From f58846593aa9809c375cb487da317647e45cf257 Mon Sep 17 00:00:00 2001 From: Kurt Frey Date: Tue, 21 Apr 2026 14:55:32 -0700 Subject: [PATCH 1/2] Docs --- .gitignore | 19 ++++++++++ docs/bib.md | 21 ++++++----- docs/index.md | 98 ++++++++++++++++++++++++++++++++++++++++++++++++-- mkdocs.yml | 13 +++---- pyproject.toml | 1 + 5 files changed, 133 insertions(+), 19 deletions(-) diff --git a/.gitignore b/.gitignore index d42b8e4..702ad5e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,21 @@ # mkdocs documentation /site + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST diff --git a/docs/bib.md b/docs/bib.md index b3a7df4..a6a5497 100644 --- a/docs/bib.md +++ b/docs/bib.md @@ -1,10 +1,13 @@ -[emod-api]: https://emod-hub.github.io/emod-api/ -[emod-generic]: https://docs.idmod.org/projects/emod-generic/en/latest/parameter-overview.html -[emodpy]: https://emod-hub.github.io/emodpy/ -[emodpy-hiv]: https://docs.idmod.org/projects/emodpy-hiv/ -[emodpy-malaria]: https://docs.idmod.org/projects/emodpy-malaria/ +[emod]: https://emod.idmod.org/EMOD/ +[emod-generic]: https://emod.idmod.org/EMOD-Generic/ +[emod-api]: https://emod.idmod.org/emod-api/ +[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://institutefordiseasemodeling.github.io/idmtools/ +[idmtools_cli]: https://institutefordiseasemodeling.github.io/idmtools/cli/ +[idmtools_config]: https://institutefordiseasemodeling.github.io/idmtools/getting-started/configuration +[idmtools_container]: https://institutefordiseasemodeling.github.io/idmtools/platforms/container/ +[idmtools_calibra]: https://institutefordiseasemodeling.github.io/idmtools-calibra/ +[pypi]: https://pypi.org/ diff --git a/docs/index.md b/docs/index.md index 1d13d5f..edbae50 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,6 +2,100 @@ title: Home --- -# Welcome to EMOD-Hub +# EMOD model documentation -Homepage for documentation. +EMOD (Epidemiological MODeling software) is a stochastic, agent-based modeling framework that simulates the simultaneous interactions of agents in an effort to recreate the complex phenomena of disease transmission. Built in C++, the models are feature-rich and designed to track the movement, development, health, and other traits of interest for individuals over a course of lifetimes. + +No new features, bug fixes, or model updates are currently planned. Community support is available through the GitHub Discussions forum, and model code will remain publicly accessible. + +## Available models and utilities + +EMOD is the disease model framework, offering disease-specific models for malaria and HIV alongside Python packages for configuring and running simulations. The idmtools package is a model-agnostic framework that handles the surrounding infrastructure: job commissioning, HPC integration, calibration, and more. While each can be used independently, we recommend using them together for a seamless, integrated workflow. + +### EMOD + +The EMOD framework is powerful and flexible, and can be customized to examine a variety of epidemiological problems. Source code is available for those interested in modifying code to create custom models, and various transmission modes are available to investigate specific disease-oriented questions. + +
+ +- :material-virus:{ .lg .middle } __EMOD__ + + --- + + The source files for building EMOD. + + [:octicons-arrow-right-24: EMOD][emod] + +- :material-virus-outline:{ .lg .middle } __EMOD-Generic__ + + --- + + Modeling framework best suited for low-complexity disease transmission, such as measles. + + [:octicons-arrow-right-24: EMOD-Generic][emod-generic] + +- :material-api:{ .lg .middle } __emod-api__ + + --- + + The Python API used for editing EMOD files. + + [:octicons-arrow-right-24: emod-api][emod-api] + +- :material-language-python:{ .lg .middle } __emodpy__ + + --- + + The Python code used to configure and run EMOD simulations. + + [:octicons-arrow-right-24: emodpy][emodpy] + +- :fontawesome-solid-mosquito:{ .lg .middle } __emodpy-malaria__ + + --- + + The malaria-specific model and Python code used to configure and run malaria-based EMOD. It includes vector transmission, within-host parasite dynamics, and malaria-specific interventions. + + [:octicons-arrow-right-24: emodpy-malaria][emodpy-malaria] + +- :material-water:{ .lg .middle } __emodpy-hiv__ + + --- + + The HIV-specific model and Python code used to configure and run HIV-based EMOD. It includes within-host viral dynamics, HIV virology parameters, and HIV-specific interventions. + + [:octicons-arrow-right-24: emodpy-hiv][emodpy-hiv] + +
+ +### idmtools + +The idmtools package is a collection of Python scripts and utilities that streamlines the full modeling workflow: input file creation, model calibration, commissioning simulations (both locally and on an HPC), and analyzing results. While idmtools is model-agnostic and compatible with custom R or Python models, it is purpose-built to work seamlessly with EMOD. + +
+ +- :material-language-python:{ .lg .middle } __idmtools__ + + --- + + Framework of Python scripts and utilities to streamline modeling workflows. + + [:octicons-arrow-right-24: idmtools][idmtools] + +- :material-language-python:{ .lg .middle } __idmtools container__ + + --- + + The local runner enabling the execution of tasks in a docker container. + + [:octicons-arrow-right-24: idmtools_local][idmtools_container] + +- :material-language-python:{ .lg .middle } __idmtools calibra__ + + --- + + Python scripts and utilities to aid in model calibration. + + [:octicons-arrow-right-24: idmtools_calibra][idmtools_calibra] + +
