EMOD-Hub · kfrey-idm · Jun 12, 2026 · Jun 2, 2026 · Jun 2, 2026 · Jun 9, 2026
diff --git a/.gitignore b/.gitignore
@@ -32,4 +32,7 @@ env.bak/
 venv.bak/
 
 # Local simulations
-Suite_*/
+LOCAL_EXP_PATH.txt
+docker_suites/
+local_python/container_assets/Eradication
+local_python/container_assets/schema.json
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # EMOD-Generic-Scripts
 
-See documentation at https://emod-hub.github.io/EMOD-Generic-Scripts/ for additional information.
+See documentation at https://emod.idmod.org/EMOD-Generic-Scripts for additional information.
 
 
 ## Contents:
@@ -9,19 +9,17 @@ See documentation at https://emod-hub.github.io/EMOD-Generic-Scripts/ for additi
 | --- | --- |
 | env_Alma10 <br /> env_Amazon2023 <br /> env_Debian13 <br /> env_Fedora42 <br /> env_Rocky10 <br /> env_Ubuntu26 | Definition files for Apptainer containers with various operating systems. Produces the the EMOD executable and schema file; creates an environment for running EMOD on COMPS with the python packages available to the embedded python interpreter. All files remain on COMPS and are provided to the various workflows as Asset Collection IDs. |
 | local_python             | Contains additional python scripts with helper functions common to all of the workflows. |
-| model_covariance01       | [Demonstration simulations for heterogeneity in individual behavior.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_covariance01.html) |
-| model_covid01            | Baseline simulations for SARS-CoV-2 in EMOD. Collab with MvG. |
+| model_covariance01       | [Demonstration simulations for heterogeneity in individual behavior.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_covariance01/) |
+| model_covid01            | Baseline simulations for SARS-CoV-2 in EMOD. |
 | model_demographics01     | Example demographics for UK measles simulations. |
-| model_demographics_wpp01 | [Example demographics using UN WPP data as inputs.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_demographics_wpp01.html) |
+| model_demographics_wpp01 | [Example demographics using UN WPP data as inputs.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_demographics_wpp01/) |
+| model_measles            | [Estimates of measles burden under various policies for age of MCV1.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_measles/) |
 | model_measles_cod01      | Documentation. |
-| model_measles_gha01      | [Examination of RDT use and measles outbreak response using Ghana as an example context.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_measles_gha01.html) |
-| model_measles_nga01      | Documentation. |
-| model_measles_nga02      | Documentation. |
-| model_measles01          | [Estimates of measles burden under various policies for age of MCV1.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_measles01.html) |
-| model_network01          | [Demonstration simulations for transmission of infectivity on a network.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_network01.html) |
+| model_measles_gha01      | [Examination of RDT use and measles outbreak response using Ghana as an example context.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_measles_gha01/) |
+| model_network01          | [Demonstration simulations for transmission of infectivity on a network.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_network01/) |
 | model_polio_nga01        | [Example outbreak simulations for cVDPV2 in Nigeria.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_polio_nga01.html) |
-| model_rubella01          | [Projections of rubella infections and estimates of CRS burden following RCV introduction.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_rubella01.html) |
-| model_transtree01        | [Demonstration of the infector labeling feature and generation of explicit transmission networks.](https://docs.idmod.org/projects/emod-generic-scripts/en/latest/examples/model_transtree01.html) |
+| model_rubella01          | [Projections of rubella infections and estimates of CRS burden following RCV introduction.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_rubella01/) |
+| model_transtree01        | [Demonstration of the infector labeling feature and generation of explicit transmission networks.](https://emod.idmod.org/EMOD-Generic-Scripts/examples/model_transtree01/) |
 | refdat_mcv1              | IHME MCV1 coverage estimates used to construct input files for EMOD simulations. |
 | refdat_namesets          | Namesets used for region identification. |
 | refdat_poppyr            | UN WPP age structured population estimates used to construct input files for EMOD simulations. |
@@ -69,17 +67,6 @@ To build the documentation locally, do the following:
 ---------------------
 
 
-## Disclaimer
-
-The code in this repository was developed by IDM and other collaborators to support our
-joint research on flexible agent-based modeling. We've made it publicly available under
-the MIT License to provide others with a better understanding of our research and an
-opportunity to build upon it for their own work. We make no representations that the code
-works as intended or that we will provide support, address issues that are found, or accept
-pull requests. You are welcome to create your own fork and modify the code to suit your own
-modeling needs as permitted under the MIT License.
-
-
 ## Project status
 
