Change organization and project name expansion

[hammer]

We decided to rename the organization to sgkit-dev and to expand sgkit to "Scalable genetics toolkit". We should make the corresponding changes and make sure all project resources work.

[jeromekelleher]

Things that might break:

• documentation hosted on GitHub pages: https://pystatgen.github.io/sgkit/latest/
• Workflows (do a grep for pystatgen in this repo?)
• Conda-package?

[benjeffery]

https://docs.github.com/en/organizations/managing-organization-settings/renaming-an-organization

Doesn't mention pages URLs redirecting

[jeromekelleher]

Related: https://gist.github.com/domenic/1f286d415559b56d725bee51a62c24a7

[hammer]

Also relevant

• Redirect GitHub Pages site when transferring repository ownership isaacs/github#492
• https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository
• https://inbo.github.io/
• Redirecting GitHub Pages after renaming a repository
• Setup a redirect on Github Pages

[hammer]

Okay going to try to change the org name now, let's see how this goes... cc @jeromekelleher

[hammer]

...and quickly encountered an issue. After the org rename, my plan was to create a new organization pystatgen, add a repo sgkit, and set up GitHub Pages to redirect to the sgkit-dev/sgkit site. Unfortunately GitHub seems to have retired this repository name:

According to StackOverflow, I can contact GitHub support to get this repository name unretired. I'll do that now.

If it takes longer than 24 hours to unretire the repo, I'll change the org name back for now. Let me know if anyone has concerns about our docs being broken longer than that...

[hammer]

Okay I've got a ticket filed with GitHub support, I expect this URL only works for me but for my own reference I'll record it here: https://support.github.com/ticket/personal/0/2699614

[hammer]

Now to change pystatgen to sgkit-dev in the repo, I got hits in these files. I think a find and replace should be fine. I'm wondering if we'll need to update our repo with some of the services we use such as Mergify and PyPI?

Mergify

.mergify.yml

Markdown docs

CONTRIBUTING.md
GOVERNANCE.md
README.md

Setup

setup.cfg

Scripts

.github/scripts/test_sgkit_bgen.py
.github/scripts/test_sgkit_plink.py
.github/scripts/test_sgkit_vcf.py

Workflows

.github/workflows/benchmark.yml
.github/workflows/build.yml
.github/workflows/check-docs.yml
.github/workflows/docs.yml
.github/workflows/upstream.yml
.github/workflows/validation.yml
.github/workflows/wheels.yml
.github/workflows/windows.yml

Benchmarks

benchmarks/asv.conf.json

Docs

docs/conf.py
docs/contributing.rst
docs/how_do_i.rst
docs/user_guide.rst
docs/_static/switcher.json
docs/examples/gwas_tutorial.ipynb:
docs/examples/relatedness_tutorial.ipynb
docs/news/introducing_sgkit.md

Code

sgkit/io/vcfzarr_reader.py
sgkit/stats/pca.py

Tests

sgkit/tests/test_ld.py
sgkit/tests/test_pc_relate.py
sgkit/tests/test_pedigree.py
sgkit/tests/test_regenie.py
sgkit/tests/test_utils.py
sgkit/tests/io/plink/test_plink_reader.py
sgkit/tests/io/vcf/test_vcf_scikit_allel.py

Validation

validation/gwas/method/pc_relate/Dockerfile
validation/gwas/method/regenie/sgkit_zarr.py
validation/gwas/method/regenie_loco_regression/GlowGR_continuous.ipynb

[hammer]

I went ahead and committed the find and replace directly at d09fe24.

Upon closer inspection there's also the issue of the email we associate with the project, [email protected]. I don't own sgkit-dev.org yet, and I can't find a password for pystatgen.org in my 1Password. I'll sort this out shortly...

[hammer]

According to https://whois.domaintools.com/pystatgen.org the registration for pystatgen.org has lapsed, so it's probably a good thing we're changing org names! I can't find where I registered that domain anyways.

I went ahead and bought sgkit.dev and set up email routing to forward [email protected] to [email protected]. I can add others if there's interest. I have updated the emails in our repo.

[hammer]

Okay docs look good at https://sgkit-dev.github.io/sgkit/latest. I noticed that for some reason https://sgkit-dev.github.io/sgkit is redirecting to https://pystatgen.github.io/sgkit/latest, and I'm not quite sure where that rule is encoded. It also seems that older versions of the docs are no longer available. I believe @tomwhite might know more about how our docs interact with GitHub Pages to figure this out?

[tomwhite]

I noticed that for some reason https://sgkit-dev.github.io/sgkit is redirecting to https://pystatgen.github.io/sgkit/latest, and I'm not quite sure where that rule is encoded.

It's in the gh-pages branch: https://github.com/sgkit-dev/sgkit/blob/gh-pages/index.html

It also seems that older versions of the docs are no longer available.

The version switcher at https://sgkit-dev.github.io/sgkit/latest/ doesn't seem to be appearing, although older versions do exist, e.g. https://sgkit-dev.github.io/sgkit/0.7.0/. However, the versions that they link to are wrong because they have the
pystatgen.github.io domain. I'm not sure there's much we can do about that.

[jeromekelleher]

Awesome! Thanks for sorting this out @hammer

[jeromekelleher]

Given that we have the sgkit.dev domain, I wonder if it would be worth making our stable docs URL point there? So, rather than https://sgkit-dev.github.io/sgkit/ have something like https://sgkit.dev/sgkit/docs or something? It's a bit easier to remember, and would be easier to keep stable long term. We can still host using GitHub pages, it's effectively just a redirect. That's what we do with tskit.dev isn't it @benjeffery?

Might be nice to just do this, as we're changing docs URLs in packages etc anyway?

[hammer]

Ah yes in my reading I've seen comments about using a custom domain like that to avoid the situation we're in currently. To be honest managing DNS is not my favorite thing in the world. I will file it as an issue and come back to it a bit later?

Also they've un-retired pystatgen/sgkit thankfully so I will set up the redirects today when I have some time and close this out!

[hammer]

Okay I've resurrected pystatgen/sgkit and https://pystatgen.github.io/sgkit now redirects to https://sgkit-dev.github.io/sgkit.

One thing I did not think about: when we bring back this repository, we lose the automatic redirects that GitHub sets up from all https://github.com/pystatgen/sgkit/* URLs to https://github.com/sgkit-dev/sgkit/* URLs.

This means links like https://github.com/pystatgen/sgkit/discussions will now 404 instead of redirecting to https://github.com/sgkit-dev/sgkit/discussions.

In short: we've gained a redirect for our Pages, but lost the redirect for our repo.

If everyone is okay with this tradeoff, I'm ready to close this out.

[jeromekelleher]

I'm good with that

[hammer]

Great filed #1212 to follow up and will close this one out for now!