Merge branch 'refs/heads/master' into hallett/fix-1420

.github/workflows/run-on-comment.yml

@@ -126,7 +126,7 @@ jobs:
     - name: Get comment-bot token
       if: always() && steps.has_permissions.outputs.result == 'true'
       id: get_comment_bot_token
-      uses: peter-murray/workflow-application-token-action@dc0413987a085fa17d19df9e47d4677cf81ffef3
+      uses: peter-murray/workflow-application-token-action@8e4e6fbf6fcc8a272781d97597969d21b3812974
       with:
         application_id: ${{ secrets.application-id }}
         application_private_key: ${{ secrets.application-private-key }}

.github/workflows/tests-unpinned.yml

@@ -0,0 +1,32 @@
+name: Tests with unpinned dependencies
+
+on:
+  schedule:
+    - cron: 0 0 15 * *
+
+jobs:
+  test:
+    name: Run tests
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.x]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          lfs: true
+      - name: Cache tox
+        uses: actions/cache@v4
+        with:
+          path: .tox
+          key: tox-${{hashFiles('pyproject.toml') }}
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install tox
+        run: python -m pip install tox
+      - name: Run tests
+        run: tox -v -e py3-latest -- pytest -n auto -vv tests --skip-slow

.github/workflows/tests.yml

@@ -10,6 +10,8 @@ on:
       - requirements/**
       - resources/**
       - src/tlo/**
+      - src/scripts/profiling/scale_run.py
+      - src/scripts/profiling/shared.py
       - tests/**
       - pyproject.toml
       - tox.ini
@@ -44,9 +46,10 @@ jobs:
         name: Set matrix
         run: |
           set -e
+          shopt -s globstar
           # Find all test files and generate their list in JSON format
           VAR_FILES="{\"include\":["
-          for file in tests/test_*.py; do
+          for file in tests/**/test_*.py; do
               VAR_FILES="${VAR_FILES}{\"file\":\"${file}\"},"
           done
           VAR_FILES="${VAR_FILES}]}"
@@ -75,4 +78,12 @@ jobs:
           tox --version
       - name: Test with tox
         run: |
-          tox -v -e py311,report -- pytest --cov --cov-report=term-missing -vv "${{ matrix.file }}"
+          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 }}

.gitignore

@@ -109,9 +109,6 @@ venv.bak/
 # PyCharm
 .idea/
 
-# TLO .rst files
-docs/reference/tlo*.rst
-
 # TLO configuration
 tlo.conf
 
@@ -124,3 +121,12 @@ profiling_results/
 
 # ignore _version.py file generated by setuptools_scm
 src/**/_version.py
+
+# Generated TLO docs files
+docs/_*.rst
+docs/_*.html
+docs/hsi_events.csv
+docs/parameters.rst
+docs/reference/modules.rst
+docs/reference/tlo*.rst
+docs/resources/**/*.rst

CITATION.cff

@@ -113,6 +113,7 @@ 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

README.md

@@ -1,5 +1,5 @@
 <div style="text-align: center" align="center">
-<img src="docs/thanzi-la-onse.png" alt="Thanzi La Onze" />
+<img src="docs/thanzi-la-onse.png" alt="Thanzi la Onse" />
 <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 Infectioous Disease Analysis][mrc-gida-link], [Imperial College London][imperial-link]
+- [MRC Centre for Global Infectious 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

@@ -195,6 +195,7 @@
   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

docs/conf.py

@@ -25,7 +25,6 @@
     'sphinx.ext.ifconfig',
     'sphinx.ext.napoleon',
     'sphinx.ext.todo',
-    'sphinx.ext.viewcode',
     'rawfiles'
 ]
 
@@ -56,7 +55,6 @@
     html_theme = 'sphinx_rtd_theme'
 
 html_use_smartypants = True
-html_last_updated_fmt = '%b %d, %Y'
 html_split_index = False
 html_show_copyright = False
 html_sidebars = {
@@ -106,6 +104,9 @@
     '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

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