Stdpopsim: update dev docs to main from master

[agladstein]

The github workflow docs still says master. It should we switched to main. https://stdpopsim.readthedocs.io/en/latest/development.html#github-workflow
We should also include instructions for how to switch fix your fork if it's old.

[agladstein]

converting master to main

git branch -m master main
git push -u origin main
git fetch upstream

[grahamgower]

The readthedocs (RTD) page hasn't been updated from the repository for a long time --- IIRC we had long-standing issues with RTD running out of memory when setting up the conda env to build the docs.

[apragsdale]

The development docs also don't explain the new process of adding species (no longer have an update_ensembl_data.py function, for example). There's been a bit of movement in the API (e.g. #839 updates a bunch of the tutorial). Until the memory issue is resolved, are we able to at least manually trigger builds of the docs when we merge PRs that update them? The last update was 2 1/2 months ago...

[agladstein]

I don't know if this is related at all, but I tried to build locally, didn't get any error, but it didn't include any updates. I was very confused. Seemed like I was on the wrong branch... But, I wasn't.

[apragsdale]

Hmm - yeah, I've been able to build locally as well without issues, but the updates I wrote do show up in my local build/html outputs. Not sure why they wouldn't be updating locally

[agladstein]

same... I was very confused and thought I was doing something dumb... But, maybe it's not me

[jeromekelleher]

@grahamgower - what's the new docs URL? We should just do the redirect from rtd to there, it's going to cause more and more confusion.

[grahamgower]

Currently living at: https://popsim-consortium.github.io/stdpopsim-docs/

[grahamgower]

There's no versioning there though. Which as far as I can tell, is the one major advantage to using readthedocs over rolling our own and hosting on github.io.

[jeromekelleher]

Ben did some versioning for the tskit docs, is that any use?

[grahamgower]

Ben did some versioning for the tskit docs, is that any use?

I see
https://tskit.dev/tskit/docs/stable/
and
https://tskit.dev/tskit/docs/latest/

But nothing like https://tskit.dev/tskit/docs/0.3.5/ and no menu with links to the various versions. But maybe I missed it? We can certainly upload tagged versions of the docs onto github.io, it's really just doing the javascript bit to insert a menu which is lacking. The menu's contents should be populated from a file, as it needs to be updated with each new tagged release. I haven't done any javascript since ~1999, so would be grateful if someone else has a pre-canned solution, or could otherwise figure it out.

[jeromekelleher]

I don't think it really matters if we have a menu, just stable and latest links is fine I think.

[agladstein]

Maybe I missed something. Is something different happening with how the docs are built?

[jeromekelleher]

Sorry @agladstein - local builds should work just fine, I've no idea what's happening there.