Merge branch 'master' into mnjowe/any_other_excel_files

UCL · Jan 7, 2025 · d545bce · d545bce
2 parents da569a6 + 05d3679
commit d545bce
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diff --git a/README.md b/README.md
@@ -58,5 +58,5 @@ This work has been funded by grants from [Wellcome](https://wellcome.org/),
 [arc-link]: https://www.ucl.ac.uk/arc
 [york-link]: https://www.york.ac.uk/
 [che-link]: https://www.york.ac.uk/che/
-[ecsea-hc-link]: https://ecsahc.org/
+[ecsa-hc-link]: https://ecsahc.org/
 [contributors-link]: https://www.tlomodel.org/contributors.html
diff --git a/pyproject.toml b/pyproject.toml
@@ -57,7 +57,7 @@ dev = [
     # Profiling
     "ansi2html",
     "psutil",
-    "pyinstrument>=4.7",
+    "pyinstrument>=4.3",
     # Building requirements files
     "pip-tools",
 ]

diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -164,7 +164,7 @@ psutil==5.9.5
     # via tlo (pyproject.toml)
 pycparser==2.21
     # via cffi
-pyinstrument==4.7.3
+pyinstrument==4.5.3
     # via tlo (pyproject.toml)
 pyjwt[crypto]==2.8.0
     # via

diff --git a/resources/ResourceFile_AntenatalCare.xlsx b/resources/ResourceFile_AntenatalCare.xlsx
diff --git a/resources/ResourceFile_AntenatalCare/parameter_values.csv b/resources/ResourceFile_AntenatalCare/parameter_values.csv
diff --git a/resources/ResourceFile_EPI_WHO_estimates.xlsx b/resources/ResourceFile_EPI_WHO_estimates.xlsx
diff --git a/resources/ResourceFile_EPI_WHO_estimates/WHO_estimates.csv b/resources/ResourceFile_EPI_WHO_estimates/WHO_estimates.csv
diff --git a/resources/ResourceFile_EPI_WHO_estimates/parameters.csv b/resources/ResourceFile_EPI_WHO_estimates/parameters.csv
diff --git a/resources/ResourceFile_EPI_WHO_estimates/vaccine_schedule.csv b/resources/ResourceFile_EPI_WHO_estimates/vaccine_schedule.csv
diff --git a/resources/ResourceFile_HIV.xlsx b/resources/ResourceFile_HIV.xlsx
diff --git a/resources/ResourceFile_HIV/DHS_prevalence.csv b/resources/ResourceFile_HIV/DHS_prevalence.csv
diff --git a/resources/ResourceFile_HIV/LHC_samples.csv b/resources/ResourceFile_HIV/LHC_samples.csv
diff --git a/resources/ResourceFile_HIV/MPHIA_incidence2020.csv b/resources/ResourceFile_HIV/MPHIA_incidence2020.csv
diff --git a/resources/ResourceFile_HIV/MPHIA_prevalence_art2020.csv b/resources/ResourceFile_HIV/MPHIA_prevalence_art2020.csv
diff --git a/resources/ResourceFile_HIV/MoH_CPT_IPT2020.csv b/resources/ResourceFile_HIV/MoH_CPT_IPT2020.csv
diff --git a/resources/ResourceFile_HIV/MoH_number_art.csv b/resources/ResourceFile_HIV/MoH_number_art.csv
diff --git a/resources/ResourceFile_HIV/MoH_numbers_tests.csv b/resources/ResourceFile_HIV/MoH_numbers_tests.csv
diff --git a/resources/ResourceFile_HIV/art_coverage.csv b/resources/ResourceFile_HIV/art_coverage.csv
diff --git a/resources/ResourceFile_HIV/calibration_from_aids_info.csv b/resources/ResourceFile_HIV/calibration_from_aids_info.csv
diff --git a/resources/ResourceFile_HIV/children0_14_prev_AIDSinfo.csv b/resources/ResourceFile_HIV/children0_14_prev_AIDSinfo.csv
diff --git a/resources/ResourceFile_HIV/hiv_prevalence.csv b/resources/ResourceFile_HIV/hiv_prevalence.csv
diff --git a/resources/ResourceFile_HIV/parameters.csv b/resources/ResourceFile_HIV/parameters.csv
diff --git a/resources/ResourceFile_HIV/scaleup_parameters.csv b/resources/ResourceFile_HIV/scaleup_parameters.csv
diff --git a/resources/ResourceFile_HIV/spectrum_treatment_cascade.csv b/resources/ResourceFile_HIV/spectrum_treatment_cascade.csv
diff --git a/resources/ResourceFile_HIV/time_since_infection_at_baselin.csv b/resources/ResourceFile_HIV/time_since_infection_at_baselin.csv
diff --git a/resources/ResourceFile_HIV/unaids_infections_art2021.csv b/resources/ResourceFile_HIV/unaids_infections_art2021.csv
diff --git a/resources/ResourceFile_HIV/unaids_mortality_dalys2021.csv b/resources/ResourceFile_HIV/unaids_mortality_dalys2021.csv
diff --git a/resources/ResourceFile_HIV/unaids_pmtct2021.csv b/resources/ResourceFile_HIV/unaids_pmtct2021.csv
diff --git a/resources/ResourceFile_HIV/unaids_program_perf.csv b/resources/ResourceFile_HIV/unaids_program_perf.csv
