Update repo descriptions, attribution, and how to use (#50)

* Use shared logo, adjust size for visibility

* Update citation to include all contributors

* Add comments for personalizing & attribution, how to use the template guide

* Add 'History' subsection to further contextualize the guide
particularly, includes mention of ABC
---------

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

Author: egrace479

CITATION.cff

@@ -1,22 +1,31 @@
-abstract: "Imageomics-focused guide to collaborative work, including GitHub and Hugging Face workflows."
+abstract: "Template guide site for collaborative work, including GitHub and Hugging Face workflows."
 authors:
 - family-names: "Campolongo"
   given-names: "Elizabeth G."
   orcid: "https://orcid.org/0000-0003-0846-2413"
 - family-names: "Thompson"
   given-names: "Matthew J."
   orcid: "https://orcid.org/0000-0003-0583-8585"
-- family-names: "Zoe"
-  given-names: "Duan"
+- family-names: Zhang
+  given-names: Net
+  orcid: "https://orcid.org/0000-0003-2664-451X"
+- family-names: "Duan"
+  given-names: "Zoe"
   orcid: "https://orcid.org/0000-0002-8547-5907"
 - family-names: "Bradley"
   given-names: "John"
   orcid: "https://orcid.org/0000-0003-3858-848X"
+- family-names: Eyriay
+  given-names: Iuliia
+  orcid: "https://orcid.org/0009-0007-1597-8684"
+- family-names: Taylor
+  given-names: Graham
+  orcid: "https://orcid.org/0000-0001-5867-3652"
 - family-names: "Lapp"
   given-names: "Hilmar"
   orcid: "https://orcid.org/0000-0001-9107-0714"
 cff-version: 1.2.0
-date-released: "2024-11-DD"
+date-released: "2025-06-DD" # to update on release
 identifiers:
   - description: "The GitHub release URL of tag v1.0.0."
     type: url
@@ -38,5 +47,5 @@ keywords:
 license: CC0-1.0
 message: "If you find these docs helpful in your research, please cite them as below."
 repository-code: "https://github.com/Imageomics/Collaborative-distributed-science-guide"
-title: "Imageomics Guide"
+title: "Collaborative Distributed Science Guide"
 version: "1.0.0"

README.md

@@ -3,14 +3,35 @@
 Welcome to the Collaborative Distributed Science Guide!
 
 Just joining or starting a new project? 
-Checkout the [Collaborative Distributed Science Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/) for guidance on conventions and best practices.
+Check out the [Collaborative Distributed Science Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/) for guidance on conventions and best practices.
 
 ## About the Guide
 
-This guide started as an Institute-internal wiki, focused on providing guidance and best practices for collaborative and interdisciplinary (computer science + biology) work. Recognizing that the topics and suggestions are broadly applicable to anyone working in similar or adjacent fields, we moved the vast majority to this [guide](https://imageomics.github.io/Collaborative-distributed-science-guide/). To increase accessibility for those less familiar with GitHub, we generated the web site from our Markdown documents (which used to be wiki pages) with [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/).
+This guide started as an Imageomics Institute-internal wiki, focused on providing guidance and best practices for collaborative and interdisciplinary (computer science + biology) work. Recognizing that the topics and suggestions are broadly applicable to anyone working in similar or adjacent fields, we moved the vast majority to this [guide](https://imageomics.github.io/Collaborative-distributed-science-guide/). To increase accessibility for those less familiar with GitHub, we generated the website from our Markdown documents (which used to be wiki pages) with [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/).
 
 Please feel free to open an [issue](https://github.com/Imageomics/Collaborative-distributed-science-guide/issues) with any questions regarding the content of this guide.
 
