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SciKit-Surgery / scikit-surgery

SciKit-Surgery - Compact Libraries for Surgical Navigation
http://scikit-surgery.github.io/scikit-surgery/
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Move SNAPPY libraries to github #51

Closed thompson318 closed 4 years ago

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Feb 5, 2020, 14:53

This is from one of our IPCAI reviewers. Could we move the core opensource libaries to github to make it easier for people to contribute?

"Gitlab isolates your efforts from the rest of the world. Currently, it does not even seem possible to sign up at https://weisslab.cs.ucl.ac.uk/. Hosting on github would increase visibility and willingness of people to submit bug reports or contribute. If you must host your own repository then at least host an official github mirror to avoid cropping up of unofficial forks."

@MattClarkson @ThomasDowrick @MianAhmad

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 5, 2020, 15:38

Seems a fair point.... If we want people outside UCL to use it we need to have a GitHub presence.

thompson318 commented 4 years ago

In GitLab by @MianAhmad on Feb 5, 2020, 15:58

Will we need to set pipeline with github?

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 5, 2020, 16:46

If we only mirror to GitHub then no, but if we used GitHub as the main host we'd have to fiddle around with it.

It seems it is possible to use a gitlab runner for GitHub projects https://docs.gitlab.com/ee/ci/ci_cd_for_external_repos/github_integration.html but it probably isn't a good idea to use our own servers for testing a publicly hosted project.

In either case some of the stuff we'd have to keep on our own runners for GPU support.

thompson318 commented 4 years ago

In GitLab by @MattClarkson on Feb 5, 2020, 18:01

Im Happy to move to Github. Just need to discuss testing.

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 6, 2020, 20:56

I gathered some opinion at RSLondon today about what we could do with this. The consensus seemed to be to that we could move to GitHub and still use our existing runners for testing. People could then fork the repo to make changes, and we have control over what is merged back into our branch.

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 7, 2020, 09:14

Any libraries that don't use VTK/Qt/GPU could use Travis or GitHub CI, but I think doing a mix and match approach is probably more hassle than just keeping everything on our own runners.

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Feb 11, 2020, 13:55

Sounds like we all agree in principal? We should aim to get this done before publication of the IPCAI paper. I don't think there's time to do it before I resubmit on Thursday, but hopefully I can slip it into the paper once it hits the editors.

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 11, 2020, 13:58

I looked into it and we can follow this guide to set up the GitHub<->GitLab link. I think we'll have to modify our gitlab configuration on the server, as if you try and do it now the 'CI/CD For External Repo' option isn't there.

image

thompson318 commented 4 years ago

In GitLab by @MattClarkson on Feb 11, 2020, 13:59

hold on. Is it possible we'd need the enterprise version? i.e. pay for it. We only have the community free version? Or did I miss something?

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Feb 11, 2020, 14:10

er..... yes. It seems you're right.

thompson318 commented 4 years ago

In GitLab by @MianAhmad on Mar 5, 2020, 10:22

I wonder if github education program is equivalent to enterprise github. I am using it to host many private repos then the free tier offer. It is offered for two years and students and staff has to fill the form on this page https://education.github.com/discount_requests/new.

The following image shows that I am using it since 2017.
Screenshot_2020-03-05_at_10.16.56

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Mar 16, 2020, 10:28

I want to get this sorted before the Snappy IPCAI paper get's published, so that the links in it are right. I've just gone through the paper and the only link to weisslab is the wiki, (https://weisslab.cs.ucl.ac.uk/WEISS/PlatformManagement/SNAPPY). So my main priority would be to migrate the wiki to github. We could use UCL's github group, so something like https://github.com/UCL/SNAPPY. That wouldn't have any issues with CI testing yet. Does that sound OK?

thompson318 commented 4 years ago

In GitLab by @MattClarkson on Mar 16, 2020, 10:32

yep.... or the alternative UCL/scikit-surgery?

Can you remind me what we decided about renaming?

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Mar 16, 2020, 10:37

I don't think we came to a decision on renaming. I didn't think scikit-surgery was catchy enough, though it is more searchable. From a practical point of view changing the name would be a substantial edit of the paper, as opposed to changing a link.

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Mar 16, 2020, 10:52

True that scikit-surgery isn't super catchy, but if we're agreed that we shouldn't use SNAPPY too much publically because it clashes with other names, then we should probably change it sooner rather than later. Given that we haven't thought of any better names in the 2ish years we've been working on it, then I'd say we're unlikely to think of anything else.

Shall we take a vote on it?

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Mar 16, 2020, 11:08

Let me try doing a find and replace on the paper, I'll just change SNAPPY to to scikit-surgery and see what it does. I will try it out tomorrow. We should move discussion on renaming back to issue #50

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Apr 3, 2020, 11:33

UCL appears to have a Azure account, so could use that for CI from github rather than travis or appveyor?

thompson318 commented 4 years ago

In GitLab by @MattClarkson on Apr 3, 2020, 11:38

we can certainly host on github.com/UCL/

but Im not sure what Azure provides ... is it Windows/Linux/Mac. The only reason Im suggesting Travis/Appveyor, is Travis=Linux/Mac and Appveyor=Windows, but I think travis now has all 3.

