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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
231 stars 32 forks source link

Change organization and project name expansion #1167

Closed hammer closed 6 months ago

hammer commented 8 months ago

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 commented 8 months ago

Things that might break:

benjeffery commented 8 months ago

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

Doesn't mention pages URLs redirecting

jeromekelleher commented 8 months ago

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

hammer commented 6 months ago

Also relevant

hammer commented 6 months ago

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

hammer commented 6 months ago

...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:

Screenshot 2024-03-28 at 9 06 00 AM

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 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

I went ahead and committed the find and replace directly at https://github.com/sgkit-dev/sgkit/commit/d09fe246fe37fa7e6a6381e4307b8ed24e5c8f6b.

Upon closer inspection there's also the issue of the email we associate with the project, project@pystatgen.org. 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 commented 6 months ago

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 project@sgkit.dev to jeff.hammerbacher@gmail.com. I can add others if there's interest. I have updated the emails in our repo.

hammer commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

Awesome! Thanks for sorting this out @hammer

jeromekelleher commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

I'm good with that

hammer commented 6 months ago

Great filed https://github.com/sgkit-dev/sgkit/issues/1212 to follow up and will close this one out for now!