From cc9024cf27bf233c7cc10cb34610b86f6ff2d40a Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Wed, 15 Oct 2025 23:36:24 -0400 Subject: [PATCH 1/8] remove hardcoding and update param values --- resources/ResourceFile_Alri/Calculations.csv | 3 -- resources/ResourceFile_Alri/Lazzerini CFR.csv | 3 -- .../ResourceFile_Alri/Parameter_values.csv | 4 +- .../ResourceFile_Alri/Pathogen_specific.csv | 3 -- src/tlo/methods/alri.py | 44 +++++++++++++++---- 5 files changed, 38 insertions(+), 19 deletions(-) delete mode 100644 resources/ResourceFile_Alri/Calculations.csv delete mode 100644 resources/ResourceFile_Alri/Lazzerini CFR.csv delete mode 100644 resources/ResourceFile_Alri/Pathogen_specific.csv diff --git a/resources/ResourceFile_Alri/Calculations.csv b/resources/ResourceFile_Alri/Calculations.csv deleted file mode 100644 index d7d0eef9fd..0000000000 --- a/resources/ResourceFile_Alri/Calculations.csv +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f93d78ef1f1bfac70eae5d8414150f811fa3bc6198b1196053d876766a758dd3 -size 10799 diff --git a/resources/ResourceFile_Alri/Lazzerini CFR.csv b/resources/ResourceFile_Alri/Lazzerini CFR.csv deleted file mode 100644 index b65822ad94..0000000000 --- a/resources/ResourceFile_Alri/Lazzerini CFR.csv +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:c599eb5bc71c447d0845a2796b5326743c4ae18d1c758ff8bcafe90b5312e5a3 -size 339 diff --git a/resources/ResourceFile_Alri/Parameter_values.csv b/resources/ResourceFile_Alri/Parameter_values.csv index 23004f9ee1..9c463c3dee 100644 --- a/resources/ResourceFile_Alri/Parameter_values.csv +++ b/resources/ResourceFile_Alri/Parameter_values.csv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:aa4d99fa2ad1e63a24d69cd955455da80404e21eacb92f776ee1c4d96f411f14 -size 9953 +oid sha256:6d97a60e3f3a9aee304f5bfbce548fb74df7e7effd3370bfec92398dcfdce275 +size 13774 diff --git a/resources/ResourceFile_Alri/Pathogen_specific.csv b/resources/ResourceFile_Alri/Pathogen_specific.csv deleted file mode 100644 index 3e1438da8f..0000000000 --- a/resources/ResourceFile_Alri/Pathogen_specific.csv +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1c5f9de464fece0d6232f54cbdf985362fcd3a833dc806108ffe0d016f6f5444 -size 1284 diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index 9c8460961d..f23f257166 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,7 +28,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor @@ -744,6 +743,29 @@ class Alri(Module, GenericFirstAppointmentsMixin): Parameter(Types.REAL, 'The probability for scheduling a follow-up appointment following treatment failure' ), + + # Module configuration parameters ----- + 'main_polling_frequency': + Parameter(Types.INT, + 'Frequency of main polling event in months' + ), + 'child_age_threshold': + Parameter(Types.INT, + 'Maximum age in years for child classification' + ), + 'inpatient_bed_days': + Parameter(Types.INT, + 'Number of bed days required for inpatient care of ALRI' + ), + 'treatment_window_days': + Parameter(Types.INT, + 'Buffer window days that ALRI treatment event can be scheduled' + ), + 'follow_up_appointment_days': + Parameter(Types.INT, + 'Days after which follow-up appointment is scheduled' + ), + } PROPERTIES = { @@ -1372,7 +1394,8 @@ def do_at_generic_first_appt( # Action taken when a child (under 5 years old) presents at a # generic appointment (emergency or non-emergency) with symptoms # of `cough` or `difficult_breathing`. - if individual_properties["age_years"] <= 5 and ( + p = self.parameters + if individual_properties["age_years"] <= p['child_age_threshold'] and ( ("cough" in symptoms) or ("difficult_breathing" in symptoms) ): self.record_sought_care_for_alri() @@ -1384,7 +1407,7 @@ def do_at_generic_first_appt( schedule_hsi_event( event, topen=self.sim.date, - tclose=self.sim.date + pd.DateOffset(days=1), + tclose=self.sim.date + pd.DateOffset(days=p['treatment_window_days']), priority=1, ) @@ -1901,7 +1924,7 @@ class AlriPollingEvent(RegularEvent, PopulationScopeEventMixin): age-groups. This is a small effect when the frequency of the polling event is high.""" def __init__(self, module): - super().__init__(module, frequency=DateOffset(months=2)) + super().__init__(module, frequency=DateOffset(months=module.parameters['main_polling_frequency'])) @property def fraction_of_year_between_polling_event(self): @@ -2273,7 +2296,8 @@ def _as_in_patient(self, facility_level): f'{self._treatment_id_stub}_Inpatient{"_Followup" if self.is_followup_following_treatment_failure else ""}' self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({}) self.ACCEPTED_FACILITY_LEVEL = facility_level - self.BEDDAYS_FOOTPRINT = self.make_beddays_footprint({'general_bed': 7}) + bed_days = self.module.parameters['inpatient_bed_days'] + self.BEDDAYS_FOOTPRINT = self.make_beddays_footprint({'general_bed': bed_days}) def _refer_to_next_level_up(self): """Schedule this event to occur again today at the next level-up (if there is a next level-up).""" @@ -2290,6 +2314,8 @@ def _next_in_sequence(seq: tuple, x: str): _next_level_up = _next_in_sequence(self._facility_levels, self.ACCEPTED_FACILITY_LEVEL) if _next_level_up is not None: + p = self.module.parameters + self.sim.modules['HealthSystem'].schedule_hsi_event( HSI_Alri_Treatment( module=self.module, @@ -2298,7 +2324,7 @@ def _next_in_sequence(seq: tuple, x: str): facility_level=_next_level_up ), topen=self.sim.date, - tclose=self.sim.date + pd.DateOffset(days=1), + tclose=self.sim.date + pd.DateOffset(days=p['treatment_window_days']), priority=0) def _refer_to_become_inpatient(self): @@ -2318,8 +2344,10 @@ def _refer_to_become_inpatient(self): priority=0) def _schedule_follow_up_following_treatment_failure(self): - """Schedule a copy of this event to occur in 5 days time as a 'follow-up' appointment at this level + """Schedule a copy of this event to occur as a 'follow-up' appointment at this level (if above "0") and as an in-patient.""" + + p = self.module.parameters self.sim.modules['HealthSystem'].schedule_hsi_event( HSI_Alri_Treatment( module=self.module, @@ -2328,7 +2356,7 @@ def _schedule_follow_up_following_treatment_failure(self): facility_level=self.ACCEPTED_FACILITY_LEVEL if self.ACCEPTED_FACILITY_LEVEL != "0" else "1a", is_followup_following_treatment_failure=True, ), - topen=self.sim.date + pd.DateOffset(days=5), + topen=self.sim.date + pd.DateOffset(days=p['follow_up_appointment_days']), tclose=None, priority=0) From 666ecefd1292e1cd56d582fc4e13cbb1e70aec7d Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Wed, 15 Oct 2025 23:41:22 -0400 Subject: [PATCH 2/8] test linting change --- src/tlo/methods/alri.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index f23f257166..48d8e733b9 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,6 +28,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor From 65a68a7d134555aa0cd5fb057d2ea14006511e56 Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Wed, 15 Oct 2025 23:48:42 -0400 Subject: [PATCH 3/8] test linting change --- src/tlo/methods/alri.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index 48d8e733b9..f23f257166 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,7 +28,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor From c5c1f49faf5427a21b9c759e3da9e4f80a5f8bab Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Mon, 27 Oct 2025 12:33:13 -0400 Subject: [PATCH 4/8] fix linting error --- src/tlo/methods/alri.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index f23f257166..48d8e733b9 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,6 +28,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor From fa7bf70eb782e94b288c3b6fcbe8345a925acbfa Mon Sep 17 00:00:00 2001 From: Margherita Molaro <48129834+marghe-molaro@users.noreply.github.com> Date: Thu, 6 Nov 2025 21:31:32 +0000 Subject: [PATCH 5/8] Add hardcoded param --- src/tlo/methods/alri.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index 48d8e733b9..8707e674ad 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -1943,7 +1943,7 @@ def get_probs_of_acquiring_pathogen(self, interval_as_fraction_of_a_year: float) # Compute the incidence rate for each person getting Alri and then convert into a probability # getting all children that do not currently have an Alri episode (never had or last episode resolved) mask_could_get_new_alri_event = ( - df.is_alive & (df.age_years < 5) & ~df.ri_current_infection_status & + df.is_alive & (df.age_years < m.parameters['child_age_threshold']) & ~df.ri_current_infection_status & ((df.ri_end_of_current_episode < self.sim.date) | pd.isnull(df.ri_end_of_current_episode)) ) From 1284bdba40dcf49076837b766cc270728c1df662 Mon Sep 17 00:00:00 2001 From: Margherita Molaro <48129834+marghe-molaro@users.noreply.github.com> Date: Thu, 6 Nov 2025 21:33:47 +0000 Subject: [PATCH 6/8] ruff fixes --- .../alri_azure_run_scenarios/base_scenario_inc_mort_plots.py | 1 - .../alri_azure_run_scenarios/base_scenario_plots.py | 1 - .../alri_calibration_plots/GBD_comparison_plots.py | 1 - .../alri_calibration_plots/analysis_Alri_default_params.py | 1 - .../analysis_Alri_with_and_without_treatment.py | 1 - .../alri_calibration_plots/analysis_effect_of_treatment.py | 1 - .../alri_calibration_plots/analysis_pulse_oximeter_vs_none.py | 1 - .../Alri_analyses/alri_calibration_plots/baseline_outputs.py | 1 - src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py | 1 - .../calc_5y_survival_following_treatment.py | 1 - src/scripts/breast_cancer_analyses/breast_cancer_analyses.py | 1 - .../calc_5y_survival_following_treatment.py | 1 - .../analysis_scripts/analysis_all_calibration.py | 1 - .../analysis_cause_of_death_and_disability_calibrations.py | 1 - .../analysis_compare_appt_usage_real_and_simulation.py | 1 - .../analysis_scripts/analysis_demography_calibrations.py | 1 - .../analysis_scripts/analysis_hsi_descriptions.py | 1 - .../analysis_scripts/analysis_hsi_events_by_date.py | 1 - .../analysis_scripts/plot_appt_use_by_hsi.py | 1 - .../calibration_analyses/analysis_scripts/plot_legends.py | 1 - .../description_of_data_only/coverage_of_gbd_causes.py | 1 - .../description_of_data_only/graph_of_gbd_data.py | 1 - .../calibration_analyses/scenarios/long_run_no_diseases.py | 1 - .../cardiometabolicdisorders_plots.py | 1 - .../cervical_cancer_analyses/cervical_cancer_analyses.py | 1 - .../cervical_cancer_calibration_check.py | 1 - .../analysis_hss_elements.py | 1 - .../analysis_vertical_programs_with_and_without_hss.py | 1 - .../roi_analysis_horizontal_vs_vertical.py | 1 - .../analysis_impact_of_consumable_scenarios.py | 1 - src/scripts/contraception/contraception_calibration.py | 1 - src/scripts/contraception/f_steril_use_2010vs2020.py | 1 - src/scripts/contraception/fnc_analyse_contraception.py | 1 - .../copd_analyses/analysis_copd_prevalence_and_deaths.py | 1 - src/scripts/copd_analyses/copd_calibrations.py | 1 - src/scripts/costing/cost_estimation.py | 1 - src/scripts/costing/costing_overview_analysis.py | 1 - src/scripts/costing/costing_validation.py | 1 - src/scripts/data_file_processing/formatting_demography_data.py | 1 - src/scripts/data_file_processing/formatting_gbd_data.py | 1 - .../consumables_availability_estimation.py | 1 - ...te_consumable_availability_scenarios_for_impact_analysis.py | 1 - src/scripts/depression_analyses/analyses_depression.py | 1 - src/scripts/dev/scenarios/test_scenario_1.py | 1 - .../dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py | 1 - src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py | 1 - .../th_testing/single_sweep/analysing_mockitis_single_sweep.py | 1 - .../dev/th_testing/single_sweep/mockitis_single_sweep.py | 1 - .../analysis_diarrhoea_with_and_without_treatment.py | 1 - .../diarrhoea_analyses/analysis_diarrhoea_with_treatment.py | 1 - .../enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py | 1 - .../enhanced_lifestyle_calibrations.py | 1 - src/scripts/epi/analysis_epi.py | 1 - src/scripts/epilepsy_analyses/analysis_epilepsy.py | 1 - src/scripts/get_properties/properties_graph.py | 1 - .../analysis_comparison_of_impact_in_different_scenarios.py | 2 +- .../analysis_effect_of_each_treatment_multiple_scenarios.py | 1 - .../analysis_impact_of_consumables_availability.py | 1 - .../scenario_impact_of_capabilities_expansion_combined.py | 1 - .../scenario_impact_of_capabilities_expansion_scaling.py | 1 - .../scenario_impact_of_capabilities_expansion_test_scaling.py | 1 - .../scenario_impact_of_const_capabilities_expansion.py | 1 - .../impact_of_mode/analysis_health_impact_of_mode.py | 1 - .../healthsystem/impact_of_mode/analysis_hsi_by_mode.py | 1 - .../impact_of_policy/analysis_effect_of_each_treatment.py | 1 - .../healthsystem/impact_of_policy/scenario_impact_of_policy.py | 1 - .../org_chart_of_hsi/plot_org_chart_treatment_ids.py | 1 - src/scripts/hiv/projections_jan2023/output_plots.py | 1 - src/scripts/htm_scenario_analyses/scenario_plots.py | 1 - .../analysis_historical_changes_in_hr.py | 1 - .../examining_data_historic_changes_in_hr.py | 1 - src/scripts/malaria/malaria_plots.py | 1 - .../analysis_scripts/analysis_utility_functions.py | 1 - .../maternal_newborn_health_thesis_analysis.py | 1 - .../calibration/calibration_outputs_with_ci.py | 2 +- src/scripts/measles/analysis_measles.py | 1 - src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py | 1 - src/scripts/measles/analysis_measles_deaths.py | 1 - src/scripts/measles/analysis_measles_scenarios.py | 1 - .../calc_5y_survival_following_treatment.py | 1 - .../oesophagealcancer_analyses/oesophagealcancer_analyses.py | 1 - .../calc_5y_survival_following_treatment.py | 1 - .../other_adult_cancers_analyses.py | 1 - .../other_adult_cancers_calibration_to_deaths.py | 1 - .../analysis_effect_of_each_treatment.py | 1 - .../analysis_impact_of_healthsystem.py | 1 - src/scripts/profiling/batch_test.py | 1 - src/scripts/profiling/heavy_use_of_bed_days.py | 1 - src/scripts/profiling/heavy_use_of_spurious_symptoms.py | 1 - .../run_full_model_with_hard_constraints_in_healthsystem.py | 1 - .../run_with_high_intensity_of_HSI_and_simplified_births.py | 1 - src/scripts/profiling/scale_run.py | 1 - src/scripts/profiling/symptom_manager_bookkeeping_profiling.py | 1 - .../calc_5y_survival_following_treatment.py | 1 - .../prostate_cancer_analyses/prostate_cancer_analyses.py | 1 - src/scripts/rti/analysis_rti.py | 1 - src/scripts/rti/analysis_rti_deaths.py | 1 - src/scripts/rti/analysis_rti_single_vs_multiple_injury.py | 1 - src/scripts/schistosomiasis/schisto_analysis.py | 1 - src/scripts/schistosomiasis/schisto_calibration_check.py | 1 - src/scripts/schistosomiasis/schisto_single_run_local.py | 1 - .../analysis_simplified_births_calibrations.py | 1 - src/scripts/tb/output_plots_tb.py | 1 - .../stunting/stunting_analysis_plots.py | 1 - src/tlo/analysis/hsi_events.py | 1 - src/tlo/analysis/life_expectancy.py | 1 - src/tlo/analysis/utils.py | 1 - src/tlo/cli.py | 1 - src/tlo/lm.py | 1 - src/tlo/logging/core.py | 1 - src/tlo/methods/alri.py | 1 - src/tlo/methods/bed_days.py | 1 - src/tlo/methods/bladder_cancer.py | 1 - src/tlo/methods/breast_cancer.py | 1 - src/tlo/methods/cardio_metabolic_disorders.py | 1 - src/tlo/methods/care_of_women_during_pregnancy.py | 1 - src/tlo/methods/causes.py | 1 - src/tlo/methods/cervical_cancer.py | 1 - src/tlo/methods/chronicsyndrome.py | 1 - src/tlo/methods/consumables.py | 1 - src/tlo/methods/contraception.py | 1 - src/tlo/methods/copd.py | 1 - src/tlo/methods/demography.py | 1 - src/tlo/methods/depression.py | 1 - src/tlo/methods/diarrhoea.py | 1 - src/tlo/methods/dxmanager.py | 1 - src/tlo/methods/enhanced_lifestyle.py | 1 - src/tlo/methods/epi.py | 1 - src/tlo/methods/epilepsy.py | 1 - src/tlo/methods/equipment.py | 1 - src/tlo/methods/healthburden.py | 1 - src/tlo/methods/healthseekingbehaviour.py | 1 - src/tlo/methods/healthsystem.py | 1 - src/tlo/methods/hiv.py | 1 - src/tlo/methods/hiv_tb_calibration.py | 1 - src/tlo/methods/hsi_event.py | 1 - src/tlo/methods/hsi_generic_first_appts.py | 1 - src/tlo/methods/labour.py | 1 - src/tlo/methods/malaria.py | 1 - src/tlo/methods/measles.py | 1 - src/tlo/methods/mockitis.py | 1 - src/tlo/methods/newborn_outcomes.py | 1 - src/tlo/methods/oesophagealcancer.py | 1 - src/tlo/methods/other_adult_cancers.py | 1 - src/tlo/methods/postnatal_supervisor.py | 1 - src/tlo/methods/pregnancy_helper_functions.py | 1 - src/tlo/methods/pregnancy_supervisor.py | 1 - src/tlo/methods/prostate_cancer.py | 1 - src/tlo/methods/rti.py | 1 - src/tlo/methods/schisto.py | 1 - src/tlo/methods/simplified_births.py | 1 - src/tlo/methods/stunting.py | 1 - src/tlo/methods/symptommanager.py | 1 - src/tlo/methods/tb.py | 1 - src/tlo/population.py | 1 - src/tlo/scenario.py | 1 - src/tlo/test/random_birth.py | 1 - src/tlo/util.py | 1 - tests/bitset_handler/conftest.py | 1 - tests/bitset_handler/test_bitset_pandas_dtype.py | 1 - tests/bitset_handler/test_bitset_set_like_interactions.py | 1 - tests/test_alri.py | 1 - tests/test_analysis.py | 1 - tests/test_antenatal_interventions.py | 1 - tests/test_basic_sims.py | 1 - tests/test_beddays.py | 1 - tests/test_bitset.py | 1 - tests/test_bladder_cancer.py | 1 - tests/test_breast_cancer.py | 1 - tests/test_cardiometabolicdisorders.py | 1 - tests/test_cervical_cancer.py | 1 - tests/test_consumables.py | 1 - tests/test_contraception.py | 1 - tests/test_control_order_of_events.py | 1 - tests/test_copd.py | 1 - tests/test_core.py | 1 - tests/test_demography.py | 1 - tests/test_depression.py | 1 - tests/test_diarrhoea.py | 1 - tests/test_docs.py | 1 - tests/test_dxmanager.py | 1 - tests/test_enhanced_lifestyle.py | 1 - tests/test_epi.py | 1 - tests/test_epilepsy.py | 1 - tests/test_equipment.py | 1 - tests/test_find_events_for_person_in_event_queue.py | 1 - tests/test_fullmodel.py | 1 - tests/test_healthburden.py | 1 - tests/test_healthcareseeking.py | 1 - tests/test_healthsystem.py | 1 - tests/test_hiv.py | 1 - tests/test_htm_scaleup.py | 1 - tests/test_labour.py | 1 - tests/test_life_expectancy.py | 1 - tests/test_lm.py | 1 - tests/test_logging.py | 1 - tests/test_logging_end_to_end.py | 1 - tests/test_malaria.py | 1 - tests/test_maternal_health_helper_and_analysis_functions.py | 1 - tests/test_measles.py | 1 - tests/test_module_dependencies.py | 1 - tests/test_newborn_outcomes.py | 1 - tests/test_oesophagealcancer.py | 1 - tests/test_other_adult_cancers.py | 1 - tests/test_population.py | 1 - tests/test_postnatal.py | 1 - tests/test_pregnancy_supervisor.py | 1 - tests/test_progressbar.py | 1 - tests/test_prostate_cancer.py | 1 - tests/test_rti.py | 1 - tests/test_scenario.py | 1 - tests/test_schisto.py | 1 - tests/test_simplified_births.py | 1 - tests/test_simulation.py | 1 - tests/test_stunting.py | 1 - tests/test_symptommanager.py | 1 - tests/test_tb.py | 1 - tests/test_utils.py | 3 +-- 218 files changed, 3 insertions(+), 219 deletions(-) diff --git a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py index b5c14fa599..8659aab8ca 100644 --- a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py +++ b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py index beda8138d8..5b590b3b3d 100644 --- a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py +++ b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py @@ -8,7 +8,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py b/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py index 2cf9cc6068..19854860f5 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py @@ -9,7 +9,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py index 19719b5344..e0695026a3 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py @@ -11,7 +11,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py index 06be9a23aa..4f2c0120c0 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py @@ -8,7 +8,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py index 59dfe7474f..c625840158 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py @@ -6,7 +6,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation from tlo.methods import ( alri, diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py index e350248505..f3e2c5fa59 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py @@ -9,7 +9,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py b/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py index 77360e618f..95196c4ccf 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py b/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py index 227e2e28d3..940ebbee47 100644 --- a/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py +++ b/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py @@ -12,7 +12,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py index 9d69c0be7f..7248c81071 100644 --- a/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py @@ -12,7 +12,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py b/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py index b94537e7ef..725c4b4eac 100644 --- a/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py +++ b/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py @@ -14,7 +14,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py index dc8a0b0ab4..afbc9d3e9a 100644 --- a/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py @@ -13,7 +13,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py index 7135d4fd89..07a4dfb178 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py @@ -8,7 +8,6 @@ import analysis_demography_calibrations import analysis_hsi_descriptions import plot_legends - from scripts.calibration_analyses.analysis_scripts import ( analysis_compare_appt_usage_real_and_simulation, plot_appt_use_by_hsi, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py index e6fa66603d..6e71403368 