Merge branch 'master' into mnjowe/convert_excel_files_to_csv_Tim_H_mo…

…dules
UCL · Jan 15, 2025 · 51b9148 · 51b9148
2 parents 2adb1c1 + f0d351b
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diff --git a/docs/conf.py b/docs/conf.py
@@ -25,7 +25,8 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.napoleon',
     'sphinx.ext.todo',
-    'rawfiles'
+    'rawfiles',
+    'sphinxcontrib.youtube',
 ]
 
 if os.getenv('SPELLCHECK'):

diff --git a/docs/index.rst b/docs/index.rst
@@ -56,6 +56,7 @@ Contents
    resources/index
    parameters
    learning
+   videos
    publications
    contributors
    contributing
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,6 @@
 sphinx>=1.3
 sphinx-rtd-theme
+sphinxcontrib-youtube
 pybtex
 pyyaml
 requests

diff --git a/docs/videos.rst b/docs/videos.rst
@@ -0,0 +1,85 @@
+===========
+HEPU Videos
+===========
+
+The *Health Economics and Policy Unit* (HEPU) is a unit within the Department of Health Systems 
+under the School of Global and Public Health at the Kamuzu University of Health Sciences. 
+It was established in 2018 with support from the Thanzi La Onse Program with the aim of promoting demand, 
+generation and use of health economics evidence in health policy and decision making.
+
+Background: Thanzi La Mawa Project
+==================================
+
+A video exploring the Thanzi La Mawa project, led by Prof Tim Hallett at Imperial. 
+In response to the need for more evidence to support resource allocation decision making processes in Malawi, 
+researchers and modellers have partnered with Kamuzu University of Health Sciences, led by Prof Joseph Mfutso-Bengo, 
+to develop a 'whole system and all-disease model' for the Malawi health system. 
+Discover how their findings could potentially revolutionize healthcare practices and policies, 
+ultimately benefiting millions of Malawians.
+
+..  youtube:: dazYfnhaNOw
+   :align: center
+
+Training and Capacity Building
+==============================
+
+A modelling short course was held in Blantyre, Malawi, from 23-26 September 2024, 
+hosted by the Health Economics and Policy Unit of Kamuzu University of Health Sciences 
+in collaboration with Imperial and University College London. 
+This course marks a significant milestone for health education in Malawi, 
+empowering local professionals with advanced modelling skills 
+to strengthen the capacity of Malawi's health systems in responding to future challenges.
+
+..  youtube:: T5WvzDFpuF4
+   :align: center
+
+Policy Think Tanks
+==================
+
+**HEPU 9th Extraordinary Think Tank Conference, Launch of Thanzi La Mawa Program.**
+
+..  youtube:: 6HCJVFV-gGI
+   :align: center
+
+**HEPU 12th Extraordinary Think Tank Conference, Christian Health Association of Malawi Service Level Agreement Value for Money Evaluation.**
+
+..  youtube:: Ce_iLowNwIQ
+   :align: center
+
+**HEPU 13th Extraordinary Think Tank Conference, Progress of the Direct Facility Financing and Financial Risk Management.**
+
+..  youtube:: tTp6FprPRGs
+   :align: center
+
+Research Seminars 
+=================
+
+**86th Research Seminar, Institutionalization of Health Technology Assessment in Malawi: A Progress Update with Dr. Lucky Ngwira.**
+
+..  youtube:: hcRNwU-SA98
+   :align: center
+
+3rd KUHeS Research Dissemination Conference
+-------------------------------------------
+
+**Performance of Pooled Donor Funding to Support the Malawi Health Service Strategic Plans in the Context of Suspended Direct Budgetary Support.**
+
+..  youtube:: RFTmfkvUbNg
+   :align: center
+
+**Advancing Universal Health Coverage: Assessing the Efficiency of Contracting Not-for-Profit Faith-Based Healthcare Providers in Malawi.**
+
+..  youtube:: RMUItOZTtWg
+   :align: center
+
+**Improved Community Governance and Public Financial Management Outcomes: Direct Facility Financing Evaluation.**
+
+..  youtube:: YqbRT3CNVQY
+   :align: center
+
+**Demonstrating the Use of VEDMAP Framework as a Research Tool for Value-Mapping and Value-Implementation Fidelity-Assessment: 
+A Case of Feasibility Study of Health Technology Assessment in Malawi.**
+
+..  youtube:: u4CZcBqRRoA
+   :align: center
+
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",
 ]
@@ -127,3 +127,4 @@ where = ["src"]
 
