoms(
-                   child_is_younger_than_2_months=False, 
+                   child_is_younger_than_2_months=False,
                    symptoms=self.sim.modules['SymptomManager'].has_what(person_id=person_id)
                )
 

src/tlo/methods/consumables.py

@@ -266,7 +266,7 @@ def _lookup_availability_of_consumables(self,
 
     def on_simulation_end(self):
         """Do tasks at the end of the simulation.
-         
+
         Raise warnings and enter to log about item_codes not recognised.
         """
         if self._not_recognised_item_codes:

src/tlo/methods/demography.py

@@ -134,7 +134,7 @@ def __init__(self, name=None, resourcefilepath=None, equal_allocation_by_distric
         ),
 
         'district_num_of_residence': Property(
-            Types.CATEGORICAL, 
+            Types.CATEGORICAL,
             'The district number in which the person is resident',
             categories=['SET_AT_RUNTIME']
         ),

src/tlo/population.py

@@ -212,7 +212,7 @@ def individual_properties(
         In this case on exit from the ``with`` block in which the context is entered,
         any updates to the individual properties will be written back to the population
         dataframe.
-        
+
         Once the ``with`` block in which the context is entered has been exited the view
         returned will raise an error on any subsequent attempts at reading or writing
         properties.

tests/test_healthburden.py

@@ -131,7 +131,7 @@ def test_arithmetic_of_disability_aggregation_calcs(seed):
     rfp = Path(os.path.dirname(__file__)) / '../resources'
 
     class ModuleWithPersonsAffected(Module):
-        
+
         def __init__(self, persons_affected, name=None):
             super().__init__(name=name)
             self.persons_affected = persons_affected
@@ -249,7 +249,7 @@ def report_daly_values(self):
         DiseaseThatCausesB(persons_affected=1),
         DiseaseThatCausesAandB(persons_affected=2),
         # intentionally two instances of DiseaseThatCausesC
-        DiseaseThatCausesC(persons_affected=3, name='DiseaseThatCausesC1'),  
+        DiseaseThatCausesC(persons_affected=3, name='DiseaseThatCausesC1'),
         DiseaseThatCausesC(persons_affected=3, name='DiseaseThatCausesC2'),
         DiseaseThatCausesNothing(),
         # Disable sorting to allow registering multiple instances of DiseaseThatCausesC

tests/test_symptommanager.py

@@ -237,7 +237,7 @@ def test_has_what_via_individual_properties(seed, supply_disease_module: bool):
     5     0           1           0
     6     0           0           1
     7     0           0           0
-    
+
     We will then assert that has_what returns the expected symptoms for the
     individuals, and that supplying either the person_id keyword or the
     individual_properties keyword gives the same answer.