Merge branch 'master' into wgraham/pyinstrument-profiling-ci

UCL · Aug 21, 2023 · 921fdb5 · 921fdb5
2 parents 03403ab + d09c7c1
commit 921fdb5
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Showing 70 changed files with 4,717 additions and 1,569 deletions.
diff --git a/.gitignore b/.gitignore
@@ -116,4 +116,6 @@ docs/reference/tlo*.rst
 # TLO configuration
 tlo.conf
 
-
+# ignore all files in outputs directory, except README
+outputs/*
+!outputs/README
diff --git a/docs/write-ups/EPI.docx b/docs/write-ups/EPI.docx
diff --git a/outputs/.gitignore b/outputs/.gitignore
diff --git a/resources/ResourceFile_EPI_WHO_estimates.xlsx b/resources/ResourceFile_EPI_WHO_estimates.xlsx
diff --git a/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx b/resources/ResourceFile_Improved_Healthsystem_And_Healthcare_Seeking.xlsx
diff --git a/resources/cmd/ResourceFile_cmd_condition_hsi.xlsx b/resources/cmd/ResourceFile_cmd_condition_hsi.xlsx
diff --git a/resources/healthsystem/ResourceFile_HealthSystem_parameters.csv b/resources/healthsystem/ResourceFile_HealthSystem_parameters.csv
diff --git a/resources/healthsystem/ResourceFile_PriorityRanking.csv b/resources/healthsystem/ResourceFile_PriorityRanking.csv
diff --git a/resources/healthsystem/consumables/ResourceFile_Consumables_availability_and_usage.csv b/resources/healthsystem/consumables/ResourceFile_Consumables_availability_and_usage.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/...m/human_resources/definitions/ResourceFile_Appts_That_Require_HCW_Who_Are_Not_Present.csv b/...m/human_resources/definitions/ResourceFile_Appts_That_Require_HCW_Who_Are_Not_Present.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/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES.xlsx
diff --git a/resources/healthsystem/real_appt_usage_data/unadjusted_real_monthly_usage_of_appt_type.csv b/resources/healthsystem/real_appt_usage_data/unadjusted_real_monthly_usage_of_appt_type.csv
diff --git a/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py b/src/scripts/calibration_analyses/analysis_scripts/analysis_all_calibration.py
@@ -1,3 +1,4 @@
+import argparse
 import glob
 import os.path
 import zipfile
@@ -12,7 +13,6 @@
     analysis_compare_appt_usage_real_and_simulation,
     plot_appt_use_by_hsi,
 )
-from tlo.analysis.utils import get_scenario_outputs
 
 
 def apply(results_folder: Path, output_folder: Path, resourcefilepath: Path = None):
@@ -60,11 +60,12 @@ def apply(results_folder: Path, output_folder: Path, resourcefilepath: Path = No
 
 
 if __name__ == "__main__":
-    outputspath = Path('./outputs/[email protected]')
-
-    # Find results folder (most recent run generated using that scenario_filename)
-    scenario_filename = 'long_run_all_diseases.py'
-    results_folder = get_scenario_outputs(scenario_filename, outputspath)[-1]
-
-    # Run all the calibrations
-    apply(results_folder=results_folder, output_folder=results_folder, resourcefilepath=Path('./resources'))
+    parser = argparse.ArgumentParser()
+    parser.add_argument("results_folder", type=Path)
+    args = parser.parse_args()
+
+    apply(
+        results_folder=args.results_folder,
+        output_folder=args.results_folder,
+        resourcefilepath=Path('./resources')
+    )
diff --git a/...ibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py b/...ibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py
@@ -4,7 +4,7 @@
 This uses the results of the Scenario defined in: src/scripts/long_run/long_run.py but it can edited to look at other
 results (change 'scenario_filename').
 """
-
+import argparse
 from pathlib import Path
 
 import numpy as np
@@ -15,7 +15,6 @@
     extract_results,
     format_gbd,
     get_color_cause_of_death_or_daly_label,
-    get_scenario_outputs,
     load_pickled_dataframes,
     make_age_grp_lookup,
     make_age_grp_types,
@@ -412,11 +411,12 @@ def shift_row_to_top(df, index_to_shift):
 
 
 if __name__ == "__main__":
-    outputspath = Path('./outputs/[email protected]')
-    rfp = Path('./resources')
-
-    # Find results folder (most recent run generated using that scenario_filename)
-    scenario_filename = 'long_run_all_diseases.py'
-    results_folder = get_scenario_outputs(scenario_filename, outputspath)[-1]
-
-    apply(results_folder=results_folder, output_folder=results_folder, resourcefilepath=rfp)
+    parser = argparse.ArgumentParser()
+    parser.add_argument("results_folder", type=Path)
+    args = parser.parse_args()
+
+    apply(
+        results_folder=args.results_folder,
+        output_folder=args.results_folder,
+        resourcefilepath=Path('./resources')
+    )