Um, conda is failing in CI. Tried saying the module does not support conda. What to do? https://github.com/nf-core/modules/pull/10925

add to the skip list

How do I do this

but since when does this tool not support conda?

It should

yeah I would check that before trying to kill conda

I tried updating the bioconda recipe, but that didn't help

what about

pkg_resources

drama?

Actually it did help, but now there is another issue, and the tool isn't maintained

the skip list: -> https://github.com/nf-core/modules/blob/master/.github/skip_nf_test.json

indeed no commits in 3 years: https://github.com/linsalrob/py_fasta_validator

😞

Who's up to take over?

Fork?

you want to join in on the fun?

Going to try update the bioconda recipe again with

--no-build-isolation

in the meantime, but would be good to get the package off pkg_resources

I've encountered a lot this issue with other process. The simplest way is to pin in the environment the python and setuptools version like for biohansel:

---
# yaml-language-server: $schema=<https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json>
channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::bio_hansel=2.6.1
  - conda-forge::numpy=1.20.1
  - conda-forge::pandas=1.2.3
  - conda-forge::python=3.9.2
  - conda-forge::setuptools=49.6

That is going to break SO MANY THINGS

What does it break ?

For what’s its worth, I had to write a specialised tool for this purpose in Go: https://github.com/GallVp/fa-lint We should probably deprecate fastavalidator and add it to the Conda skip list as it is not being maintained by the developer.

I did see this tool, looks great. I haven't approved/merged fastavalidator yet, perhaps you would like to write a small advert for fa-lint on the PR?

@Cameron Lloyd I have added a deprecation message and a conda CI exclusion: https://github.com/nf-core/modules/pull/11012 The original commit is also included.