hpvsim 2.2.4__tar.gz → 2.2.6__tar.gz

{hpvsim-2.2.4 → hpvsim-2.2.6}/.github/workflows/pypi_release.yaml

@@ -1,6 +1,7 @@
-name: Publish to PyPI
+name: Publish HPVsim to PyPI (manual)
 
 on:
+  workflow_dispatch:
   push:
     tags:
       - 'v*'

{hpvsim-2.2.4 → hpvsim-2.2.6}/.github/workflows/tests.yaml

@@ -1,5 +1,7 @@
 name: HPVsim CI tests
 on:
+  workflow_call:
+  workflow_dispatch:
   pull_request:
   schedule:
     - cron: "0 0 * * *"
@@ -12,7 +14,7 @@ jobs:
       fail-fast: false
       max-parallel: 8
       matrix:
-        python-version: [ '3.12' ]
+        python-version: [ '3.13' ]
     name: Install and test
     steps:
       - name: Checkout sources
@@ -23,6 +25,8 @@ jobs:
           architecture: x64
       - name: Install HPVsim
         run:  pip install -e .
+      - name: Download data on first load
+        run: hpvsim-download-data
       - name: Install tests
         working-directory: ./tests
         run: pip install -r requirements.txt

{hpvsim-2.2.4 → hpvsim-2.2.6}/.readthedocs.yaml

@@ -7,9 +7,12 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.9"
+    python: "3.13"
+  jobs:
+    post_install:
+      - hpvsim-download-data
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

{hpvsim-2.2.4 → hpvsim-2.2.6}/CHANGELOG.rst

@@ -9,6 +9,18 @@ All notable changes to the codebase are documented in this file. Changes that ma
    :depth: 1
 
 
+Version 2.2.6 (2026-04-17)
+---------------------------
+- Reconcile different copies of repository
+- *Github info* PR `75 <https://github.com/starsimhub/hpvsim/pull/75>`__
+
+
+Version 2.2.5 (2025-10-27)
+---------------------------
+- Small bugfix for campaign vaccination
+- *Github info* PR `689 <https://github.com/starsimhub/hpvsim_orig/pull/689>`__
+
+
 Version 2.2.4 (2025-08-20)
 ---------------------------
 - Fixes a bug in analyzer results for cancer by age and HIV status

{hpvsim-2.2.4 → hpvsim-2.2.6}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023-2025 Bill & Melinda Gates Foundation
+Copyright (c) 2023-2026 Gates Foundation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{hpvsim-2.2.4/hpvsim.egg-info → hpvsim-2.2.6}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: hpvsim
-Version: 2.2.4
+Version: 2.2.6
 Summary: HPVsim: Human Papillomavirus Simulator
 Author: Robyn Stuart, Jamie Cohen, Cliff Kerr, Romesh Abeysuriya, Mariah Boudreau, Daniel Klein, Hao Hu
 Maintainer-email: HPVsim Team <info@hpvsim.org>
 License-Expression: MIT
 Project-URL: Website, https://hpvsim.org
-Project-URL: Source, https://github.com/institutefordiseasemodeling/hpvsim/
+Project-URL: Source, https://github.com/starsimhub/hpvsim/
 Keywords: HPV,human papillomavirus,cervical cancer,agent-based model,disease modeling,simulation
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -65,7 +65,7 @@ HPVsim has been used for analyses in several countries. Academic papers that hav
 Installation
 ------------
 
-The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB).
+The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB). You can also download the data manually by running ``hpvsim-download-data`` from the terminal.
 
 
 Usage and documentation
@@ -77,7 +77,7 @@ Documentation is available at https://docs.hpvsim.org. Additional usage examples
 Contributing
 ------------
 
-If you wish to contribute, please follow the Starsim style guide at: https://github.com/amath-idm/styleguide. See the code of conduct readme for more information.
+If you wish to contribute, please follow the Starsim style guide at: https://github.com/starsimhub/styleguide. See the code of conduct readme for more information.
 
