Cervical cancer

.github/workflows/run-profiling.yaml

@@ -163,7 +163,7 @@ jobs:
       ## The token provided needs contents and pages access to the target repo
       ## Token can be (re)generated by a member of the UCL organisation, 
       ## the current member is the rc-softdev-admin.
-      ## [17-07-2024] New token generated, will expire 10-07-2025
+      ## [10-07-2023] The current token will expire 10-07-2024
       - name: Push results to profiling repository
         uses: dmnemec/[email protected]
         env:

.github/workflows/tests.yml

@@ -10,8 +10,6 @@ on:
       - requirements/**
       - resources/**
       - src/tlo/**
-      - src/scripts/profiling/scale_run.py
-      - src/scripts/profiling/shared.py
       - tests/**
       - pyproject.toml
       - tox.ini
@@ -77,12 +75,4 @@ jobs:
           tox --version
       - name: Test with tox
         run: |
-          tox -v -e py311 -- pytest --show-capture=no -vv "${{ matrix.file }}" --junit-xml="${{ matrix.file }}.results.xml"
-      - name: Generate test report
-        if: always()
-        uses: pmeier/pytest-results-action@fc6576eced1f411ea48ab10e917d9cfce2960e29
-        with:
-          path: ${{ matrix.file }}.results.xml
-          summary: true
-          display-options: fEX
-          title: Results for ${{ matrix.file }}
+          tox -v -e py311,report -- pytest --cov --cov-report=term-missing -vv "${{ matrix.file }}"

.gitignore

@@ -109,6 +109,9 @@ venv.bak/
 # PyCharm
 .idea/
 
+# TLO .rst files
+docs/reference/tlo*.rst
+
 # TLO configuration
 tlo.conf
 
@@ -121,11 +124,3 @@ profiling_results/
 
 # ignore _version.py file generated by setuptools_scm
 src/**/_version.py
-
-# Generated TLO docs files
-docs/_*.rst
-docs/hsi_events.csv
-docs/parameters.rst
-docs/reference/modules.rst
-docs/reference/tlo*.rst
-docs/resources/**/*.rst

CITATION.cff

@@ -113,11 +113,6 @@ authors:
   family-names: Janoušková
   orcid: https://orcid.org/0000-0002-4104-0119
   affiliation: University College London
-  website: https://profiles.ucl.ac.uk/90260
-- given-names: Rachel
-  family-names: Murray-Watson
-  affiliation: Imperial College London
-  orcid: https://orcid.org/0000-0001-9079-5975
 repository-code: https://github.com/UCL/TLOmodel
 url: https://tlomodel.org
 abstract: Our fundamental aim is to develop the use of epidemiological and economic

README.md

@@ -1,5 +1,5 @@
 <div style="text-align: center" align="center">
-<img src="docs/thanzi-la-onse.png" alt="Thanzi la Onse" />
+<img src="docs/thanzi-la-onse.png" alt="Thanzi La Onze" />
 <br />
 <h1>Thanzi la Onse model</h1>
 </div>
@@ -24,7 +24,7 @@ The __Thanzi la Onse model (TLOmodel)__ is a part of the [Thanzi la Onse][thanzi
 TLOmodel is developed in a collaboration between:
 
 - [Kamuzu University of Health Sciences][kuhes-link]
-- [MRC Centre for Global Infectious Disease Analysis][mrc-gida-link], [Imperial College London][imperial-link]
+- [MRC Centre for Global Infectioous Disease Analysis][mrc-gida-link], [Imperial College London][imperial-link]
 - [Institute for Global Health][igh-link], [University College London][ucl-link]
 - [Centre for Advanced Research Computing][arc-link], [University College London][ucl-link]
 - [Centre for Health Economics][che-link], [University of York][york-link]