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py index 491284b83b..b85a42c907 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py @@ -5,7 +5,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py index 64ac672158..d7b2f8b46d 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py @@ -17,7 +17,6 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.ticker import FormatStrFormatter - from tlo.analysis.utils import ( extract_results, format_gbd, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py index da337130af..6d1eec4cc1 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py @@ -6,7 +6,6 @@ import pandas as pd import squarify from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( COARSE_APPT_TYPE_TO_COLOR_MAP, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py index 996579d80c..acf4ee50ec 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( extract_results, diff --git a/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py b/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py index 2aa3dae473..6e3797e7dd 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py +++ b/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py @@ -4,7 +4,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( bin_hsi_event_details, diff --git a/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py b/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py index d2aaf664fa..6791a34d21 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py +++ b/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, get_coarse_appt_type, diff --git a/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py b/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py index 4d10e1d9d7..b8e131f7bc 100644 --- a/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py +++ b/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py @@ -4,7 +4,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Module, Simulation from tlo.analysis.utils import format_gbd from tlo.methods import ( diff --git a/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py b/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py index 5fec646268..f7f5c36101 100644 --- a/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py +++ b/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py @@ -6,7 +6,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo.analysis.utils import format_gbd # Where will outputs go diff --git a/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py b/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py index 872a0b245a..23c97328f6 100644 --- a/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py +++ b/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py @@ -10,7 +10,6 @@ """ import pandas as pd - from tlo import Date, logging from tlo.methods import contraception, demography, hiv from tlo.scenario import BaseScenario diff --git a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py index 59c04ea02c..c244088865 100644 --- a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py +++ b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py b/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py index 387a997a90..a9e23b4f1b 100644 --- a/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py +++ b/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py @@ -14,7 +14,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py b/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py index 4e6a9e9aa9..4a4d17e048 100644 --- a/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py +++ b/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py @@ -5,7 +5,6 @@ """ import matplotlib.pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, get_root_path from tlo.methods import ( diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py index 76708f7c25..0e12a8ccdd 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import extract_results, make_age_grp_lookup, summarize diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py index f0dd083d97..c0fc37b5bb 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import extract_results, make_age_grp_lookup, summarize diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py index 8d43c24b2f..fbe81051a5 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py @@ -20,7 +20,6 @@ import pandas as pd import seaborn as sns from adjustText import adjust_text # For the CEA plane figure to avoid overlaps in data labels - from scripts.costing.cost_estimation import ( apply_discounting_to_cost_data, do_line_plot_of_cost, diff --git a/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py b/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py index 004624fbcb..c8e439de7c 100644 --- a/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py +++ b/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py @@ -15,7 +15,6 @@ import pandas as pd import seaborn as sns from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( extract_params, diff --git a/src/scripts/contraception/contraception_calibration.py b/src/scripts/contraception/contraception_calibration.py index ed519fb4ac..5ec5d197b9 100644 --- a/src/scripts/contraception/contraception_calibration.py +++ b/src/scripts/contraception/contraception_calibration.py @@ -11,7 +11,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import make_calendar_period_lookup from tlo.methods import contraception, demography, enhanced_lifestyle, healthsystem, symptommanager diff --git a/src/scripts/contraception/f_steril_use_2010vs2020.py b/src/scripts/contraception/f_steril_use_2010vs2020.py index 013e704312..103f306337 100644 --- a/src/scripts/contraception/f_steril_use_2010vs2020.py +++ b/src/scripts/contraception/f_steril_use_2010vs2020.py @@ -7,7 +7,6 @@ import pandas as pd from matplotlib import dates as mdates - from tlo.analysis.utils import parse_log_file # ### TO SET ################################################################################################# diff --git a/src/scripts/contraception/fnc_analyse_contraception.py b/src/scripts/contraception/fnc_analyse_contraception.py index 025997df06..413e30ac9a 100644 --- a/src/scripts/contraception/fnc_analyse_contraception.py +++ b/src/scripts/contraception/fnc_analyse_contraception.py @@ -13,7 +13,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import extract_results, parse_log_file, summarize diff --git a/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py b/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py index d7f2ebcec7..837f9c2a69 100644 --- a/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py +++ b/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py @@ -8,7 +8,6 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.font_manager import FontProperties - from tlo import Date, Simulation from tlo.analysis.utils import ( compare_number_of_deaths, diff --git a/src/scripts/copd_analyses/copd_calibrations.py b/src/scripts/copd_analyses/copd_calibrations.py index 9cef13b297..c5f1b15ee0 100644 --- a/src/scripts/copd_analyses/copd_calibrations.py +++ b/src/scripts/copd_analyses/copd_calibrations.py @@ -6,7 +6,6 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.font_manager import FontProperties - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/src/scripts/costing/cost_estimation.py b/src/scripts/costing/cost_estimation.py index bf5a129c0e..6ee6bf0d2d 100644 --- a/src/scripts/costing/cost_estimation.py +++ b/src/scripts/costing/cost_estimation.py @@ -12,7 +12,6 @@ import numpy as np import pandas as pd import squarify - from tlo import Date from tlo.analysis.utils import ( extract_results, diff --git a/src/scripts/costing/costing_overview_analysis.py b/src/scripts/costing/costing_overview_analysis.py index d9184218fd..5c70b81697 100644 --- a/src/scripts/costing/costing_overview_analysis.py +++ b/src/scripts/costing/costing_overview_analysis.py @@ -14,7 +14,6 @@ import matplotlib.pyplot as plt import pandas as pd import seaborn as sns - from scripts.costing.cost_estimation import ( create_summary_treemap_by_cost_subgroup, do_line_plot_of_cost, diff --git a/src/scripts/costing/costing_validation.py b/src/scripts/costing/costing_validation.py index 5909e8525d..aba851c2c0 100644 --- a/src/scripts/costing/costing_validation.py +++ b/src/scripts/costing/costing_validation.py @@ -7,7 +7,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from scripts.costing.cost_estimation import ( do_stacked_bar_plot_of_cost_by_category, estimate_input_cost_of_scenarios, diff --git a/src/scripts/data_file_processing/formatting_demography_data.py b/src/scripts/data_file_processing/formatting_demography_data.py index f48e89812e..c0b0557739 100644 --- a/src/scripts/data_file_processing/formatting_demography_data.py +++ b/src/scripts/data_file_processing/formatting_demography_data.py @@ -30,7 +30,6 @@ import numpy as np import pandas as pd - from tlo.analysis.utils import make_calendar_period_lookup from tlo.util import create_age_range_lookup diff --git a/src/scripts/data_file_processing/formatting_gbd_data.py b/src/scripts/data_file_processing/formatting_gbd_data.py index 62c3b7010b..bc1ef7fc86 100644 --- a/src/scripts/data_file_processing/formatting_gbd_data.py +++ b/src/scripts/data_file_processing/formatting_gbd_data.py @@ -22,7 +22,6 @@ from pathlib import Path import pandas as pd - from tlo.analysis.utils import ( make_age_grp_lookup, make_age_grp_types, diff --git a/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py b/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py index e8812a93c6..9489f6c8b7 100644 --- a/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py +++ b/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py @@ -29,7 +29,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.methods.consumables import check_format_of_consumables_file # Set local shared folder source diff --git a/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py b/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py index 9ca0554650..b7ea085364 100644 --- a/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py +++ b/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py @@ -46,7 +46,6 @@ import pandas as pd import seaborn as sns from plotnine import aes, element_text, geom_bar, ggplot, labs, theme, ylim # for ggplots from R - from tlo.methods.consumables import check_format_of_consumables_file # define a timestamp for script outputs diff --git a/src/scripts/depression_analyses/analyses_depression.py b/src/scripts/depression_analyses/analyses_depression.py index 4429027cdf..0e39e23a91 100644 --- a/src/scripts/depression_analyses/analyses_depression.py +++ b/src/scripts/depression_analyses/analyses_depression.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/dev/scenarios/test_scenario_1.py b/src/scripts/dev/scenarios/test_scenario_1.py index 0804725540..b7cfdf8fe3 100644 --- a/src/scripts/dev/scenarios/test_scenario_1.py +++ b/src/scripts/dev/scenarios/test_scenario_1.py @@ -1,5 +1,4 @@ import numpy as np - from tlo import Date, logging from tlo.methods import ( contraception, diff --git a/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py b/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py index d23cc587d3..e6557c79fc 100644 --- a/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py +++ b/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py @@ -5,7 +5,6 @@ from pathlib import Path import matplotlib.pyplot as plt - from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py b/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py index eb47e54e3f..0c1ac87e75 100644 --- a/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py +++ b/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py @@ -7,7 +7,6 @@ """ import numpy as np - from tlo import Date, logging from tlo.methods import ( demography, diff --git a/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py b/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py index 78c84b010f..5f3513a2f5 100644 --- a/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py +++ b/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py @@ -6,7 +6,6 @@ import matplotlib.pyplot as plt import numpy as np - from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py b/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py index 637a7db114..815f447d12 100644 --- a/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py +++ b/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py @@ -7,7 +7,6 @@ """ import numpy as np - from tlo import Date, logging from tlo.methods import ( demography, diff --git a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py index 615e07c1f1..42c26852a2 100644 --- a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py +++ b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py @@ -8,7 +8,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py index ff20947b7c..0b9245dcb9 100644 --- a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py +++ b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py @@ -10,7 +10,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py index b8f2de5a55..2dcda42458 100644 --- a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py +++ b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py @@ -10,7 +10,6 @@ import matplotlib.pyplot as plt import pandas as pd from matplotlib import ticker - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import demography, enhanced_lifestyle, simplified_births diff --git a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py index db89bef880..5d2d997334 100644 --- a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py +++ b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd from matplotlib import ticker - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import demography, enhanced_lifestyle, simplified_births diff --git a/src/scripts/epi/analysis_epi.py b/src/scripts/epi/analysis_epi.py index 197388372e..98f158b36c 100644 --- a/src/scripts/epi/analysis_epi.py +++ b/src/scripts/epi/analysis_epi.py @@ -4,7 +4,6 @@ import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/epilepsy_analyses/analysis_epilepsy.py b/src/scripts/epilepsy_analyses/analysis_epilepsy.py index 1fd20d0334..7a199e6d7d 100644 --- a/src/scripts/epilepsy_analyses/analysis_epilepsy.py +++ b/src/scripts/epilepsy_analyses/analysis_epilepsy.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/get_properties/properties_graph.py b/src/scripts/get_properties/properties_graph.py index 8c79787cc6..5c10e811c4 100644 --- a/src/scripts/get_properties/properties_graph.py +++ b/src/scripts/get_properties/properties_graph.py @@ -10,7 +10,6 @@ from typing import Any, Mapping, Set, Type, Union import numpy as np - import tlo.methods from tlo import Module from tlo.analysis.utils import _standardize_short_treatment_id diff --git a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py index ba989f2272..7379f6d178 100644 --- a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py +++ b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py @@ -6,11 +6,11 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt +from tlo.analysis.utils import get_color_short_treatment_id from src.scripts.healthsystem.effects_of_each_treatment_multi_scenario.analysis_effect_of_each_treatment_multiple_scenarios import ( apply, ) -from tlo.analysis.utils import get_color_short_treatment_id outputs = Path("./outputs/tbh03@ic.ac.uk/") diff --git a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py index 25533960d7..ebe243eaf1 100644 --- a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py +++ b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from scripts.calibration_analyses.analysis_scripts import plot_legends from scripts.healthsystem.effects_of_each_treatment_multi_scenario.scenario_effect_of_each_treatment_status_quo import ( EffectOfEachTreatmentStatusQuo, diff --git a/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py b/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py index 37c0c1e5a7..7c257109da 100644 --- a/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py +++ b/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py @@ -5,7 +5,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo.analysis.utils import ( extract_params, extract_results, 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..99fb47e1aa 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 @@ -16,7 +16,6 @@ from typing import Dict import pandas as pd - from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel 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..753a9a1449 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 @@ -16,7 +16,6 @@ from typing import Dict import pandas as pd - from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel 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..2a93d03344 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 @@ -16,7 +16,6 @@ from typing import Dict import pandas as pd - from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py index be0a641504..bc8c88c385 100644 --- a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py +++ b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py @@ -16,7 +16,6 @@ from typing import Dict import pandas as pd - from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py b/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py index 0fa3595aab..fe20090b3f 100644 --- a/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py +++ b/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py @@ -8,7 +8,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py b/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py index f616632a8c..63741b448f 100644 --- a/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py +++ b/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py @@ -6,7 +6,6 @@ from typing import Tuple import pandas as pd - from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py b/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py index 216636669a..5ca9e174ee 100644 --- a/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py +++ b/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from scripts.calibration_analyses.analysis_scripts import plot_legends from tlo import Date from tlo.analysis.utils import ( diff --git a/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py b/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py index 2554d78583..9f32481479 100644 --- a/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py +++ b/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py @@ -16,7 +16,6 @@ from typing import Dict import pandas as pd - from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py b/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py index e80cda3128..ad3529efb6 100644 --- a/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py +++ b/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py @@ -7,7 +7,6 @@ import pandas as pd import pydot - from tlo.analysis.utils import ( get_color_short_treatment_id, get_filtered_treatment_ids, diff --git a/src/scripts/hiv/projections_jan2023/output_plots.py b/src/scripts/hiv/projections_jan2023/output_plots.py index 4ae8a1531d..efebff8696 100644 --- a/src/scripts/hiv/projections_jan2023/output_plots.py +++ b/src/scripts/hiv/projections_jan2023/output_plots.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.analysis.utils import compare_number_of_deaths from tlo.util import read_csv_files diff --git a/src/scripts/htm_scenario_analyses/scenario_plots.py b/src/scripts/htm_scenario_analyses/scenario_plots.py index c209c60f6e..0919114c92 100644 --- a/src/scripts/htm_scenario_analyses/scenario_plots.py +++ b/src/scripts/htm_scenario_analyses/scenario_plots.