@ThomasDowrick - can you clarify?

thompson318 commented 4 years ago

In GitLab by @StephenThompson on Apr 3, 2020, 11:45

I googled "tox azure" and got this. It implies it covers our target platforms and can be set up to use tox more easily than travis at least, but I really don't know.

https://github.com/tox-dev/azure-pipelines-template

thompson318 commented 4 years ago

In GitLab by @MattClarkson on Apr 3, 2020, 11:46

I don't know if @ThomasDowrick is available (Childcare), but you could as on RITS slack channel. Jonathan Cooper would know.

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Apr 3, 2020, 12:28

I haven't used the Azure stuff much - I think asking RITS might be a good idea as I know they have used it a bit and can give some feedback on it (Some of it wasn't great if I recall...)

thompson318 commented 4 years ago

In GitLab by @ThomasDowrick on Apr 3, 2020, 12:30

I think we can @DavidPerez-Suarez @JonathanCooper - have either of you used Azure Pipelines for CI before?

In brief, we're moving some of our repos from here to GitHub and are thinking about where to host CI. Since UCL has an Azure service/account, there might be some additional features we get?

thompson318 commented 4 years ago

In GitLab by @JonathanCooper on Apr 6, 2020, 09:28

Mose was looking into CI options along with David, so I'll defer to them!

thompson318 commented 4 years ago

In GitLab by @MianAhmad on Apr 6, 2020, 10:19

So I did some search on weekend and most of the cloud dont provide Mac VM because according to the Apple license Mac OS can only be installed on Apple hardware. Since cloud uses all VM's therefore cant give you apple. (May be some illegal ways are available to install apple on VM but not legal).

Some clouds put a mac hardware to provide mac OS to customers but they are very expensive.

thompson318 commented 4 years ago

I've moved the wiki from https://weisslab.cs.ucl.ac.uk/WEISS/PlatformManagement/SNAPPY to https://github.com/UCL/scikit-surgery/wiki The platform related issues have moved with it.

I've also moved the minimal code from https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/SNAPPY/scikit-surgery to https://github.com/UCL/scikit-surgery/ so now we have code and wiki in the same place. The second move involved leaving the 4 raised issues on scikit-surgery behind. but these were not very interesting and in any case remain on weisslab for anyone interested.

tdowrick commented 4 years ago

Moving scikit-surgerycore

tdowrick commented 4 years ago

@thompson318 @MattClarkson should we do something like the above for each repo when we move it? Any other checkboxes to add?

thompson318 commented 4 years ago

Looks reasonable, thanks. Could add one to check that read the docs is working, and maybe that all relevant links have been changed to github.

tdowrick commented 4 years ago

Moving scikit-surgeryimage

~I have set up GitHub Actions, but it isn't working on Linux yet.~

tdowrick commented 4 years ago

scikit-surgerynditracker

tdowrick commented 4 years ago

scikit-surgeryarucotracker

thompson318 commented 4 years ago

scikit-surgerybard

thompson318 commented 4 years ago

snappysonic

thompson318 commented 4 years ago

sciikit-surgeryvtk

tdowrick commented 4 years ago

I can look at the CI for vtk - can you make me an admin on the repo?

thompson318 commented 4 years ago

I'm just transfering files/issues. I think it will take about two hours.

thompson318 commented 4 years ago

OK, you should have admin access now.

tdowrick commented 4 years ago

Thanks. CI definitely more fiddly with this library, but I'll keep working on it.

JonathanCooper commented 4 years ago

Hey folks! Just wanted to flag to you that you are tagging the wrong Jonathan Cooper!

tdowrick commented 4 years ago

scikit-surgeryspeech

tdowrick commented 4 years ago

For reference, this is the tool we've been using to transfer issues between Gitlab/Github. Runs relateively slowly (can take several hours) but is simple enough to run.

tdowrick commented 4 years ago

scikit-surgerytf

tdowrick commented 4 years ago

@thompson318 What has been your process for removing project from weisslab? Are you archiving them or just deleting?

thompson318 commented 4 years ago

I haven't been doing either yet, I just changed the readme to say "XXX had moved to github please visit ". Then disabling everything in the settings. Have a look at surgerycore on weisslab for an example. So if someone is looking for it on weisslab they will still be able to find it and get redirected. I didn't want them to just disappear from weisslab straight away.

tdowrick commented 4 years ago

Thanks - I'll do the same.

tdowrick commented 4 years ago

scikit-surgerybk

tdowrick commented 4 years ago

I have finished surgeryvtk and surgerytf. In both cases there were issues with getting the Mac CI to run correctly. We decided it was better to skip these, as Linux/Windows CI working and we have been able to test locally on Mac, rather than spend (lots of) time trying to fix the problem.

tdowrick commented 4 years ago

scikit-surgeryutils

MattClarkson commented 4 years ago

@thompson318 - most of this issue is done? close?

thompson318 commented 4 years ago

There's a couple of things to do on snappysonic first. (see list above)