 
 Disclaimer

{hpvsim-2.2.4 → hpvsim-2.2.6}/README.rst

@@ -35,7 +35,7 @@ HPVsim has been used for analyses in several countries. Academic papers that hav
 Installation
 ------------
 
-The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB).
+The easiest way to install is simply via pip: ``pip install hpvsim``. Alternatively, you can clone this repository, then run ``pip install -e .`` (don't forget the dot!) in this folder to install ``hpvsim`` and its dependencies. This will make ``hpvsim`` available on the Python path. The first time HPVsim is imported, it will automatically download the required data files (~30 MB). You can also download the data manually by running ``hpvsim-download-data`` from the terminal.
 
 
 Usage and documentation
@@ -47,7 +47,7 @@ Documentation is available at https://docs.hpvsim.org. Additional usage examples
 Contributing
 ------------
 
-If you wish to contribute, please follow the Starsim style guide at: https://github.com/amath-idm/styleguide. See the code of conduct readme for more information.
+If you wish to contribute, please follow the Starsim style guide at: https://github.com/starsimhub/styleguide. See the code of conduct readme for more information.
 
 
 Disclaimer

{hpvsim-2.2.4 → hpvsim-2.2.6}/docs/_templates/page.html

@@ -2,15 +2,6 @@
 
 {% set css_files = css_files + ["_static/theme_overrides.css"] %}
 
-{% block htmltitle %}
-{{ super() }}
-
-{% if not READTHEDOCS %}
-<meta name="robots" content="none">
-{% endif %}
-
-{% endblock %}
-
 {% block extrahead %}
 
 <script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':

{hpvsim-2.2.4 → hpvsim-2.2.6}/docs/conf.py

@@ -101,9 +101,6 @@ html_context = {
     },
     "default_mode": "light",
 }
-# Add any extra paths that contain custom files
-if not on_rtd:
-    html_extra_path = ['robots.txt']
 
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.

{hpvsim-2.2.4 → hpvsim-2.2.6}/docs/requirements.txt

@@ -6,7 +6,7 @@ pydata-sphinx-theme
 sphinx-design
 readthedocs-sphinx-search
 ipykernel # For tutorials
-nbconvert==7.13.0 # For tutorials; >=7.14 does not work
+nbconvert==7.17.0 # For tutorials; >=7.14 does not work
 nbsphinx # For tutorials
 plantweb
 ipykernel

