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Reorganize docs, add several new guides#685

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garrettjstevens merged 18 commits intomainfrom
admin_and_customization_docs
Oct 14, 2025
Merged

Reorganize docs, add several new guides#685
garrettjstevens merged 18 commits intomainfrom
admin_and_customization_docs

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@garrettjstevens
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Draft PR for now since it's still a work in progress, but I wanted to share some screenshots and get feedback while working on it.

Here's what I'm thinking of changing the outline of the docs to:

image

I'd also like to eventually have a "Users" section with various examples of how to work on different types of annotations.

@garrettjstevens garrettjstevens self-assigned this Sep 22, 2025
@garrettjstevens garrettjstevens changed the title Admin and customization docs Improve admin docs, add. customization docs Sep 22, 2025
@garrettjstevens garrettjstevens changed the title Improve admin docs, add. customization docs Improve admin docs, add customization docs Sep 22, 2025
@garrettjstevens garrettjstevens force-pushed the admin_and_customization_docs branch 2 times, most recently from ae7004a to 65a6a99 Compare October 2, 2025 22:51
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After working with it some more, the above changes to the docs didn't really seem to work. I tried to look at it as if I was new to Apollo and realized the "Administrators" section was unclear since it had so many things. Also, having a separate page for every action in the CLI and GUI docs seemed like it would be hard to create and maintain.

After looking over a bunch of other docs sites, I settled on a three main docs sections that seem pretty standard: "Try it out", "Installation", and "Guides", as well as an additional "Developers" section that most projects don't need, but is important for us.

Each page in the "Guides" section will have both CLI and GUI instructions for that topic, if applicable, and I think it makes it a lot easier to find information on a certain topic.

image

I still think we need a users guide section, but I now think it needs to be a completely separate section from the docs on the website.

@alpapan
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alpapan commented Oct 9, 2025

I like it based on screenshots - i'd only change changelog to audit changes since changelog for me means code and audit is a standard term in biocuration.

i hope i can find some time to look at the content (but now need to get some Zs)

@garrettjstevens garrettjstevens force-pushed the admin_and_customization_docs branch from c42253e to b82f35e Compare October 13, 2025 20:12
@garrettjstevens garrettjstevens marked this pull request as ready for review October 13, 2025 20:15
@garrettjstevens garrettjstevens force-pushed the admin_and_customization_docs branch from ab62c74 to 08ca5ba Compare October 14, 2025 01:49
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I'm going to merge the guides that are done for now and add/update more in a future PR.

@garrettjstevens garrettjstevens changed the title Improve admin docs, add customization docs Reorganize docs, add several new guides Oct 14, 2025
@garrettjstevens garrettjstevens merged commit e279eac into main Oct 14, 2025
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@garrettjstevens garrettjstevens deleted the admin_and_customization_docs branch October 14, 2025 02:30
cmdcolin pushed a commit to cmdcolin/Apollo3 that referenced this pull request Mar 16, 2026
* Organize and add more admin docs

* Use pngquant on images

* More docs restructuring

* Add guides section to docs

* Work on admin, assembly, and CLI guides

* Rename CLI guide directory

* Add login instructions to CLI docs

* Add docs for adding and removing assemblies

* Add doc describing features and how to import them

* Add JBrowse configuration docs

* Add evidence track docs

* Add changelog docs

* Improve doc code block theming

* Add screenshots/examples to evidence tracks guide

* Update theme and coloring docs

* Spell and grammar check

* Remove guides that aren't finished yet

* Run pngquant
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2 participants