 EMOD-Hub projects are provided as open source software under the MIT License for

diff --git a/docker/emod_env/Dockerfile b/docker/emod_env/Dockerfile
diff --git a/docker/emod_exe/Dockerfile b/docker/emod_exe/Dockerfile
diff --git a/docker/emodpy/Dockerfile b/docker/emodpy/Dockerfile
@@ -1,11 +1,11 @@
-FROM ubuntu:24.04
+FROM ubuntu:26.04
 #
 RUN apt-get update
 RUN apt-get -y upgrade
 #
-RUN apt-get -y install python3
-RUN apt-get -y install python3-pip
-RUN apt-get -y install python3-venv
+RUN apt-get install -y python3
+RUN apt-get install -y python3-pip
+RUN apt-get install -y python3-venv
 #
 RUN apt-get clean
 #
@@ -14,4 +14,4 @@ RUN python3 -m venv $PY_VENV
 ENV PATH="$PY_VENV/bin:$PATH"
 #
 RUN pip3 install pip --upgrade
-RUN pip3 install emodpy~=3.1
+RUN pip3 install emodpy~=3.2
diff --git a/docs/bib.md b/docs/bib.md
@@ -1,10 +1,7 @@
-[emod-api]: https://emod-hub.github.io/emod-api/
-[emod-generic]: https://emod-hub.github.io/EMOD-Generic/
-[emodpy]: https://emod-hub.github.io/emodpy/
-[emodpy-hiv]: https://emod-hub.github.io/emodpy-hiv/
-[emodpy-malaria]: https://emod-hub.github.io/emodpy-malaria/
+[emod-api]: https://emod.idmod.org/emod-api/
+[emod-generic]: https://emod.idmod.org/EMOD-Generic/
+[emodpy]: https://emod.idmod.org/emodpy/
+[emodpy-hiv]: https://emod.idmod.org/emodpy-hiv/
+[emodpy-malaria]: https://emod.idmod.org/emodpy-malaria/
 [idmod]: https://www.idmod.org/
-[idmtools]: https://docs.idmod.org/projects/idmtools/
-[idmtools_cli]: https://docs.idmod.org/projects/idmtools/en/latest/cli/cli_index.html
-[idmtools_config]: https://docs.idmod.org/projects/idmtools/en/latest/configuration.html
-[idm_pypi]: https://packages.idmod.org/
+[idmtools]: https://docs.idmod.org/idmtools/
diff --git a/docs/examples/figures/ref_gha_obr_contours.png b/docs/examples/figures/ref_gha_obr_contours.png
diff --git a/docs/examples/figures/ref_gha_timeseries.png b/docs/examples/figures/ref_gha_timeseries.png
diff --git a/docs/examples/model_measles01.md → docs/examples/model_measles.md b/docs/examples/model_measles01.md → docs/examples/model_measles.md
diff --git a/docs/examples/model_measles_gha01.md b/docs/examples/model_measles_gha01.md
@@ -14,11 +14,11 @@ Measles infectivity moved between nodes based on a gravity-type network model. A
 
 Each agent represented 25 individuals. Prevalence could fall to zero during the simulation, but exogeneous importation ensured long-term elimination did not occur. Importation probability was proportional to population. Simulations started in 2008. Outputs prior to 2011 were ignored because initial measles immunity is only roughly approximate and a few years of simulated time are required to establish internal consistency. Each simulation time step represents 5 days.
 
-Parameters in the baseline model were adjusted to fit observed timeseries of measles incidence. A Poisson-based likelihood function was maximized over one free parameter that scales total incidence and was interpreted as a reporting rate.
+Parameters in the baseline model were adjusted to fit observed timeseries of measles incidence. A Poisson-based likelihood function was maximized over two free parameters that scale total incidence; this scaling was interpreted as a reporting rate.
 
 ![Figure 3: Baseline timeseries and reporting rate](figures/ref_gha_timeseries.png)
 
-Posterior estimates suggest around 4% of measles infections are captured in case reports.
+Posterior estimates suggest around 2% of measles infections are captured in case reports, and a modest annual improvement to the reporting rate.
 
 Test scenarios implemented hypothetical regional outbreak response SIAs starting in 2022. These responses were triggered based on varying thresholds of observed cases. Spatially heterogeneous reporting rates were assumed with a mean reporting rate of 4%
 

diff --git a/docs/examples/model_measles_nga01.md b/docs/examples/model_measles_nga01.md
diff --git a/docs/examples/model_measles_nga02.md b/docs/examples/model_measles_nga02.md
diff --git a/local_python/container_assets/Dockerfile b/local_python/container_assets/Dockerfile
@@ -0,0 +1,3 @@
+FROM ghcr.io/emod-hub/emod-ubuntu-runtime:latest
+#
+RUN pip3 install emod-api~=3.1
diff --git a/local_python/container_assets/Eradication b/local_python/container_assets/Eradication
diff --git a/local_python/container_assets/README.md b/local_python/container_assets/README.md
@@ -0,0 +1,7 @@
+## Local execution
+
+This directory is the destination for an executable and schema extracted to from the emod-generic Python package.
+These files are only used when running locally via Docker Desktop, and require the `local` optional dependencies
+to also be installed.
+
+The Dockerfile in this directory is used to add the emod-api package to the default EMOD-Hub runtime environment.