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import pandas as pd import seaborn as sns - from tlo import Date from tlo.analysis.utils import ( extract_params, diff --git a/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py b/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py index affa7c8603..558097a6a9 100644 --- a/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py +++ b/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from scripts.impact_of_historical_changes_in_hr.scenario_historical_changes_in_hr import ( HistoricalChangesInHRH, ) diff --git a/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py b/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py index b018fb3513..aa0fdb5f1a 100644 --- a/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py +++ b/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd from scipy.optimize import curve_fit - from tlo.analysis.utils import get_root_path # Path to shared folder diff --git a/src/scripts/malaria/malaria_plots.py b/src/scripts/malaria/malaria_plots.py index ab09f47e25..a1aed71c41 100644 --- a/src/scripts/malaria/malaria_plots.py +++ b/src/scripts/malaria/malaria_plots.py @@ -7,7 +7,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.util import read_csv_files resourcefilepath = Path("./resources") diff --git a/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py b/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py index dfb44abd97..db029a9f08 100644 --- a/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py +++ b/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py @@ -1,7 +1,6 @@ import numpy as np import scipy.stats as st from matplotlib import pyplot as plt - from tlo.analysis.utils import extract_results plt.style.use('seaborn-darkgrid') diff --git a/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py b/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py index b3e64e1217..18c3275f46 100644 --- a/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py +++ b/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py @@ -10,7 +10,6 @@ return_95_CI_across_runs, ) from matplotlib import pyplot as plt - from tlo.analysis.utils import extract_results, get_scenario_outputs plt.style.use('seaborn-darkgrid') diff --git a/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py b/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py index 1ca54f24b8..d9f7915baa 100644 --- a/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py +++ b/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py @@ -5,9 +5,9 @@ import pandas as pd import scipy.stats as st from matplotlib import pyplot as plt +from tlo.analysis.utils import extract_results, get_scenario_outputs from src.scripts.maternal_perinatal_analyses.analysis_scripts import analysis_utility_functions -from tlo.analysis.utils import extract_results, get_scenario_outputs plt.style.use('seaborn') diff --git a/src/scripts/measles/analysis_measles.py b/src/scripts/measles/analysis_measles.py index 0f6661421d..54ca3cc66e 100644 --- a/src/scripts/measles/analysis_measles.py +++ b/src/scripts/measles/analysis_measles.py @@ -3,7 +3,6 @@ # import time import matplotlib.pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py b/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py index be8a90265f..ea43652570 100644 --- a/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py +++ b/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py @@ -4,7 +4,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_deaths.py b/src/scripts/measles/analysis_measles_deaths.py index 86a41cd59f..d58c3c45ea 100644 --- a/src/scripts/measles/analysis_measles_deaths.py +++ b/src/scripts/measles/analysis_measles_deaths.py @@ -2,7 +2,6 @@ from pathlib import Path import matplotlib.pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_scenarios.py b/src/scripts/measles/analysis_measles_scenarios.py index 58b0db6e59..2f0e1ff9ed 100644 --- a/src/scripts/measles/analysis_measles_scenarios.py +++ b/src/scripts/measles/analysis_measles_scenarios.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py index cb4cd7db50..46838f325d 100644 --- a/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py @@ -13,7 +13,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py b/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py index 204e52467a..66e879bc5a 100644 --- a/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py +++ b/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py @@ -13,7 +13,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py b/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py index a3d5d2cf31..3ec2c9c107 100644 --- a/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py @@ -13,7 +13,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py index 83ad74152d..a6c1552a4f 100644 --- a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py +++ b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py @@ -14,7 +14,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import compare_number_of_deaths, make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py index 36937944cf..6b38646398 100644 --- a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py +++ b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py @@ -6,7 +6,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths from tlo.methods import ( diff --git a/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py b/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py index 021590ba48..af1f68840d 100644 --- a/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py +++ b/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from scripts.calibration_analyses.analysis_scripts import plot_legends from scripts.healthsystem.org_chart_of_hsi import plot_org_chart_treatment_ids from scripts.overview_paper.B_finding_effects_of_each_treatment.scenario_effect_of_each_treatment import ( diff --git a/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py b/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py index faac171620..41d0564951 100644 --- a/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py +++ b/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, diff --git a/src/scripts/profiling/batch_test.py b/src/scripts/profiling/batch_test.py index f69bb6cbd6..dc46087820 100644 --- a/src/scripts/profiling/batch_test.py +++ b/src/scripts/profiling/batch_test.py @@ -11,7 +11,6 @@ import pandas as pd import shared - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/profiling/heavy_use_of_bed_days.py b/src/scripts/profiling/heavy_use_of_bed_days.py index 647a5bd948..7cd4310be1 100644 --- a/src/scripts/profiling/heavy_use_of_bed_days.py +++ b/src/scripts/profiling/heavy_use_of_bed_days.py @@ -4,7 +4,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation from tlo.methods import demography, healthsystem diff --git a/src/scripts/profiling/heavy_use_of_spurious_symptoms.py b/src/scripts/profiling/heavy_use_of_spurious_symptoms.py index 2550c374f8..87ea16d1ef 100644 --- a/src/scripts/profiling/heavy_use_of_spurious_symptoms.py +++ b/src/scripts/profiling/heavy_use_of_spurious_symptoms.py @@ -4,7 +4,6 @@ from pathlib import Path from pandas import DateOffset - from tlo import Date, Simulation, logging from tlo.methods import demography, healthsystem, simplified_births, symptommanager diff --git a/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py b/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py index 9ea33cba69..4f71c06f75 100644 --- a/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py +++ b/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py @@ -13,7 +13,6 @@ import pandas as pd import shared - from tlo import Date, Simulation, logging from tlo.methods import ( cardio_metabolic_disorders, diff --git a/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py b/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py index 599101dddd..e758fa3f50 100644 --- a/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py +++ b/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py @@ -15,7 +15,6 @@ import pandas as pd import shared - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.lm import LinearModel, LinearModelType diff --git a/src/scripts/profiling/scale_run.py b/src/scripts/profiling/scale_run.py index 5a5889bf95..9f02670c34 100644 --- a/src/scripts/profiling/scale_run.py +++ b/src/scripts/profiling/scale_run.py @@ -11,7 +11,6 @@ from pyinstrument import Profiler from shared import print_checksum, schedule_profile_log - from tlo import Date, Simulation, logging from tlo.analysis.utils import LogsDict from tlo.analysis.utils import parse_log_file as parse_log_file_fn diff --git a/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py b/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py index 5dd6076361..280b9b8e42 100644 --- a/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py +++ b/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py @@ -7,7 +7,6 @@ from pathlib import Path import numpy as np - from tlo import Date, Simulation from tlo.methods import demography, symptommanager diff --git a/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py index 36c2dc9557..49a85e8097 100644 --- a/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py @@ -13,7 +13,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py b/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py index 51d205cd5d..8b850bf082 100644 --- a/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py +++ b/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py @@ -14,7 +14,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti.py b/src/scripts/rti/analysis_rti.py index 3231d27d5a..2c063e8726 100644 --- a/src/scripts/rti/analysis_rti.py +++ b/src/scripts/rti/analysis_rti.py @@ -2,7 +2,6 @@ import numpy as np from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti_deaths.py b/src/scripts/rti/analysis_rti_deaths.py index eca62cf283..19201ea5aa 100644 --- a/src/scripts/rti/analysis_rti_deaths.py +++ b/src/scripts/rti/analysis_rti_deaths.py @@ -1,6 +1,5 @@ import numpy as np from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py b/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py index b36d8ae372..a1ae201d70 100644 --- a/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py +++ b/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py @@ -1,6 +1,5 @@ import numpy as np from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/schistosomiasis/schisto_analysis.py b/src/scripts/schistosomiasis/schisto_analysis.py index c7362d29a0..672634728c 100644 --- a/src/scripts/schistosomiasis/schisto_analysis.py +++ b/src/scripts/schistosomiasis/schisto_analysis.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib.dates import DateFormatter - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import contraception, demography, healthburden, healthsystem, schisto diff --git a/src/scripts/schistosomiasis/schisto_calibration_check.py b/src/scripts/schistosomiasis/schisto_calibration_check.py index 3c46bdad76..2f87d4a5c7 100644 --- a/src/scripts/schistosomiasis/schisto_calibration_check.py +++ b/src/scripts/schistosomiasis/schisto_calibration_check.py @@ -5,7 +5,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import ( format_gbd, diff --git a/src/scripts/schistosomiasis/schisto_single_run_local.py b/src/scripts/schistosomiasis/schisto_single_run_local.py index 6e84efb3e1..4341200c46 100644 --- a/src/scripts/schistosomiasis/schisto_single_run_local.py +++ b/src/scripts/schistosomiasis/schisto_single_run_local.py @@ -7,7 +7,6 @@ import matplotlib.pyplot as plt import pandas as pd - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py b/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py index c3aa6689d6..bbddc029f3 100644 --- a/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py +++ b/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt - from tlo import Date, Simulation, logging from tlo.analysis.utils import make_calendar_period_lookup, make_calendar_period_type from tlo.methods import demography, simplified_births diff --git a/src/scripts/tb/output_plots_tb.py b/src/scripts/tb/output_plots_tb.py index 2078fdfc88..ebbdb2db61 100644 --- a/src/scripts/tb/output_plots_tb.py +++ b/src/scripts/tb/output_plots_tb.py @@ -9,7 +9,6 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd - from tlo.analysis.utils import compare_number_of_deaths from tlo.util import read_csv_files diff --git a/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py b/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py index 6a3a5d31a1..3e1fdbeb9c 100644 --- a/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py +++ b/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py @@ -4,7 +4,6 @@ import pandas as pd from matplotlib import pyplot as plt from scipy.stats import norm - from tlo import Date, Simulation from tlo.analysis.utils import extract_results, get_scenario_outputs, summarize from tlo.methods import demography, enhanced_lifestyle, healthsystem, simplified_births, stunting diff --git a/src/tlo/analysis/hsi_events.py b/src/tlo/analysis/hsi_events.py index f5082c6e3a..5332f27d5b 100644 --- a/src/tlo/analysis/hsi_events.py +++ b/src/tlo/analysis/hsi_events.py @@ -13,7 +13,6 @@ from typing import Any, Iterable, List, Mapping, Optional, Set, Union import pandas as pd - import tlo.methods from tlo import Date, Module, Simulation from tlo.analysis.utils import get_root_path diff --git a/src/tlo/analysis/life_expectancy.py b/src/tlo/analysis/life_expectancy.py index ebde940f66..d0d1de57d6 100644 --- a/src/tlo/analysis/life_expectancy.py +++ b/src/tlo/analysis/life_expectancy.py @@ -9,7 +9,6 @@ from typing import Dict, Tuple import pandas as pd - from tlo.analysis.utils import ( extract_results, get_scenario_info, diff --git a/src/tlo/analysis/utils.py b/src/tlo/analysis/utils.py index cbc9aee900..02d175ef76 100644 --- a/src/tlo/analysis/utils.py +++ b/src/tlo/analysis/utils.py @@ -20,7 +20,6 @@ import pandas as pd import scipy.stats as st import squarify - from tlo import Date, Simulation, logging, util from tlo.logging.reader import LogData from tlo.util import ( diff --git a/src/tlo/cli.py b/src/tlo/cli.py index 9436d060ff..d6097accd9 100644 --- a/src/tlo/cli.py +++ b/src/tlo/cli.py @@ -22,7 +22,6 @@ from azure.keyvault.secrets import SecretClient from azure.storage.fileshare import ShareClient, ShareDirectoryClient, ShareFileClient from git import Repo - from tlo.analysis.utils import parse_log_file from tlo.scenario import SampleRunner, ScenarioLoader diff --git a/src/tlo/lm.py b/src/tlo/lm.py index a7538a1a7a..87459d693a 100644 --- a/src/tlo/lm.py +++ b/src/tlo/lm.py @@ -8,7 +8,6 @@ import numpy as np import pandas as pd from pandas.core.computation.parsing import clean_column_name - from tlo import logging logger = logging.getLogger(__name__) diff --git a/src/tlo/logging/core.py b/src/tlo/logging/core.py index dc3beaf2f1..4dee050f4d 100644 --- a/src/tlo/logging/core.py +++ b/src/tlo/logging/core.py @@ -11,7 +11,6 @@ import numpy as np import pandas as pd - from tlo.logging import encoding LogLevel: TypeAlias = int diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index 8707e674ad..0fff41b27b 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,7 +28,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/bed_days.py b/src/tlo/methods/bed_days.py index a47b75b16a..1ad08bb217 100644 --- a/src/tlo/methods/bed_days.py +++ b/src/tlo/methods/bed_days.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd - from tlo import Date, Property, Types, logging # --------------------------------------------------------------------------------------------------------- diff --git a/src/tlo/methods/bladder_cancer.py b/src/tlo/methods/bladder_cancer.py index c84d0050db..be59f2e6a0 100644 --- a/src/tlo/methods/bladder_cancer.py +++ b/src/tlo/methods/bladder_cancer.py @@ -11,7 +11,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/breast_cancer.py b/src/tlo/methods/breast_cancer.py index 2d093ac010..f532b29627 100644 --- a/src/tlo/methods/breast_cancer.py +++ b/src/tlo/methods/breast_cancer.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/cardio_metabolic_disorders.py b/src/tlo/methods/cardio_metabolic_disorders.py index 0d52f3fa80..8fa71a0bf6 100644 --- a/src/tlo/methods/cardio_metabolic_disorders.py +++ b/src/tlo/methods/cardio_metabolic_disorders.py @@ -19,7 +19,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/care_of_women_during_pregnancy.py b/src/tlo/methods/care_of_women_during_pregnancy.py index 4cdf3339bb..386d5289b1 100644 --- a/src/tlo/methods/care_of_women_during_pregnancy.py +++ b/src/tlo/methods/care_of_women_during_pregnancy.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata, pregnancy_helper_functions diff --git a/src/tlo/methods/causes.py b/src/tlo/methods/causes.py index f2b881be8e..438a0e6a22 100644 --- a/src/tlo/methods/causes.py +++ b/src/tlo/methods/causes.py @@ -7,7 +7,6 @@ from typing import Union import pandas as pd - from tlo.methods import Metadata diff --git a/src/tlo/methods/cervical_cancer.py b/src/tlo/methods/cervical_cancer.py index 3d5647494b..2fab397ba3 100644 --- a/src/tlo/methods/cervical_cancer.py +++ b/src/tlo/methods/cervical_cancer.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/chronicsyndrome.py b/src/tlo/methods/chronicsyndrome.py index db9303da5c..c3dede39be 100644 --- a/src/tlo/methods/chronicsyndrome.py +++ b/src/tlo/methods/chronicsyndrome.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/consumables.py b/src/tlo/methods/consumables.py index c16b22e6cd..98aff365ba 100644 --- a/src/tlo/methods/consumables.py +++ b/src/tlo/methods/consumables.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd - from tlo import logging logger = logging.getLogger('tlo.methods.healthsystem') diff --git a/src/tlo/methods/contraception.py b/src/tlo/methods/contraception.py index 6f56a55cc7..0a2bbf6329 100644 --- a/src/tlo/methods/contraception.py +++ b/src/tlo/methods/contraception.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/copd.py b/src/tlo/methods/copd.py index eeb08f0445..1c4f84bcf0 100644 --- a/src/tlo/methods/copd.py +++ b/src/tlo/methods/copd.py @@ -4,7 +4,6 @@ from typing import TYPE_CHECKING, Dict, List, Optional import pandas as pd - from tlo import Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/demography.py b/src/tlo/methods/demography.py index 2acaad75eb..83f75abbfe 100644 --- a/src/tlo/methods/demography.py +++ b/src/tlo/methods/demography.py @@ -13,7 +13,6 @@ import numpy as np import pandas as pd - from tlo import ( DAYS_IN_MONTH, DAYS_IN_YEAR, diff --git a/src/tlo/methods/depression.py b/src/tlo/methods/depression.py index f198c4699c..28ed747b6a 100644 --- a/src/tlo/methods/depression.py +++ b/src/tlo/methods/depression.py @@ -8,7 +8,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/diarrhoea.py b/src/tlo/methods/diarrhoea.py index c5320ca555..2f64cda66c 100644 --- a/src/tlo/methods/diarrhoea.py +++ b/src/tlo/methods/diarrhoea.py @@ -23,7 +23,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/dxmanager.py b/src/tlo/methods/dxmanager.py index b46dd58f87..f32bfb9d21 100644 --- a/src/tlo/methods/dxmanager.py +++ b/src/tlo/methods/dxmanager.py @@ -8,7 +8,6 @@ import numpy as np import pandas as pd from pandas.api.types import is_bool_dtype, is_categorical_dtype, is_float_dtype - from tlo import logging from tlo.events import IndividualScopeEventMixin diff --git a/src/tlo/methods/enhanced_lifestyle.py b/src/tlo/methods/enhanced_lifestyle.py index d9164f04fd..f96dee7f15 100644 --- a/src/tlo/methods/enhanced_lifestyle.py +++ b/src/tlo/methods/enhanced_lifestyle.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/epi.py b/src/tlo/methods/epi.py index 4bc298aefc..7c91c4cadd 100644 --- a/src/tlo/methods/epi.py +++ b/src/tlo/methods/epi.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/epilepsy.py b/src/tlo/methods/epilepsy.py index 1ed2989733..af82288350 100644 --- a/src/tlo/methods/epilepsy.py +++ b/src/tlo/methods/epilepsy.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/equipment.py b/src/tlo/methods/equipment.py index 64e833fb06..4b9b9dc613 100644 --- a/src/tlo/methods/equipment.py +++ b/src/tlo/methods/equipment.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd - from tlo import logging from tlo.logging.helpers import get_dataframe_row_as_dict_for_logging diff --git a/src/tlo/methods/healthburden.py b/src/tlo/methods/healthburden.py index 54db8bf8fb..da3fe9141d 100644 --- a/src/tlo/methods/healthburden.py +++ b/src/tlo/methods/healthburden.py @@ -8,7 +8,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Types, logging from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/healthseekingbehaviour.py b/src/tlo/methods/healthseekingbehaviour.py index 5fdab960d3..cfd075d4f2 100644 --- a/src/tlo/methods/healthseekingbehaviour.py +++ b/src/tlo/methods/healthseekingbehaviour.py @@ -12,7 +12,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Types from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent from tlo.lm import LinearModel diff --git a/src/tlo/methods/healthsystem.py b/src/tlo/methods/healthsystem.py index 98c07aa4df..719f5bdc0c 100644 --- a/src/tlo/methods/healthsystem.py +++ b/src/tlo/methods/healthsystem.py @@ -13,7 +13,6 @@ import numpy as np import pandas as pd from pandas.testing import assert_series_equal - from tlo import Date, DateOffset, Module, Parameter, Population, Property, Types, logging from tlo.analysis.utils import ( # get_filtered_treatment_ids, flatten_multi_index_series_into_dict_for_logging, diff --git a/src/tlo/methods/hiv.py b/src/tlo/methods/hiv.py index 8b40e37a34..c685d246fd 100644 --- a/src/tlo/methods/hiv.py +++ b/src/tlo/methods/hiv.py @@ -30,7 +30,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/hiv_tb_calibration.py b/src/tlo/methods/hiv_tb_calibration.py index 2fdb1fded0..3cf93ff9f9 100644 --- a/src/tlo/methods/hiv_tb_calibration.py +++ b/src/tlo/methods/hiv_tb_calibration.py @@ -11,7 +11,6 @@ from typing import Optional import pandas as pd - from tlo import Module, logging from tlo.util import read_csv_files diff --git a/src/tlo/methods/hsi_event.py b/src/tlo/methods/hsi_event.py index 946fdd9087..d86dba3485 100644 --- a/src/tlo/methods/hsi_event.py +++ b/src/tlo/methods/hsi_event.py @@ -4,7 +4,6 @@ from typing import TYPE_CHECKING, Dict, Iterable, Literal, NamedTuple, Optional, Set, Tuple, Union import numpy as np - from tlo import Date, logging from tlo.events import Event diff --git a/src/tlo/methods/hsi_generic_first_appts.py b/src/tlo/methods/hsi_generic_first_appts.py index 37f6c5e261..ba77db7c4b 100644 --- a/src/tlo/methods/hsi_generic_first_appts.py +++ b/src/tlo/methods/hsi_generic_first_appts.py @@ -12,7 +12,6 @@ from typing import TYPE_CHECKING, Any, Dict, List, Protocol, Set, Union import numpy as np - from tlo import Date, Module, logging from tlo.events import IndividualScopeEventMixin from tlo.methods.hsi_event import HSI_Event diff --git a/src/tlo/methods/labour.py b/src/tlo/methods/labour.py index 8cd97da57f..67d6d2f53d 100644 --- a/src/tlo/methods/labour.py +++ b/src/tlo/methods/labour.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd import scipy.stats - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType diff --git a/src/tlo/methods/malaria.py b/src/tlo/methods/malaria.py index 82d82b1a4c..481e2b3c44 100644 --- a/src/tlo/methods/malaria.py +++ b/src/tlo/methods/malaria.