busco: Added versions, miniprot dependency

[emwjacobson]

As of version 5.6 of Busco, miniprot is added as a dependency. Added the latest point release of each minor version as well.

Maintainer is listed as @snehring

[snehring]

It looks like 5.6.0 also added a dependency for py-requests

Suggested change

	depends_on("miniprot", when="@5.6:", type="run")
	depends_on("miniprot", when="@5.6:", type="run")
	depends_on("py-requests", when="@5.6:", type="run")

I don't see any other obvious added deps, but I'm not infallible.

[snehring]

numpy's already implicit with biopython, but I'm good with being explicit. Are you sure about some of the versions you've changed? I don't think prodigal was included until 5.0., same with sepp.

[emwjacobson]

I could have sworn that I made a comment addressing the changed, but I guess I didn't actually send it... weird.

I'll be honest that I had Claude attempt to do most of the digging here, but I did my best to to verify the usages:

• py-biopython
  • Brought version down to 4:, as that's when it was included despite 4.0.0 not being a package within Spack
  • (new file in 4.0.0) https://gitlab.com/ezlab/busco/-/compare/3.0.2...4.0.0?file_path=src%2Fbusco%2FAnalysis.py#2e93f7e0e2fd4edc2763be000d7339cf2a01055c
• py-numpy
  • As you mentioned it's included implicitly through py-biopython. I dont think it hurts to make it explicit either.
• prodigal, sepp
  • I'll admit I'm not experienced with Busco, so my knowledge might be limited here, but the changelog seems to imply that prodigal support was added in 4.0.0?
  • https://gitlab.com/ezlab/busco/-/compare/3.0.2...4.0.0
  • (new file in 4.0.0, "ProdigalRunner" and "SEPPRunner" classes) https://gitlab.com/ezlab/busco/-/compare/3.0.2...4.0.0?file_path=src%2Fbusco%2FBuscoTools.py#200a2d1cfa2fb65158ca0f851c48c1054f174e7a
• bbmap
  • Seemed to be added with 5.4.0's release
  • https://gitlab.com/ezlab/busco/-/compare/5.3.2...5.4.0
  • (new file in 5.4.0) https://gitlab.com/ezlab/busco/-/compare/5.3.2...5.4.0?file_path=src%2Fbusco%2Fbusco_tools%2Fbbtools.py#61301d7e3fa29db93f2995bd68925a68fb7b173d
• miniprot
  • I bumped this down from 5.6: -> 5.5: from my original commit, as it was initially introduced in 5.5 as a beta.
  • https://gitlab.com/ezlab/busco/-/compare/5.4.7...5.5.0
  • (new file in 5.5.0) https://gitlab.com/ezlab/busco/-/compare/5.4.7...5.5.0?file_path=src%2Fbusco%2Fbusco_tools%2Fminiprot.py#b826b997d532a7f5cba04586f00fb10ce71521cf
• py-requests
  • From your original suggestion
• py-matplotlib
  • Introduced in 6.0.0
  • (new file in 6.0.0) https://gitlab.com/ezlab/busco/-/compare/5.8.3...6.0.0?file_path=src%2Fbusco%2FBuscoPlot.py#a9c13ced7c704a4cc71dd2ea83083d7b5d414299

[snehring]

You're probably correct. I was running off the commit history of the wrappers, it's possible they didn't start doing it that way until 5.0.

[snehring]

lgtm