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/data/products_dx.csv

@@ -93,6 +93,12 @@ hpv,susceptible,hpv18,inadequate,0
 hpv,susceptible,hi5,positive,0
 hpv,susceptible,hi5,negative,1
 hpv,susceptible,hi5,inadequate,0
+hpv,susceptible,hpv45,positive,0
+hpv,susceptible,hpv45,negative,1
+hpv,susceptible,hpv45,inadequate,0
+hpv,susceptible,hi4,positive,0
+hpv,susceptible,hi4,negative,1
+hpv,susceptible,hi4,inadequate,0
 hpv,susceptible,ohr,positive,0
 hpv,susceptible,ohr,negative,1
 hpv,susceptible,ohr,inadequate,0
@@ -111,6 +117,12 @@ hpv,latent,hpv18,inadequate,0
 hpv,latent,hi5,positive,0
 hpv,latent,hi5,negative,1
 hpv,latent,hi5,inadequate,0
+hpv,latent,hpv45,positive,0
+hpv,latent,hpv45,negative,1
+hpv,latent,hpv45,inadequate,0
+hpv,latent,hi4,positive,0
+hpv,latent,hi4,negative,1
+hpv,latent,hi4,inadequate,0
 hpv,latent,ohr,positive,0
 hpv,latent,ohr,negative,1
 hpv,latent,ohr,inadequate,0
@@ -129,6 +141,12 @@ hpv,precin,hpv18,inadequate,0
 hpv,precin,hi5,positive,0.9
 hpv,precin,hi5,negative,0.1
 hpv,precin,hi5,inadequate,0
+hpv,precin,hpv45,positive,0.9
+hpv,precin,hpv45,negative,0.1
+hpv,precin,hpv45,inadequate,0
+hpv,precin,hi4,positive,0.9
+hpv,precin,hi4,negative,0.1
+hpv,precin,hi4,inadequate,0
 hpv,precin,ohr,positive,0.9
 hpv,precin,ohr,negative,0.1
 hpv,precin,ohr,inadequate,0
@@ -147,6 +165,12 @@ hpv,cin,hpv18,inadequate,0
 hpv,cin,hi5,positive,0.9
 hpv,cin,hi5,negative,0.1
 hpv,cin,hi5,inadequate,0
+hpv,cin,hpv45,positive,0.9
+hpv,cin,hpv45,negative,0.1
+hpv,cin,hpv45,inadequate,0
+hpv,cin,hi4,positive,0.9
+hpv,cin,hi4,negative,0.1
+hpv,cin,hi4,inadequate,0
 hpv,cin,ohr,positive,0.9
 hpv,cin,ohr,negative,0.1
 hpv,cin,ohr,inadequate,0
@@ -165,6 +189,12 @@ hpv,cancerous,hpv18,inadequate,0
 hpv,cancerous,hi5,positive,0.9
 hpv,cancerous,hi5,negative,0.1
 hpv,cancerous,hi5,inadequate,0
+hpv,cancerous,hpv45,positive,0.9
+hpv,cancerous,hpv45,negative,0.1
+hpv,cancerous,hpv45,inadequate,0
+hpv,cancerous,hi4,positive,0.9
+hpv,cancerous,hi4,negative,0.1
+hpv,cancerous,hi4,inadequate,0
 hpv,cancerous,ohr,positive,0.9
 hpv,cancerous,ohr,negative,0.1
 hpv,cancerous,ohr,inadequate,0
@@ -183,6 +213,12 @@ hpv1618,susceptible,hpv18,inadequate,0
 hpv1618,susceptible,hi5,positive,0
 hpv1618,susceptible,hi5,negative,1
 hpv1618,susceptible,hi5,inadequate,0
+hpv1618,susceptible,hpv45,positive,0
+hpv1618,susceptible,hpv45,negative,1
+hpv1618,susceptible,hpv45,inadequate,0
+hpv1618,susceptible,hi4,positive,0
+hpv1618,susceptible,hi4,negative,1
+hpv1618,susceptible,hi4,inadequate,0
 hpv1618,susceptible,ohr,positive,0