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, List, Literal, Optional, Union import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, Predictor diff --git a/src/tlo/methods/measles.py b/src/tlo/methods/measles.py index 075cc1c67c..3f0939c02b 100644 --- a/src/tlo/methods/measles.py +++ b/src/tlo/methods/measles.py @@ -5,7 +5,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/mockitis.py b/src/tlo/methods/mockitis.py index 6e0a43f278..d9eea86943 100644 --- a/src/tlo/methods/mockitis.py +++ b/src/tlo/methods/mockitis.py @@ -4,7 +4,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/newborn_outcomes.py b/src/tlo/methods/newborn_outcomes.py index 131589b88a..ed52d6b944 100644 --- a/src/tlo/methods/newborn_outcomes.py +++ b/src/tlo/methods/newborn_outcomes.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin from tlo.lm import LinearModel diff --git a/src/tlo/methods/oesophagealcancer.py b/src/tlo/methods/oesophagealcancer.py index 4ffd6fca08..5c7ee1b96a 100644 --- a/src/tlo/methods/oesophagealcancer.py +++ b/src/tlo/methods/oesophagealcancer.py @@ -12,7 +12,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/other_adult_cancers.py b/src/tlo/methods/other_adult_cancers.py index 42278b35b9..ab6e885c9e 100644 --- a/src/tlo/methods/other_adult_cancers.py +++ b/src/tlo/methods/other_adult_cancers.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/postnatal_supervisor.py b/src/tlo/methods/postnatal_supervisor.py index 109b7d5694..9a6ee88f5a 100644 --- a/src/tlo/methods/postnatal_supervisor.py +++ b/src/tlo/methods/postnatal_supervisor.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging, util from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel diff --git a/src/tlo/methods/pregnancy_helper_functions.py b/src/tlo/methods/pregnancy_helper_functions.py index 76076a5dcf..4520255b4a 100644 --- a/src/tlo/methods/pregnancy_helper_functions.py +++ b/src/tlo/methods/pregnancy_helper_functions.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo import logging diff --git a/src/tlo/methods/pregnancy_supervisor.py b/src/tlo/methods/pregnancy_supervisor.py index 1be38175f7..b8c1d79607 100644 --- a/src/tlo/methods/pregnancy_supervisor.py +++ b/src/tlo/methods/pregnancy_supervisor.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo import ( DAYS_IN_MONTH, DAYS_IN_YEAR, diff --git a/src/tlo/methods/prostate_cancer.py b/src/tlo/methods/prostate_cancer.py index abd280b325..fc77f40357 100644 --- a/src/tlo/methods/prostate_cancer.py +++ b/src/tlo/methods/prostate_cancer.py @@ -10,7 +10,6 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/rti.py b/src/tlo/methods/rti.py index 994b8d1054..653d5c675d 100644 --- a/src/tlo/methods/rti.py +++ b/src/tlo/methods/rti.py @@ -9,7 +9,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/schisto.py b/src/tlo/methods/schisto.py index b7079e95d3..20b56a384e 100644 --- a/src/tlo/methods/schisto.py +++ b/src/tlo/methods/schisto.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/simplified_births.py b/src/tlo/methods/simplified_births.py index 940692bb62..d8ad4c9e89 100644 --- a/src/tlo/methods/simplified_births.py +++ b/src/tlo/methods/simplified_births.py @@ -8,7 +8,6 @@ from typing import List, Optional import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods.contraception import get_medium_variant_asfr_from_wpp_resourcefile diff --git a/src/tlo/methods/stunting.py b/src/tlo/methods/stunting.py index 7c2d83cc40..3938339fa2 100644 --- a/src/tlo/methods/stunting.py +++ b/src/tlo/methods/stunting.py @@ -17,7 +17,6 @@ import numpy as np import pandas as pd from scipy.stats import norm - from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/symptommanager.py b/src/tlo/methods/symptommanager.py index 9f246b9845..ac3c1ccc76 100644 --- a/src/tlo/methods/symptommanager.py +++ b/src/tlo/methods/symptommanager.py @@ -19,7 +19,6 @@ import numpy as np import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/tb.py b/src/tlo/methods/tb.py index d9ba7309e0..b08f063f70 100644 --- a/src/tlo/methods/tb.py +++ b/src/tlo/methods/tb.py @@ -8,7 +8,6 @@ from typing import Optional import pandas as pd - from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/population.py b/src/tlo/population.py index 26af2f3185..d3d19d17f0 100644 --- a/src/tlo/population.py +++ b/src/tlo/population.py @@ -6,7 +6,6 @@ from typing import Any, Dict, Optional, Set import pandas as pd - from tlo import Property, logging logger = logging.getLogger(__name__) diff --git a/src/tlo/scenario.py b/src/tlo/scenario.py index cd83d0e63f..9cf84fadd7 100644 --- a/src/tlo/scenario.py +++ b/src/tlo/scenario.py @@ -69,7 +69,6 @@ def draw_parameters(self, draw_number, rng): from typing import List, Optional import numpy as np - from tlo import Date, Simulation, logging from tlo.util import str_to_pandas_date diff --git a/src/tlo/test/random_birth.py b/src/tlo/test/random_birth.py index 22a20879b1..fae5e29f0c 100644 --- a/src/tlo/test/random_birth.py +++ b/src/tlo/test/random_birth.py @@ -10,7 +10,6 @@ """ import pandas as pd - from tlo import DateOffset, Module, Parameter, Property, Types from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/util.py b/src/tlo/util.py index efe17a9920..dcbfad0cc9 100644 --- a/src/tlo/util.py +++ b/src/tlo/util.py @@ -9,7 +9,6 @@ import pandas as pd from pandas import DataFrame, DateOffset from pandas._typing import DtypeArg - from tlo import Population, Property, Types # Default mother_id value, assigned to individuals initialised as adults at the start of the simulation. diff --git a/tests/bitset_handler/conftest.py b/tests/bitset_handler/conftest.py index 5cd111ae62..7d3372c117 100644 --- a/tests/bitset_handler/conftest.py +++ b/tests/bitset_handler/conftest.py @@ -13,7 +13,6 @@ import pytest from numpy.random import PCG64, Generator from numpy.typing import NDArray - from tlo.bitset_handler.bitset_extension import BitsetArray, BitsetDtype, ElementType diff --git a/tests/bitset_handler/test_bitset_pandas_dtype.py b/tests/bitset_handler/test_bitset_pandas_dtype.py index 156f9e49e6..b6644074bf 100644 --- a/tests/bitset_handler/test_bitset_pandas_dtype.py +++ b/tests/bitset_handler/test_bitset_pandas_dtype.py @@ -2,7 +2,6 @@ import pytest from pandas.tests.extension.base import BaseDtypeTests - from tlo.bitset_handler.bitset_extension import BitsetDtype diff --git a/tests/bitset_handler/test_bitset_set_like_interactions.py b/tests/bitset_handler/test_bitset_set_like_interactions.py index 801703ce24..aa6360e124 100644 --- a/tests/bitset_handler/test_bitset_set_like_interactions.py +++ b/tests/bitset_handler/test_bitset_set_like_interactions.py @@ -6,7 +6,6 @@ import pandas as pd import pytest - from tlo.bitset_handler.bitset_extension import BitsetDtype, CastableForPandasOps, ElementType diff --git a/tests/test_alri.py b/tests/test_alri.py index 3d13041a61..2829d8fca8 100644 --- a/tests/test_alri.py +++ b/tests/test_alri.py @@ -7,7 +7,6 @@ import pandas as pd import pytest from pandas import DateOffset - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_analysis.py b/tests/test_analysis.py index d419f5a92e..760af188cd 100644 --- a/tests/test_analysis.py +++ b/tests/test_analysis.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, DateOffset, Module, Property, Simulation, Types, logging from tlo.analysis.utils import ( colors_in_matplotlib, diff --git a/tests/test_antenatal_interventions.py b/tests/test_antenatal_interventions.py index 8237301668..b629bba013 100644 --- a/tests/test_antenatal_interventions.py +++ b/tests/test_antenatal_interventions.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation from tlo.lm import LinearModel, LinearModelType, Predictor from tlo.methods import ( diff --git a/tests/test_basic_sims.py b/tests/test_basic_sims.py index c56ae74554..997aa073e3 100644 --- a/tests/test_basic_sims.py +++ b/tests/test_basic_sims.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, DateOffset, Module, Property, Simulation, Types, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.test import random_birth, random_death diff --git a/tests/test_beddays.py b/tests/test_beddays.py index 4ddfe4c84f..29b3a248f1 100644 --- a/tests/test_beddays.py +++ b/tests/test_beddays.py @@ -6,7 +6,6 @@ import pandas as pd import pytest - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/tests/test_bitset.py b/tests/test_bitset.py index 0ca60f5c5e..044cc1c15e 100644 --- a/tests/test_bitset.py +++ b/tests/test_bitset.py @@ -3,7 +3,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Population from tlo.lm import LinearModel, LinearModelType, Predictor from tlo.util import BitsetDType, BitsetHandler diff --git a/tests/test_bladder_cancer.py b/tests/test_bladder_cancer.py index e0979df6a1..b0e60407fd 100644 --- a/tests/test_bladder_cancer.py +++ b/tests/test_bladder_cancer.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( bladder_cancer, diff --git a/tests/test_breast_cancer.py b/tests/test_breast_cancer.py index 7b1eb96334..b98671c935 100644 --- a/tests/test_breast_cancer.py +++ b/tests/test_breast_cancer.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( breast_cancer, diff --git a/tests/test_cardiometabolicdisorders.py b/tests/test_cardiometabolicdisorders.py index daa4fc5cb2..bbd5ec83e6 100644 --- a/tests/test_cardiometabolicdisorders.py +++ b/tests/test_cardiometabolicdisorders.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.methods import ( cardio_metabolic_disorders, diff --git a/tests/test_cervical_cancer.py b/tests/test_cervical_cancer.py index 21ccc741c4..41dc8b9fa3 100644 --- a/tests/test_cervical_cancer.py +++ b/tests/test_cervical_cancer.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, DateOffset, Simulation from tlo.methods import ( cervical_cancer, diff --git a/tests/test_consumables.py b/tests/test_consumables.py index a8114aa8d8..a2bb4285e1 100644 --- a/tests/test_consumables.py +++ b/tests/test_consumables.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Module, Simulation from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin diff --git a/tests/test_contraception.py b/tests/test_contraception.py index 37a2ab3fee..3ba567352c 100644 --- a/tests/test_contraception.py +++ b/tests/test_contraception.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import contraception, demography, enhanced_lifestyle, healthsystem, symptommanager diff --git a/tests/test_control_order_of_events.py b/tests/test_control_order_of_events.py index a355f0a622..b02a2ae3c9 100644 --- a/tests/test_control_order_of_events.py +++ b/tests/test_control_order_of_events.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent diff --git a/tests/test_copd.py b/tests/test_copd.py index 08d2b1a464..d27f37792e 100644 --- a/tests/test_copd.py +++ b/tests/test_copd.py @@ -4,7 +4,6 @@ import numpy as np import pytest - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/tests/test_core.py b/tests/test_core.py index 5981c2be3f..10b27bff97 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -4,7 +4,6 @@ import pandas as pd import pytest - from tlo import Module, Parameter, Property, Types diff --git a/tests/test_demography.py b/tests/test_demography.py index 71a24caf8c..761a691fd1 100644 --- a/tests/test_demography.py +++ b/tests/test_demography.py @@ -5,7 +5,6 @@ import pandas as pd import pytest from pytest import approx - from tlo import DAYS_IN_MONTH, DAYS_IN_YEAR, Date, Module, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import Metadata, demography diff --git a/tests/test_depression.py b/tests/test_depression.py index e5da67195d..30308059d1 100644 --- a/tests/test_depression.py +++ b/tests/test_depression.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Simulation from tlo.lm import LinearModel, LinearModelType from tlo.methods import ( diff --git a/tests/test_diarrhoea.py b/tests/test_diarrhoea.py index 4864dcdd74..600d82c849 100644 --- a/tests/test_diarrhoea.py +++ b/tests/test_diarrhoea.py @@ -8,7 +8,6 @@ import pandas as pd import pytest from pandas import DateOffset - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_docs.py b/tests/test_docs.py index cf18097ce2..aabe82e0d9 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -1,7 +1,6 @@ import importlib import pytest - from tlo.docs import ( extract_bases, generate_module_dict, diff --git a/tests/test_dxmanager.py b/tests/test_dxmanager.py index 507c9eec85..5d2ea0eae8 100644 --- a/tests/test_dxmanager.py +++ b/tests/test_dxmanager.py @@ -4,7 +4,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.events import IndividualScopeEventMixin from tlo.methods import ( diff --git a/tests/test_enhanced_lifestyle.py b/tests/test_enhanced_lifestyle.py index 07cc21cef1..d01bfd700f 100644 --- a/tests/test_enhanced_lifestyle.py +++ b/tests/test_enhanced_lifestyle.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, DateOffset, Module, Simulation from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods import demography, enhanced_lifestyle diff --git a/tests/test_epi.py b/tests/test_epi.py index f81c7603bb..67e7905bc0 100644 --- a/tests/test_epi.py +++ b/tests/test_epi.py @@ -4,7 +4,6 @@ import pandas as pd import pytest from pandas import DateOffset - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import PopulationScopeEventMixin, RegularEvent diff --git a/tests/test_epilepsy.py b/tests/test_epilepsy.py index 13fb80bdfe..d3fc005375 100644 --- a/tests/test_epilepsy.py +++ b/tests/test_epilepsy.py @@ -2,7 +2,6 @@ from pathlib import Path import pytest - from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_equipment.py b/tests/test_equipment.py index 85b5e1a83c..567b4106e4 100644 --- a/tests/test_equipment.py +++ b/tests/test_equipment.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Module, Simulation from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin diff --git a/tests/test_find_events_for_person_in_event_queue.py b/tests/test_find_events_for_person_in_event_queue.py index 0f79c4224e..2c6c903d37 100644 --- a/tests/test_find_events_for_person_in_event_queue.py +++ b/tests/test_find_events_for_person_in_event_queue.py @@ -3,7 +3,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation from tlo.methods import ( chronicsyndrome, diff --git a/tests/test_fullmodel.py b/tests/test_fullmodel.py index 0a0a554433..98e8b8451b 100644 --- a/tests/test_fullmodel.py +++ b/tests/test_fullmodel.py @@ -7,7 +7,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation, logging from tlo.methods.fullmodel import fullmodel from tlo.util import hash_dataframe diff --git a/tests/test_healthburden.py b/tests/test_healthburden.py index 4b28b3fd85..7ccbddca1a 100644 --- a/tests/test_healthburden.py +++ b/tests/test_healthburden.py @@ -5,7 +5,6 @@ import pandas as pd import pytest from pytest import approx - from tlo import DAYS_IN_YEAR, Date, Module, Simulation, logging from tlo.analysis.utils import get_mappers_in_fullmodel, parse_log_file from tlo.events import Event, IndividualScopeEventMixin diff --git a/tests/test_healthcareseeking.py b/tests/test_healthcareseeking.py index 165980efa9..d244ee62da 100644 --- a/tests/test_healthcareseeking.py +++ b/tests/test_healthcareseeking.py @@ -7,7 +7,6 @@ import numpy as np import pandas as pd from pandas import DateOffset - from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import Event, IndividualScopeEventMixin diff --git a/tests/test_healthsystem.py b/tests/test_healthsystem.py index 0c1a03932b..579253493e 100644 --- a/tests/test_healthsystem.py +++ b/tests/test_healthsystem.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Module, Simulation, logging from tlo.analysis.hsi_events import get_details_of_defined_hsi_events from tlo.analysis.utils import get_filtered_treatment_ids, parse_log_file diff --git a/tests/test_hiv.py b/tests/test_hiv.py index 640554e840..a6e0fc5d45 100644 --- a/tests/test_hiv.py +++ b/tests/test_hiv.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Simulation from tlo.lm import LinearModel from tlo.methods import ( diff --git a/tests/test_htm_scaleup.py b/tests/test_htm_scaleup.py index 63f6cba6ba..d9867af2f8 100644 --- a/tests/test_htm_scaleup.py +++ b/tests/test_htm_scaleup.py @@ -4,7 +4,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_labour.py b/tests/test_labour.py index b280cede9e..3ce22f1ec6 100644 --- a/tests/test_labour.py +++ b/tests/test_labour.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_life_expectancy.py b/tests/test_life_expectancy.py index 0a77f02310..2d4d3d93c5 100644 --- a/tests/test_life_expectancy.py +++ b/tests/test_life_expectancy.py @@ -5,7 +5,6 @@ import numpy as np import pandas as pd - from tlo.analysis.life_expectancy import ( get_life_expectancy_estimates, get_probability_of_premature_death, diff --git a/tests/test_lm.py b/tests/test_lm.py index b2cb6f1c72..a7076416fe 100644 --- a/tests/test_lm.py +++ b/tests/test_lm.py @@ -6,7 +6,6 @@ import numpy as np import pandas as pd import pytest - from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/tests/test_logging.py b/tests/test_logging.py index 6d094623c4..457e9a47ff 100644 --- a/tests/test_logging.py +++ b/tests/test_logging.py @@ -10,7 +10,6 @@ import numpy as np import pandas as pd import pytest - import tlo.logging as logging import tlo.logging.core as core diff --git a/tests/test_logging_end_to_end.py b/tests/test_logging_end_to_end.py index 4948c7a744..b166a36af2 100644 --- a/tests/test_logging_end_to_end.py +++ b/tests/test_logging_end_to_end.py @@ -6,7 +6,6 @@ import pandas as pd from pytest import fixture - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file diff --git a/tests/test_malaria.py b/tests/test_malaria.py index b20d598606..41df332969 100644 --- a/tests/test_malaria.py +++ b/tests/test_malaria.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.events import IndividualScopeEventMixin from tlo.methods import ( diff --git a/tests/test_maternal_health_helper_and_analysis_functions.py b/tests/test_maternal_health_helper_and_analysis_functions.py index a762fe4155..bcac1ff398 100644 --- a/tests/test_maternal_health_helper_and_analysis_functions.py +++ b/tests/test_maternal_health_helper_and_analysis_functions.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd - from tlo import Date, Simulation from tlo.methods import ( care_of_women_during_pregnancy, diff --git a/tests/test_measles.py b/tests/test_measles.py index 5acdc4df4d..640de20d66 100644 --- a/tests/test_measles.py +++ b/tests/test_measles.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation, logging from tlo.methods import ( demography, diff --git a/tests/test_module_dependencies.py b/tests/test_module_dependencies.py index a50d5d158b..fd36d9e37d 100644 --- a/tests/test_module_dependencies.py +++ b/tests/test_module_dependencies.py @@ -6,7 +6,6 @@ from types import GeneratorType import pytest - from tlo import Date, Module, Simulation, logging from tlo.dependencies import ( ModuleDependencyError, diff --git a/tests/test_newborn_outcomes.py b/tests/test_newborn_outcomes.py index d75022043b..ba276706b5 100644 --- a/tests/test_newborn_outcomes.py +++ b/tests/test_newborn_outcomes.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_oesophagealcancer.py b/tests/test_oesophagealcancer.py index 8ec2b51736..54e8df2a1a 100644 --- a/tests/test_oesophagealcancer.py +++ b/tests/test_oesophagealcancer.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_other_adult_cancers.py b/tests/test_other_adult_cancers.py index 12e3607d91..4b77f7c552 100644 --- a/tests/test_other_adult_cancers.py +++ b/tests/test_other_adult_cancers.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_population.py b/tests/test_population.py index e8a549209d..11bf4f2c6f 100644 --- a/tests/test_population.py +++ b/tests/test_population.py @@ -1,7 +1,6 @@ import numpy as np import pandas as pd import pytest - from tlo.core import Property, Types from tlo.population import Population diff --git a/tests/test_postnatal.py b/tests/test_postnatal.py index 001866d4cf..f291083b2c 100644 --- a/tests/test_postnatal.py +++ b/tests/test_postnatal.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_pregnancy_supervisor.py b/tests/test_pregnancy_supervisor.py index ee56c3a1fc..46444d29ae 100644 --- a/tests/test_pregnancy_supervisor.py +++ b/tests/test_pregnancy_supervisor.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd import pytest - from tlo import DAYS_IN_MONTH, DAYS_IN_YEAR, Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.lm import LinearModel, LinearModelType diff --git a/tests/test_progressbar.py b/tests/test_progressbar.py index bda0376cb9..7050fe5ac3 100644 --- a/tests/test_progressbar.py +++ b/tests/test_progressbar.py @@ -1,5 +1,4 @@ import pytest - from tlo import progressbar diff --git a/tests/test_prostate_cancer.py b/tests/test_prostate_cancer.py index bae5d4fcf4..2839944a71 100644 --- a/tests/test_prostate_cancer.py +++ b/tests/test_prostate_cancer.