diff --git a/mkdocs.yml b/mkdocs.yml index 4e7db35..4bd20e3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,5 +1,5 @@ site_name: EMOD-Hub -site_url: https://emod-hub.github.io/ +site_url: https://emod.idmod.org/ repo_name: EMOD-Hub/emod-hub.github.io repo_url: https://github.com/EMOD-Hub/emod-hub.github.io/ @@ -30,17 +30,13 @@ theme: nav: - Home: index.md - - Related projects: - - emodpy: https://emod-hub.github.io/emodpy/ - - emod-api: https://emod-hub.github.io/emod-api/ - - EMOD-Generic: https://emod-hub.github.io/EMOD-Generic/ - - idmtools: https://docs.idmod.org/projects/idmtools/ plugins: - search: - autorefs: - include-markdown: - glightbox: + - table-reader: - mkdocstrings: markdown_extensions: @@ -54,6 +50,9 @@ markdown_extensions: - pymdownx.blocks.details: # allows nesting of collapsible code - pymdownx.caret: # superscripts - pymdownx.details: # collapsible elements + - pymdownx.emoji: # emojis and icons + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg - pymdownx.highlight: # syntax highlighting for code blocks linenums: true # adds line numbers to code blocks automatically anchor_linenums: true # adds HTML anchors (#L1, #L2, etc.) to each line so you can link to specific ones. @@ -90,8 +89,6 @@ extra: link: http://www.youtube.com/@institutefordiseasemodelin1987 - icon: fontawesome/brands/linkedin link: https://linkedin.com/company/institute-disease-modeling - - icon: fontawesome/brands/slack - link: https://gatesfoundation.enterprise.slack.com/ analytics: provider: custom property: GTM-NK4K647 diff --git a/pyproject.toml b/pyproject.toml index 538c5ed..669e9b2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,7 @@ docs = [ "mkdocstrings-python", "mkdocs-autoapi", "mkdocs-glightbox", + "mkdocs-table-reader-plugin", ] lint = [ ] From 1037ac7757b1b13ed18caf6604385b6c1010957e Mon Sep 17 00:00:00 2001 From: Kurt Frey Date: Tue, 21 Apr 2026 15:31:43 -0700 Subject: [PATCH 2/2] Updates --- docs/bib.md | 4 ++++ docs/index.md | 43 +++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 45 insertions(+), 2 deletions(-) diff --git a/docs/bib.md b/docs/bib.md index a6a5497..b0b6d29 100644 --- a/docs/bib.md +++ b/docs/bib.md @@ -1,9 +1,13 @@ [emod]: https://emod.idmod.org/EMOD/ [emod-generic]: https://emod.idmod.org/EMOD-Generic/ +[emod-generic-scripts]: https://emod.idmod.org/EMOD-Generic-Scripts/ [emod-api]: https://emod.idmod.org/emod-api/ [emodpy]: https://emod.idmod.org/emodpy/ [emodpy-hiv]: https://emod.idmod.org/emodpy-hiv/ +[emodpy-hiv_tutorial]: https://github.com/EMOD-Hub/emodpy-hiv/tree/main/tutorials [emodpy-malaria]: https://emod.idmod.org/emodpy-malaria/ +[emodpy-malaria_tutorial]: https://github.com/EMOD-Hub/emodpy-malaria/blob/main/getting_started.md +[emodpy-workflow]: https://emod.idmod.org/emodpy-workflow/ [idmod]: https://www.idmod.org/ [idmtools]: https://institutefordiseasemodeling.github.io/idmtools/ [idmtools_cli]: https://institutefordiseasemodeling.github.io/idmtools/cli/ diff --git a/docs/index.md b/docs/index.md index edbae50..8451ba2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -8,6 +8,45 @@ EMOD (Epidemiological MODeling software) is a stochastic, agent-based modeling f No new features, bug fixes, or model updates are currently planned. Community support is available through the GitHub Discussions forum, and model code will remain publicly accessible. +## Getting started + +
+ +- :material-school:{ .lg .middle } __emodpy-hiv__ + + --- + + Tutorials for emodpy-hiv. + + [:octicons-arrow-right-24: emodpy-hiv][emodpy-hiv_tutorial] + +- :material-school:{ .lg .middle } __emodpy-malaria__ + + --- + + Tutorials for emodpy-malaria. + + [:octicons-arrow-right-24: emodpy-malaria][emodpy-malaria_tutorial] + +- :material-school:{ .lg .middle } __emodpy-workflow__ + + --- + + Workflow examples with emodpy-hiv. + + [:octicons-arrow-right-24: emodpy-workflow][emodpy-workflow] + +- :material-school:{ .lg .middle } __EMOD-Generic-Scripts__ + + --- + + Example models for the Generic branch of EMOD. + + [:octicons-arrow-right-24: EMOD-Generic-Scripts][emod-generic-scripts] + +
+ + ## Available models and utilities EMOD is the disease model framework, offering disease-specific models for malaria and HIV alongside Python packages for configuring and running simulations. The idmtools package is a model-agnostic framework that handles the surrounding infrastructure: job commissioning, HPC integration, calibration, and more. While each can be used independently, we recommend using them together for a seamless, integrated workflow. @@ -88,7 +127,7 @@ The idmtools package is a collection of Python scripts and utilities that stream The local runner enabling the execution of tasks in a docker container. - [:octicons-arrow-right-24: idmtools_local][idmtools_container] + [:octicons-arrow-right-24: idmtools-local][idmtools_container] - :material-language-python:{ .lg .middle } __idmtools calibra__ @@ -96,6 +135,6 @@ The idmtools package is a collection of Python scripts and utilities that stream Python scripts and utilities to aid in model calibration. - [:octicons-arrow-right-24: idmtools_calibra][idmtools_calibra] + [:octicons-arrow-right-24: idmtools-calibra][idmtools_calibra]