 hpv1618,susceptible,ohr,negative,1
 hpv1618,susceptible,ohr,inadequate,0
@@ -201,6 +237,12 @@ hpv1618,latent,hpv18,inadequate,0
 hpv1618,latent,hi5,positive,0
 hpv1618,latent,hi5,negative,1
 hpv1618,latent,hi5,inadequate,0
+hpv1618,latent,hpv45,positive,0
+hpv1618,latent,hpv45,negative,1
+hpv1618,latent,hpv45,inadequate,0
+hpv1618,latent,hi4,positive,0
+hpv1618,latent,hi4,negative,1
+hpv1618,latent,hi4,inadequate,0
 hpv1618,latent,ohr,positive,0
 hpv1618,latent,ohr,negative,1
 hpv1618,latent,ohr,inadequate,0
@@ -219,6 +261,12 @@ hpv1618,precin,hpv18,inadequate,0
 hpv1618,precin,hi5,positive,0
 hpv1618,precin,hi5,negative,1
 hpv1618,precin,hi5,inadequate,0
+hpv1618,precin,hpv45,positive,0
+hpv1618,precin,hpv45,negative,1
+hpv1618,precin,hpv45,inadequate,0
+hpv1618,precin,hi4,positive,0
+hpv1618,precin,hi4,negative,1
+hpv1618,precin,hi4,inadequate,0
 hpv1618,precin,ohr,positive,0
 hpv1618,precin,ohr,negative,1
 hpv1618,precin,ohr,inadequate,0
@@ -237,6 +285,12 @@ hpv1618,cin,hpv18,inadequate,0
 hpv1618,cin,hi5,positive,0
 hpv1618,cin,hi5,negative,1
 hpv1618,cin,hi5,inadequate,0
+hpv1618,cin,hpv45,positive,0
+hpv1618,cin,hpv45,negative,1
+hpv1618,cin,hpv45,inadequate,0
+hpv1618,cin,hi4,positive,0
+hpv1618,cin,hi4,negative,1
+hpv1618,cin,hi4,inadequate,0
 hpv1618,cin,ohr,positive,0
 hpv1618,cin,ohr,negative,1
 hpv1618,cin,ohr,inadequate,0
@@ -255,6 +309,24 @@ hpv1618,cancerous,hpv18,inadequate,0
 hpv1618,cancerous,hrhpv,positive,0
 hpv1618,cancerous,hrhpv,negative,1
 hpv1618,cancerous,hrhpv,inadequate,0
+hpv1618,cancerous,hi5,positive,0
+hpv1618,cancerous,hi5,negative,1
+hpv1618,cancerous,hi5,inadequate,0
+hpv1618,cancerous,hpv45,positive,0
+hpv1618,cancerous,hpv45,negative,1
+hpv1618,cancerous,hpv45,inadequate,0
+hpv1618,cancerous,hi4,positive,0
+hpv1618,cancerous,hi4,negative,1
+hpv1618,cancerous,hi4,inadequate,0
+hpv1618,cancerous,ohr,positive,0
+hpv1618,cancerous,ohr,negative,1
+hpv1618,cancerous,ohr,inadequate,0
+hpv1618,cancerous,hr,positive,0
+hpv1618,cancerous,hr,negative,1
+hpv1618,cancerous,hr,inadequate,0
+hpv1618,cancerous,lr,positive,0
+hpv1618,cancerous,lr,negative,1
+hpv1618,cancerous,lr,inadequate,0
 hpv_type,susceptible,hpv16,positive_1618,0
 hpv_type,susceptible,hpv16,positive_ohr,0
 hpv_type,susceptible,hpv16,negative,1
@@ -267,6 +339,14 @@ hpv_type,susceptible,hi5,positive_1618,0
 hpv_type,susceptible,hi5,positive_ohr,0
 hpv_type,susceptible,hi5,negative,1
 hpv_type,susceptible,hi5,inadequate,0
+hpv_type,susceptible,hpv45,positive_1618,0
+hpv_type,susceptible,hpv45,positive_ohr,0
+hpv_type,susceptible,hpv45,negative,1