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_rti.py b/tests/test_rti.py index 2b65595782..4d8a1fd88b 100644 --- a/tests/test_rti.py +++ b/tests/test_rti.py @@ -3,7 +3,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_scenario.py b/tests/test_scenario.py index 1feac8ef87..ccd9985e0f 100644 --- a/tests/test_scenario.py +++ b/tests/test_scenario.py @@ -3,7 +3,6 @@ from pathlib import Path import pytest - from tlo.scenario import BaseScenario, SampleRunner, ScenarioLoader diff --git a/tests/test_schisto.py b/tests/test_schisto.py index 02bbba707f..985fc00c7f 100644 --- a/tests/test_schisto.py +++ b/tests/test_schisto.py @@ -6,7 +6,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_simplified_births.py b/tests/test_simplified_births.py index 8474223508..5a291e4667 100644 --- a/tests/test_simplified_births.py +++ b/tests/test_simplified_births.py @@ -4,7 +4,6 @@ import numpy as np import pandas as pd import pytest - from tlo import Date, Simulation, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods import demography, simplified_births diff --git a/tests/test_simulation.py b/tests/test_simulation.py index 90abe68761..c30a714e60 100644 --- a/tests/test_simulation.py +++ b/tests/test_simulation.py @@ -3,7 +3,6 @@ import numpy as np import pytest - from tlo import Date, DateOffset, Module, Population, Simulation, logging from tlo.analysis.utils import merge_log_files, parse_log_file from tlo.methods.fullmodel import fullmodel diff --git a/tests/test_stunting.py b/tests/test_stunting.py index 676d29970b..e2ebe4dfd8 100644 --- a/tests/test_stunting.py +++ b/tests/test_stunting.py @@ -6,7 +6,6 @@ import pytest from pytest import approx from scipy.stats import norm - from tlo import Date, Simulation from tlo.lm import LinearModel, Predictor from tlo.methods import demography, enhanced_lifestyle, healthsystem, simplified_births, stunting diff --git a/tests/test_symptommanager.py b/tests/test_symptommanager.py index cdc6de7293..f66e303861 100644 --- a/tests/test_symptommanager.py +++ b/tests/test_symptommanager.py @@ -6,7 +6,6 @@ import pytest from pandas import DateOffset - from tlo import Date, Simulation from tlo.methods import ( chronicsyndrome, diff --git a/tests/test_tb.py b/tests/test_tb.py index 513d2a52ae..19434aac38 100644 --- a/tests/test_tb.py +++ b/tests/test_tb.py @@ -5,7 +5,6 @@ import pandas as pd import pytest - from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_utils.py b/tests/test_utils.py index ee9426f607..5b268a297e 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -9,9 +9,8 @@ import numpy as np import pandas as pd import pytest -from scipy.stats import chisquare - import tlo.util +from scipy.stats import chisquare from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import demography From df6367b0288b5d1d72a99c9390a2249b6c3dfe4e Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Fri, 7 Nov 2025 08:37:11 -0500 Subject: [PATCH 7/8] update notes and ref column --- resources/ResourceFile_Alri/Parameter_values.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/ResourceFile_Alri/Parameter_values.csv b/resources/ResourceFile_Alri/Parameter_values.csv index 9c463c3dee..bc0344cf03 100644 --- a/resources/ResourceFile_Alri/Parameter_values.csv +++ b/resources/ResourceFile_Alri/Parameter_values.csv @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6d97a60e3f3a9aee304f5bfbce548fb74df7e7effd3370bfec92398dcfdce275 +oid sha256:405ff935edd10c3073839f820ebfd8c99d9179147a38ef5459e8c20c63121119 size 13774 From 709a93815474cb8b19cf679bc91d540e4c052754 Mon Sep 17 00:00:00 2001 From: mmsuarezcosta Date: Fri, 7 Nov 2025 08:42:06 -0500 Subject: [PATCH 8/8] revert ruff fixes on documents outside alri module --- .../alri_azure_run_scenarios/base_scenario_inc_mort_plots.py | 1 + .../alri_azure_run_scenarios/base_scenario_plots.py | 1 + .../alri_calibration_plots/GBD_comparison_plots.py | 1 + .../alri_calibration_plots/analysis_Alri_default_params.py | 1 + .../analysis_Alri_with_and_without_treatment.py | 1 + .../alri_calibration_plots/analysis_effect_of_treatment.py | 1 + .../alri_calibration_plots/analysis_pulse_oximeter_vs_none.py | 1 + .../Alri_analyses/alri_calibration_plots/baseline_outputs.py | 1 + src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py | 1 + .../calc_5y_survival_following_treatment.py | 1 + src/scripts/breast_cancer_analyses/breast_cancer_analyses.py | 1 + .../calc_5y_survival_following_treatment.py | 1 + .../analysis_scripts/analysis_all_calibration.py | 1 + .../analysis_cause_of_death_and_disability_calibrations.py | 1 + .../analysis_compare_appt_usage_real_and_simulation.py | 1 + .../analysis_scripts/analysis_demography_calibrations.py | 1 + .../analysis_scripts/analysis_hsi_descriptions.py | 1 + .../analysis_scripts/analysis_hsi_events_by_date.py | 1 + .../analysis_scripts/plot_appt_use_by_hsi.py | 1 + .../calibration_analyses/analysis_scripts/plot_legends.py | 1 + .../description_of_data_only/coverage_of_gbd_causes.py | 1 + .../description_of_data_only/graph_of_gbd_data.py | 1 + .../calibration_analyses/scenarios/long_run_no_diseases.py | 1 + .../cardiometabolicdisorders_plots.py | 1 + .../cervical_cancer_analyses/cervical_cancer_analyses.py | 1 + .../cervical_cancer_calibration_check.py | 1 + .../analysis_hss_elements.py | 1 + .../analysis_vertical_programs_with_and_without_hss.py | 1 + .../roi_analysis_horizontal_vs_vertical.py | 1 + .../analysis_impact_of_consumable_scenarios.py | 1 + src/scripts/contraception/contraception_calibration.py | 1 + src/scripts/contraception/f_steril_use_2010vs2020.py | 1 + src/scripts/contraception/fnc_analyse_contraception.py | 1 + .../copd_analyses/analysis_copd_prevalence_and_deaths.py | 1 + src/scripts/copd_analyses/copd_calibrations.py | 1 + src/scripts/costing/cost_estimation.py | 1 + src/scripts/costing/costing_overview_analysis.py | 1 + src/scripts/costing/costing_validation.py | 1 + src/scripts/data_file_processing/formatting_demography_data.py | 1 + src/scripts/data_file_processing/formatting_gbd_data.py | 1 + .../consumables_availability_estimation.py | 1 + ...te_consumable_availability_scenarios_for_impact_analysis.py | 1 + src/scripts/depression_analyses/analyses_depression.py | 1 + src/scripts/dev/scenarios/test_scenario_1.py | 1 + .../dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py | 1 + src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py | 1 + .../th_testing/single_sweep/analysing_mockitis_single_sweep.py | 1 + .../dev/th_testing/single_sweep/mockitis_single_sweep.py | 1 + .../analysis_diarrhoea_with_and_without_treatment.py | 1 + .../diarrhoea_analyses/analysis_diarrhoea_with_treatment.py | 1 + .../enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py | 1 + .../enhanced_lifestyle_calibrations.py | 1 + src/scripts/epi/analysis_epi.py | 1 + src/scripts/epilepsy_analyses/analysis_epilepsy.py | 1 + src/scripts/get_properties/properties_graph.py | 1 + .../analysis_comparison_of_impact_in_different_scenarios.py | 2 +- .../analysis_effect_of_each_treatment_multiple_scenarios.py | 1 + .../analysis_impact_of_consumables_availability.py | 1 + .../scenario_impact_of_capabilities_expansion_combined.py | 1 + .../scenario_impact_of_capabilities_expansion_scaling.py | 1 + .../scenario_impact_of_capabilities_expansion_test_scaling.py | 1 + .../scenario_impact_of_const_capabilities_expansion.py | 1 + .../impact_of_mode/analysis_health_impact_of_mode.py | 1 + .../healthsystem/impact_of_mode/analysis_hsi_by_mode.py | 1 + .../impact_of_policy/analysis_effect_of_each_treatment.py | 1 + .../healthsystem/impact_of_policy/scenario_impact_of_policy.py | 1 + .../org_chart_of_hsi/plot_org_chart_treatment_ids.py | 1 + src/scripts/hiv/projections_jan2023/output_plots.py | 1 + src/scripts/htm_scenario_analyses/scenario_plots.py | 1 + .../analysis_historical_changes_in_hr.py | 1 + .../examining_data_historic_changes_in_hr.py | 1 + src/scripts/malaria/malaria_plots.py | 1 + .../analysis_scripts/analysis_utility_functions.py | 1 + .../maternal_newborn_health_thesis_analysis.py | 1 + .../calibration/calibration_outputs_with_ci.py | 2 +- src/scripts/measles/analysis_measles.py | 1 + src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py | 1 + src/scripts/measles/analysis_measles_deaths.py | 1 + src/scripts/measles/analysis_measles_scenarios.py | 1 + .../calc_5y_survival_following_treatment.py | 1 + .../oesophagealcancer_analyses/oesophagealcancer_analyses.py | 1 + .../calc_5y_survival_following_treatment.py | 1 + .../other_adult_cancers_analyses.py | 1 + .../other_adult_cancers_calibration_to_deaths.py | 1 + .../analysis_effect_of_each_treatment.py | 1 + .../analysis_impact_of_healthsystem.py | 1 + src/scripts/profiling/batch_test.py | 1 + src/scripts/profiling/heavy_use_of_bed_days.py | 1 + src/scripts/profiling/heavy_use_of_spurious_symptoms.py | 1 + .../run_full_model_with_hard_constraints_in_healthsystem.py | 1 + .../run_with_high_intensity_of_HSI_and_simplified_births.py | 1 + src/scripts/profiling/scale_run.py | 1 + src/scripts/profiling/symptom_manager_bookkeeping_profiling.py | 1 + .../calc_5y_survival_following_treatment.py | 1 + .../prostate_cancer_analyses/prostate_cancer_analyses.py | 1 + src/scripts/rti/analysis_rti.py | 1 + src/scripts/rti/analysis_rti_deaths.py | 1 + src/scripts/rti/analysis_rti_single_vs_multiple_injury.py | 1 + src/scripts/schistosomiasis/schisto_analysis.py | 1 + src/scripts/schistosomiasis/schisto_calibration_check.py | 1 + src/scripts/schistosomiasis/schisto_single_run_local.py | 1 + .../analysis_simplified_births_calibrations.py | 1 + src/scripts/tb/output_plots_tb.py | 1 + .../stunting/stunting_analysis_plots.py | 1 + src/tlo/analysis/hsi_events.py | 1 + src/tlo/analysis/life_expectancy.py | 1 + src/tlo/analysis/utils.py | 1 + src/tlo/cli.py | 1 + src/tlo/lm.py | 1 + src/tlo/logging/core.py | 1 + src/tlo/methods/alri.py | 1 + src/tlo/methods/bed_days.py | 1 + src/tlo/methods/bladder_cancer.py | 1 + src/tlo/methods/breast_cancer.py | 1 + src/tlo/methods/cardio_metabolic_disorders.py | 1 + src/tlo/methods/care_of_women_during_pregnancy.py | 1 + src/tlo/methods/causes.py | 1 + src/tlo/methods/cervical_cancer.py | 1 + src/tlo/methods/chronicsyndrome.py | 1 + src/tlo/methods/consumables.py | 1 + src/tlo/methods/contraception.py | 1 + src/tlo/methods/copd.py | 1 + src/tlo/methods/demography.py | 1 + src/tlo/methods/depression.py | 1 + src/tlo/methods/diarrhoea.py | 1 + src/tlo/methods/dxmanager.py | 1 + src/tlo/methods/enhanced_lifestyle.py | 1 + src/tlo/methods/epi.py | 1 + src/tlo/methods/epilepsy.py | 1 + src/tlo/methods/equipment.py | 1 + src/tlo/methods/healthburden.py | 1 + src/tlo/methods/healthseekingbehaviour.py | 1 + src/tlo/methods/healthsystem.py | 1 + src/tlo/methods/hiv.py | 1 + src/tlo/methods/hiv_tb_calibration.py | 1 + src/tlo/methods/hsi_event.py | 1 + src/tlo/methods/hsi_generic_first_appts.py | 1 + src/tlo/methods/labour.py | 1 + src/tlo/methods/malaria.py | 1 + src/tlo/methods/measles.py | 1 + src/tlo/methods/mockitis.py | 1 + src/tlo/methods/newborn_outcomes.py | 1 + src/tlo/methods/oesophagealcancer.py | 1 + src/tlo/methods/other_adult_cancers.py | 1 + src/tlo/methods/postnatal_supervisor.py | 1 + src/tlo/methods/pregnancy_helper_functions.py | 1 + src/tlo/methods/pregnancy_supervisor.py | 1 + src/tlo/methods/prostate_cancer.py | 1 + src/tlo/methods/rti.py | 1 + src/tlo/methods/schisto.py | 1 + src/tlo/methods/simplified_births.py | 1 + src/tlo/methods/stunting.py | 1 + src/tlo/methods/symptommanager.py | 1 + src/tlo/methods/tb.py | 1 + src/tlo/population.py | 1 + src/tlo/scenario.py | 1 + src/tlo/test/random_birth.py | 1 + src/tlo/util.py | 1 + tests/bitset_handler/conftest.py | 1 + tests/bitset_handler/test_bitset_pandas_dtype.py | 1 + tests/bitset_handler/test_bitset_set_like_interactions.py | 1 + tests/test_alri.py | 1 + tests/test_analysis.py | 1 + tests/test_antenatal_interventions.py | 1 + tests/test_basic_sims.py | 1 + tests/test_beddays.py | 1 + tests/test_bitset.py | 1 + tests/test_bladder_cancer.py | 1 + tests/test_breast_cancer.py | 1 + tests/test_cardiometabolicdisorders.py | 1 + tests/test_cervical_cancer.py | 1 + tests/test_consumables.py | 1 + tests/test_contraception.py | 1 + tests/test_control_order_of_events.py | 1 + tests/test_copd.py | 1 + tests/test_core.py | 1 + tests/test_demography.py | 1 + tests/test_depression.py | 1 + tests/test_diarrhoea.py | 1 + tests/test_docs.py | 1 + tests/test_dxmanager.py | 1 + tests/test_enhanced_lifestyle.py | 1 + tests/test_epi.py | 1 + tests/test_epilepsy.py | 1 + tests/test_equipment.py | 1 + tests/test_find_events_for_person_in_event_queue.py | 1 + tests/test_fullmodel.py | 1 + tests/test_healthburden.py | 1 + tests/test_healthcareseeking.py | 1 + tests/test_healthsystem.py | 1 + tests/test_hiv.py | 1 + tests/test_htm_scaleup.py | 1 + tests/test_labour.py | 1 + tests/test_life_expectancy.py | 1 + tests/test_lm.py | 1 + tests/test_logging.py | 1 + tests/test_logging_end_to_end.py | 1 + tests/test_malaria.py | 1 + tests/test_maternal_health_helper_and_analysis_functions.py | 1 + tests/test_measles.py | 1 + tests/test_module_dependencies.py | 1 + tests/test_newborn_outcomes.py | 1 + tests/test_oesophagealcancer.py | 1 + tests/test_other_adult_cancers.py | 1 + tests/test_population.py | 1 + tests/test_postnatal.py | 1 + tests/test_pregnancy_supervisor.py | 1 + tests/test_progressbar.py | 1 + tests/test_prostate_cancer.py | 1 + tests/test_rti.py | 1 + tests/test_scenario.py | 1 + tests/test_schisto.py | 1 + tests/test_simplified_births.py | 1 + tests/test_simulation.py | 1 + tests/test_stunting.py | 1 + tests/test_symptommanager.py | 1 + tests/test_tb.py | 1 + tests/test_utils.py | 3 ++- 218 files changed, 219 insertions(+), 3 deletions(-) diff --git a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py index 8659aab8ca..b5c14fa599 100644 --- a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py +++ b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_inc_mort_plots.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py index 5b590b3b3d..beda8138d8 100644 --- a/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py +++ b/src/scripts/Alri_analyses/alri_azure_run_scenarios/base_scenario_plots.py @@ -8,6 +8,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py b/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py index 19854860f5..2cf9cc6068 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py @@ -9,6 +9,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py index e0695026a3..19719b5344 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py @@ -11,6 +11,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py index 4f2c0120c0..06be9a23aa 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py @@ -8,6 +8,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py index c625840158..59dfe7474f 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py @@ -6,6 +6,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation from tlo.methods import ( alri, diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py index f3e2c5fa59..e350248505 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py @@ -9,6 +9,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py b/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py index 95196c4ccf..77360e618f 100644 --- a/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py +++ b/src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py b/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py index 940ebbee47..227e2e28d3 100644 --- a/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py +++ b/src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py @@ -12,6 +12,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py index 7248c81071..9d69c0be7f 100644 --- a/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/bladder_cancer_analyses/calc_5y_survival_following_treatment.py @@ -12,6 +12,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py b/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py index 725c4b4eac..b94537e7ef 100644 --- a/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py +++ b/src/scripts/breast_cancer_analyses/breast_cancer_analyses.py @@ -14,6 +14,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py index afbc9d3e9a..dc8a0b0ab4 100644 --- a/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/breast_cancer_analyses/calc_5y_survival_following_treatment.py @@ -13,6 +13,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py index 07a4dfb178..7135d4fd89 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py @@ -8,6 +8,7 @@ import analysis_demography_calibrations import analysis_hsi_descriptions import plot_legends + from scripts.calibration_analyses.analysis_scripts import ( analysis_compare_appt_usage_real_and_simulation, plot_appt_use_by_hsi, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py index 6e71403368..e6fa66603d 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py index b85a42c907..491284b83b 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_compare_appt_usage_real_and_simulation.py @@ -5,6 +5,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py index d7b2f8b46d..64ac672158 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_demography_calibrations.py @@ -17,6 +17,7 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.ticker import FormatStrFormatter + from tlo.analysis.utils import ( extract_results, format_gbd, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py index 6d1eec4cc1..da337130af 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_descriptions.py @@ -6,6 +6,7 @@ import pandas as pd import squarify from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( COARSE_APPT_TYPE_TO_COLOR_MAP, diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py index acf4ee50ec..996579d80c 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py +++ b/src/scripts/calibration_analyses/analysis_scripts/analysis_hsi_events_by_date.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( extract_results, diff --git a/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py b/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py index 6e3797e7dd..2aa3dae473 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py +++ b/src/scripts/calibration_analyses/analysis_scripts/plot_appt_use_by_hsi.py @@ -4,6 +4,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( bin_hsi_event_details, diff --git a/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py b/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py index 6791a34d21..d2aaf664fa 100644 --- a/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py +++ b/src/scripts/calibration_analyses/analysis_scripts/plot_legends.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, get_coarse_appt_type, diff --git a/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py b/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py index b8e131f7bc..4d10e1d9d7 100644 --- a/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py +++ b/src/scripts/calibration_analyses/description_of_data_only/coverage_of_gbd_causes.py @@ -4,6 +4,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Module, Simulation from tlo.analysis.utils import format_gbd from tlo.methods import ( diff --git a/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py b/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py index f7f5c36101..5fec646268 100644 --- a/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py +++ b/src/scripts/calibration_analyses/description_of_data_only/graph_of_gbd_data.py @@ -6,6 +6,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo.analysis.utils import format_gbd # Where will outputs go diff --git a/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py b/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py index 23c97328f6..872a0b245a 100644 --- a/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py +++ b/src/scripts/calibration_analyses/scenarios/long_run_no_diseases.py @@ -10,6 +10,7 @@ """ import pandas as pd + from tlo import Date, logging from tlo.methods import contraception, demography, hiv from tlo.scenario import BaseScenario diff --git a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py index c244088865..59c04ea02c 100644 --- a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py +++ b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py b/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py index a9e23b4f1b..387a997a90 100644 --- a/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py +++ b/src/scripts/cervical_cancer_analyses/cervical_cancer_analyses.py @@ -14,6 +14,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py b/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py index 4a4d17e048..4e6a9e9aa9 100644 --- a/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py +++ b/src/scripts/cervical_cancer_analyses/cervical_cancer_calibration_check.py @@ -5,6 +5,7 @@ """ import matplotlib.pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, get_root_path from tlo.methods import ( diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py index 0e12a8ccdd..76708f7c25 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_hss_elements.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import extract_results, make_age_grp_lookup, summarize diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py index c0fc37b5bb..f0dd083d97 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/analysis_vertical_programs_with_and_without_hss.