How do I have to declare a pip package in the environment.yml to fix the linting:

╭─ [✗] 1 Module Test Failed ──────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                 ╷                                                ╷                                                              │
│ Module name     │ File path                                      │ Test message                                                 │
│╶────────────────┼────────────────────────────────────────────────┼─────────────────────────────────────────────────────────────╴│
│ crabs/dbimport  │ modules/nf-core/crabs/dbimport/environment.yml │ The environment.yml of the module crabs/dbimport is not      │
│                 │                                                │ valid: {'pip': ['crabs==0.2']} is not of type 'string'.      │
│                 │                                                │ Check the entry for dependencies.                            │
│                 ╵                                                ╵                                                              │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Another issue in the env JSON schema 😛 I'll see if I can fix it

I mean it makes sense to allow pip packages, no?

Yep but I also added the requirement for version pinning

Can we go ahead with your PR? 🙂 I think it was approved, right?

yeah sorry I was busy and forgot to merge 😛 doing that right now!

I was just careful haha, thanks!

thanks for reminding me 🙂

There might still be some things that are not working: https://github.com/nf-core/modules/actions/runs/10768533070/job/29857872603?pr=6526 https://github.com/nf-core/modules/actions/runs/10768650885/job/29858215361?pr=6583

yes that's intended. You need to hardpin your versions (just use the ones from the container). This to ensure full reproducibility between conda and the containers

I copy-pasted the environment from the wave container

Yeah sorry we discussed this in the maintainers group (that's the reason it took so long to merge it in)

ok so even the pip version I guess

yes indeed 😛

When I do that and run lint locally I get: TypeError: '<' not supported between instances of 'dict' and 'str'

Can you show me what you have?

This is the env file

channels:
  - conda-forge
  - bioconda
dependencies:
  - bioconda::cutadapt=4.9
  - bioconda::muscle=3.8.31
  - bioconda::vsearch=2.28.1
  - conda-forge::wget=1.20.3
  - conda-forge::pip=24.2
  - pip:
      - crabs==0.2.0

it looks fine hmmm

That seems like an issue in tools. It seems like there is no pip support for that 😕 can you bring this up in #CE5LG7WMB ?

I also get this in, https://github.com/nf-core/modules/pull/6526. Can make it run fine in conda now, but fails in linting.