+hpv_type,susceptible,hpv45,inadequate,0
+hpv_type,susceptible,hi4,positive_1618,0
+hpv_type,susceptible,hi4,positive_ohr,0
+hpv_type,susceptible,hi4,negative,1
+hpv_type,susceptible,hi4,inadequate,0
 hpv_type,susceptible,ohr,positive_1618,0
 hpv_type,susceptible,ohr,positive_ohr,0
 hpv_type,susceptible,ohr,negative,1
@@ -291,6 +371,14 @@ hpv_type,latent,hi5,positive_1618,0
 hpv_type,latent,hi5,positive_ohr,0
 hpv_type,latent,hi5,negative,1
 hpv_type,latent,hi5,inadequate,0
+hpv_type,latent,hpv45,positive_1618,0
+hpv_type,latent,hpv45,positive_ohr,0
+hpv_type,latent,hpv45,negative,1
+hpv_type,latent,hpv45,inadequate,0
+hpv_type,latent,hi4,positive_1618,0
+hpv_type,latent,hi4,positive_ohr,0
+hpv_type,latent,hi4,negative,1
+hpv_type,latent,hi4,inadequate,0
 hpv_type,latent,ohr,positive_1618,0
 hpv_type,latent,ohr,positive_ohr,0
 hpv_type,latent,ohr,negative,1
@@ -315,6 +403,14 @@ hpv_type,precin,hi5,positive_1618,0
 hpv_type,precin,hi5,positive_ohr,0.9
 hpv_type,precin,hi5,negative,0.1
 hpv_type,precin,hi5,inadequate,0
+hpv_type,precin,hpv45,positive_1618,0
+hpv_type,precin,hpv45,positive_ohr,0.9
+hpv_type,precin,hpv45,negative,0.1
+hpv_type,precin,hpv45,inadequate,0
+hpv_type,precin,hi4,positive_1618,0
+hpv_type,precin,hi4,positive_ohr,0.9
+hpv_type,precin,hi4,negative,0.1
+hpv_type,precin,hi4,inadequate,0
 hpv_type,precin,ohr,positive_1618,0
 hpv_type,precin,ohr,positive_ohr,0.9
 hpv_type,precin,ohr,negative,0.1
@@ -339,6 +435,14 @@ hpv_type,cin,hi5,positive_1618,0
 hpv_type,cin,hi5,positive_ohr,0.9
 hpv_type,cin,hi5,negative,0.1
 hpv_type,cin,hi5,inadequate,0
+hpv_type,cin,hpv45,positive_1618,0
+hpv_type,cin,hpv45,positive_ohr,0.9
+hpv_type,cin,hpv45,negative,0.1
+hpv_type,cin,hpv45,inadequate,0
+hpv_type,cin,hi4,positive_1618,0
+hpv_type,cin,hi4,positive_ohr,0.9
+hpv_type,cin,hi4,negative,0.1
+hpv_type,cin,hi4,inadequate,0
 hpv_type,cin,ohr,positive_1618,0
 hpv_type,cin,ohr,positive_ohr,0.9
 hpv_type,cin,ohr,negative,0.1
@@ -363,6 +467,14 @@ hpv_type,cancerous,hi5,positive_1618,0
 hpv_type,cancerous,hi5,positive_ohr,0.9
 hpv_type,cancerous,hi5,negative,0.1
 hpv_type,cancerous,hi5,inadequate,0
+hpv_type,cancerous,hpv45,positive_1618,0
+hpv_type,cancerous,hpv45,positive_ohr,0.9
+hpv_type,cancerous,hpv45,negative,0.1
+hpv_type,cancerous,hpv45,inadequate,0
+hpv_type,cancerous,hi4,positive_1618,0
+hpv_type,cancerous,hi4,positive_ohr,0.9
+hpv_type,cancerous,hi4,negative,0.1
+hpv_type,cancerous,hi4,inadequate,0
 hpv_type,cancerous,ohr,positive_1618,0
 hpv_type,cancerous,ohr,positive_ohr,0.9
 hpv_type,cancerous,ohr,negative,0.1

