Port HowTo to main NIU website

[adamltyson]

This PR closes #290

Working on this made me more convinced that this PR is necessary. The HowTo guide has languished somewhat. Lots of links don't work, partially because we don't look at it much, nevermind everyone else.

So far I've just very naively copied the content from HowTo to here. Not sure if we want to anything more, such as add a card on the main site or something to promote it more.

N.B. I need to do a final check to make sure all the content makes sense in its new place.

Once merged, we should do something about neuroinformatics-unit/HowTo#78, neuroinformatics-unit/HowTo#80, neuroinformatics-unit/HowTo#81, neuroinformatics-unit/HowTo#82.

I suggest we just merge this as is, and work on improving the guide and it's accessibility separately, unless anyone has any ideas for things we should do now?

[adamltyson]

Once merged, I will redirect the howto domain to this new page

[lochhh]

If we care about preserving commit history of HowTo, we could consider using git-filter-repo to rewrite HowTo's history (in a throw-away "filtered" clone) so the paths match where we will put the files in the website repo. Roughly we are mapping:

• HowTo: docs/source/_static/X → Website: docs/source/_static/howto/X (selected files only)
• HowTo: docs/source/Y → Website: docs/source/howto/Y (everything else)

We can then add the filtered clone as a remote to the website repo, and merge it into the website repo

[adamltyson]

Do we care though? I figured for a docs site, this was overkill. It's always taken a very long time when we've done in the past for BrainGlobe.

[lochhh]

Wdyt about something like this:

This surfaces the howto site, without needing to merge both repos. We could also do the same for the software skills site?

[adamltyson]

Im not sure that helps greatly. We want people to be able to go to one place and search. I think having multiple sites is a convenience for developers, but doesn't help users much. We lose out a lot by not having all our resources in one place as much as possible.

[niksirbi]

Thanks for taking the initiative @adamltyson.

PRs neuroinformatics-unit/HowTo#80 and neuroinformatics-unit/HowTo#81 are very close to merrging, and I could do that tomorrow while also fixing the broken links.

Could we not hold off merging this one until Friday? I wouldn't want to go through re-opening neuroinformatics-unit/HowTo#80 here, I'd just merge it on HowTo and then copy the whole updated file to this PR.

[adamltyson]

Yeah no rush!

[niksirbi]

I've merged 3 PRs on HowTo: 84 (fixing linkcheck errors), 80 (a typo fix) and 81 (the updated SLEAP HPC guide). Should I also port these changes onto this branch?

[adamltyson]

yeah if you don't mind. you may get a merge error with the linkcheck fixes (i also fixed them here), but feel free to just keep your changes

[niksirbi]

I reasoned that this was a suitable task for @claude.

I ported the three recently merged HowTo PRs (84, 80, 81) onto this branch. Since the files live in different locations here, these were applied by 'hand' rather than cherry-picked. Where the two repos had diverging linkcheck fixes, I kept HowTo PR 84's approach as agreed.

Changes

• Linkcheck config (conf.py): ignore all of gin.g-node.org (slow/times out) and cambridgeneurotech.com (returns HTTP 415), and dropped the now-redundant GIN wiki anchor-ignore entries. From Fix linkcheck errors HowTo#84.
• Electrophysiology reference links — replaced pubmed/eLife URLs with stable DOI links in resources.md and the example-pipelines README.rst. From Fix linkcheck errors HowTo#84.
• GIN guide typo: git upload → gin upload. From Fix typo HowTo#80.
• SLEAP HPC guide: full rewrite for the new PyTorch-backed SLEAP module (sleap train/track, YAML configs, new SLURM args) plus a Legacy (TensorFlow) modules section. From Update SLEAP module guide for the new pytorch version HowTo#81.

Notes

This branch had already independently picked up most of PR 84's content fixes, so those weren't re-touched.
The GIN "movement" references link is left as-is; the version here (/latest/...#sample-data) is already newer than PR 84's.

[niksirbi]

From my POV this can be merged.

However:

• we should definitely open an issue about refactoring the abundance of guides and resources under 'More' into a more logical organisation.
• what's our plan about the open HowTo issues, should we transfer those as well after this PR is merged?
• The currently open 2 HowTo PRs (one by me and one by @sfmig) would have to be re-opened against this repo). Presumably not too much pain since they're both still in draft?