Fix imports

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>

.pre-commit-config.yaml

@@ -2,26 +2,29 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
+
   - repo: https://github.com/tox-dev/pyproject-fmt
     rev: "2.2.4"
     hooks:
       - id: pyproject-fmt
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.9.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
-        args: [--fix, --exit-non-zero-on-fix]
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
@@ -32,22 +35,25 @@ repos:
         args: [--fix=lf]
       - id: trailing-whitespace
       - id: check-case-conflict
-      # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
+
   - repo: local
     hooks:
       - id: forbid-to-commit
-        name: Don't commit rej files
+        name: Don't commit .rej files
         entry: |
           Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
           Fix the merge conflicts manually and remove the .rej files.
         language: fail
         files: '.*\.rej$'
-    - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.14.1
-      hooks:
-          - id: mypy
-            args: [--no-strict-optional, --ignore-missing-imports]
-            additional_dependencies:
-                ["types-setuptools", "types-requests", "types-attrs"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies:
+          - types-setuptools
+          - types-requests
+          - types-attrs

src/spatialdata_db/lamin_spatialdatadb_curator.py

@@ -1,20 +1,18 @@
-from lamindb.curators import SpatialDataCurator
-from spatialdata import SpatialData
 import bionty as bt
 import lamindb as ln
+from lamindb.base.types import FieldAttr
+from lamindb.curators._spatial import SpatialDataCurator
+from lamindb.models import Record
+from spatialdata import SpatialData
 
-from lnschema_core import Record
-from lnschema_core.types import FieldAttr
-from lnschema_core import (
-    Record,
-)
 
 class SpatialDataDBCurator(SpatialDataCurator):
+    """Custom Curator for SpatialDataDB"""
 
     DEFAULT_CATEGORICALS = {
         "assay": bt.ExperimentalFactor.name,
         "chemistry_version": ln.ULabel.name,
-        'organism': bt.Organism.name,
+        "organism": bt.Organism.name,
         "tissue": bt.Tissue.name,
         "disease": bt.Disease.name,
         "license": ln.ULabel.name,
@@ -29,11 +27,11 @@ class SpatialDataDBCurator(SpatialDataCurator):
         "preproc_version": "unknown",
     }
 
-    FIXED_SOURCES = {
-            # TODO: fix ontologies
-        }
+    FIXED_SOURCES = {  # type: ignore
+        # TODO: fix ontologies
+    }
 
-    DEFAULT_VAR_INDEX = {'table': bt.Gene.ensembl_gene_id}
+    DEFAULT_VAR_INDEX = {"table": bt.Gene.ensembl_gene_id}
 
     def __init__(
         self,
@@ -49,9 +47,7 @@ def __init__(
         sample_metadata_key: str = "sample",
     ):
         if categoricals is None:
-            categoricals = dict([(
-                sample_metadata_key, self.DEFAULT_CATEGORICALS
-            )])
+            categoricals = {sample_metadata_key: self.DEFAULT_CATEGORICALS}
 
         super().__init__(
             sdata,
@@ -63,4 +59,4 @@ def __init__(
             sources=sources,
             exclude=exclude,
             sample_metadata_key=sample_metadata_key,
-        )
+        )