diff --git a/resources/ResourceFile_LabourSkilledBirthAttendance.xlsx b/resources/ResourceFile_LabourSkilledBirthAttendance.xlsx
diff --git a/resources/ResourceFile_LabourSkilledBirthAttendance/parameter_values.csv b/resources/ResourceFile_LabourSkilledBirthAttendance/parameter_values.csv
diff --git a/resources/ResourceFile_Measles.xlsx b/resources/ResourceFile_Measles.xlsx
diff --git a/resources/ResourceFile_Measles/beta.csv b/resources/ResourceFile_Measles/beta.csv
diff --git a/resources/ResourceFile_Measles/cfr.csv b/resources/ResourceFile_Measles/cfr.csv
diff --git a/resources/ResourceFile_Measles/parameters.csv b/resources/ResourceFile_Measles/parameters.csv
diff --git a/resources/ResourceFile_Measles/symptoms.csv b/resources/ResourceFile_Measles/symptoms.csv
diff --git a/resources/ResourceFile_NewbornOutcomes.xlsx b/resources/ResourceFile_NewbornOutcomes.xlsx
diff --git a/resources/ResourceFile_NewbornOutcomes/parameter_values.csv b/resources/ResourceFile_NewbornOutcomes/parameter_values.csv
diff --git a/resources/ResourceFile_PostnatalSupervisor.xlsx b/resources/ResourceFile_PostnatalSupervisor.xlsx
diff --git a/resources/ResourceFile_PostnatalSupervisor/parameter_values.csv b/resources/ResourceFile_PostnatalSupervisor/parameter_values.csv
diff --git a/resources/ResourceFile_PregnancySupervisor.xlsx b/resources/ResourceFile_PregnancySupervisor.xlsx
diff --git a/resources/ResourceFile_PregnancySupervisor/parameter_values.csv b/resources/ResourceFile_PregnancySupervisor/parameter_values.csv
diff --git a/resources/ResourceFile_Schisto.xlsx b/resources/ResourceFile_Schisto.xlsx
diff --git a/resources/ResourceFile_Schisto/DALYs.csv b/resources/ResourceFile_Schisto/DALYs.csv
diff --git a/resources/ResourceFile_Schisto/District_Params_haematobium.csv b/resources/ResourceFile_Schisto/District_Params_haematobium.csv
diff --git a/resources/ResourceFile_Schisto/District_Params_mansoni.csv b/resources/ResourceFile_Schisto/District_Params_mansoni.csv
diff --git a/resources/ResourceFile_Schisto/MDA_historical_Coverage.csv b/resources/ResourceFile_Schisto/MDA_historical_Coverage.csv
diff --git a/resources/ResourceFile_Schisto/MDA_prognosed_Coverage.csv b/resources/ResourceFile_Schisto/MDA_prognosed_Coverage.csv
diff --git a/resources/ResourceFile_Schisto/Parameters.csv b/resources/ResourceFile_Schisto/Parameters.csv
diff --git a/resources/ResourceFile_Schisto/Symptoms.csv b/resources/ResourceFile_Schisto/Symptoms.csv
diff --git a/resources/ResourceFile_TB.xlsx b/resources/ResourceFile_TB.xlsx
diff --git a/resources/ResourceFile_TB/IPTdistricts.csv b/resources/ResourceFile_TB/IPTdistricts.csv
diff --git a/resources/ResourceFile_TB/NTP2019.csv b/resources/ResourceFile_TB/NTP2019.csv
diff --git a/resources/ResourceFile_TB/WHO_activeTB2023.csv b/resources/ResourceFile_TB/WHO_activeTB2023.csv
diff --git a/resources/ResourceFile_TB/WHO_latentTB2017.csv b/resources/ResourceFile_TB/WHO_latentTB2017.csv
diff --git a/resources/ResourceFile_TB/WHO_mdrTB2017.csv b/resources/ResourceFile_TB/WHO_mdrTB2017.csv
diff --git a/resources/ResourceFile_TB/WHO_tx_success_rates2021.csv b/resources/ResourceFile_TB/WHO_tx_success_rates2021.csv
diff --git a/resources/ResourceFile_TB/additional_params.csv b/resources/ResourceFile_TB/additional_params.csv
diff --git a/resources/ResourceFile_TB/all_districts.csv b/resources/ResourceFile_TB/all_districts.csv
diff --git a/resources/ResourceFile_TB/calibrated_transmission_rates.csv b/resources/ResourceFile_TB/calibrated_transmission_rates.csv
diff --git a/resources/ResourceFile_TB/cases2010district.csv b/resources/ResourceFile_TB/cases2010district.csv
diff --git a/resources/ResourceFile_TB/details_rates.csv b/resources/ResourceFile_TB/details_rates.csv
diff --git a/resources/ResourceFile_TB/followup.csv b/resources/ResourceFile_TB/followup.csv
diff --git a/resources/ResourceFile_TB/ipt_coverage.csv b/resources/ResourceFile_TB/ipt_coverage.csv
diff --git a/resources/ResourceFile_TB/latent_TB2014_summary.csv b/resources/ResourceFile_TB/latent_TB2014_summary.csv
