Generate Releases and version more frequently

[mfansler]

I am interested in packaging ArchR as a Conda package, which could help alleviate installation issues. However, it appears master has had minor patching since the last Release. Also, dev has had many changes and end-users do appear to use this. It would be helpful to capture fixes and features in Releases. Note that one has the ability to mark Releases as beta, in case one wishes to signal uncertainty about their stability.

[immanuelazn]

Hi Mervin,

I've seen your recent work with respect to getting a conda package built for ArchR, and am really greatful for that work. I am currently doing some final checks with making sure that the brunt of the function reference, and vignettes work within my containerized environment.

Once that is done, I will update 1.0.2 to reflect the current state of master, and 1.0.3 to reflect the current state of dev as a pre-release.

Best,

Immanuel

[immanuelazn]

Hi Mervin, sorry for the late reply! Lots of other things coming up on my end and I do apologize.
1.0.3 will likely be held with respect to the current environment requirements in 1.0.2. Contradicting the Issue auto-reply, I would recommend building for R 4.1.1 and Bioconductor 3.14 instead as the vignettes were built using them.

I would like to also caveat that ArchR has some heavily suggested dependencies that are not listed within the DESCRIPTION file (see this file). I noticed that your conda build does not currently have them listed in your meta.yaml. Is there any way of getting these packages incorporated as well?

I will add a sub-release to 1.0.3 to support 4.4.1 and bioconductor 3.19 once the deprecated APIs are updated.

Thanks again for putting in the effort here. Completely acknowledge it is a mess and we're trying to fix it ASAP on our end too!

[mfansler]

"...I would recommend building for R 4.1.1 and Bioconductor 3.14 instead as the vignettes were built using them."

R packages on Bioconda/Conda Forge don't constrain further than x.x for R builds, so R 4.1.3 builds will run on all v4.1. Other than R's warning about this, I never seen a concrete report where a package we built had an issue working across R patches. We can adjust the constraints to Bioconductor 3.14.

Personally, I'd like to add some unit testing. Rather than trusting that specifying versions is functional, it's better practice to empirically test API calls that are essential. At some point I will try adding something to the Conda recipe, but may also be worth considering adding here, especially as you're refactoring for an R 4.4-compatible version.

"...ArchR has some heavily suggested dependencies that are not listed within the DESCRIPTION file..."

We could do something like issue a r-archr-full or r-archr-recommended metapackage that installs r-archr plus additional suggested dependencies. A major audience for Conda Forge/Bioconda are workflow engineers who prefer minimal install options to run lightweight non-interactive pipelines. For that reason, it's generally better that the minimal install is the default package (r-archr) and any bundle(s) with extra features be something users must deliberately specify.

[immanuelazn]

Having a metapackage would seem like a good idea once I get this work done!

Just to be clear, there are a decent chunk of unit tests that are added in 1.0.3, and can be tested using your typical devtools workflow. I understand it is suboptimal, but currently what I'm doing for ArchR's "test coverage" as of right now is just making sure the vignettes, and the unit tests are able to run.

[mfansler]

I see there is a release! 🎉

For reference, here's the corresponding Bioconda PR. Any suggestion on what R version I should be aiming at? Right now trying R 4.3, which is our latest available.

[immanuelazn]

Thanks for being on top of this and sorry for the delayed response! I was thinking to keeping 1.0.3 to be working with 4.1, and releasing a sub-version with some fixes to dependencies. One of them being the one you pointed out with ggplot legends.

On my end, the fixes are working on both 4.3 and 4.4. I'll ping this discussion board when they're merged in and I create a new release for that.