Improve pylint compatibility - sbol3.provelance

[GeneCodeSavvy]

Hello,

PR for #433

After analyzing the pylint reports and wanted to share my observations:

1. Wildcard Imports Inflate Warning Counts:
   The ~9,000 unused-import warnings appear to stem from a pattern where from . import * statements pull in unused modules/classes. For example, in provenance.py (line 6), a single wildcard import triggers 247 unused-import warnings, each for an unused item. This suggests that many warnings are redundant and could be resolved by replacing wildcard imports with explicit imports of only necessary classes/functions.

2. Why provenance.py?:

   • It contributes 5.75% of all pylint errors (e.g., class redefinitions, missing docstrings).
   • Its wildcard imports alone generate ~10% of the file’s warnings.

This PR:

1. Not Yet Complete
2. It eliminates wildcard-import and unused-import.
3. Added some scratch changes in .gitignore and setup.cfg for my convenience. That will be removed after the final changes.

Further changes:

1. provelance.py has functions with access to protected methods like in this case.

def build_usage(identity: str, *, type_uri: str = PROV_USAGE) -> SBOLObject:
    obj = Usage(entity=PYSBOL3_MISSING, identity=identity, type_uri=type_uri)
    # Remove the placeholder values
    obj._properties[PROV_ENTITY] = []
    return obj

2. too-many-arguments is also common refactor recommendation. Like in the case below.

class Usage(CustomIdentified):
    def __init__(self, entity: str,
                 *, roles: Optional[str, list[str]] = None,
                 name: str = None, description: str = None,
                 derived_from: List[str] = None,
                 generated_by: List[str] = None,
                 measures: List[SBOLObject] = None,
                 identity: str = None,
                 type_uri: str = PROV_USAGE) -> None:
        super().__init__(identity=identity, type_uri=type_uri,
                         name=name, description=description,
                         derived_from=derived_from, generated_by=generated_by,
                         measures=measures)
        self.entity: uri_singleton = URIProperty(self, PROV_ENTITY, 1, 1,
                                                 initial_value=entity)
        self.roles: uri_list = URIProperty(self, PROV_ROLES, 0, math.inf,
                                           initial_value=roles)

Please help with these cases.

Thank you for your guidance!
— Harsh

pylint sbol3/provelance.py
Previous score : 0 / 10
Current score : 8.35 / 10

[tcmitchell]

The builds are failing. This PR cannot be merged until the builds are passing. Please let us know if you need help fixing the builds.

[GeneCodeSavvy]

@tcmitchell done, I had removed the pylint config without realising it would interfere with CI / CD

[tcmitchell]

For both too-many-arguments and protected-access, just leave those checks disabled for now. Those are not the low-hanging fruit. There are something like 45 pylint warnings. My suggestion on the issue was to start with the easy ones and work towards the harder ones. If you need advice on them, they probably don't qualify as "easy".

[GeneCodeSavvy]

Okay, then this PR will be merged?