Fix serializing optional Collection attributes

[gadomski]

Description:

The underlying problem is that, when creating a Collection from a dict, some values are pulled out to Collection-level attributes, e.g.

pystac/pystac/collection.py

Lines 644 to 646 in 114b1a1

	assets: Optional[Dict[str, Any]] = {
	k: Asset.from_dict(v) for k, v in d.get("assets", {}).items()
	}

However, those values are not removed from the original dictionary d, and that original dictionary is used to populate extra_fields:

pystac/pystac/collection.py

Line 657 in 114b1a1

extra_fields=d,

This means that the assets attribute of a Collection isn't the only place where assets (and other attributes) are stored, and in fact when a collection is turned back into a dictionary, those assets are re-populated from extra_fields:

pystac/pystac/catalog.py

Lines 516 to 517 in 114b1a1

	for key in self.extra_fields:
	d[key] = self.extra_fields[key]

This fixes the issue by popping these optional attributes out of the source dictionary, and by checking for these attributes' presence in a better way (i.e. before we were checking if lists were not None 😞).

PR Checklist:

• Code is formatted (run pre-commit run --all-files)
• Tests pass (run scripts/test)
• Documentation has been updated to reflect changes, if applicable
• This PR maintains or improves overall codebase code coverage.
• Changes are added to the CHANGELOG. See the docs for information about adding to the changelog.

[codecov-commenter]

Codecov Report

Base: 94.34% // Head: 94.37% // Increases project coverage by +0.02% 🎉

Coverage data is based on head (80aa478) compared to base (e8da685).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #916      +/-   ##
==========================================
+ Coverage   94.34%   94.37%   +0.02%     
==========================================
  Files          83       83              
  Lines       11989    12015      +26     
  Branches     1134     1136       +2     
==========================================
+ Hits        11311    11339      +28     
  Misses        496      496              
+ Partials      182      180       -2     

Impacted Files	Coverage Δ
pystac/catalog.py	91.58% <100.00%> (+0.24%)	⬆️
pystac/collection.py	92.88% <100.00%> (+0.45%)	⬆️
tests/test_collection.py	99.60% <100.00%> (+0.04%)	⬆️

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