diff --git a/resources/ResourceFile_TB/parameters.csv b/resources/ResourceFile_TB/parameters.csv
diff --git a/resources/ResourceFile_TB/pulm_tb.csv b/resources/ResourceFile_TB/pulm_tb.csv
diff --git a/resources/ResourceFile_TB/scaleup_parameters.csv b/resources/ResourceFile_TB/scaleup_parameters.csv
diff --git a/resources/ResourceFile_TB/testing_rates.csv b/resources/ResourceFile_TB/testing_rates.csv
diff --git a/resources/contraception/ResourceFile_Contraception.xlsx b/resources/contraception/ResourceFile_Contraception.xlsx
diff --git a/resources/contraception/ResourceFile_Contraception/Discontinuation_ByAge.csv b/resources/contraception/ResourceFile_Contraception/Discontinuation_ByAge.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Discontinuation_ByMethod.csv b/resources/contraception/ResourceFile_Contraception/Discontinuation_ByMethod.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Failure_ByMethod.csv b/resources/contraception/ResourceFile_Contraception/Failure_ByMethod.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Initiation_AfterBirth.csv b/resources/contraception/ResourceFile_Contraception/Initiation_AfterBirth.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Initiation_ByAge.csv b/resources/contraception/ResourceFile_Contraception/Initiation_ByAge.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Initiation_ByMethod.csv b/resources/contraception/ResourceFile_Contraception/Initiation_ByMethod.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Interventions_PPFP.csv b/resources/contraception/ResourceFile_Contraception/Interventions_PPFP.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Interventions_Pop.csv b/resources/contraception/ResourceFile_Contraception/Interventions_Pop.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Method_Use_In_2010.csv b/resources/contraception/ResourceFile_Contraception/Method_Use_In_2010.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Pregnancy_NotUsing_HIVeffect.csv b/resources/contraception/ResourceFile_Contraception/Pregnancy_NotUsing_HIVeffect.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Pregnancy_NotUsing_In_2010.csv b/resources/contraception/ResourceFile_Contraception/Pregnancy_NotUsing_In_2010.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Prob_Switch_From.csv b/resources/contraception/ResourceFile_Contraception/Prob_Switch_From.csv
diff --git a/resources/contraception/ResourceFile_Contraception/Prob_Switch_From_And_To.csv b/resources/contraception/ResourceFile_Contraception/Prob_Switch_From_And_To.csv
diff --git a/resources/contraception/ResourceFile_Contraception/simplified_labour_parameters.csv b/resources/contraception/ResourceFile_Contraception/simplified_labour_parameters.csv
diff --git a/resources/healthsystem/consumables/ResourceFile_Consumables_availability_small.csv b/resources/healthsystem/consumables/ResourceFile_Consumables_availability_small.csv
diff --git a/resources/healthsystem/consumables/ResourceFile_consumables_matched.csv b/resources/healthsystem/consumables/ResourceFile_consumables_matched.csv
diff --git a/resources/healthsystem/human_resources/actual/ResourceFile_Daily_Capabilities.csv b/resources/healthsystem/human_resources/actual/ResourceFile_Daily_Capabilities.csv
diff --git a/resources/healthsystem/human_resources/definitions/ResourceFile_Appt_Time_Table.csv b/resources/healthsystem/human_resources/definitions/ResourceFile_Appt_Time_Table.csv
diff --git a/resources/healthsystem/human_resources/funded/ResourceFile_Daily_Capabilities.csv b/resources/healthsystem/human_resources/funded/ResourceFile_Daily_Capabilities.csv
diff --git a/resources/healthsystem/human_resources/funded_plus/ResourceFile_Daily_Capabilities.csv b/resources/healthsystem/human_resources/funded_plus/ResourceFile_Daily_Capabilities.csv
diff --git a/...es/healthsystem/human_resources/scaling_capabilities/ResourceFile_dynamic_HR_scaling.xlsx b/...es/healthsystem/human_resources/scaling_capabilities/ResourceFile_dynamic_HR_scaling.xlsx
diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx