Bioconda build on OSx after recent changes

[raufs]

Hi Martin,

Bioconda recently had a major update which caused some recipes to fail to build, including pyrodigal, but only on OSx: https://github.com/bioconda/bioconda-recipes/wiki/build-failures

Just want to report it here in case you had not seen it.

Thank you again for all the awesome Python bindings and software! Rauf

[althonos]

Thanks for the heads-up!

It looks like there is an issue with the cpu-features compilation, which is okay, given that I was planning to replace it by the archspec package for convenience. I'll make the necessary changes and hopefully the new version builds without issue.

[raufs]

Thank you Martin for updating pyrodigal to the next version so quickly! I saw you ran into the same issue I have been seeing in bioconda for zol with build failure on OSx still occurring. I was secretly hoping by resolving pyrodigal's built it might resolve the issue for zol as well, which uses it as a key dependency, but definitely seems independent and related to mambabuild as suggested by someone on bioconda issues.

[raufs]

Hi Martin, looks like I was able to get the checks to pass and build on OSx after changing python listing in the requirements - run subsection to python >=3. Not sure why this solved the issue exactly and because artifacts are not building/fetching currently its difficult to test if there are any problems - I think it just means that python3 is required to be present on the target system.

EDIT: To clarify, I updated zol - not pyrodigal - but I took a look at the pyrodigal recipe and think it might work there as well.

[althonos]

Hi @raufs , Thanks for the hint :smile: I tried updating the run section as well but I'm still hitting issues in the build process. I'll try to force python >=3 in all stages of the recipe to see if it resolves something.

[raufs]

Something odd is going on with bioconda utils I think, now getting the same error except on linux checks and the last successful commit for zol, after adding the >3, didn't actually get registered.

:man_shrugging: hopefully gets resolved

[althonos]

Yes this is annoying, and since it impacts a lot of people I guess the Bioconda people will have to resolve it at some point but we can only wait for now :unamused: If this takes too long I'll create a recipe on conda-forge.

[althonos]

Looks like it's fixed :)