♻️ Re-purpose BaseCurator as Curator and introduce CatCurator

[falexwolf]

Is part of a sequence of PRs that refactors the curators:

• 🎨 Let Curator.validate() throw an error #2417
• ♻️ Refactor organism handling in curators #2415
• 🚚 Bulk-rename old-style curators to CatCurator #2413
• 🎨 Self-contained definition of CellxGene schema #2412
• 🚚 Move PertCurator from wetlab here and add CellxGene Curator test #2408
• 🚚 Move CellxGene Curator from cellxgene-lamin here #2403
• ✨ Schema-based curators: DataFrameCurator #2388

Consolidate under Curator

Rename BaseCurator to Curator and eliminate the previous Curator 1080aed

The private attributes of Curator enable the most basic curation functionality.

class Curator:
    def __init__(self, dataset: Any):
        self._dataset: Any = dataset  # pass the dataset as a UPathStr or data object
        self._artifact: Artifact = None  # pass the dataset as a (non-curated) artifact
        self._cat_curator: CatCurator = None
        self._validated: bool = False

Consolidate under CatCurator 99e145b

Rename .fields and ._fields to .categoricals and ._categoricals, respectively

The private attributes of CatCurator extend Curator to enable curating categoricals.

class CatCurator(Curator):
    def __init__(
        self, *, dataset, categoricals, sources, organism, exclude, columns_field=None
    ):
        super().__init__(dataset=dataset)
        self._categoricals = categoricals or {}
        self._non_validated = None
        self._organism = organism
        self._sources = sources or {}
        self._exclude = exclude or {}
        self._columns_field = columns_field
        self._validate_category_error_messages: str = ""

DataFrameCatCurator, AnnDataCatCurator, and MuDataCatCurator now all leverage these fields. They also all leverage CatCurator.save_artifact().

TiledbsomaCatCurator and SpatialDataCatCurator both have more custom logic that should be consolidated in another PR.

[github-actions]

🚀 Deployed on https://679f6e2aafa20e128025eac3--lamindb-qnwk.netlify.app

[codecov]

Codecov Report

Attention: Patch coverage is 95.83333% with 7 lines in your changes missing coverage. Please review.

Project coverage is 91.54%. Comparing base (d503387) to head (cc65789).
Report is 35 commits behind head on main.

Files with missing lines	Patch %	Lines
lamindb/curators/__init__.py	95.80%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2416      +/-   ##
==========================================
- Coverage   91.71%   91.54%   -0.17%     
==========================================
  Files          62       62              
  Lines        9138     9572     +434     
==========================================
+ Hits         8381     8763     +382     
- Misses        757      809      +52     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.