Fix/remove deprecated linters

[kenibrewer]

With the migration of linting functionality out of the core vscode python extension to individual extensions (https://github.com/microsoft/vscode-python/wiki/Migration-to-Python-Tools-Extensions), these linter paths are no longer needed. In addition, with the adoption of ruff for python formatting & linting, these linters may also be no longer correct in some settings.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 73.60%. Comparing base (b0a268b) to head (a059e16).

❗ Current head a059e16 differs from pull request most recent head 622601e. Consider uploading reports for the commit 622601e to get more accurate results

Additional details and impacted files

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[mashehu]

yes, makes sense to me. We should maybe add then ruff to the vs-code extension set (and the gitpod.yml), since this is our default linter for python code.

[kenibrewer]

@mashehu This is my first PR against the tools repo. I couldn't find a CONTRIUBTING.md or documentation section on the website relevant to contributing here. Can you point me towards any instructions I can view?

The specific item I'm confused about is what I need to do in terms of modifying the CHANGELOG.md file.

[mashehu]

our contributing guidelines here: https://github.com/nf-core/tools/blob/master/.github/CONTRIBUTING.md

we don't have any strict rules for the changelog (actually we have changelog.py which should have run automatically on this, but for some reason skipped this PR 👀 ). I added an entry for your changes. Thanks again for having a look into these settings and extensions!

[kenibrewer]

Thanks @mashehu ! I'm not in the habit of checking .github for the CONTRIBUTING.md file, but know to do so in the future.