+### How to Use the Guide
+
+This Guide is set up as a template repository such that there are two primary means of interacting with it:
+1. Building a personalized version of the Guide: select "Use this Template" at the top of the repo to generate your own version. This will create a new repository (generated from the template repo) that does _not_ share the commit history of the template. Updates could still be added from the template upstream through [`git cherry-pick`](https://git-scm.com/docs/git-cherry-pick). More details are provided below, in [Personalizing the Guide](#personalizing-the-guide).
+2. Contributing to the Guide: fork this repo, make changes, and submit a pull request (PR) for review. Some guidance is provided in the [Pull Request Guide](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/The-GitHub-Pull-Request-Guide/); please provide a detailed description of your changes and review the contributing guidelines (coming soon).
+
+### Personalizing the Guide
+
+Welcome to your new guide repo! The first step in updating your new guide is to give it a name; ideally this should match the name you give to the repo when using the template. You will need to update the name and hardcoded repo links across various files.
+
+Primary pages to personalize are:
+
+- [`mkdocs.yaml`](mkdocs.yaml) has comments indicating locations to personalize (e.g., updating name, logos, socials). All pages use relative links within the repository, so those connections only need to be updated if adding or removing pages.
+- [`index.md`](docs/index.md): this is the homepage for the site and should reflect your organization or group's priorities.
+- [`CITATION.cff`](CITATION.cff): please set the Collaborative Distributed Science Guide citation as a reference in your citation file after making your own modifications (see [template](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/GitHub-Repo-Guide/#citation) for guidance on formatting).
+- [`Digital-products-release-licensing-policy.md`](docs/wiki-guide/Digital-products-release-licensing-policy.md): at a minimum, links should be redirected to your GitHub and Hugging Face organization pages.
+    - Other locations in pages such as the [`GitHub-Repo-Guide`](docs/wiki-guide/GitHub-Repo-Guide.md) and [`Hugging-Face-Repo-Guide.md`](docs/wiki-guide/Hugging-Face-Repo-Guide.md) also have links to our organization pages. A search and replace for "Imageomics" can be done to update these.
+- [`Technical-Infrastructure.md`](docs/wiki-guide/Technical-Infrastructure.md): this page is Imageomics-specific and includes internal-only links.
+- [Glossary for Imageomics](docs/wiki-guide/Glossary-for-Imageomics.md): this page should be updated to a topic relevant to your field or focus.
+- Templates should be updated for your organization (mainly the `Acknowledgements` sections, pre-filled URL suggestions, domain-specific suggestions and guidance).
+
 ### Testing
 To test this site locally, first clone this repository, then create an environment with `requirements.txt`
 ```
@@ -21,3 +42,10 @@ and run `mkdocs serve`:
 mkdocs serve
 ```
 Then the site will run at http://127.0.0.1:8000/Collaborative-distributed-science-guide/.
+
+### History
+This guide was developed alongside the [Imageomics Guide](https://imageomics.github.io/Imageomics-guide/), which houses the information needed to get started with and use institute resources readily available to all members. However, most of its content is applicable to anyone working more broadly in the field of [_imageomics_](https://imageomics.github.io/Collaborative-distributed-science-guide/wiki-guide/Glossary-for-Imageomics.md/#imageomics) or adjacent fields of computer and data science, and it is tailored to help domain scientists bridging that gap. _This guide_ is intended to serve as a template for others wishing to develop a similar organization-specific guide, and this solution was born out of the desire to do so for the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org) while limiting duplicative updates between guides (Imageomics and ABC share some team members on this project). The general structure of the website should be broadly applicable, but see [Personalizing the Guide](#personalizing-the-guide) for suggestions on tailoring it for the particular organization or group's needs.
+
+## Acknowledgments
+
+This work was supported by both the [Imageomics Institute](https://imageomics.org) and the [AI and Biodiversity Change (ABC) Global Center](http://abcresearchcenter.org). The Imageomics Institute is funded by the US National Science Foundation's Harnessing the Data Revolution (HDR) program under [Award #2118240](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240) (Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning). The ABC Global Climate Center is funded by the US National Science Foundation under [Award No. 2330423](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330423&HistoricalAwards=false) and Natural Sciences and Engineering Research Council of Canada under [Award No. 585136](https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=782440). This guide draws on research supported by the Social Sciences and Humanities Research Council. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, Natural Sciences and Engineering Research Council of Canada, or Social Sciences and Humanities Research Council.

docs/logos/Imageomics_ABC.png

@@ -9,3 +9,17 @@
 .md-footer-generator {
   order: 3;
 }
+
+/*
+Make logo larger to be legible,
+based on this suggestion: https://github.com/squidfunk/mkdocs-material/discussions/2933#discussioncomment-1168075
+*/
+ .md-header__button.md-logo {
+  margin: 0;
+  padding: 1;
+}
+
+.md-header__button.md-logo img, .md-header__button.md-logo svg {
+  height: 2.8rem;
+  width: 2.8rem;
+}

docs/logos/Imageomics_logo_butterfly.png

@@ -1,18 +1,17 @@
-site_name: "Collaborative Distributed Science Guide"
-site_description: "A guide to collaborative work (originally for Imageomics), including GitHub and Hugging Face workflows."
-site_author: "Imageomics Institute"
-site_url: "https://Imageomics.github.io/Collaborative-distributed-science-guide/"
-edit_uri: view/main/docs
+site_name: "Collaborative Distributed Science Guide"  # Update guide name here
+site_description: "A guide to collaborative work (originally for Imageomics), including GitHub and Hugging Face workflows."  # Update description
+site_author: "Imageomics Institute"    # Update organization/author name
+site_url: "https://Imageomics.github.io/Collaborative-distributed-science-guide/"  # Update your site URL
 
-repo_url: https://github.com/Imageomics/Collaborative-distributed-science-guide
-edit_uri: blob/main/docs/
+repo_url: https://github.com/Imageomics/Collaborative-distributed-science-guide  # Update your repository URL
+edit_uri: edit/main/docs/
 
 theme:
   name: material
   icon:
     view: material/eye
-  logo: logos/Imageomics_logo_butterfly.png
-  favicon: logos/Imageomics_logo_butterfly.png
+  logo: logos/Imageomics_ABC.png    # Set your logo
+  favicon: logos/Imageomics_ABC.png    # Set your logo or favicon of choice
   palette:
     # Palette toggle for automatic mode
     - media: "(prefers-color-scheme)"
@@ -42,6 +41,8 @@ extra_css:
 
 extra:
   social:
+  # Switch to your socials, more info from MkDocs: 
+  # https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#social-links
     - icon: fontawesome/brands/github
       link: https://github.com/Imageomics
     - icon: simple/huggingface
@@ -59,6 +60,8 @@ extra:
     - icon: octicons/link-16
       link: https://imageomics.org
 
+# Add your own copyright notice, but please include the note 
+# "This guide was generated from the <a href="https://github.com/Imageomics/Collaborative-distributed-science-guide" target="_blank"><u>Collaborative Distributed Science Guide</u></a>, developed by the <a href="https://imageomics.org" target="_blank"><u>Imageomics Institute</u></a> and the <a href="http://abcresearchcenter.org/" target="_blank"><u>AI and Biodiversity Change (ABC) Global Center</u></a>."
 copyright: >
   This work was supported by both the <a href="https://imageomics.org" target="_blank"><u>Imageomics Institute</u></a> and the <a href="http://abcresearchcenter.org/" target="_blank"><u>AI and Biodiversity Change (ABC) Global Center</u></a>. 
 
@@ -96,6 +99,7 @@ markdown_extensions:
       title: 📖 On This Page
 
 nav:
+# These are all relative links within the repo, only update if adding or deleting pages
   - Home: index.md
   - GitHub Guide:
       - "Repo Guide": wiki-guide/GitHub-Repo-Guide.md