Doc updates

.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

docs/bib.md

@@ -1,10 +1,17 @@
-[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-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://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/

docs/index.md

@@ -2,6 +2,139 @@
 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.
+
+## Getting started
+
+<div class="grid cards" markdown>
+
+-   :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]
+
+</div>
+
+
+## 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.
+
+<div class="grid cards" markdown>
+
+-   :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]
+
+</div>
+
+### 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.
+
+<div class="grid cards" markdown>
+
+-   :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]
+
+</div>

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

pyproject.toml

@@ -34,6 +34,7 @@ docs = [
     "mkdocstrings-python",
     "mkdocs-autoapi",
     "mkdocs-glightbox",
+    "mkdocs-table-reader-plugin",
 ]
 lint = [
 ]