Docs update (#70)

Author: kfrey-idm

README.md

@@ -10,14 +10,15 @@ Python 3.13 is the recommended and supported version.
 
 ## Documentation
 
-Documentation available at https://emod-hub.github.io/emodpy/.
+Documentation available at https://emod.idmod.org/emodpy/
 
 To build the documentation locally, do the following:
 
 1. Create and activate a venv.
 2. Navigate to the root directory of the repo.
     ```
     python -m pip install .[docs]
+    mkdocs serve
     ```
 
 ## Running tests

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

@@ -6,15 +6,20 @@ title: Home
 
 The emodpy package is a collection of Python scripts for using EMOD. It integrates the configuring of EMOD with idmtools ability to run a model on different platforms. Typical use of emodpy is as part of a disease specific package like [emodpy-malaria][emodpy-malaria] or [emodpy-hiv][emodpy-hiv].
 
-
-See [idmtools documentation][idmtools] for a diagram showing how idmtools and each of the related packages are used in an end-to-end workflow using EMOD as the disease transmission model.
+See the [idmtools documentation][idmtools] for a diagram showing how idmtools and each of the related packages are used in an end-to-end workflow using EMOD as the disease transmission model.
 
 ## Installation
 
-The emodpy package is currently available on a [Python package index server][idm_pypi] managed by the [Institute for Disease Modeling][idmod].
+### Python Version
+
+Python 3.13 is the recommended and supported version.
+
+### Installing the Package
+
+The emodpy package is currently available on the [Python package index][pypi].
 
 Typically, emodpy is installed as part of [emodpy-malaria][emodpy-malaria] or [emodpy-hiv.][emodpy-hiv]. It can be installed independently as below:
 
 ```
-pip install emodpy --extra-index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+pip install emodpy
 ```

mkdocs.yml

@@ -1,5 +1,5 @@
 site_name: emodpy
-site_url: https://emod-hub.github.io/emodpy/
+site_url: https://emod.idmod.org/emodpy/
 repo_name: EMOD-Hub/emodpy
 repo_url: https://github.com/EMOD-Hub/emodpy/
 
@@ -31,16 +31,14 @@ theme:
 nav:
   - Home: index.md
   - API reference: autoapi/
-  - Related projects:
-    - emod-api: https://emod-hub.github.io/emod-api/
-    - EMOD-Generic: https://docs.idmod.org/projects/emod-generic
-    - idmtools: https://docs.idmod.org/projects/idmtools/
+  - Related projects: https://emod.idmod.org/
 
 plugins:
   - search:
   - autorefs:
   - include-markdown:
   - glightbox:
+  - table-reader:
   - mkdocs-autoapi:
       autoapi_ignore:
         - .github/**/*
@@ -62,6 +60,9 @@ 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.
@@ -98,8 +99,6 @@ 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

@@ -40,6 +40,7 @@ docs = [
     "mkdocstrings-python",
     "mkdocs-autoapi",
     "mkdocs-glightbox",
+    "mkdocs-table-reader-plugin",
 ]
 lint = [
     "flake8",