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tidyomics / tidyomicsWorkshop

Tidy genomic and transcriptomic analyses
https://tidyomics.github.io/tidyomicsWorkshop/
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making repo event/workshop specific + versioning #2

Open stemangiola opened 1 year ago

stemangiola commented 1 year ago

@mikelove I usually make the repo and package name specific for a conference for reproducibility's sake. What do you think? Would you prefer a unique repo that evolves through the workshops we give?

Also, for the versioning, do you have any preference?

For example, tidytranscriptomics increments Y in every workshop X.Y.Z, which would be 0.16.0. But of course, we should find a common one.

mikelove commented 1 year ago

I was thinking it’s less work to use same repo and make git tags and GitHub releases linked to tags.

No pref for version number, we can go with your paradigm.

stemangiola commented 1 year ago

I was thinking it’s less work to use same repo and make git tags and GitHub releases linked to tags.

It sounds scalable, and I like the idea. But what about when workshops need different material, how the stable version of the workshop would look like?

Should we modularise in vignettes and propose different vignette combinations for different workshops? Should we use branches and/or tags to modularise the development?

No pref for version number, we can go with your paradigm.

If you really don't have any paradigm going on, we could start from 0.16.0, but I have not strong feelings about it

Btw I just wrapped up teaching tidySE, tidybulk, plyranges and nullranges at CSAMA. Students loved it!

Amazing, having a vignette about the common use would be awesome. Actually the most interesting thing!

stemangiola commented 1 year ago

Also, a little thought should be given to: if we want this repository to be the only workshop repo and last a long time with this name so as not to break any back compatibility with old workshop versions, should we name it tidyomic... in the perspective that the ecosystem and our team will grow.

Again not a strong feeling, just some brainstorming that is better to do now rather than later ;)

mikelove commented 1 year ago

I like branching for different flavors, but I guess as they diverge substantially make a new repo. But avoiding year/conference name in repo name.

I had a breakthrough in conceiving of the peak-gene correlation problem for large datasets. I’ll work it up.

mikelove commented 1 year ago

Also, I’m thinking of moving tidy-ranges-tutorials over to this org. Does that make sense?

mikelove commented 1 year ago

Sure, I’m happy with a catchy name!

Should the org name have the hyphen or no?

stemangiola commented 1 year ago

Sure, I’m happy with a catchy name! Should the org name have the hyphen or no?

I was referring to the repo name, not the org name. But for the workshop repo name, you mentioned that if many things change (workshop on omics rather than genome transcriptome), we can create a new repo. To which I agree with.

For the org name, I like tidyomics.. but as I think the tidyomics repo will be born soon ;) it is a bit backward to have

tidy-omics/tidyomics as org/repo name.

stemangiola commented 1 year ago

Also, I’m thinking of moving tidy-ranges-tutorials over to this org. Does that make sense?

Another thing that would be cool is to move the tidytranscriptomics blog we have, which can become (be renamed to) tidy omics blog.

https://stemangiola.github.io/tidytranscriptomics/

I don't have the throughput alone to maintain. And a blog, I think, is a good meeting place for the community.

mikelove commented 1 year ago

Would you like to rename the org to "tidybiology" (no hypen)?

And then we have:

tidybiology/TidyGenomicsTranscriptomicsWorkshop tidybiology/tidyomics (the blog) tidybiology/tidy-ranges-tutorial

The first one is a bit long and cumbersome, any better suggestion?

It has to be CamelCase right? Bc it is a package name?

stemangiola commented 1 year ago

Would you like to rename the org to "tidybiology" (no hypen)?

sure. If you google tidy-biology, or tidybiology, this is a terms that has been used for a while with a heterogeneous focus, not sure what you think. Have a look.

The first one is a bit long and cumbersome, any better suggestion?

How about tidyomicsWorkshop? With the perspective that we will generalise it in the future? too confusing?

mikelove commented 1 year ago

I like tidyomicsWorkshop for this repo, as it is more general. We can branch it off when needed, but this would be like the general interest introduction workshop that can be re-used in different contexts.

I think it's ok to have an org name that is already used as a repo name elsewhere, I see there is a Duke professor teaching a class by this name. I think it's fair game to have the organization by this name, as we are open to contributions. We are trying to put together a lot of disparate work enabling use of tidyverse packages and coding paradigm for applications in biology. Tidy + biology seem then an obvious name for the effort. And there is already tidyomics the organization, so we can't use that.

If you're good with this, I will change org + repo to: tidybiology/tidyomicsWorkshop

stemangiola commented 1 year ago

Last question/thought: will we be likely to include any biology that is not "omics"? If so what could an example ebe?

stemangiola commented 1 year ago

Anyway, I am happy to change to tidybiology

mikelove commented 1 year ago

The two that come to mind that are not really 'omics are: flow cytometry and imaging.

mikelove commented 1 year ago

I'd also propose, maybe right before the BioC meeting, to change the Bioc Slack channel to #tidybiology and invite others to join this effort. Thoughts?

mikelove commented 1 year ago

Ok, I made the change to org and repo name, now i will update the GH actions stuff.

stemangiola commented 1 year ago

I'd also propose, maybe right before the BioC meeting, to change the Bioc Slack channel to #tidybiology and invite others to join this effort. Thoughts?

I also like the biocviews tidybiology

Now you are making me think, if tidyomics does not include cytometry, and we want to be inclusive, does make sense to push tidyomics at all (e.g. workshop, mother repo, blog)?

sorry to go into brainstorming mode again? but better to discuss these thing earlier rather than later

tidybiology, tidyomics, tidybioverse

mikelove commented 1 year ago

I think it's ok for this repo (but happy to discuss). I was thinking this workshop would be mostly written by us + our collaborators/teams, on the topic of combining tidytranscriptomics packages, enhanced with plyranges and/or nullranges routines. If we in the future plan for a longer set of material, also including cytometry and/or imaging, we can use a new workshop name.