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import extract_results, make_age_grp_lookup, summarize diff --git a/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py b/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py index fbe81051a5..8d43c24b2f 100644 --- a/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py +++ b/src/scripts/comparison_of_horizontal_and_vertical_programs/economic_analysis_for_manuscript/roi_analysis_horizontal_vs_vertical.py @@ -20,6 +20,7 @@ import pandas as pd import seaborn as sns from adjustText import adjust_text # For the CEA plane figure to avoid overlaps in data labels + from scripts.costing.cost_estimation import ( apply_discounting_to_cost_data, do_line_plot_of_cost, diff --git a/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py b/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py index c8e439de7c..004624fbcb 100644 --- a/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py +++ b/src/scripts/consumables_analyses/analysis_impact_of_consumable_scenarios.py @@ -15,6 +15,7 @@ import pandas as pd import seaborn as sns from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( extract_params, diff --git a/src/scripts/contraception/contraception_calibration.py b/src/scripts/contraception/contraception_calibration.py index 5ec5d197b9..ed519fb4ac 100644 --- a/src/scripts/contraception/contraception_calibration.py +++ b/src/scripts/contraception/contraception_calibration.py @@ -11,6 +11,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import make_calendar_period_lookup from tlo.methods import contraception, demography, enhanced_lifestyle, healthsystem, symptommanager diff --git a/src/scripts/contraception/f_steril_use_2010vs2020.py b/src/scripts/contraception/f_steril_use_2010vs2020.py index 103f306337..013e704312 100644 --- a/src/scripts/contraception/f_steril_use_2010vs2020.py +++ b/src/scripts/contraception/f_steril_use_2010vs2020.py @@ -7,6 +7,7 @@ import pandas as pd from matplotlib import dates as mdates + from tlo.analysis.utils import parse_log_file # ### TO SET ################################################################################################# diff --git a/src/scripts/contraception/fnc_analyse_contraception.py b/src/scripts/contraception/fnc_analyse_contraception.py index 413e30ac9a..025997df06 100644 --- a/src/scripts/contraception/fnc_analyse_contraception.py +++ b/src/scripts/contraception/fnc_analyse_contraception.py @@ -13,6 +13,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import extract_results, parse_log_file, summarize diff --git a/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py b/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py index 837f9c2a69..d7f2ebcec7 100644 --- a/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py +++ b/src/scripts/copd_analyses/analysis_copd_prevalence_and_deaths.py @@ -8,6 +8,7 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.font_manager import FontProperties + from tlo import Date, Simulation from tlo.analysis.utils import ( compare_number_of_deaths, diff --git a/src/scripts/copd_analyses/copd_calibrations.py b/src/scripts/copd_analyses/copd_calibrations.py index c5f1b15ee0..9cef13b297 100644 --- a/src/scripts/copd_analyses/copd_calibrations.py +++ b/src/scripts/copd_analyses/copd_calibrations.py @@ -6,6 +6,7 @@ import pandas as pd from matplotlib import pyplot as plt from matplotlib.font_manager import FontProperties + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/src/scripts/costing/cost_estimation.py b/src/scripts/costing/cost_estimation.py index 6ee6bf0d2d..bf5a129c0e 100644 --- a/src/scripts/costing/cost_estimation.py +++ b/src/scripts/costing/cost_estimation.py @@ -12,6 +12,7 @@ import numpy as np import pandas as pd import squarify + from tlo import Date from tlo.analysis.utils import ( extract_results, diff --git a/src/scripts/costing/costing_overview_analysis.py b/src/scripts/costing/costing_overview_analysis.py index 5c70b81697..d9184218fd 100644 --- a/src/scripts/costing/costing_overview_analysis.py +++ b/src/scripts/costing/costing_overview_analysis.py @@ -14,6 +14,7 @@ import matplotlib.pyplot as plt import pandas as pd import seaborn as sns + from scripts.costing.cost_estimation import ( create_summary_treemap_by_cost_subgroup, do_line_plot_of_cost, diff --git a/src/scripts/costing/costing_validation.py b/src/scripts/costing/costing_validation.py index aba851c2c0..5909e8525d 100644 --- a/src/scripts/costing/costing_validation.py +++ b/src/scripts/costing/costing_validation.py @@ -7,6 +7,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from scripts.costing.cost_estimation import ( do_stacked_bar_plot_of_cost_by_category, estimate_input_cost_of_scenarios, diff --git a/src/scripts/data_file_processing/formatting_demography_data.py b/src/scripts/data_file_processing/formatting_demography_data.py index c0b0557739..f48e89812e 100644 --- a/src/scripts/data_file_processing/formatting_demography_data.py +++ b/src/scripts/data_file_processing/formatting_demography_data.py @@ -30,6 +30,7 @@ import numpy as np import pandas as pd + from tlo.analysis.utils import make_calendar_period_lookup from tlo.util import create_age_range_lookup diff --git a/src/scripts/data_file_processing/formatting_gbd_data.py b/src/scripts/data_file_processing/formatting_gbd_data.py index bc1ef7fc86..62c3b7010b 100644 --- a/src/scripts/data_file_processing/formatting_gbd_data.py +++ b/src/scripts/data_file_processing/formatting_gbd_data.py @@ -22,6 +22,7 @@ from pathlib import Path import pandas as pd + from tlo.analysis.utils import ( make_age_grp_lookup, make_age_grp_types, diff --git a/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py b/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py index 9489f6c8b7..e8812a93c6 100644 --- a/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py +++ b/src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py @@ -29,6 +29,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.methods.consumables import check_format_of_consumables_file # Set local shared folder source diff --git a/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py b/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py index b7ea085364..9ca0554650 100644 --- a/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py +++ b/src/scripts/data_file_processing/healthsystem/consumables/generating_consumable_scenarios/generate_consumable_availability_scenarios_for_impact_analysis.py @@ -46,6 +46,7 @@ import pandas as pd import seaborn as sns from plotnine import aes, element_text, geom_bar, ggplot, labs, theme, ylim # for ggplots from R + from tlo.methods.consumables import check_format_of_consumables_file # define a timestamp for script outputs diff --git a/src/scripts/depression_analyses/analyses_depression.py b/src/scripts/depression_analyses/analyses_depression.py index 0e39e23a91..4429027cdf 100644 --- a/src/scripts/depression_analyses/analyses_depression.py +++ b/src/scripts/depression_analyses/analyses_depression.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/dev/scenarios/test_scenario_1.py b/src/scripts/dev/scenarios/test_scenario_1.py index b7cfdf8fe3..0804725540 100644 --- a/src/scripts/dev/scenarios/test_scenario_1.py +++ b/src/scripts/dev/scenarios/test_scenario_1.py @@ -1,4 +1,5 @@ import numpy as np + from tlo import Date, logging from tlo.methods import ( contraception, diff --git a/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py b/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py index e6557c79fc..d23cc587d3 100644 --- a/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py +++ b/src/scripts/dev/th_testing/2D_grid/analysing_mockitis_2D_grid.py @@ -5,6 +5,7 @@ from pathlib import Path import matplotlib.pyplot as plt + from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py b/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py index 0c1ac87e75..eb47e54e3f 100644 --- a/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py +++ b/src/scripts/dev/th_testing/2D_grid/mockitis_2D_grid.py @@ -7,6 +7,7 @@ """ import numpy as np + from tlo import Date, logging from tlo.methods import ( demography, diff --git a/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py b/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py index 5f3513a2f5..78c84b010f 100644 --- a/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py +++ b/src/scripts/dev/th_testing/single_sweep/analysing_mockitis_single_sweep.py @@ -6,6 +6,7 @@ import matplotlib.pyplot as plt import numpy as np + from tlo.analysis.utils import ( extract_params, extract_results, diff --git a/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py b/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py index 815f447d12..637a7db114 100644 --- a/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py +++ b/src/scripts/dev/th_testing/single_sweep/mockitis_single_sweep.py @@ -7,6 +7,7 @@ """ import numpy as np + from tlo import Date, logging from tlo.methods import ( demography, diff --git a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py index 42c26852a2..615e07c1f1 100644 --- a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py +++ b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_and_without_treatment.py @@ -8,6 +8,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py index 0b9245dcb9..ff20947b7c 100644 --- a/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py +++ b/src/scripts/diarrhoea_analyses/analysis_diarrhoea_with_treatment.py @@ -10,6 +10,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py index 2dcda42458..b8f2de5a55 100644 --- a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py +++ b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py @@ -10,6 +10,7 @@ import matplotlib.pyplot as plt import pandas as pd from matplotlib import ticker + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import demography, enhanced_lifestyle, simplified_births diff --git a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py index 5d2d997334..db89bef880 100644 --- a/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py +++ b/src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_calibrations.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd from matplotlib import ticker + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import demography, enhanced_lifestyle, simplified_births diff --git a/src/scripts/epi/analysis_epi.py b/src/scripts/epi/analysis_epi.py index 98f158b36c..197388372e 100644 --- a/src/scripts/epi/analysis_epi.py +++ b/src/scripts/epi/analysis_epi.py @@ -4,6 +4,7 @@ import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/epilepsy_analyses/analysis_epilepsy.py b/src/scripts/epilepsy_analyses/analysis_epilepsy.py index 7a199e6d7d..1fd20d0334 100644 --- a/src/scripts/epilepsy_analyses/analysis_epilepsy.py +++ b/src/scripts/epilepsy_analyses/analysis_epilepsy.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/get_properties/properties_graph.py b/src/scripts/get_properties/properties_graph.py index 5c10e811c4..8c79787cc6 100644 --- a/src/scripts/get_properties/properties_graph.py +++ b/src/scripts/get_properties/properties_graph.py @@ -10,6 +10,7 @@ from typing import Any, Mapping, Set, Type, Union import numpy as np + import tlo.methods from tlo import Module from tlo.analysis.utils import _standardize_short_treatment_id diff --git a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py index 7379f6d178..ba989f2272 100644 --- a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py +++ b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_comparison_of_impact_in_different_scenarios.py @@ -6,11 +6,11 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt -from tlo.analysis.utils import get_color_short_treatment_id from src.scripts.healthsystem.effects_of_each_treatment_multi_scenario.analysis_effect_of_each_treatment_multiple_scenarios import ( apply, ) +from tlo.analysis.utils import get_color_short_treatment_id outputs = Path("./outputs/tbh03@ic.ac.uk/") diff --git a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py index ebe243eaf1..25533960d7 100644 --- a/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py +++ b/src/scripts/healthsystem/effects_of_each_treatment_multi_scenario/analysis_effect_of_each_treatment_multiple_scenarios.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from scripts.calibration_analyses.analysis_scripts import plot_legends from scripts.healthsystem.effects_of_each_treatment_multi_scenario.scenario_effect_of_each_treatment_status_quo import ( EffectOfEachTreatmentStatusQuo, diff --git a/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py b/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py index 7c257109da..37c0c1e5a7 100644 --- a/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py +++ b/src/scripts/healthsystem/impact_of_cons_availability/analysis_impact_of_consumables_availability.py @@ -5,6 +5,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo.analysis.utils import ( extract_params, extract_results, 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 99fb47e1aa..a46dfa75fe 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 @@ -16,6 +16,7 @@ from typing import Dict import pandas as pd + from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel 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 753a9a1449..28cd7ff171 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 @@ -16,6 +16,7 @@ from typing import Dict import pandas as pd + from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel 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 2a93d03344..5d29102e8b 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 @@ -16,6 +16,7 @@ from typing import Dict import pandas as pd + from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py index bc8c88c385..be0a641504 100644 --- a/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py +++ b/src/scripts/healthsystem/impact_of_const_capabilities_expansion/scenario_impact_of_const_capabilities_expansion.py @@ -16,6 +16,7 @@ from typing import Dict import pandas as pd + from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py b/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py index fe20090b3f..0fa3595aab 100644 --- a/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py +++ b/src/scripts/healthsystem/impact_of_mode/analysis_health_impact_of_mode.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py b/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py index 63741b448f..f616632a8c 100644 --- a/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py +++ b/src/scripts/healthsystem/impact_of_mode/analysis_hsi_by_mode.py @@ -6,6 +6,7 @@ from typing import Tuple import pandas as pd + from tlo import Date from tlo.analysis.utils import extract_results, summarize diff --git a/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py b/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py index 5ca9e174ee..216636669a 100644 --- a/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py +++ b/src/scripts/healthsystem/impact_of_policy/analysis_effect_of_each_treatment.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from scripts.calibration_analyses.analysis_scripts import plot_legends from tlo import Date from tlo.analysis.utils import ( diff --git a/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py b/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py index 9f32481479..2554d78583 100644 --- a/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py +++ b/src/scripts/healthsystem/impact_of_policy/scenario_impact_of_policy.py @@ -16,6 +16,7 @@ from typing import Dict import pandas as pd + from tlo import Date, logging from tlo.analysis.utils import get_parameters_for_status_quo, mix_scenarios from tlo.methods.fullmodel import fullmodel diff --git a/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py b/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py index ad3529efb6..e80cda3128 100644 --- a/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py +++ b/src/scripts/healthsystem/org_chart_of_hsi/plot_org_chart_treatment_ids.py @@ -7,6 +7,7 @@ import pandas as pd import pydot + from tlo.analysis.utils import ( get_color_short_treatment_id, get_filtered_treatment_ids, diff --git a/src/scripts/hiv/projections_jan2023/output_plots.py b/src/scripts/hiv/projections_jan2023/output_plots.py index efebff8696..4ae8a1531d 100644 --- a/src/scripts/hiv/projections_jan2023/output_plots.py +++ b/src/scripts/hiv/projections_jan2023/output_plots.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.analysis.utils import compare_number_of_deaths from tlo.util import read_csv_files diff --git a/src/scripts/htm_scenario_analyses/scenario_plots.py b/src/scripts/htm_scenario_analyses/scenario_plots.py index 0919114c92..c209c60f6e 100644 --- a/src/scripts/htm_scenario_analyses/scenario_plots.py +++ b/src/scripts/htm_scenario_analyses/scenario_plots.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import pandas as pd import seaborn as sns + from tlo import Date from tlo.analysis.utils import ( extract_params, diff --git a/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py b/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py index 558097a6a9..affa7c8603 100644 --- a/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py +++ b/src/scripts/impact_of_historical_changes_in_hr/analysis_historical_changes_in_hr.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from scripts.impact_of_historical_changes_in_hr.scenario_historical_changes_in_hr import ( HistoricalChangesInHRH, ) diff --git a/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py b/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py index aa0fdb5f1a..b018fb3513 100644 --- a/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py +++ b/src/scripts/impact_of_historical_changes_in_hr/examining_data_historic_changes_in_hr.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd from scipy.optimize import curve_fit + from tlo.analysis.utils import get_root_path # Path to shared folder diff --git a/src/scripts/malaria/malaria_plots.py b/src/scripts/malaria/malaria_plots.py index a1aed71c41..ab09f47e25 100644 --- a/src/scripts/malaria/malaria_plots.py +++ b/src/scripts/malaria/malaria_plots.py @@ -7,6 +7,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.util import read_csv_files resourcefilepath = Path("./resources") diff --git a/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py b/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py index db029a9f08..dfb44abd97 100644 --- a/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py +++ b/src/scripts/maternal_perinatal_analyses/analysis_scripts/analysis_utility_functions.py @@ -1,6 +1,7 @@ import numpy as np import scipy.stats as st from matplotlib import pyplot as plt + from tlo.analysis.utils import extract_results plt.style.use('seaborn-darkgrid') diff --git a/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py b/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py index 18c3275f46..b3e64e1217 100644 --- a/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py +++ b/src/scripts/maternal_perinatal_analyses/analysis_scripts/maternal_newborn_health_thesis_analysis.py @@ -10,6 +10,7 @@ return_95_CI_across_runs, ) from matplotlib import pyplot as plt + from tlo.analysis.utils import extract_results, get_scenario_outputs plt.style.use('seaborn-darkgrid') diff --git a/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py b/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py index d9f7915baa..1ca54f24b8 100644 --- a/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py +++ b/src/scripts/maternal_perinatal_analyses/calibration/calibration_outputs_with_ci.py @@ -5,9 +5,9 @@ import pandas as pd import scipy.stats as st from matplotlib import pyplot as plt -from tlo.analysis.utils import extract_results, get_scenario_outputs from src.scripts.maternal_perinatal_analyses.analysis_scripts import analysis_utility_functions +from tlo.analysis.utils import extract_results, get_scenario_outputs plt.style.use('seaborn') diff --git a/src/scripts/measles/analysis_measles.py b/src/scripts/measles/analysis_measles.py index 54ca3cc66e..0f6661421d 100644 --- a/src/scripts/measles/analysis_measles.py +++ b/src/scripts/measles/analysis_measles.py @@ -3,6 +3,7 @@ # import time import matplotlib.pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py b/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py index ea43652570..be8a90265f 100644 --- a/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py +++ b/src/scripts/measles/analysis_measles_compare_deaths_to_gbd.py @@ -4,6 +4,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_deaths.py b/src/scripts/measles/analysis_measles_deaths.py index d58c3c45ea..86a41cd59f 100644 --- a/src/scripts/measles/analysis_measles_deaths.py +++ b/src/scripts/measles/analysis_measles_deaths.py @@ -2,6 +2,7 @@ from pathlib import Path import matplotlib.pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/measles/analysis_measles_scenarios.py b/src/scripts/measles/analysis_measles_scenarios.py index 2f0e1ff9ed..58b0db6e59 100644 --- a/src/scripts/measles/analysis_measles_scenarios.py +++ b/src/scripts/measles/analysis_measles_scenarios.py @@ -2,6 +2,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py index 46838f325d..cb4cd7db50 100644 --- a/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/oesophagealcancer_analyses/calc_5y_survival_following_treatment.py @@ -13,6 +13,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py b/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py index 66e879bc5a..204e52467a 100644 --- a/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py +++ b/src/scripts/oesophagealcancer_analyses/oesophagealcancer_analyses.py @@ -13,6 +13,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py b/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py index 3ec2c9c107..a3d5d2cf31 100644 --- a/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/other_adult_cancers_analyses/calc_5y_survival_following_treatment.py @@ -13,6 +13,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py index a6c1552a4f..83ad74152d 100644 --- a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py +++ b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_analyses.py @@ -14,6 +14,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import compare_number_of_deaths, make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py index 6b38646398..36937944cf 100644 --- a/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py +++ b/src/scripts/other_adult_cancers_analyses/other_adult_cancers_calibration_to_deaths.py @@ -6,6 +6,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths from tlo.methods import ( diff --git a/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py b/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py index af1f68840d..021590ba48 100644 --- a/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py +++ b/src/scripts/overview_paper/B_finding_effects_of_each_treatment/analysis_effect_of_each_treatment.