Fabian Egli

Refactoring will help, too. e.g. extracting functions from classes as done in https://github.com/nf-core/tools/commit/91199fc7e7ad08b73f6e754f304ba4a88572638f.

May I ask why you want to filter the warnings? If it doesn't break a workflow, they actually let you now about potential issues. In this case once the nodes.py...

A DeprecationWarning means that a function that is used is *now* working as expected, but it is deprecated and will (probably) stop working in the future. It is basically a...

Just a small comment on the `PytestRemovedIn8Warning`. This means in pytest version 8 this warning will be an error. If the source of the warning hasn't been dealt with then...

@mahesh-panchal Can you quickly tell me how I can run the tests locally? Or how else I can access the container in which they run? I am familiar with Python...

**tl;dr**: Unsurprisingly there's still use of the old Python path handling. It is originating from pytest workflow 1.6 and will be resolved in the next release. **How to find out**:...

@mahesh-panchal This "failure" will manifest independent of Gitpod, so it might be good to title this issue something not Gitpod specific like "pytest version 7 throwing PytestRemovedIn8Warning because of py.path.local...

Yes, I tried that on Gitpod. The `--git-aware` flag in ``` PROFILE=docker pytest --tag fastqc --symlink --keep-workflow-wd --git-aware ``` solves the `UserWarning: .git dir detected`.

> OK. So once `mamba search pytest-workflow` shows 1.7.0, a pull request should be made to change: https://github.com/nf-core/tools/blob/dev/nf_core/gitpod/gitpod.Dockerfile. Thanks for looking into this @fabianegli. Have I missed any other action...

Is there a really good reason why random arguments should not fail? If not I would make it fail with a clear message what was too much.