contributors.yaml

@@ -4,7 +4,7 @@
   affiliation: "Imperial College London"
   website: "https://www.imperial.ac.uk/people/timothy.hallett"
   github-username: tbhallett
-  role: Project Lead
+  role: Joint lead epidemiology
   contributions:
     - Epidemiology and modelling
     - Software development
@@ -14,7 +14,7 @@
   affiliation: "University College London"
   website: "https://profiles.ucl.ac.uk/5430"
   github-username: andrew-phillips-1
-  role: Lead Epidemiology
+  role: Joint lead epidemiology
   contributions:
     - Epidemiology and modelling
     - Software development
@@ -102,6 +102,7 @@
   website: "https://www.york.ac.uk/che/staff/research/sakshi-mohan/"
   github-username: sakshimohan
   contributions:
+    - Epidemiology and modelling
     - Health economics
     - Software development
 - given-names: Wingston
@@ -195,7 +196,6 @@
   family-names: Janoušková
   orcid: "https://orcid.org/0000-0002-4104-0119"
   affiliation: "University College London"
-  website: "https://profiles.ucl.ac.uk/90260"
   github-username: EvaJanouskova
   contributions:
     - Epidemiology and modelling
@@ -206,14 +206,15 @@
   affiliation: University College London
   website: "https://profiles.ucl.ac.uk/954"
   contributions:
-    - Clinical process modelling
+    - Clinical consultant 
 - given-names: Paul
   family-names: Revill
   orcid: "https://orcid.org/0000-0001-8632-0600"
   affiliation: University of York
   website: "https://www.york.ac.uk/che/staff/research/paul-revill/"
   github-username: paulrevill
-  role: "Lead Health-Economics"
+  contributions:
+    - Health economics
 - given-names: Wiktoria
   family-names: Tafesse
   orcid: "https://orcid.org/0000-0002-0076-8285"
@@ -236,7 +237,7 @@
   website: "https://www.york.ac.uk/che/staff/students/newton-chagoma/"
   github-username: nchagoma503
   contributions:
-    - Health economics
+    - Health economics  
 - given-names: Martin
   family-names: Chalkley
   orcid: "https://orcid.org/0000-0002-1091-8259"
@@ -272,31 +273,3 @@
   family-names: Uwais
   website: "https://uk.linkedin.com/in/leila-uwais-597705142"
   github-username: Leila-Uwais
-- given-names: Dominic
-  family-names: Nkhoma
-  affiliation: "Kamuzu University of Health Sciences"
-  orcid: "https://orcid.org/0000-0001-6125-6630"
-  contributions:
-      - Policy translation
-  website: "https://mw.linkedin.com/in/dominicnkhoma1978"
-- given-names: Gerald
-  family-names: Manthalu
-  affiliation: "Department of Planning and Policy Development, Ministry of Health and Population, Lilongwe, Malawi"
-  orcid: "https://orcid.org/0000-0002-3501-8601"
-  contributions:
-      - Policy translation
-- given-names: Rachel
-  family-names: Murray-Watson
-  affiliation: "Imperial College London"
-  orcid: https://orcid.org/0000-0001-9079-5975
-  github-username: RachelMurray-Watson
-  contributions:
-    - Epidemiology and modelling
-    - Software development
-- given-names: Victor
-  family-names: Mwapasa
-  orcid: "https://orcid.org/0000-0002-2748-8902"
-  affiliation: "Kamuzu University of Health Sciences"
-  website: "https://www.kuhes.ac.mw/prof-victor-mwapasa/"
-  contributions:
-    - Clinical process modelling

docs/conf.py

@@ -106,9 +106,6 @@
     'exclude-members': '__dict__, name, rng, sim'  # , read_parameters',
 }
 
-# Include both class level and __init__ docstring content in class documentation
-autoclass_content = 'both'
-
 # The checker can't see private repos
 linkcheck_ignore = ['^https://github.com/UCL/TLOmodel.*',
                     'https://www.who.int/bulletin/volumes/88/8/09-068213/en/nn']

docs/index.rst

@@ -52,7 +52,6 @@ Contents
    azure_batch
    reference/index
    resources/index
-   parameters
    learning
    publications
    contributors

docs/publications.rst

@@ -14,26 +14,21 @@ Overview of the Model
 
 Analyses Using The Model
 ========================
-* `Health workforce needs in Malawi: analysis of the Thanzi La Onse integrated epidemiological model of care <https://human-resources-health.biomedcentral.com/articles/10.1186/s12960-024-00949-2>`_
-
-* `A new approach to Health Benefits Package design: an application of the Thanzi La Onse model in Malawi <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012462>`_
 
 * `The Changes in Health Service Utilisation in Malawi During the COVID-19 Pandemic <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0290823>`_
 
 * `Modeling Contraception and Pregnancy in Malawi: A Thanzi La Onse Mathematical Modeling Study <https://onlinelibrary.wiley.com/doi/10.1111/sifp.12255>`_
 
 * `Factors Associated with Consumable Stock-Outs in Malawi: Evidence from a Facility Census <https://www.sciencedirect.com/science/article/pii/S2214109X24000950>`_
 
-* `The Effects of Health System Frailties on the Projected Impact of the HIV and TB Programmes in Malawi <https://www.sciencedirect.com/science/article/pii/S2214109X24002596>`_
+* `The Effects of Health System Frailties on the Projected Impact of the HIV and TB Programmes in Malawi <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4508436>`_
 
 * `Estimating the health burden of road traffic injuries in Malawi using an individual-based model <https://injepijournal.biomedcentral.com/articles/10.1186/s40621-022-00386-6>`_
 
 * `The potential impact of intervention strategies on COVID-19 transmission in Malawi: A mathematical modelling study. <https://bmjopen.bmj.com/content/11/7/e045196>`_
 
 * `The potential impact of including pre-school aged children in the praziquantel mass-drug administration programmes on the S.haematobium infections in Malawi: a modelling study <https://www.medrxiv.org/content/10.1101/2020.12.09.20246652v1>`_
 
-* `A Decade of Progress in HIV, Malaria, and Tuberculosis Initiatives in Malawi. <https://www.medrxiv.org/content/10.1101/2024.10.08.24315077v1>`_
-
 
 Healthcare Seeking Behaviour
 ============================

docs/tlo_contributors.py

@@ -98,12 +98,11 @@ def categorized_contributor_lists_html(
     with open(args.contributors_file_path, "r") as f:
         contributors = yaml.safe_load(f)
     contribution_categories = (
-        "Clinical process modelling",
         "Epidemiology and modelling",
         "Health economics",
-        "Policy translation",
-        "Project management",
         "Software development",
+        "Clinical consultant",
+        "Project management",
     )
     category_predicates = {
         "Scientific leads": lambda c: "lead" in c.get("role", "").lower(),