452 Fix Header + Footer + Add Homepage

[davidsmejia]

Purpose

• Add homepage to the examples site
• fix scaling of header/navbar
• adds footer/fix layout
• adds documentation for the homepage
• rerenders all the things
• fixes the fonts by adding the font file to be downloaded and renaming google-analytics.html -> header-includes.html

Issue addressed

#452

Gotchas the reviewer should know about

• Imported the vendor dependencies from a cdn which I would consider "production ready".
• The homepage has to be rendered and committed since snakemake --forceall won't trigger the rule for the homepage.

Remaining concerns and questions

• Navbar couldnt be dynamically included - if it were the relative links would have to be updated to go from root (which would break local dev unless you spun up a server)

[davidsmejia]

Add link to refine.bio in how to use section

[jashapiro]

Navbar couldnt be dynamically included - if it were the relative links would have to be updated to go from root (which would break local dev unless you spun up a server)

I get this, but I worry that having two navbars we have to update down the line will be confusing. Can we somehow put index.html at homepage/index.html or something like that with a redirect? My other thought was some kind of js to rewrite the links, but that seems even more hackish?

[jashapiro]

Since this keeps popping up in my slack reminders, I am submitting a new comment as a "review".

Overall, this looks great, but having two separate header locations to keep track of and keep updated strikes me as a problem we should solve. I had an idea in my earlier comment #457 (comment), but I don't know how workable it is...

My other question is if we want to incorporate #454 into this PR (or merge that first?)

[davidsmejia]

• add footer to homepage
• make the footer wider and at the bottom of the doc
• add github action to inject the header on deploy
• align the set up and other section on the homepage

[davidsmejia]

This looks good as an approach to getting thing inserted semi-dynamically. I'm fine with making the chances on commit rather than trying to set up actions to do it. Hopefully we are not updating all of this too often.

I have a few comments about some snakemake changes that I think could make --forceall option work, but I'm not sure whether or not you tried that already. One other possibility is to make the navbar and footer files inputs to the snakemake rules, which should force rendering of everything when those change even without forceall, but I'm less sold on that in general.

One thing I ran into and I have no idea what is going on is that the navbar isn't getting styled properly (font only, it looks like?) in Safari on a mac for the internal pages. Looks fine with Brave, but not right with Safari, and the home page looks fine in either.

Home page:

Internal pages:

Looks like the google font was only being included with the changes I made for the homepage.. If it had ever appeared correctly before it was because it was cached in your browser. Good catch I made some changes to fix that and include the style sheet on the notebooks!

[jashapiro]

Kinda minor, but I noticed in refinebio-examples/03-rnaseq/pathway-analysis_rnaseq_01_ora.html that one of the image files was not loaded because the AWS object was not public. Since the rendered html file embeds images, (Rmarkdown), this failed load is now baked in to the current rendered files. Rerendering should fix it, and while I am pretty confident that should be the only file affected, we might want to think about how to check for any other cases.

[jashapiro]

This all looks good to me! There is the one note about rerendering for a broken image that I made earlier, but otherwise, pretty! #457 (comment)