Fix #354: Remove empty RDF Description nodes after unsetModifiedDates

[dyrpsf]

Description

Updated the SBase::reconstructRDFAnnotation() cleanup logic in src/sbml/SBase.cpp. Added a routine at the end of the function to iterate backwards through the RDF node's children and delete any <rdf:Description> elements that have zero inner children. If the parent <rdf:RDF> block becomes completely empty as a result, it is also safely removed.
I also added a unit test (test_SBase_unsetModifiedDates_issue354) in src/sbml/test/TestSBase.cpp to explicitly verify that no detritus is left behind when dates are removed.

Motivation and Context

Previously, calling unsetModifiedDates would successfully remove the date nodes but leave behind empty <rdf:Description rdf:about="#foo"/> elements in the XML tree. Over multiple cycles, these empty tags would accumulate as detritus in the model's annotation. This change ensures the XML tree remains clean after node removal.
Fixes #354

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Change in documentation

Checklist:

• I have updated all documentation necessary.
• I have checked spelling in (new) comments.

Testing

• Testing is done automatically and codecov shows test coverage
• This cannot be tested automatically ```

[fbergmann]

@dyrpsf thank you for this

[dyrpsf]

Hi @fbergmann, thanks for the approval!

I just pushed a quick update to fix the CI build failures. There was a syntax error in the unit test I added (mistakenly calling the date methods on Model instead of ModelHistory), which caused the test suite to fail compilation.

The tests should compile cleanly and pass now. Let me know if anything else is needed before this can be merged!

[dyrpsf]

Hi @fbergmann,

Apologies for the back-and-forth on the CI checks! I just pushed another small commit to fix the compilation error in the new test suite.

I had mistakenly tried to call unsetModifiedDates() directly on the ModelHistory object in the test, which caused the build matrix to fail. I've corrected it to call the method properly on the Model object (via SBase), while ensuring the memory cleanups (delete h; and delete d;) remain intact.

The extensive CMake builds should compile cleanly and pass this time. Thanks again for your patience and the approval!