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from scripts.calibration_analyses.analysis_scripts import plot_legends from scripts.healthsystem.org_chart_of_hsi import plot_org_chart_treatment_ids from scripts.overview_paper.B_finding_effects_of_each_treatment.scenario_effect_of_each_treatment import ( diff --git a/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py b/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py index 41d0564951..faac171620 100644 --- a/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py +++ b/src/scripts/overview_paper/C_impact_of_healthsystem_assumptions/analysis_impact_of_healthsystem.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date from tlo.analysis.utils import ( CAUSE_OF_DEATH_OR_DALY_LABEL_TO_COLOR_MAP, diff --git a/src/scripts/profiling/batch_test.py b/src/scripts/profiling/batch_test.py index dc46087820..f69bb6cbd6 100644 --- a/src/scripts/profiling/batch_test.py +++ b/src/scripts/profiling/batch_test.py @@ -11,6 +11,7 @@ import pandas as pd import shared + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/profiling/heavy_use_of_bed_days.py b/src/scripts/profiling/heavy_use_of_bed_days.py index 7cd4310be1..647a5bd948 100644 --- a/src/scripts/profiling/heavy_use_of_bed_days.py +++ b/src/scripts/profiling/heavy_use_of_bed_days.py @@ -4,6 +4,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation from tlo.methods import demography, healthsystem diff --git a/src/scripts/profiling/heavy_use_of_spurious_symptoms.py b/src/scripts/profiling/heavy_use_of_spurious_symptoms.py index 87ea16d1ef..2550c374f8 100644 --- a/src/scripts/profiling/heavy_use_of_spurious_symptoms.py +++ b/src/scripts/profiling/heavy_use_of_spurious_symptoms.py @@ -4,6 +4,7 @@ from pathlib import Path from pandas import DateOffset + from tlo import Date, Simulation, logging from tlo.methods import demography, healthsystem, simplified_births, symptommanager diff --git a/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py b/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py index 4f71c06f75..9ea33cba69 100644 --- a/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py +++ b/src/scripts/profiling/run_full_model_with_hard_constraints_in_healthsystem.py @@ -13,6 +13,7 @@ import pandas as pd import shared + from tlo import Date, Simulation, logging from tlo.methods import ( cardio_metabolic_disorders, diff --git a/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py b/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py index e758fa3f50..599101dddd 100644 --- a/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py +++ b/src/scripts/profiling/run_with_high_intensity_of_HSI_and_simplified_births.py @@ -15,6 +15,7 @@ import pandas as pd import shared + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.lm import LinearModel, LinearModelType diff --git a/src/scripts/profiling/scale_run.py b/src/scripts/profiling/scale_run.py index 9f02670c34..5a5889bf95 100644 --- a/src/scripts/profiling/scale_run.py +++ b/src/scripts/profiling/scale_run.py @@ -11,6 +11,7 @@ from pyinstrument import Profiler from shared import print_checksum, schedule_profile_log + from tlo import Date, Simulation, logging from tlo.analysis.utils import LogsDict from tlo.analysis.utils import parse_log_file as parse_log_file_fn diff --git a/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py b/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py index 280b9b8e42..5dd6076361 100644 --- a/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py +++ b/src/scripts/profiling/symptom_manager_bookkeeping_profiling.py @@ -7,6 +7,7 @@ from pathlib import Path import numpy as np + from tlo import Date, Simulation from tlo.methods import demography, symptommanager diff --git a/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py b/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py index 49a85e8097..36c2dc9557 100644 --- a/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py +++ b/src/scripts/prostate_cancer_analyses/calc_5y_survival_following_treatment.py @@ -13,6 +13,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py b/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py index 8b850bf082..51d205cd5d 100644 --- a/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py +++ b/src/scripts/prostate_cancer_analyses/prostate_cancer_analyses.py @@ -14,6 +14,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo import Date, Simulation from tlo.analysis.utils import make_age_grp_types, parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti.py b/src/scripts/rti/analysis_rti.py index 2c063e8726..3231d27d5a 100644 --- a/src/scripts/rti/analysis_rti.py +++ b/src/scripts/rti/analysis_rti.py @@ -2,6 +2,7 @@ import numpy as np from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti_deaths.py b/src/scripts/rti/analysis_rti_deaths.py index 19201ea5aa..eca62cf283 100644 --- a/src/scripts/rti/analysis_rti_deaths.py +++ b/src/scripts/rti/analysis_rti_deaths.py @@ -1,5 +1,6 @@ import numpy as np from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py b/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py index a1ae201d70..b36d8ae372 100644 --- a/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py +++ b/src/scripts/rti/analysis_rti_single_vs_multiple_injury.py @@ -1,5 +1,6 @@ import numpy as np from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/src/scripts/schistosomiasis/schisto_analysis.py b/src/scripts/schistosomiasis/schisto_analysis.py index 672634728c..c7362d29a0 100644 --- a/src/scripts/schistosomiasis/schisto_analysis.py +++ b/src/scripts/schistosomiasis/schisto_analysis.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib.dates import DateFormatter + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import contraception, demography, healthburden, healthsystem, schisto diff --git a/src/scripts/schistosomiasis/schisto_calibration_check.py b/src/scripts/schistosomiasis/schisto_calibration_check.py index 2f87d4a5c7..3c46bdad76 100644 --- a/src/scripts/schistosomiasis/schisto_calibration_check.py +++ b/src/scripts/schistosomiasis/schisto_calibration_check.py @@ -5,6 +5,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import ( format_gbd, diff --git a/src/scripts/schistosomiasis/schisto_single_run_local.py b/src/scripts/schistosomiasis/schisto_single_run_local.py index 4341200c46..6e84efb3e1 100644 --- a/src/scripts/schistosomiasis/schisto_single_run_local.py +++ b/src/scripts/schistosomiasis/schisto_single_run_local.py @@ -7,6 +7,7 @@ import matplotlib.pyplot as plt import pandas as pd + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py b/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py index bbddc029f3..c3aa6689d6 100644 --- a/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py +++ b/src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd from matplotlib import pyplot as plt + from tlo import Date, Simulation, logging from tlo.analysis.utils import make_calendar_period_lookup, make_calendar_period_type from tlo.methods import demography, simplified_births diff --git a/src/scripts/tb/output_plots_tb.py b/src/scripts/tb/output_plots_tb.py index ebbdb2db61..2078fdfc88 100644 --- a/src/scripts/tb/output_plots_tb.py +++ b/src/scripts/tb/output_plots_tb.py @@ -9,6 +9,7 @@ import matplotlib.pyplot as plt import numpy as np import pandas as pd + from tlo.analysis.utils import compare_number_of_deaths from tlo.util import read_csv_files diff --git a/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py b/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py index 3e1fdbeb9c..6a3a5d31a1 100644 --- a/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py +++ b/src/scripts/undernutrition_analyses/stunting/stunting_analysis_plots.py @@ -4,6 +4,7 @@ import pandas as pd from matplotlib import pyplot as plt from scipy.stats import norm + from tlo import Date, Simulation from tlo.analysis.utils import extract_results, get_scenario_outputs, summarize from tlo.methods import demography, enhanced_lifestyle, healthsystem, simplified_births, stunting diff --git a/src/tlo/analysis/hsi_events.py b/src/tlo/analysis/hsi_events.py index 5332f27d5b..f5082c6e3a 100644 --- a/src/tlo/analysis/hsi_events.py +++ b/src/tlo/analysis/hsi_events.py @@ -13,6 +13,7 @@ from typing import Any, Iterable, List, Mapping, Optional, Set, Union import pandas as pd + import tlo.methods from tlo import Date, Module, Simulation from tlo.analysis.utils import get_root_path diff --git a/src/tlo/analysis/life_expectancy.py b/src/tlo/analysis/life_expectancy.py index d0d1de57d6..ebde940f66 100644 --- a/src/tlo/analysis/life_expectancy.py +++ b/src/tlo/analysis/life_expectancy.py @@ -9,6 +9,7 @@ from typing import Dict, Tuple import pandas as pd + from tlo.analysis.utils import ( extract_results, get_scenario_info, diff --git a/src/tlo/analysis/utils.py b/src/tlo/analysis/utils.py index 02d175ef76..cbc9aee900 100644 --- a/src/tlo/analysis/utils.py +++ b/src/tlo/analysis/utils.py @@ -20,6 +20,7 @@ import pandas as pd import scipy.stats as st import squarify + from tlo import Date, Simulation, logging, util from tlo.logging.reader import LogData from tlo.util import ( diff --git a/src/tlo/cli.py b/src/tlo/cli.py index d6097accd9..9436d060ff 100644 --- a/src/tlo/cli.py +++ b/src/tlo/cli.py @@ -22,6 +22,7 @@ from azure.keyvault.secrets import SecretClient from azure.storage.fileshare import ShareClient, ShareDirectoryClient, ShareFileClient from git import Repo + from tlo.analysis.utils import parse_log_file from tlo.scenario import SampleRunner, ScenarioLoader diff --git a/src/tlo/lm.py b/src/tlo/lm.py index 87459d693a..a7538a1a7a 100644 --- a/src/tlo/lm.py +++ b/src/tlo/lm.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd from pandas.core.computation.parsing import clean_column_name + from tlo import logging logger = logging.getLogger(__name__) diff --git a/src/tlo/logging/core.py b/src/tlo/logging/core.py index 4dee050f4d..dc3beaf2f1 100644 --- a/src/tlo/logging/core.py +++ b/src/tlo/logging/core.py @@ -11,6 +11,7 @@ import numpy as np import pandas as pd + from tlo.logging import encoding LogLevel: TypeAlias = int diff --git a/src/tlo/methods/alri.py b/src/tlo/methods/alri.py index 0fff41b27b..8707e674ad 100644 --- a/src/tlo/methods/alri.py +++ b/src/tlo/methods/alri.py @@ -28,6 +28,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/bed_days.py b/src/tlo/methods/bed_days.py index 1ad08bb217..a47b75b16a 100644 --- a/src/tlo/methods/bed_days.py +++ b/src/tlo/methods/bed_days.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd + from tlo import Date, Property, Types, logging # --------------------------------------------------------------------------------------------------------- diff --git a/src/tlo/methods/bladder_cancer.py b/src/tlo/methods/bladder_cancer.py index be59f2e6a0..c84d0050db 100644 --- a/src/tlo/methods/bladder_cancer.py +++ b/src/tlo/methods/bladder_cancer.py @@ -11,6 +11,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/breast_cancer.py b/src/tlo/methods/breast_cancer.py index f532b29627..2d093ac010 100644 --- a/src/tlo/methods/breast_cancer.py +++ b/src/tlo/methods/breast_cancer.py @@ -10,6 +10,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/cardio_metabolic_disorders.py b/src/tlo/methods/cardio_metabolic_disorders.py index 8fa71a0bf6..0d52f3fa80 100644 --- a/src/tlo/methods/cardio_metabolic_disorders.py +++ b/src/tlo/methods/cardio_metabolic_disorders.py @@ -19,6 +19,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/care_of_women_during_pregnancy.py b/src/tlo/methods/care_of_women_during_pregnancy.py index 386d5289b1..4cdf3339bb 100644 --- a/src/tlo/methods/care_of_women_during_pregnancy.py +++ b/src/tlo/methods/care_of_women_during_pregnancy.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata, pregnancy_helper_functions diff --git a/src/tlo/methods/causes.py b/src/tlo/methods/causes.py index 438a0e6a22..f2b881be8e 100644 --- a/src/tlo/methods/causes.py +++ b/src/tlo/methods/causes.py @@ -7,6 +7,7 @@ from typing import Union import pandas as pd + from tlo.methods import Metadata diff --git a/src/tlo/methods/cervical_cancer.py b/src/tlo/methods/cervical_cancer.py index 2fab397ba3..3d5647494b 100644 --- a/src/tlo/methods/cervical_cancer.py +++ b/src/tlo/methods/cervical_cancer.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/chronicsyndrome.py b/src/tlo/methods/chronicsyndrome.py index c3dede39be..db9303da5c 100644 --- a/src/tlo/methods/chronicsyndrome.py +++ b/src/tlo/methods/chronicsyndrome.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/consumables.py b/src/tlo/methods/consumables.py index 98aff365ba..c16b22e6cd 100644 --- a/src/tlo/methods/consumables.py +++ b/src/tlo/methods/consumables.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd + from tlo import logging logger = logging.getLogger('tlo.methods.healthsystem') diff --git a/src/tlo/methods/contraception.py b/src/tlo/methods/contraception.py index 0a2bbf6329..6f56a55cc7 100644 --- a/src/tlo/methods/contraception.py +++ b/src/tlo/methods/contraception.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/copd.py b/src/tlo/methods/copd.py index 1c4f84bcf0..eeb08f0445 100644 --- a/src/tlo/methods/copd.py +++ b/src/tlo/methods/copd.py @@ -4,6 +4,7 @@ from typing import TYPE_CHECKING, Dict, List, Optional import pandas as pd + from tlo import Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/demography.py b/src/tlo/methods/demography.py index 83f75abbfe..2acaad75eb 100644 --- a/src/tlo/methods/demography.py +++ b/src/tlo/methods/demography.py @@ -13,6 +13,7 @@ import numpy as np import pandas as pd + from tlo import ( DAYS_IN_MONTH, DAYS_IN_YEAR, diff --git a/src/tlo/methods/depression.py b/src/tlo/methods/depression.py index 28ed747b6a..f198c4699c 100644 --- a/src/tlo/methods/depression.py +++ b/src/tlo/methods/depression.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/diarrhoea.py b/src/tlo/methods/diarrhoea.py index 2f64cda66c..c5320ca555 100644 --- a/src/tlo/methods/diarrhoea.py +++ b/src/tlo/methods/diarrhoea.py @@ -23,6 +23,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/dxmanager.py b/src/tlo/methods/dxmanager.py index f32bfb9d21..b46dd58f87 100644 --- a/src/tlo/methods/dxmanager.py +++ b/src/tlo/methods/dxmanager.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd from pandas.api.types import is_bool_dtype, is_categorical_dtype, is_float_dtype + from tlo import logging from tlo.events import IndividualScopeEventMixin diff --git a/src/tlo/methods/enhanced_lifestyle.py b/src/tlo/methods/enhanced_lifestyle.py index f96dee7f15..d9164f04fd 100644 --- a/src/tlo/methods/enhanced_lifestyle.py +++ b/src/tlo/methods/enhanced_lifestyle.py @@ -7,6 +7,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/epi.py b/src/tlo/methods/epi.py index 7c91c4cadd..4bc298aefc 100644 --- a/src/tlo/methods/epi.py +++ b/src/tlo/methods/epi.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/epilepsy.py b/src/tlo/methods/epilepsy.py index af82288350..1ed2989733 100644 --- a/src/tlo/methods/epilepsy.py +++ b/src/tlo/methods/epilepsy.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/equipment.py b/src/tlo/methods/equipment.py index 4b9b9dc613..64e833fb06 100644 --- a/src/tlo/methods/equipment.py +++ b/src/tlo/methods/equipment.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd + from tlo import logging from tlo.logging.helpers import get_dataframe_row_as_dict_for_logging diff --git a/src/tlo/methods/healthburden.py b/src/tlo/methods/healthburden.py index da3fe9141d..54db8bf8fb 100644 --- a/src/tlo/methods/healthburden.py +++ b/src/tlo/methods/healthburden.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Types, logging from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/healthseekingbehaviour.py b/src/tlo/methods/healthseekingbehaviour.py index cfd075d4f2..5fdab960d3 100644 --- a/src/tlo/methods/healthseekingbehaviour.py +++ b/src/tlo/methods/healthseekingbehaviour.py @@ -12,6 +12,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Types from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent from tlo.lm import LinearModel diff --git a/src/tlo/methods/healthsystem.py b/src/tlo/methods/healthsystem.py index 719f5bdc0c..98c07aa4df 100644 --- a/src/tlo/methods/healthsystem.py +++ b/src/tlo/methods/healthsystem.py @@ -13,6 +13,7 @@ import numpy as np import pandas as pd from pandas.testing import assert_series_equal + from tlo import Date, DateOffset, Module, Parameter, Population, Property, Types, logging from tlo.analysis.utils import ( # get_filtered_treatment_ids, flatten_multi_index_series_into_dict_for_logging, diff --git a/src/tlo/methods/hiv.py b/src/tlo/methods/hiv.py index c685d246fd..8b40e37a34 100644 --- a/src/tlo/methods/hiv.py +++ b/src/tlo/methods/hiv.py @@ -30,6 +30,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/hiv_tb_calibration.py b/src/tlo/methods/hiv_tb_calibration.py index 3cf93ff9f9..2fdb1fded0 100644 --- a/src/tlo/methods/hiv_tb_calibration.py +++ b/src/tlo/methods/hiv_tb_calibration.py @@ -11,6 +11,7 @@ from typing import Optional import pandas as pd + from tlo import Module, logging from tlo.util import read_csv_files diff --git a/src/tlo/methods/hsi_event.py b/src/tlo/methods/hsi_event.py index d86dba3485..946fdd9087 100644 --- a/src/tlo/methods/hsi_event.py +++ b/src/tlo/methods/hsi_event.py @@ -4,6 +4,7 @@ from typing import TYPE_CHECKING, Dict, Iterable, Literal, NamedTuple, Optional, Set, Tuple, Union import numpy as np + from tlo import Date, logging from tlo.events import Event diff --git a/src/tlo/methods/hsi_generic_first_appts.py b/src/tlo/methods/hsi_generic_first_appts.py index ba77db7c4b..37f6c5e261 100644 --- a/src/tlo/methods/hsi_generic_first_appts.py +++ b/src/tlo/methods/hsi_generic_first_appts.py @@ -12,6 +12,7 @@ from typing import TYPE_CHECKING, Any, Dict, List, Protocol, Set, Union import numpy as np + from tlo import Date, Module, logging from tlo.events import IndividualScopeEventMixin from tlo.methods.hsi_event import HSI_Event diff --git a/src/tlo/methods/labour.py b/src/tlo/methods/labour.py index 67d6d2f53d..8cd97da57f 100644 --- a/src/tlo/methods/labour.py +++ b/src/tlo/methods/labour.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd import scipy.stats + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType diff --git a/src/tlo/methods/malaria.py b/src/tlo/methods/malaria.py index 481e2b3c44..82d82b1a4c 100644 --- a/src/tlo/methods/malaria.py +++ b/src/tlo/methods/malaria.py @@ -10,6 +10,7 @@ from typing import TYPE_CHECKING, List, Literal, Optional, Union import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, Predictor diff --git a/src/tlo/methods/measles.py b/src/tlo/methods/measles.py index 3f0939c02b..075cc1c67c 100644 --- a/src/tlo/methods/measles.py +++ b/src/tlo/methods/measles.py @@ -5,6 +5,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/mockitis.py b/src/tlo/methods/mockitis.py index d9eea86943..6e0a43f278 100644 --- a/src/tlo/methods/mockitis.py +++ b/src/tlo/methods/mockitis.py @@ -4,6 +4,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/newborn_outcomes.py b/src/tlo/methods/newborn_outcomes.py index ed52d6b944..131589b88a 100644 --- a/src/tlo/methods/newborn_outcomes.py +++ b/src/tlo/methods/newborn_outcomes.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin from tlo.lm import LinearModel diff --git a/src/tlo/methods/oesophagealcancer.py b/src/tlo/methods/oesophagealcancer.py index 5c7ee1b96a..4ffd6fca08 100644 --- a/src/tlo/methods/oesophagealcancer.py +++ b/src/tlo/methods/oesophagealcancer.py @@ -12,6 +12,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/other_adult_cancers.py b/src/tlo/methods/other_adult_cancers.py index ab6e885c9e..42278b35b9 100644 --- a/src/tlo/methods/other_adult_cancers.py +++ b/src/tlo/methods/other_adult_cancers.py @@ -10,6 +10,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/postnatal_supervisor.py b/src/tlo/methods/postnatal_supervisor.py index 9a6ee88f5a..109b7d5694 100644 --- a/src/tlo/methods/postnatal_supervisor.py +++ b/src/tlo/methods/postnatal_supervisor.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging, util from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel diff --git a/src/tlo/methods/pregnancy_helper_functions.py b/src/tlo/methods/pregnancy_helper_functions.py index 4520255b4a..76076a5dcf 100644 --- a/src/tlo/methods/pregnancy_helper_functions.py +++ b/src/tlo/methods/pregnancy_helper_functions.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo import logging diff --git a/src/tlo/methods/pregnancy_supervisor.py b/src/tlo/methods/pregnancy_supervisor.py index b8c1d79607..1be38175f7 100644 --- a/src/tlo/methods/pregnancy_supervisor.py +++ b/src/tlo/methods/pregnancy_supervisor.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo import ( DAYS_IN_MONTH, DAYS_IN_YEAR, diff --git a/src/tlo/methods/prostate_cancer.py b/src/tlo/methods/prostate_cancer.py index fc77f40357..abd280b325 100644 --- a/src/tlo/methods/prostate_cancer.py +++ b/src/tlo/methods/prostate_cancer.py @@ -10,6 +10,7 @@ from typing import TYPE_CHECKING, List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/rti.py b/src/tlo/methods/rti.py index 653d5c675d..994b8d1054 100644 --- a/src/tlo/methods/rti.py +++ b/src/tlo/methods/rti.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/schisto.py b/src/tlo/methods/schisto.py index 20b56a384e..b7079e95d3 100644 --- a/src/tlo/methods/schisto.py +++ b/src/tlo/methods/schisto.