diff --git a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_combined.py b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_combined.py
index a46dfa75fe..c76becfd78 100644
--- a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_combined.py
+++ b/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(),
diff --git a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_scaling.py b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_scaling.py
index 28cd7ff171..1b64e1713b 100644
--- a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_scaling.py
+++ b/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(
diff --git a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_test_scaling.py b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_test_scaling.py
index 5d29102e8b..78ffd1dbcb 100644
--- a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_capabilities_expansion_test_scaling.py
+++ b/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(),
diff --git a/src/scripts/profiling/run_profiling.py b/src/scripts/profiling/run_profiling.py
index 882894d6af..20386fe13b 100644
--- a/src/scripts/profiling/run_profiling.py
+++ b/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(
diff --git a/src/scripts/profiling/scale_run.py b/src/scripts/profiling/scale_run.py
index 735d1e7ba3..c4dfa57e46 100644
--- a/src/scripts/profiling/scale_run.py
+++ b/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
)
diff --git a/src/scripts/task_runner/generate_html.py b/src/scripts/task_runner/generate_html.py
index b9116c57f2..1a9b4a385b 100644
--- a/src/scripts/task_runner/generate_html.py
+++ b/src/scripts/task_runner/generate_html.py
@@ -101,8 +101,8 @@ def get_html_for_commit(commit_dir: Path) -> str:
$title
- This page was generated on $generated_time. The
- calibration workflow runs every
+ This page was generated on $generated_time. The
+ calibration workflow runs every
night on the latest new commit on the master branch. toggle incomplete
$body
diff --git a/src/tlo/analysis/utils.py b/src/tlo/analysis/utils.py
index 2808ab57a5..4a71c8500b 100644
--- a/src/tlo/analysis/utils.py
+++ b/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
diff --git a/src/tlo/core.py b/src/tlo/core.py
index 9fbbf08893..c6364458dc 100644
--- a/src/tlo/core.py
+++ b/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)
```
diff --git a/src/tlo/logging/helpers.py b/src/tlo/logging/helpers.py
index 99fc51c473..ec6239239c 100644
--- a/src/tlo/logging/helpers.py
+++ b/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
diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py
index f004e19819..b9f3048071 100644
--- a/src/tlo/methods/alri.py
+++ b/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)
)
diff --git a/src/tlo/methods/consumables.py b/src/tlo/methods/consumables.py
index 674035ad98..01264cb1f0 100644
--- a/src/tlo/methods/consumables.py
+++ b/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:
diff --git a/src/tlo/methods/demography.py b/src/tlo/methods/demography.py
index e58f3895f4..3b4d20265e 100644
--- a/src/tlo/methods/demography.py
+++ b/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']
),
diff --git a/src/tlo/population.py b/src/tlo/population.py
index 37f5fccfdf..26af2f3185 100644
--- a/src/tlo/population.py
+++ b/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.
diff --git a/tests/test_healthburden.py b/tests/test_healthburden.py
index 585549e9db..a01a00f585 100644
--- a/tests/test_healthburden.py
+++ b/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
diff --git a/tests/test_symptommanager.py b/tests/test_symptommanager.py
index 73ea7619d0..05981a8867 100644
--- a/tests/test_symptommanager.py
+++ b/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.