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/data/products_tx.csv

@@ -8,48 +8,64 @@ excision,cancerous,all,0
 txvx1,latent,hpv16,0.01
 txvx1,latent,hpv18,0.01
 txvx1,latent,hi5,0.01
+txvx1,latent,hpv45,0.01
+txvx1,latent,hi4,0.01
 txvx1,latent,ohr,0.01
 txvx1,latent,hr,0.01
 txvx1,latent,lr,0.01
 txvx1,precin,hpv16,0.01
 txvx1,precin,hpv18,0.01
 txvx1,precin,hi5,0.01
+txvx1,precin,hpv45,0.01
+txvx1,precin,hi4,0.01
 txvx1,precin,ohr,0.01
 txvx1,precin,hr,0.01
 txvx1,precin,lr,0.01
 txvx1,cin,hpv16,0.01
 txvx1,cin,hpv18,0.01
 txvx1,cin,hi5,0.01
+txvx1,cin,hpv45,0.01
+txvx1,cin,hi4,0.01
 txvx1,cin,ohr,0.01
 txvx1,cin,hr,0.01
 txvx1,cin,lr,0.01
 txvx1,cancerous,hpv16,0
 txvx1,cancerous,hpv18,0
 txvx1,cancerous,hi5,0
+txvx1,cancerous,hpv45,0
+txvx1,cancerous,hi4,0
 txvx1,cancerous,ohr,0
 txvx1,cancerous,hr,0
 txvx1,cancerous,lr,0
 txvx2,latent,hpv16,0.9
 txvx2,latent,hpv18,0.9
 txvx2,latent,hi5,0.01
+txvx2,latent,hpv45,0.01
+txvx2,latent,hi4,0.01
 txvx2,latent,ohr,0.01
 txvx2,latent,hr,0.01
 txvx2,latent,lr,0.01
 txvx2,precin,hpv16,0.9
 txvx2,precin,hpv18,0.9
 txvx2,precin,hi5,0.01
+txvx2,precin,hpv45,0.01
+txvx2,precin,hi4,0.01
 txvx2,precin,ohr,0.01
 txvx2,precin,hr,0.01
 txvx2,precin,lr,0.01
 txvx2,cin,hpv16,0.5
 txvx2,cin,hpv18,0.5
 txvx2,cin,hi5,0.01
+txvx2,cin,hpv45,0.01
+txvx2,cin,hi4,0.01
 txvx2,cin,ohr,0.01
 txvx2,cin,hr,0.01
 txvx2,cin,lr,0.01
 txvx2,cancerous,hpv16,0
 txvx2,cancerous,hpv18,0
 txvx2,cancerous,hi5,0
+txvx2,cancerous,hpv45,0
+txvx2,cancerous,hi4,0
 txvx2,cancerous,ohr,0
 txvx2,cancerous,hr,0
 txvx2,cancerous,lr,0

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/data/products_txvx.csv

@@ -2,12 +2,16 @@ name,genotype,rel_imm
 txvx1,hpv16,1
 txvx1,hpv18,1
 txvx1,hi5,0.5
+txvx1,hpv45,0.5
+txvx1,hi4,0.5
 txvx1,ohr,0.5
 txvx1,hr,0.5
 txvx1,lr,0.3
 txvx2,hpv16,1
 txvx2,hpv18,1
 txvx2,hi5,0.5
+txvx2,hpv45,0.5
+txvx2,hi4,0.5
 txvx2,ohr,0.5
 txvx2,hr,0.5
 txvx2,lr,0.3

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/data/products_vx.csv

@@ -2,18 +2,24 @@ name,genotype,rel_imm
 bivalent,hpv16,1
 bivalent,hpv18,1
 bivalent,hi5,0.5
+bivalent,hpv45,0.5
+bivalent,hi4,0.5
 bivalent,ohr,0.1
 bivalent,hr,0.3
 bivalent,lr,0.3
 quadrivalent,hpv16,1
 quadrivalent,hpv18,1
 quadrivalent,hi5,0.5
+quadrivalent,hpv45,0.5
+quadrivalent,hi4,0.5
 quadrivalent,ohr,0.1
 quadrivalent,hr,0.3
 quadrivalent,lr,1
 nonavalent,hpv16,1
 nonavalent,hpv18,1
 nonavalent,hi5,1
+nonavalent,hpv45,1
+nonavalent,hi4,1
 nonavalent,ohr,0.1
 nonavalent,hr,0.5
 nonavalent,lr,1

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/interventions.py

@@ -390,8 +390,9 @@ class CampaignDelivery(Intervention):
         elif len(self.prob) == 1:
             self.prob = np.array([self.prob[0]] * len(self.timepoints))
         else:
-            errormsg = f'Length of years incompatible with length of probabilities: {len(self.years)} vs {len(self.prob)}'
-            raise ValueError(errormsg)
+            if len(self.prob) != len(self.years):
+                errormsg = f'Length of years incompatible with length of probabilities: {len(self.years)} vs {len(self.prob)}'
+                raise ValueError(errormsg)
 
         # Lastly, adjust the annual probability by the sim's timestep, if it's an annual probability
         if self.annual_prob: self.prob = 1-(1-self.prob)**sim['dt']

