remove the leading ./ from paths created in snakebids

[akhanf]

Proposed changes

This removes the leading ./ from the default root path used with snakebids apps, since this now results in a CRITICAL warning in snakemake

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!

• Changes have been tested to ensure that fix is effective or that a feature works.
• Changes pass the unit tests
• I have included necessary documentation or comments (as necessary)
• Any dependent changes have been merged and published

Notes

All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.37%. Comparing base (0f07ece) to head (85b520c).
Report is 6 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #462   +/-   ##
=======================================
  Coverage   94.37%   94.37%           
=======================================
  Files          55       55           
  Lines        2222     2222           
=======================================
  Hits         2097     2097           
  Misses        125      125           

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

[akhanf]

OK I had to update some tests, but things are passing now.
Also had a new test error in poetry check --lock appear, wondering if it is related to the new poetry 2.0.0 release in the last week? I've disabled that check for the time being..

[pvandyken]

Once I get time again to actually get some updates on this, I'd like to swap poetry for uv anyway, so I'm fine with temporary degredation. I'll merge