Fix load_document_by_uri method

[GlassOfWhiskey]

This commit adjusts the load_document_by_uri method, ensuring that the LoadingOptions object used to parse the document contains the correct values for fileuri and baseuri.

[codecov]

Codecov Report

Attention: Patch coverage is 80.00000% with 2 lines in your changes missing coverage. Please review.

Project coverage is 34.04%. Comparing base (3fbfa1b) to head (5e811ce).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cwl_utils/parser/__init__.py	80.00%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #345      +/-   ##
==========================================
+ Coverage   33.85%   34.04%   +0.18%     
==========================================
  Files          30       30              
  Lines       35230    35237       +7     
  Branches     9467     9470       +3     
==========================================
+ Hits        11928    11995      +67     
+ Misses      20653    20598      -55     
+ Partials     2649     2644       -5     

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