 [tool.setuptools_scm]
 version_file  = "src/tlo/_version.py"
+git_describe_command = ["git", "describe", "--dirty", "--tags", "--long", "--match", 'v[0-9]*']
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_Alri.xlsx b/resources/ResourceFile_Alri.xlsx
diff --git a/resources/ResourceFile_Alri/Calculations.csv b/resources/ResourceFile_Alri/Calculations.csv
diff --git a/resources/ResourceFile_Alri/GBD_Malawi_estimates.csv b/resources/ResourceFile_Alri/GBD_Malawi_estimates.csv
diff --git a/resources/ResourceFile_Alri/Lazzerini CFR.csv b/resources/ResourceFile_Alri/Lazzerini CFR.csv
diff --git a/resources/ResourceFile_Alri/McAllister_2019.csv b/resources/ResourceFile_Alri/McAllister_2019.csv
diff --git a/resources/ResourceFile_Alri/Parameter_values.csv b/resources/ResourceFile_Alri/Parameter_values.csv
diff --git a/resources/ResourceFile_Alri/Pathogen_specific.csv b/resources/ResourceFile_Alri/Pathogen_specific.csv
diff --git a/resources/ResourceFile_Depression.xlsx b/resources/ResourceFile_Depression.xlsx
diff --git a/resources/ResourceFile_Depression/parameter_values.csv b/resources/ResourceFile_Depression/parameter_values.csv
diff --git a/resources/ResourceFile_Diarrhoea.xlsx b/resources/ResourceFile_Diarrhoea.xlsx
diff --git a/resources/ResourceFile_Diarrhoea/Parameter_values.csv b/resources/ResourceFile_Diarrhoea/Parameter_values.csv
diff --git a/resources/ResourceFile_RTI.xlsx b/resources/ResourceFile_RTI.xlsx
diff --git a/resources/ResourceFile_RTI/parameter_values.csv b/resources/ResourceFile_RTI/parameter_values.csv
diff --git a/resources/epilepsy/ResourceFile_Epilepsy.xlsx b/resources/epilepsy/ResourceFile_Epilepsy.xlsx
diff --git a/resources/epilepsy/ResourceFile_Epilepsy/Structure, parameters, refs.csv b/resources/epilepsy/ResourceFile_Epilepsy/Structure, parameters, refs.csv
diff --git a/resources/epilepsy/ResourceFile_Epilepsy/additional info.csv b/resources/epilepsy/ResourceFile_Epilepsy/additional info.csv
diff --git a/resources/epilepsy/ResourceFile_Epilepsy/parameter_values.csv b/resources/epilepsy/ResourceFile_Epilepsy/parameter_values.csv
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
@@ -17,6 +17,7 @@
     load_pickled_dataframes,
     summarize,
 )
+from tlo.util import read_csv_files
 
 resourcefilepath = Path("./resources")
 datestamp = datetime.date.today().strftime("__%Y_%m_%d")
@@ -124,14 +125,14 @@ def get_under5_person_years(py_):
 draw = 0
 
 # import GBD data for Malawi's ALRI burden estimates
-GBD_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="GBD_Malawi_estimates",
+GBD_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="GBD_Malawi_estimates",
 )
 # import McAllister estimates for Malawi's ALRI incidence
-McAllister_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="McAllister_2019",
+McAllister_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="McAllister_2019",
 )
 
 plt.style.use("ggplot")

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
@@ -17,6 +17,7 @@
     load_pickled_dataframes,
     summarize,
 )
+from tlo.util import read_csv_files
 
 resourcefilepath = Path("./resources")
 datestamp = datetime.date.today().strftime("__%Y_%m_%d")
@@ -155,14 +156,14 @@ def get_person_years(draw, run):
 end_date = 2031
 
 # import GBD data for Malawi's ALRI burden estimates
-GBD_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="GBD_Malawi_estimates",
+GBD_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="GBD_Malawi_estimates",
     )
 # import McAllister estimates for Malawi's ALRI incidence
-McAllister_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="McAllister_2019",
+McAllister_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="McAllister_2019",
     )
 
 plt.style.use("ggplot")

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
@@ -22,6 +22,7 @@
     simplified_births,
     symptommanager,
 )
+from tlo.util import read_csv_files
 
 # %%
 outputpath = Path("./outputs")
@@ -141,14 +142,14 @@
 end_date = 2026
 
 # import GBD data for Malawi's ALRI burden estimates
-GBD_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="GBD_Malawi_estimates",
+GBD_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="GBD_Malawi_estimates",
     )
 # import McAllister estimates for Malawi's ALRI incidence
-McAllister_data = pd.read_excel(
-    Path(resourcefilepath) / "ResourceFile_Alri.xlsx",
-    sheet_name="McAllister_2019",
+McAllister_data = read_csv_files(
+    Path(resourcefilepath) / "ResourceFile_Alri",
+    files="McAllister_2019",
     )
 
 plt.style.use("ggplot")

diff --git a/src/scripts/epi/analysis_epi.py b/src/scripts/epi/analysis_epi.py
@@ -1,5 +1,4 @@
 import datetime
-import os
 import time
 from pathlib import Path
 
@@ -18,6 +17,7 @@
     simplified_births,
     symptommanager,
 )
+from tlo.util import read_csv_files
 
 start_time = time.time()
 
@@ -86,8 +86,7 @@
 
 # ------------------------------------- DATA  ------------------------------------- #
 # import vaccine coverage data
-workbook = pd.read_excel(os.path.join(resourcefilepath,
-                                      'ResourceFile_EPI_WHO_estimates.xlsx'), sheet_name=None)
+workbook = read_csv_files(Path(resourcefilepath)/'ResourceFile_EPI_WHO_estimates', files=None)
 
 coverage_data = workbook["WHO_estimates"]
 

diff --git a/src/scripts/hiv/projections_jan2023/calibration_script.py b/src/scripts/hiv/projections_jan2023/calibration_script.py
@@ -31,10 +31,8 @@
 
 """
 
-import os
 import random
-
-import pandas as pd
+from pathlib import Path
 
 from tlo import Date, logging
 from tlo.methods import (
@@ -51,6 +49,7 @@
     tb,
 )
 from tlo.scenario import BaseScenario
+from tlo.util import read_csv_files
 
 number_of_draws = 1
 runs_per_draw = 5
@@ -68,9 +67,9 @@ def __init__(self):
         self.number_of_draws = number_of_draws
         self.runs_per_draw = runs_per_draw
 
-        self.sampled_parameters = pd.read_excel(
-            os.path.join(self.resources, "../../../../resources/ResourceFile_HIV/parameters.csv"),
-            sheet_name="LHC_samples",
+        self.sampled_parameters = read_csv_files(
+            Path("./resources")/"ResourceFile_HIV",
+            files="LHC_samples",
         )
 
     def log_configuration(self):