some mypy fixes

Author: Arina Danilina

pyproject.toml

@@ -122,6 +122,8 @@ ignore = [
     "D107",
     # Missing docstring in magic method
     "D105",
+    # Use `X | Y` for type annotations
+    "UP007",
 ]
 line-length = 120
 select = [

src/moscot/base/problems/_mixins.py

@@ -122,7 +122,7 @@ def _annotation_mapping(
         forward: bool,
         source: K,
         target: K,
-        key: str,
+        key: str | None = None,
         other_adata: Optional[str] = None,
         scale_by_marginals: bool = True,
         cell_transition_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
@@ -342,10 +342,10 @@ def _annotation_mapping(
                     filter_key=key,
                     filter_value=source,
                 )
-                out_len = self[(source, target)].solution.shape[1]
+                out_len = self.solutions[(source, target)].shape[1]
                 batch_size = batch_size if batch_size is not None else out_len
                 for batch in range(0, out_len, batch_size):
-                    tm_batch = self.push(
+                    tm_batch : ArrayLike = self.push(  # type: ignore[attr-defined]
                         source=source,
                         target=target,
                         data=None,
@@ -366,10 +366,10 @@ def _annotation_mapping(
                     filter_key=key,
                     filter_value=target,
                 )
-                out_len = self[(source, target)].solution.shape[0]
+                out_len = self.solutions[(source, target)].shape[0]
                 batch_size = batch_size if batch_size is not None else out_len
                 for batch in range(0, out_len, batch_size):
-                    tm_batch = self.pull(
+                    tm_batch : ArrayLike = self.pull(  # type: ignore[attr-defined]
                         source=source,
                         target=target,
                         data=None,

src/moscot/problems/cross_modality/_mixins.py

@@ -25,6 +25,8 @@ class CrossModalityTranslationMixinProtocol(AnalysisMixinProtocol[K, B]):
     def _cell_transition(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
         ...
 
+    def _annotation_mapping(self: AnalysisMixinProtocol[K, B], *args: Any, **kwargs: Any) -> pd.DataFrame:
+        ...
 
 class CrossModalityTranslationMixin(AnalysisMixin[K, B]):
     """Cross modality translation analysis mixin class."""
@@ -184,13 +186,13 @@ def cell_transition(  # type: ignore[misc]
             key_added=key_added,
         )
 
-    def annotation_mapping(
+    def annotation_mapping(  # type: ignore[misc]
         self: CrossModalityTranslationMixinProtocol[K, B],
         mapping_mode: Literal["sum", "max"],
         annotation_label: str,
         forward: bool,
-        source: K = "src",
-        target: K = "tgt",
+        source: str = "src",
+        target: str = "tgt",
         scale_by_marginals: bool = True,
         other_adata: Optional[str] = None,
         cell_transition_kwargs: Mapping[str, Any] = types.MappingProxyType({}),
@@ -202,7 +204,7 @@ def annotation_mapping(
             target=target,
             key=self.batch_key,
             forward=forward,
-            other_adata=self.adata_tgt,
+            other_adata=self.adata_tgt if other_adata is None else other_adata,
             scale_by_marginals=scale_by_marginals,
             cell_transition_kwargs=cell_transition_kwargs,
         )

src/moscot/problems/space/_mixins.py

@@ -284,8 +284,8 @@ def cell_transition(  # type: ignore[misc]
             key_added=key_added,
         )
 
-    def annotation_mapping(
-        self: AnalysisMixinProtocol[K, B],
+    def annotation_mapping(  # type: ignore[misc]
+        self: SpatialAlignmentMixinProtocol[K, B],
         mapping_mode: Literal["sum", "max"],
         annotation_label: str,
         forward: bool,
@@ -299,7 +299,7 @@ def annotation_mapping(
             annotation_label=annotation_label,
             source=source,
             target=target,
-            key=self._batch_key,
+            key=self.batch_key,
             forward=forward,
             scale_by_marginals=scale_by_marginals,
             cell_transition_kwargs=cell_transition_kwargs,
@@ -594,12 +594,12 @@ def cell_transition(  # type: ignore[misc]
             key_added=key_added,
         )
 
-    def annotation_mapping(
-        self: AnalysisMixinProtocol[K, B],
+    def annotation_mapping(  # type: ignore[misc]
+        self: SpatialMappingMixinProtocol[K, B],
         mapping_mode: Literal["sum", "max"],
         annotation_label: str,
-        source: str,
-        target: str = "tgt",
+        source: K,
+        target: K | str = "tgt",
         forward: bool = False,
         scale_by_marginals: bool = True,
         cell_transition_kwargs: Mapping[str, Any] = types.MappingProxyType({}),

src/moscot/problems/time/_mixins.py

@@ -69,6 +69,13 @@ def _cell_transition(
     ) -> pd.DataFrame:
         ...
 
+    def _annotation_mapping(
+        self: AnalysisMixinProtocol[K, B],
+        *args: Any,
+        **kwargs: Any,
+    ) -> pd.DataFrame:
+        ...
+
     def _sample_from_tmap(
         self: TemporalMixinProtocol[K, B],
         source: K,