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/parameters.py

@@ -267,7 +267,9 @@ def get_genotype_choices():
     choices = {
         'hpv16':    ['hpv16', '16'],
         'hpv18':    ['hpv18', '18'],
+        'hpv45':    ['hpv45', '45'],
         'hi5':      ['hi5hpv', 'hi5hpv', 'cross-protective'],
+        'hi4':      ['hi4', 'hi4hpv'],
         'ohr':      ['ohrhpv', 'non-cross-protective'],
         'hr':       ['allhr', 'allhrhpv', 'hrhpv', 'oncogenic', 'hr10', 'hi10'],
         'lo':       ['lohpv'],
@@ -347,6 +349,16 @@ def get_genotype_pars(default=False, genotype=None):
     pars.hpv18.rel_beta         = 0.75  # Relative transmissibility, current estimate from Harvard model calibration of m2f tx
     pars.hpv18.sero_prob        = 0.56 # https://www.sciencedirect.com/science/article/pii/S2666679022000027#fig1
 
+    # using same parameter values as high-risk oncogenic types included in 9valent vaccine (31, 33, 45, 52, 58)
+    # Warning: this should not be used in conjuction with hi5 or hr
+    pars.hpv45 = sc.objdict()
+    pars.hpv45.dur_precin       = dict(dist='lognormal', par1=2.5, par2=9)  # Duration of infection prior to precancer
+    pars.hpv45.dur_cin          = dict(dist='lognormal', par1=4.5, par2=20) # Duration of infection prior to cancer
+    pars.hpv45.cin_fn           = dict(form='logf2', k=0.2, x_infl=0, ttc=50)  # Function mapping duration of infection to probability of developing cin
+    pars.hpv45.cancer_fn        = dict(method='cin_integral', transform_prob=1.5e-3)  # Function mapping duration of infection to severity
+    pars.hpv45.rel_beta         = 0.9 # placeholder
+    pars.hpv45.sero_prob        = 0.60 # placeholder
+
     # High-risk oncogenic types included in 9valent vaccine: 31, 33, 45, 52, 58
     pars.hi5 = sc.objdict()
     pars.hi5.dur_precin         = dict(dist='lognormal', par1=2.5, par2=9)  # Duration of infection prior to precancer
@@ -356,6 +368,16 @@ def get_genotype_pars(default=False, genotype=None):
     pars.hi5.rel_beta           = 0.9 # placeholder
     pars.hi5.sero_prob          = 0.60 # placeholder
 
+    # High-risk oncogenic types included in 9valent vaccine, excluding 45: 31, 33, 52, 58
+    # Warning: this should not be used in conjunction with hi5 or hr
+    pars.hi4 = sc.objdict()
+    pars.hi4.dur_precin         = dict(dist='lognormal', par1=2.5, par2=9)  # Duration of infection prior to precancer
+    pars.hi4.dur_cin            = dict(dist='lognormal', par1=4.5, par2=20) # Duration of infection prior to cancer
+    pars.hi4.cin_fn             = dict(form='logf2', k=0.2, x_infl=0, ttc=50)  # Function mapping duration of infection to probability of developing cin
+    pars.hi4.cancer_fn          = dict(method='cin_integral', transform_prob=1.5e-3)  # Function mapping duration of infection to severity
+    pars.hi4.rel_beta           = 0.9 # placeholder
+    pars.hi4.sero_prob          = 0.60 # placeholder
+
     # Other high-risk: oncogenic but not covered in 9valent vaccine: 35, 39, 51, 56, 59
     pars.ohr = sc.objdict()
     pars.ohr.dur_precin         = dict(dist='lognormal', par1=2.5, par2=9)  # Duration of infection prior to precancer
@@ -366,7 +388,7 @@ def get_genotype_pars(default=False, genotype=None):
     pars.ohr.sero_prob          = 0.60 # placeholder
 
