Update template site homepage (#52)

* Ref #49: redesign collab infrastructure diagram & rename

* Add joint components to template site homepage

* intro linking to 'About this Guide' for more context and personalization instructions

* shared logo
---------

Co-authored-by: Graham Taylor <[email protected]>

Author: egrace479

.gitignore

@@ -4,3 +4,6 @@
 # Additional
 __pycache__
 
+# MkDocs build output
+site/
+

.markdownlint.json

@@ -1,5 +1,6 @@
 {
   "MD007": { "indent": 4 },
   "no-hard-tabs": false,
-  "MD013": false
+  "MD013": false,
+  "MD026": { "punctuation": ".,;:!" }
 }

docs/index.md

@@ -1,30 +1,33 @@
 # Welcome to the Collaborative Distributed Science Guide!
 
-This website hosts guides to Imageomics workflows, documentation, and general best-practices for collaborative science. We aim to provide a helpful resource for a broad base of scientists working in the field of [_imageomics_](wiki-guide/Glossary-for-Imageomics.md/#imageomics) and beyond.
+This website hosts guides to FAIR (findable, accessible, interoperable, reusable) and reproducible workflows, documentation, and general best-practices for collaborative science. We aim to provide a helpful resource for scientists working in [_imageomics_](wiki-guide/Glossary-for-Imageomics.md/#imageomics) and related interdisciplinary fields.
 
-It houses the information needed to get started with and use institute resources readily available to all members. However, most of this guide is applicable to anyone working more broadly in the field of imageomics or adjacent fields of computer and data science, and it is tailored to help domain scientists bridging that gap.
+For information about customizing this guide template, see [About the Guide](https://github.com/Imageomics/Collaborative-distributed-science-guide?tab=readme-ov-file#about-the-guide).
 
 ## Highlights
 
-There are many pages of useful information contained in this guide covering a range of topics from project management and workflows, to repositories and archives, to a glossary of _imageomics-related_ terms for improved interdisciplinary communication.
+There are many pages of useful information contained in this guide covering a range of topics from project management and workflows, to repositories and archives, to a glossary of scientific terms for improved interdisciplinary communication.
 
 ### Just starting a project?
+
 Check out our guides to get your project off on the right foot!
 
-- [The GitHub Repo Guide](wiki-guide/GitHub-Repo-Guide.md): This page reviews expected and suggested GitHub repository contents, as well as structural considerations. 
+- [The GitHub Repo Guide](wiki-guide/GitHub-Repo-Guide.md): This page reviews expected and suggested GitHub repository contents, as well as structural considerations.
 
 - [The Hugging Face Repo Guide](wiki-guide/Hugging-Face-Repo-Guide.md): Analogous expected and suggested repository contents for Hugging Face repositories; there are notable differences from GitHub in both content and structure.
 
 - [FAIR Guide](wiki-guide/FAIR-Guide.md): Guide to producing FAIR digital products, from metadata collection through product documentation and publication. This builds on the content in both the GitHub and Hugging Face Repository Guides, providing checklists to ensure [code](wiki-guide/Code-Checklist.md), [data](wiki-guide/Data-Checklist.md), and [model](wiki-guide/Model-Checklist.md) repositories are FAIR. The latter two closely follow our [HF Templates](wiki-guide/About-Templates.md).
 
 ### Project repo up, what's next?
+
 Check out our workflow guides for how to interact with your new repo:
 
 - [The GitHub Workflow](wiki-guide/The-GitHub-Workflow.md): This page mainly focuses on branching and the PR process.
 
 - [The Hugging Face Workflow](wiki-guide/The-Hugging-Face-Workflow.md): Analogous workflow directions for Hugging Face; there are notable differences from GitHub in how this process works practically, though the concept is the same.
 
 ### Project management or organization got you down?
+
 Discover new tools to help:
 
 - [Guide to GitHub Projects](wiki-guide/Guide-to-GitHub-Projects.md): This page focuses on GitHub's project management tool, Projects, which integrates issues and pull requests into a unified task board to keep tabs on how your project is progressing. Labels, milestones, and assignee tags provide improved organization, and allow for more focused views.
@@ -33,39 +36,33 @@ Discover new tools to help:
 
 - [Virtual Environments](wiki-guide/Virtual-Environments.md): Summary of `conda` and `pip` environments: how to make, use, and share them.
 
-
-## Collaborative Infrastructure We Use
+## Collaborative Infrastructure used by Imageomics and ABC
 
 - GitHub
-    - [Institute Code Repositories](https://github.com/Imageomics) where we store our code (software + tools).
+    - [Imageomics](https://github.com/Imageomics) and [ABC](https://github.com/ABC-Center) Code Repositories, where we store our code (software + tools).
     - GitHub's [Docs](https://docs.github.com/en)
         - [Repositories](https://docs.github.com/en/repositories)
         - [GitHub Projects](https://docs.github.com/en/issues/planning-and-tracking-with-projects)
 - Hugging Face
-    - [Imageomics Organization page](https://huggingface.co/imageomics) where we store our datasets and models (and their metadata).
+    - [Imageomics](https://huggingface.co/imageomics) and [ABC](https://hf.co/ABC-Center) Organization Pages, where we store our datasets and models (and their metadata).
     - Additionally, use [Hugging Face Spaces](https://huggingface.co/docs/hub/spaces) to run demos of models and other projects.
     - Hugging Face's [Docs](https://huggingface.co/docs)
         - [Model Hub](https://huggingface.co/docs/hub/models-the-hub)
         - [Datasets](https://huggingface.co/docs/hub/datasets-overview)
 
 ### Collaborative Infrastructure Diagram
-![tech_infrastructure_diagram](wiki-guide/images/index/382108831-1173cd79-db94-4326-8b6e-dcbdeb8939cd.png)
 
+![tech_infrastructure_diagram](wiki-guide/images/index/collaborative-infrastructure-diagram.png)
 
-## Imageomics Branding (Logos)
+## `<Organization>` Branding (Logos)
 
-We have two versions of the logo, a [fish](logos/Imageomics_logo_fish.png) and a [butterfly](logos/Imageomics_logo_butterfly.png), which should be used for scientific posters, conference, workshop, and meeting marketing materials, etc. Choice of logo is based on user preference.
-
-![butterfly logo](logos/Imageomics_logo_butterfly.png){: style="width:45%"}
-![fish logo](logos/Imageomics_logo_fish.png){: style="width:45%"}
+Since this is a joint Imageomics and ABC project, we have a special combined logo:
 
+![combined Imageomics and ABC logo](logos/Imageomics_ABC.png){: style="width:75%"}
 
 ## Other pages of note
+
 - [Glossary for Imageomics](wiki-guide/Glossary-for-Imageomics.md): Collection of terms used in imageomics. The goal is to ensure all participating domains are represented, thus facilitating interdisciplinary communication. This is a group effort, please check it out and add terms you think should be there!
 - [Command Line Cheat Sheet](wiki-guide/Command-Line-Cheat-Sheet.md): Collection of useful bash and git commands with some git tips.
 
-
-<br>
-<br>
-
 !!! question "[Questions, Comments, or Concerns?](https://github.com/Imageomics/Collaborative-distributed-science-guide/issues)"