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.analysis.utils import flatten_multi_index_series_into_dict_for_logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/methods/simplified_births.py b/src/tlo/methods/simplified_births.py index d8ad4c9e89..940692bb62 100644 --- a/src/tlo/methods/simplified_births.py +++ b/src/tlo/methods/simplified_births.py @@ -8,6 +8,7 @@ from typing import List, Optional import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods.contraception import get_medium_variant_asfr_from_wpp_resourcefile diff --git a/src/tlo/methods/stunting.py b/src/tlo/methods/stunting.py index 3938339fa2..7c2d83cc40 100644 --- a/src/tlo/methods/stunting.py +++ b/src/tlo/methods/stunting.py @@ -17,6 +17,7 @@ import numpy as np import pandas as pd from scipy.stats import norm + from tlo import DAYS_IN_YEAR, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/methods/symptommanager.py b/src/tlo/methods/symptommanager.py index ac3c1ccc76..9f246b9845 100644 --- a/src/tlo/methods/symptommanager.py +++ b/src/tlo/methods/symptommanager.py @@ -19,6 +19,7 @@ import numpy as np import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata diff --git a/src/tlo/methods/tb.py b/src/tlo/methods/tb.py index b08f063f70..d9ba7309e0 100644 --- a/src/tlo/methods/tb.py +++ b/src/tlo/methods/tb.py @@ -8,6 +8,7 @@ from typing import Optional import pandas as pd + from tlo import Date, DateOffset, Module, Parameter, Property, Types, logging from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/src/tlo/population.py b/src/tlo/population.py index d3d19d17f0..26af2f3185 100644 --- a/src/tlo/population.py +++ b/src/tlo/population.py @@ -6,6 +6,7 @@ from typing import Any, Dict, Optional, Set import pandas as pd + from tlo import Property, logging logger = logging.getLogger(__name__) diff --git a/src/tlo/scenario.py b/src/tlo/scenario.py index 9cf84fadd7..cd83d0e63f 100644 --- a/src/tlo/scenario.py +++ b/src/tlo/scenario.py @@ -69,6 +69,7 @@ def draw_parameters(self, draw_number, rng): from typing import List, Optional import numpy as np + from tlo import Date, Simulation, logging from tlo.util import str_to_pandas_date diff --git a/src/tlo/test/random_birth.py b/src/tlo/test/random_birth.py index fae5e29f0c..22a20879b1 100644 --- a/src/tlo/test/random_birth.py +++ b/src/tlo/test/random_birth.py @@ -10,6 +10,7 @@ """ import pandas as pd + from tlo import DateOffset, Module, Parameter, Property, Types from tlo.events import Event, IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/src/tlo/util.py b/src/tlo/util.py index dcbfad0cc9..efe17a9920 100644 --- a/src/tlo/util.py +++ b/src/tlo/util.py @@ -9,6 +9,7 @@ import pandas as pd from pandas import DataFrame, DateOffset from pandas._typing import DtypeArg + from tlo import Population, Property, Types # Default mother_id value, assigned to individuals initialised as adults at the start of the simulation. diff --git a/tests/bitset_handler/conftest.py b/tests/bitset_handler/conftest.py index 7d3372c117..5cd111ae62 100644 --- a/tests/bitset_handler/conftest.py +++ b/tests/bitset_handler/conftest.py @@ -13,6 +13,7 @@ import pytest from numpy.random import PCG64, Generator from numpy.typing import NDArray + from tlo.bitset_handler.bitset_extension import BitsetArray, BitsetDtype, ElementType diff --git a/tests/bitset_handler/test_bitset_pandas_dtype.py b/tests/bitset_handler/test_bitset_pandas_dtype.py index b6644074bf..156f9e49e6 100644 --- a/tests/bitset_handler/test_bitset_pandas_dtype.py +++ b/tests/bitset_handler/test_bitset_pandas_dtype.py @@ -2,6 +2,7 @@ import pytest from pandas.tests.extension.base import BaseDtypeTests + from tlo.bitset_handler.bitset_extension import BitsetDtype diff --git a/tests/bitset_handler/test_bitset_set_like_interactions.py b/tests/bitset_handler/test_bitset_set_like_interactions.py index aa6360e124..801703ce24 100644 --- a/tests/bitset_handler/test_bitset_set_like_interactions.py +++ b/tests/bitset_handler/test_bitset_set_like_interactions.py @@ -6,6 +6,7 @@ import pandas as pd import pytest + from tlo.bitset_handler.bitset_extension import BitsetDtype, CastableForPandasOps, ElementType diff --git a/tests/test_alri.py b/tests/test_alri.py index 2829d8fca8..3d13041a61 100644 --- a/tests/test_alri.py +++ b/tests/test_alri.py @@ -7,6 +7,7 @@ import pandas as pd import pytest from pandas import DateOffset + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_analysis.py b/tests/test_analysis.py index 760af188cd..d419f5a92e 100644 --- a/tests/test_analysis.py +++ b/tests/test_analysis.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, DateOffset, Module, Property, Simulation, Types, logging from tlo.analysis.utils import ( colors_in_matplotlib, diff --git a/tests/test_antenatal_interventions.py b/tests/test_antenatal_interventions.py index b629bba013..8237301668 100644 --- a/tests/test_antenatal_interventions.py +++ b/tests/test_antenatal_interventions.py @@ -2,6 +2,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation from tlo.lm import LinearModel, LinearModelType, Predictor from tlo.methods import ( diff --git a/tests/test_basic_sims.py b/tests/test_basic_sims.py index 997aa073e3..c56ae74554 100644 --- a/tests/test_basic_sims.py +++ b/tests/test_basic_sims.py @@ -2,6 +2,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, DateOffset, Module, Property, Simulation, Types, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.test import random_birth, random_death diff --git a/tests/test_beddays.py b/tests/test_beddays.py index 29b3a248f1..4ddfe4c84f 100644 --- a/tests/test_beddays.py +++ b/tests/test_beddays.py @@ -6,6 +6,7 @@ import pandas as pd import pytest + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent diff --git a/tests/test_bitset.py b/tests/test_bitset.py index 044cc1c15e..0ca60f5c5e 100644 --- a/tests/test_bitset.py +++ b/tests/test_bitset.py @@ -3,6 +3,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Population from tlo.lm import LinearModel, LinearModelType, Predictor from tlo.util import BitsetDType, BitsetHandler diff --git a/tests/test_bladder_cancer.py b/tests/test_bladder_cancer.py index b0e60407fd..e0979df6a1 100644 --- a/tests/test_bladder_cancer.py +++ b/tests/test_bladder_cancer.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( bladder_cancer, diff --git a/tests/test_breast_cancer.py b/tests/test_breast_cancer.py index b98671c935..7b1eb96334 100644 --- a/tests/test_breast_cancer.py +++ b/tests/test_breast_cancer.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( breast_cancer, diff --git a/tests/test_cardiometabolicdisorders.py b/tests/test_cardiometabolicdisorders.py index bbd5ec83e6..daa4fc5cb2 100644 --- a/tests/test_cardiometabolicdisorders.py +++ b/tests/test_cardiometabolicdisorders.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.methods import ( cardio_metabolic_disorders, diff --git a/tests/test_cervical_cancer.py b/tests/test_cervical_cancer.py index 41dc8b9fa3..21ccc741c4 100644 --- a/tests/test_cervical_cancer.py +++ b/tests/test_cervical_cancer.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, DateOffset, Simulation from tlo.methods import ( cervical_cancer, diff --git a/tests/test_consumables.py b/tests/test_consumables.py index a2bb4285e1..a8114aa8d8 100644 --- a/tests/test_consumables.py +++ b/tests/test_consumables.py @@ -7,6 +7,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Module, Simulation from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin diff --git a/tests/test_contraception.py b/tests/test_contraception.py index 3ba567352c..37a2ab3fee 100644 --- a/tests/test_contraception.py +++ b/tests/test_contraception.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import contraception, demography, enhanced_lifestyle, healthsystem, symptommanager diff --git a/tests/test_control_order_of_events.py b/tests/test_control_order_of_events.py index b02a2ae3c9..a355f0a622 100644 --- a/tests/test_control_order_of_events.py +++ b/tests/test_control_order_of_events.py @@ -2,6 +2,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import PopulationScopeEventMixin, Priority, RegularEvent diff --git a/tests/test_copd.py b/tests/test_copd.py index d27f37792e..08d2b1a464 100644 --- a/tests/test_copd.py +++ b/tests/test_copd.py @@ -4,6 +4,7 @@ import numpy as np import pytest + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file, unflatten_flattened_multi_index_in_logging from tlo.methods import ( diff --git a/tests/test_core.py b/tests/test_core.py index 10b27bff97..5981c2be3f 100644 --- a/tests/test_core.py +++ b/tests/test_core.py @@ -4,6 +4,7 @@ import pandas as pd import pytest + from tlo import Module, Parameter, Property, Types diff --git a/tests/test_demography.py b/tests/test_demography.py index 761a691fd1..71a24caf8c 100644 --- a/tests/test_demography.py +++ b/tests/test_demography.py @@ -5,6 +5,7 @@ import pandas as pd import pytest from pytest import approx + from tlo import DAYS_IN_MONTH, DAYS_IN_YEAR, Date, Module, Simulation, logging from tlo.analysis.utils import compare_number_of_deaths, parse_log_file from tlo.methods import Metadata, demography diff --git a/tests/test_depression.py b/tests/test_depression.py index 30308059d1..e5da67195d 100644 --- a/tests/test_depression.py +++ b/tests/test_depression.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Simulation from tlo.lm import LinearModel, LinearModelType from tlo.methods import ( diff --git a/tests/test_diarrhoea.py b/tests/test_diarrhoea.py index 600d82c849..4864dcdd74 100644 --- a/tests/test_diarrhoea.py +++ b/tests/test_diarrhoea.py @@ -8,6 +8,7 @@ import pandas as pd import pytest from pandas import DateOffset + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_docs.py b/tests/test_docs.py index aabe82e0d9..cf18097ce2 100644 --- a/tests/test_docs.py +++ b/tests/test_docs.py @@ -1,6 +1,7 @@ import importlib import pytest + from tlo.docs import ( extract_bases, generate_module_dict, diff --git a/tests/test_dxmanager.py b/tests/test_dxmanager.py index 5d2ea0eae8..507c9eec85 100644 --- a/tests/test_dxmanager.py +++ b/tests/test_dxmanager.py @@ -4,6 +4,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.events import IndividualScopeEventMixin from tlo.methods import ( diff --git a/tests/test_enhanced_lifestyle.py b/tests/test_enhanced_lifestyle.py index d01bfd700f..07cc21cef1 100644 --- a/tests/test_enhanced_lifestyle.py +++ b/tests/test_enhanced_lifestyle.py @@ -7,6 +7,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, DateOffset, Module, Simulation from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods import demography, enhanced_lifestyle diff --git a/tests/test_epi.py b/tests/test_epi.py index 67e7905bc0..f81c7603bb 100644 --- a/tests/test_epi.py +++ b/tests/test_epi.py @@ -4,6 +4,7 @@ import pandas as pd import pytest from pandas import DateOffset + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import PopulationScopeEventMixin, RegularEvent diff --git a/tests/test_epilepsy.py b/tests/test_epilepsy.py index d3fc005375..13fb80bdfe 100644 --- a/tests/test_epilepsy.py +++ b/tests/test_epilepsy.py @@ -2,6 +2,7 @@ from pathlib import Path import pytest + from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_equipment.py b/tests/test_equipment.py index 567b4106e4..85b5e1a83c 100644 --- a/tests/test_equipment.py +++ b/tests/test_equipment.py @@ -7,6 +7,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Module, Simulation from tlo.analysis.utils import parse_log_file from tlo.events import IndividualScopeEventMixin diff --git a/tests/test_find_events_for_person_in_event_queue.py b/tests/test_find_events_for_person_in_event_queue.py index 2c6c903d37..0f79c4224e 100644 --- a/tests/test_find_events_for_person_in_event_queue.py +++ b/tests/test_find_events_for_person_in_event_queue.py @@ -3,6 +3,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation from tlo.methods import ( chronicsyndrome, diff --git a/tests/test_fullmodel.py b/tests/test_fullmodel.py index 98e8b8451b..0a0a554433 100644 --- a/tests/test_fullmodel.py +++ b/tests/test_fullmodel.py @@ -7,6 +7,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation, logging from tlo.methods.fullmodel import fullmodel from tlo.util import hash_dataframe diff --git a/tests/test_healthburden.py b/tests/test_healthburden.py index 7ccbddca1a..4b28b3fd85 100644 --- a/tests/test_healthburden.py +++ b/tests/test_healthburden.py @@ -5,6 +5,7 @@ import pandas as pd import pytest from pytest import approx + from tlo import DAYS_IN_YEAR, Date, Module, Simulation, logging from tlo.analysis.utils import get_mappers_in_fullmodel, parse_log_file from tlo.events import Event, IndividualScopeEventMixin diff --git a/tests/test_healthcareseeking.py b/tests/test_healthcareseeking.py index d244ee62da..165980efa9 100644 --- a/tests/test_healthcareseeking.py +++ b/tests/test_healthcareseeking.py @@ -7,6 +7,7 @@ import numpy as np import pandas as pd from pandas import DateOffset + from tlo import Date, Module, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.events import Event, IndividualScopeEventMixin diff --git a/tests/test_healthsystem.py b/tests/test_healthsystem.py index 579253493e..0c1a03932b 100644 --- a/tests/test_healthsystem.py +++ b/tests/test_healthsystem.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Module, Simulation, logging from tlo.analysis.hsi_events import get_details_of_defined_hsi_events from tlo.analysis.utils import get_filtered_treatment_ids, parse_log_file diff --git a/tests/test_hiv.py b/tests/test_hiv.py index a6e0fc5d45..640554e840 100644 --- a/tests/test_hiv.py +++ b/tests/test_hiv.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Simulation from tlo.lm import LinearModel from tlo.methods import ( diff --git a/tests/test_htm_scaleup.py b/tests/test_htm_scaleup.py index d9867af2f8..63f6cba6ba 100644 --- a/tests/test_htm_scaleup.py +++ b/tests/test_htm_scaleup.py @@ -4,6 +4,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_labour.py b/tests/test_labour.py index 3ce22f1ec6..b280cede9e 100644 --- a/tests/test_labour.py +++ b/tests/test_labour.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_life_expectancy.py b/tests/test_life_expectancy.py index 2d4d3d93c5..0a77f02310 100644 --- a/tests/test_life_expectancy.py +++ b/tests/test_life_expectancy.py @@ -5,6 +5,7 @@ import numpy as np import pandas as pd + from tlo.analysis.life_expectancy import ( get_life_expectancy_estimates, get_probability_of_premature_death, diff --git a/tests/test_lm.py b/tests/test_lm.py index a7076416fe..b2cb6f1c72 100644 --- a/tests/test_lm.py +++ b/tests/test_lm.py @@ -6,6 +6,7 @@ import numpy as np import pandas as pd import pytest + from tlo.lm import LinearModel, LinearModelType, Predictor diff --git a/tests/test_logging.py b/tests/test_logging.py index 457e9a47ff..6d094623c4 100644 --- a/tests/test_logging.py +++ b/tests/test_logging.py @@ -10,6 +10,7 @@ import numpy as np import pandas as pd import pytest + import tlo.logging as logging import tlo.logging.core as core diff --git a/tests/test_logging_end_to_end.py b/tests/test_logging_end_to_end.py index b166a36af2..4948c7a744 100644 --- a/tests/test_logging_end_to_end.py +++ b/tests/test_logging_end_to_end.py @@ -6,6 +6,7 @@ import pandas as pd from pytest import fixture + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file diff --git a/tests/test_malaria.py b/tests/test_malaria.py index 41df332969..b20d598606 100644 --- a/tests/test_malaria.py +++ b/tests/test_malaria.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.events import IndividualScopeEventMixin from tlo.methods import ( diff --git a/tests/test_maternal_health_helper_and_analysis_functions.py b/tests/test_maternal_health_helper_and_analysis_functions.py index bcac1ff398..a762fe4155 100644 --- a/tests/test_maternal_health_helper_and_analysis_functions.py +++ b/tests/test_maternal_health_helper_and_analysis_functions.py @@ -2,6 +2,7 @@ from pathlib import Path import pandas as pd + from tlo import Date, Simulation from tlo.methods import ( care_of_women_during_pregnancy, diff --git a/tests/test_measles.py b/tests/test_measles.py index 640de20d66..5acdc4df4d 100644 --- a/tests/test_measles.py +++ b/tests/test_measles.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation, logging from tlo.methods import ( demography, diff --git a/tests/test_module_dependencies.py b/tests/test_module_dependencies.py index fd36d9e37d..a50d5d158b 100644 --- a/tests/test_module_dependencies.py +++ b/tests/test_module_dependencies.py @@ -6,6 +6,7 @@ from types import GeneratorType import pytest + from tlo import Date, Module, Simulation, logging from tlo.dependencies import ( ModuleDependencyError, diff --git a/tests/test_newborn_outcomes.py b/tests/test_newborn_outcomes.py index ba276706b5..d75022043b 100644 --- a/tests/test_newborn_outcomes.py +++ b/tests/test_newborn_outcomes.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_oesophagealcancer.py b/tests/test_oesophagealcancer.py index 54e8df2a1a..8ec2b51736 100644 --- a/tests/test_oesophagealcancer.py +++ b/tests/test_oesophagealcancer.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_other_adult_cancers.py b/tests/test_other_adult_cancers.py index 4b77f7c552..12e3607d91 100644 --- a/tests/test_other_adult_cancers.py +++ b/tests/test_other_adult_cancers.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_population.py b/tests/test_population.py index 11bf4f2c6f..e8a549209d 100644 --- a/tests/test_population.py +++ b/tests/test_population.py @@ -1,6 +1,7 @@ import numpy as np import pandas as pd import pytest + from tlo.core import Property, Types from tlo.population import Population diff --git a/tests/test_postnatal.py b/tests/test_postnatal.py index f291083b2c..001866d4cf 100644 --- a/tests/test_postnatal.py +++ b/tests/test_postnatal.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_pregnancy_supervisor.py b/tests/test_pregnancy_supervisor.py index 46444d29ae..ee56c3a1fc 100644 --- a/tests/test_pregnancy_supervisor.py +++ b/tests/test_pregnancy_supervisor.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd import pytest + from tlo import DAYS_IN_MONTH, DAYS_IN_YEAR, Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.lm import LinearModel, LinearModelType diff --git a/tests/test_progressbar.py b/tests/test_progressbar.py index 7050fe5ac3..bda0376cb9 100644 --- a/tests/test_progressbar.py +++ b/tests/test_progressbar.py @@ -1,4 +1,5 @@ import pytest + from tlo import progressbar diff --git a/tests/test_prostate_cancer.py b/tests/test_prostate_cancer.py index 2839944a71..bae5d4fcf4 100644 --- a/tests/test_prostate_cancer.py +++ b/tests/test_prostate_cancer.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import DAYS_IN_YEAR, Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_rti.py b/tests/test_rti.py index 4d8a1fd88b..2b65595782 100644 --- a/tests/test_rti.py +++ b/tests/test_rti.py @@ -3,6 +3,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_scenario.py b/tests/test_scenario.py index ccd9985e0f..1feac8ef87 100644 --- a/tests/test_scenario.py +++ b/tests/test_scenario.py @@ -3,6 +3,7 @@ from pathlib import Path import pytest + from tlo.scenario import BaseScenario, SampleRunner, ScenarioLoader diff --git a/tests/test_schisto.py b/tests/test_schisto.py index 985fc00c7f..02bbba707f 100644 --- a/tests/test_schisto.py +++ b/tests/test_schisto.py @@ -6,6 +6,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation from tlo.methods import ( demography, diff --git a/tests/test_simplified_births.py b/tests/test_simplified_births.py index 5a291e4667..8474223508 100644 --- a/tests/test_simplified_births.py +++ b/tests/test_simplified_births.py @@ -4,6 +4,7 @@ import numpy as np import pandas as pd import pytest + from tlo import Date, Simulation, logging from tlo.events import PopulationScopeEventMixin, RegularEvent from tlo.methods import demography, simplified_births diff --git a/tests/test_simulation.py b/tests/test_simulation.py index c30a714e60..90abe68761 100644 --- a/tests/test_simulation.py +++ b/tests/test_simulation.py @@ -3,6 +3,7 @@ import numpy as np import pytest + from tlo import Date, DateOffset, Module, Population, Simulation, logging from tlo.analysis.utils import merge_log_files, parse_log_file from tlo.methods.fullmodel import fullmodel diff --git a/tests/test_stunting.py b/tests/test_stunting.py index e2ebe4dfd8..676d29970b 100644 --- a/tests/test_stunting.py +++ b/tests/test_stunting.py @@ -6,6 +6,7 @@ import pytest from pytest import approx from scipy.stats import norm + from tlo import Date, Simulation from tlo.lm import LinearModel, Predictor from tlo.methods import demography, enhanced_lifestyle, healthsystem, simplified_births, stunting diff --git a/tests/test_symptommanager.py b/tests/test_symptommanager.py index f66e303861..cdc6de7293 100644 --- a/tests/test_symptommanager.py +++ b/tests/test_symptommanager.py @@ -6,6 +6,7 @@ import pytest from pandas import DateOffset + from tlo import Date, Simulation from tlo.methods import ( chronicsyndrome, diff --git a/tests/test_tb.py b/tests/test_tb.py index 19434aac38..513d2a52ae 100644 --- a/tests/test_tb.py +++ b/tests/test_tb.py @@ -5,6 +5,7 @@ import pandas as pd import pytest + from tlo import Date, Simulation, logging from tlo.analysis.utils import parse_log_file from tlo.methods import ( diff --git a/tests/test_utils.py b/tests/test_utils.py index 5b268a297e..ee9426f607 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -9,8 +9,9 @@ import numpy as np import pandas as pd import pytest -import tlo.util from scipy.stats import chisquare + +import tlo.util from tlo import Date, Simulation from tlo.analysis.utils import parse_log_file from tlo.methods import demography