Update primerforge to 1.2.5

[BiocondaBot]

Update primerforge: 1.1.1 → 1.2.5

Info	Link or Description
Recipe	recipes/primerforge (click to view/edit other files)
Summary	primerForge: software to identify primers that can be used to distinguish genomes
Home	https://github.com/dr-joe-wirth/primerForge
Releases	https://github.com/dr-joe-wirth/primerForge/tags
Recipe Maintainer(s)	@dr-joe-wirth
Author	@dr-joe-wirth

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This pull request was automatically generated (see docs).

[dr-joe-wirth]

not sure how to fix this. in my environment.yml file, it did not work when I specified it as @martin-g did. It only worked when I allowed pip to install the package.

i'd gladly change it, but i'm unsure how to track down and resolve the conflict.

[martin-g]

Which version has been installed by pip ? Maybe we can try with exact version instead of a range ?!

[dr-joe-wirth]

Which version has been installed by pip ? Maybe we can try with exact version instead of a range ?!

version 2.1.1. So i had thought that specfiying khmer >=2.1 would be sufficient.

https://pypi.org/project/khmer/

just checked the bioconda page for khmer...it appears that 2.1.1 is not a version there.

looks like maybe the problem is the version of python it is dependent on:

depends python: >=3.6,<3.7.0a0

primerforge would need at least v3.9+ since it uses typehinting which wasn't formally supported until 3.9. I would expect to get a lot of errors saying like "cannot subset type tuple" because a function's signature line had something like def f(n:int) -> tuple[str,int]:. I am not entirely sure what version of python allows this, but i know with certainty that 3.7 would complain.

[dr-joe-wirth]

would including a line like pip install khmer in a build.sh file be compliant with bioconda syntax? or is this still a bad practice?

[rpetit3]

I think we have a few options

1. Try building khmer 2.1.1 with latest python pinnings
2. try rebuilding khmer 2.1 with latest python pinnings
3. (do not recommend) pingeon-hole primerforge to only work with python 3.6 (which might not even be supported by primerforge)

[rpetit3]

would including a line like pip install khmer in a build.sh file be compliant with bioconda syntax? or is this still a bad practice?

You are correct, this wouldn't be allowed