Mark conda-skeleton as pending deprecation

[jsmolic]

conda skeleton has not been updated in recent years and does not work reliably anymore due to bugs in the codebase (e.g. #1, #2, #3, #4) Additionally, more modern and faster alternatives such as grayskull and rattler-build generate-recipe are available.

This PR marks conda skeleton as pending deprecation. conda build will still provide skeleton command until 27.9 release, when it is scheduled to be removed. Users are encouraged to use grayskull instead of conda skeleton.

Changes in the PR:

• Mark conda-skeleton and all related modules as pending deprecation
• Update the code in few places to use inspect.signature which works better with the decorators.
• Update the test suite to expect the deprecation warning

Description

Checklist - did you ...

• Add a file to the news directory (using the template) for the next release's release notes?
• Add / update necessary tests?
• Add / update outdated documentation?

[codspeed-hq]

Merging this PR will not alter performance

✅ 5 untouched benchmarks

---

_{Comparing jsmolic:deprecate-skeleton (b9adb27) with main (ea47346)¹}

Footnotes

1. No successful run was found on main (1be6657) during the generation of this report, so ea47346 was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩

[danyeaw]

Hey @jsmolic, thanks for working on this, this looks really good! I noticed that if users do call skeleton from the CLI they will get multiple layers of deprecations:

1. CLI module
2. api.skeletonize
3. Each API backend

What if we:

1. Remove @deprecated from each skeletonize function
2. Add deprecated.module(...) at the top of each skeleton backend file
3. Keep one CLI-level decorator on main_skeleton.execute

I think that is the pattern that #4251 used.

Also, should we add a warning on the skeleton tutorial and command docs that it is pending deprecation and shouldn't be used for new conda recipes?

[danyeaw]

Since grayskull only provides PyPI and CRAN support, maybe we should soften the wording for the other backends?

[isuruf]

Conda skeleton is the most complete CRAN recipe generator there is. I'm against deprecating this feature.

[jezdez]

@isuruf Would you be interested in maintaining it (e.g. outside of conda-build)? Do you know who would? Would porting it to grayskull be an enabler or create stop energy?

[wolfv]

@isuruf any pointers as to what is missing from rattler-build generate-recipe cran foobar? We'd be happy to implement the missing features!!

[isuruf]

@wolfv, look at https://github.com/conda-forge/r-gmp-feedstock/blob/main/recipe/meta.yaml for example and compare that with the recipe you get from rattler-build. Deps are wrong. License files is missing. cross-r-base is missing. R_ARGS env variable passing to R CMD is missing. rpaths are missing.

[isuruf]

@isuruf Would you be interested in maintaining it (e.g. outside of conda-build)? Do you know who would? Would porting it to grayskull be an enabler or create stop energy?

Porting it to grayskull would be ideal. Might be a good GSoC project.

[dbast]

If somebody ports the R skeleton part, also this cleanup / skeleton-post-process code could be incorporated https://github.com/bgruening/conda_r_skeleton_helper

[jaimergp]

Conda skeleton is the most complete CRAN recipe generator there is.

That doesn't mean is fully functional though. R maintainers often comment on needing https://github.com/bgruening/conda_r_skeleton_helper on top (references: #general > R staged recipes reviews @ 💬, https://github.com/conda-forge/staged-recipes/blob/cedb79676c03427ee863d404581eed31d9710685/.github/ISSUE_TEMPLATE/package-request.yml?plain=1#L19, https://github.com/conda-forge/conda-forge.github.io/blob/67fc9430a8c64445244769e0ee8efbd9d46c3ac4/docs/maintainer/adding_pkgs.mdx?plain=1#L49-L51).

Even if this feature is deprecated, an older conda-build version can be installed (e.g. pixi exec --with conda-build=3.27 conda skeleton cran ...) since this is mostly used as a CLI.

[jaimergp]

@pb01ka, I think you were also looking into this at some point, weren't you?

[pb01ka]

@pb01ka, I think you were also looking into this at some point, weren't you?

AFAICT, I wasn't specifically looking into this topic (i.e., Mark conda-skeleton as pending deprecation). I did my research on the broader topic of comparing different tools for R recipe generation. The issue is open at prefix-dev/rattler-build#2563

Refer the first point,

• conda skeleton cran - broken in all recent conda-build releases; requires a downgrade to v3.27.0; users are being directed away from it; refer - Monitoring grayskull support for R package recipes bgruening/conda_r_skeleton_helper#58 and specifically, Monitoring grayskull support for R package recipes bgruening/conda_r_skeleton_helper#58 (comment)

Also the response received at prefix-dev/rattler-build#2563 (comment), prefix-dev/rattler-build#2563 (comment) and prefix-dev/rattler-build#2563 (comment). Quoting one specific response,

Yes, that's a misinterpretation. 99.9% of R packages are in CRAN so R packages in github is a niche problem. conda skeleton cran is still the best way to generate R recipes.

[isuruf]

That doesn't mean is fully functional though. R maintainers often comment on needing https://github.com/bgruening/conda_r_skeleton_helper on top

Sure, but we can't do that for rattler-build or grayskull.

[isuruf]

Refer the first point,
conda skeleton cran - broken in all recent conda-build releases

As I said in the other issue, this is a non-issue (at least for 99.9% of cases). Please stop spreading FUD.

[pb01ka]

As I said in the other issue, this is a non-issue (at least for 99.9% of cases). Please stop spreading FUD.

Yes. I have linked your responses as well in my comment above. The issue description in rattler-build also quotes your correction.

Please let me know if I missed anything.