environment-schema.json does not accept some needed scenarios

[toniher]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Current environment-schema.json checking environment.yml for Conda packages is not accepting certain situations that are needed, for example for GPU-enabled wheels. I imagine it was not noticed before because the pre-commit hook is checking only environment.yml , but not environment.gpu.yml

The file where I noticed it:

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
dependencies:
  - python=3.11
  - pip
  - pip:
      - "https://github.com/abetlen/llama-cpp-python/releases/download/v0.3.23/llama_cpp_python-0.3.23-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"

Equivalent GPU one:

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
dependencies:
  - python=3.11
  - pip
  - "conda-forge::cuda-version=12.4"
  - "conda-forge::cuda-runtime"
  - pip:
      - "https://github.com/abetlen/llama-cpp-python/releases/download/v0.3.23-cu124/llama_cpp_python-0.3.23-py3-none-linux_x86_64.whl"

Command used and terminal output

check-jsonschema --schemafile ../../../environment-schema.json environment.yml
check-jsonschema --schemafile ../../../environment-schema.json environment.gpu.yml

Relevant files

No response

System information

No response

[toniher]

Hi @mashehu I have a PR for also accepting these two cases I describe. I can provide it if needed. However, I don't know if you might be considering more potential scenarios.

[mashehu]

thanks! please make a PR, than we can discuss around that.