     # All other high-risk types: 31, 33, 35, 39, 45, 51, 52, 56, 58, 59
-    # Warning: this should not be used in conjuction with hi5 or ohr
+    # Warning: this should not be used in conjuction with hi5, 45/hi4, or ohr
     pars.hr = sc.objdict()
     pars.hr.dur_precin       = dict(dist='lognormal', par1=2, par2=10)  # Duration of infection prior to precancer
     pars.hr.dur_cin          = dict(dist='lognormal', par1=4, par2=4) # Duration of infection prior to cancer
@@ -396,7 +418,9 @@ def get_cross_immunity(cross_imm_med=None, cross_imm_high=None, own_imm_hr=None,
         hpv16 = dict(
             hpv16=1.0, # Default for own-immunity
             hpv18=cross_imm_high,
+            hpv45=cross_imm_med,
             hi5=cross_imm_med,
+            hi4=cross_imm_med,
             ohr=cross_imm_med,
             hr=cross_imm_med,
             lr=cross_imm_med,
@@ -405,7 +429,20 @@ def get_cross_immunity(cross_imm_med=None, cross_imm_high=None, own_imm_hr=None,
         hpv18 = dict(
             hpv16=cross_imm_high,
             hpv18=1.0,  # Default for own-immunity
+            hpv45=cross_imm_med,
             hi5=cross_imm_med,
+            hi4=cross_imm_med,
+            ohr=cross_imm_med,
+            hr=cross_imm_med,
+            lr=cross_imm_med,
+        ),
+
+        hpv45 = dict(
+            hpv16=cross_imm_med,
+            hpv18=cross_imm_med,
+            hpv45=own_imm_hr,
+            hi5=cross_imm_med,
+            hi4=cross_imm_med,
             ohr=cross_imm_med,
             hr=cross_imm_med,
             lr=cross_imm_med,
@@ -414,7 +451,20 @@ def get_cross_immunity(cross_imm_med=None, cross_imm_high=None, own_imm_hr=None,
         hi5=dict(
             hpv16=cross_imm_med,
             hpv18=cross_imm_med,
+            hpv45=cross_imm_med,
             hi5=own_imm_hr,
+            hi4=cross_imm_med,
+            ohr=cross_imm_med,
+            hr=cross_imm_med,
+            lr=cross_imm_med,
+        ),
+
+        hi4=dict(
+            hpv16=cross_imm_med,
+            hpv18=cross_imm_med,
+            hpv45=cross_imm_med,
+            hi5=cross_imm_med,
+            hi4=own_imm_hr,
             ohr=cross_imm_med,
             hr=cross_imm_med,
             lr=cross_imm_med,
@@ -423,16 +473,31 @@ def get_cross_immunity(cross_imm_med=None, cross_imm_high=None, own_imm_hr=None,
         ohr=dict(
             hpv16=cross_imm_med,
             hpv18=cross_imm_med,
+            hpv45=cross_imm_med,
             hi5=cross_imm_med,
+            hi4=cross_imm_med,
             ohr=own_imm_hr,
             hr=cross_imm_med,
             lr=cross_imm_med,
         ),
 
+        hr=dict(
+            hpv16=cross_imm_med,
+            hpv18=cross_imm_med,
+            hpv45=cross_imm_med,
+            hi5=cross_imm_med,
+            hi4=cross_imm_med,
+            ohr=cross_imm_med,
+            hr=own_imm_hr,
+            lr=cross_imm_med,
+        ),
+
         lr=dict(
             hpv16=cross_imm_med,
             hpv18=cross_imm_med,
+            hpv45=cross_imm_med,
             hi5=cross_imm_med,
+            hi4=cross_imm_med,
             ohr=cross_imm_med,
             hr=cross_imm_med,
             lr=own_imm_hr,

{hpvsim-2.2.4 → hpvsim-2.2.6}/hpvsim/version.py

@@ -4,6 +4,6 @@ Version and license information.
 
 __all__ = ['__version__', '__versiondate__', '__license__']
 
-__version__ = '2.2.4'
-__versiondate__ = '2025-08-20'
-__license__ = f'HPVsim {__version__} ({__versiondate__}) — © 2023-2025 by IDM'
+__version__ = '2.2.6'
+__versiondate__ = '2026-04-17'
+__license__ = f'HPVsim {__version__} ({__versiondate__}) — © 2023-2026 by the Gates Foundation'