Update primerforge to 1.5.1

[BiocondaBot]

Update primerforge: 1.1.1 → 1.5.1

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

[dr-joe-wirth]

@rpetit3 thanks for the input. Here are my thoughts.

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)

TL;DR

Option 3 is probably a bad choice; where can I find resources for doing options 1 or 2?

full response

I think option 1 is the best option, but khmer 2.1.1 does not have a conda recipe. So maybe that means option 2 is better? To be honest, I don't really know how we would go about rebuilding a recipe with the latest python pinnings. Is there a reference available that I could use to figure this out?

Option 3 is not good because I know for sure that the inclusion of type hinting without importing typing is not supported below python 3.9. If I had said like from typing import List, Dict, Tuple then it may have been compatible with lower versions. Obviously I would prefer not to rewrite the entire code base just to make a functioning conda installation especially when my pip installer works just fine.

As a note, khmer does not work with python 3.12 because SafeConfigParser was replaced with ConfigParser. But the pip installation does work with python >=3,9,<3.12.

additional note

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

Ok thanks for clearing that up. I had started working on this as a solution (this is what I was trying to do in my build.sh file, but I will discard this work and move things back to how they were.

[dr-joe-wirth]

this recipe should work once the recipe for khmer is working with higher versions of python3. I am trying to do this in PR #49359

[dr-joe-wirth]

updated the version, but this recipe is still broken since the recipe for khmer is incompatible with the python3 versions required for primerForge

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces several updates to the meta.yaml file for the primerForge package. The version number is increased from 1.1.1 to 1.5.1, and the source URL is updated to reflect the new version's tarball. The SHA256 checksum is also modified to correspond with the new version's archive. In the requirements section, the Python version constraints have been adjusted from >=3.11 to >=3.9,<3.12, thus expanding the range of compatible Python versions. Additionally, three new dependencies have been added: ispcr, khmer >=2.1.1, and pyahocorasick. The existing dependencies, which include biopython, numpy, and primer3-py, remain unchanged. These modifications primarily focus on version updates, the inclusion of new dependencies, and adjustments to the Python version compatibility.

Possibly related PRs

• Update meta.yaml for spec2vec #49857: Updates the meta.yaml file for the spec2vec package, including changes to versioning and dependencies.
• Update PhyloAcc recipe #51090: Modifies the meta.yaml file for the PhyloAcc package to change the Python version compatibility, aligning with the adjustments made in the primerForge package.
• Update meta.yaml, VITAP v.1.7 #51220: Updates the meta.yaml file for the vitap package with a new version and changes to dependencies, reflecting a similar pattern of updates as seen in the primerForge package.

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 459b4a4 and 02a31d1.

📒 Files selected for processing (1)

• recipes/primerforge/meta.yaml (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/primerforge/meta.yaml

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