Support for conda

[Dhananjhay]

Proposed changes

This PR adds a conditional import for the ruamel_yaml dependency. This change is necessary because the conda package manager installs the package as ruamel_yaml, while pip installs it as ruamel. This discrepancy leads to import errors when working in a conda environment. The conditional import ensures we are agnostic to the installation method, preventing the import error.

Bug Fix:
This PR resolves the import error issue that occurs when the ruamel.yaml module is installed via conda. By handling both cases, it ensures the code works in both pip and conda environments.

Checklist

• 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

[akhanf]

Looks good to me

[Dhananjhay]

It'll be nice to close this PR soon and merge the necessary changes now that snakebids v0.13.1 is available on bio-conda ecosystem (https://anaconda.org/bioconda/snakebids)

[akhanf]

What would we need to do to get the unit tests passing? Looks like pyright type checking is failing.. I'm not exactly sure why changing how its imported affects this, but if we can sort that out then we can merge in.

[Dhananjhay]

@akhanf This new commit skips type checking ruamel_yaml package coming from conda - reason why pyright tests were failing because ruamel_yaml is raumel.yaml in pypi. I was able to run the pyright tests locally without any errors!

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 94.29%. Comparing base (0f07ece) to head (4c87db2).
Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
snakebids/io/yaml.py	60.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #459      +/-   ##
==========================================
- Coverage   94.37%   94.29%   -0.09%     
==========================================
  Files          55       55              
  Lines        2222     2225       +3     
==========================================
+ Hits         2097     2098       +1     
- Misses        125      127       +2     

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[akhanf]

Looks good to me, and passing tests, so I will merge this in..

[akhanf]

hmm, looks like the tests didn't actually run in the checks (which I thought they did), so they seem to be failing in main now..