moscot 0.4.1__tar.gz → 0.4.2__tar.gz

{moscot-0.4.1 → moscot-0.4.2}/.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 3.0.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.25.0]
         files: ^src
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -23,7 +23,7 @@ repos:
       - id: prettier
         language_version: system
   - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
         additional_dependencies: [toml]
@@ -63,7 +63,7 @@ repos:
       - id: doc8
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.3
+    rev: v0.9.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{moscot-0.4.1 → moscot-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: moscot
-Version: 0.4.1
+Version: 0.4.2
 Summary: Multi-omic single-cell optimal transport tools
 Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
 Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
@@ -98,6 +98,7 @@ Requires-Dist: sphinx-tippy>=0.4.1; extra == "docs"
 Requires-Dist: myst-nb>=0.17.1; extra == "docs"
 Requires-Dist: ipython>=7.20.0; extra == "docs"
 Requires-Dist: sphinx_design>=0.3.0; extra == "docs"
+Dynamic: license-file
 
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{moscot-0.4.1 → moscot-0.4.2}/src/moscot/base/solver.py

@@ -41,7 +41,7 @@ class TagConverter:  # noqa: D101
         **kwargs: Any,
     ) -> TaggedArrayData:
         def to_tuple(
-            data: Optional[Union[ArrayLike, Tuple[ArrayLike, ArrayLike]]]
+            data: Optional[Union[ArrayLike, Tuple[ArrayLike, ArrayLike]]],
         ) -> Tuple[Optional[ArrayLike], Optional[ArrayLike]]:
             if not isinstance(data, tuple):
                 return data, None

{moscot-0.4.1 → moscot-0.4.2}/src/moscot/plotting/_utils.py

@@ -358,7 +358,7 @@ def _contrasting_color(r: int, g: int, b: int) -> str:
 
 
 def _input_to_adatas(
-    inp: Union[AnnData, Tuple[AnnData, AnnData], "CompoundProblem"]  # type: ignore[type-arg]
+    inp: Union[AnnData, Tuple[AnnData, AnnData], "CompoundProblem"],  # type: ignore[type-arg]
 ) -> Tuple[AnnData, AnnData]:
     from moscot.base.problems import CompoundProblem
 

{moscot-0.4.1 → moscot-0.4.2}/src/moscot/problems/space/_mixins.py

@@ -138,15 +138,29 @@ class SpatialAlignmentMixin(AnalysisMixin[K, B]):
         aligned_maps, aligned_metadata = self._interpolate_scheme(
             reference=reference, mode=mode, spatial_key=spatial_key  # type: ignore[arg-type]
         )
-        aligned_basis = np.vstack([aligned_maps[k] for k in self._policy._cat])
+
+        batch_categories = self.adata.obs[self._policy.key].cat.categories
+        batch_indices = {}
+        result = np.zeros((self.adata.n_obs, aligned_maps[list(aligned_maps.keys())[0]].shape[1]))
+
+        # Create batch to index mapping
+        for cat in batch_categories:
+            batch_indices[cat] = np.where(self.adata.obs[self._policy.key] == cat)[0]
+
+        # Assign aligned coordinates to the correct positions in result array
+        for cat, indices in batch_indices.items():
+            if cat in aligned_maps:
+                result[indices] = aligned_maps[cat]
 
         if key_added is None:
-            return aligned_basis, aligned_metadata
+            return result, aligned_metadata
 
-        self.adata.obsm[key_added] = aligned_basis
+        self.adata.obsm[key_added] = result
         if mode == "affine":  # noqa: RET503
             self.adata.uns.setdefault(key_added, {})
-            self.adata.uns[key_added]["alignment_metadata"] = aligned_metadata  # noqa: RET503
+            self.adata.uns[key_added]["alignment_metadata"] = aligned_metadata
+
+        return None
 
     def cell_transition(
         self,
@@ -399,7 +413,6 @@ class SpatialMappingMixin(AnalysisMixin[K, B], AbstractSpSc):
 
         corrs: Union[Dict[Tuple[K, K], Dict[Any, pd.Series]], Dict[Tuple[K, K], pd.Series]] = {}
         for key, val in self.solutions.items():
-
             # create mask corresponding to the current batch of spatial data
             index_obs = (
                 (self.adata_sp.obs[self._policy.key] == key[0])

{moscot-0.4.1 → moscot-0.4.2}/src/moscot/utils/subset_policy.py

@@ -314,7 +314,7 @@ class SimplePlanPolicy(SubsetPolicy[K], abc.ABC):
         return list(self._graph)
 
 
-class StarPolicy(SimplePlanPolicy[K]):
+class StarPolicy(OrderedPolicy[K]):
     r"""Policy with a star topology.
 
     Parameters

{moscot-0.4.1 → moscot-0.4.2}/src/moscot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: moscot
-Version: 0.4.1
+Version: 0.4.2
 Summary: Multi-omic single-cell optimal transport tools
 Author: Dominik Klein, Giovanni Palla, Michal Klein, Zoe Piran, Marius Lange
 Maintainer-email: Dominik Klein <dominik.klein@helmholtz-muenchen.de>, Giovanni Palla <giovanni.palla@helmholtz-muenchen.de>, Michal Klein <michal.klein@helmholtz-muenchen.de>
@@ -98,6 +98,7 @@ Requires-Dist: sphinx-tippy>=0.4.1; extra == "docs"
 Requires-Dist: myst-nb>=0.17.1; extra == "docs"
 Requires-Dist: ipython>=7.20.0; extra == "docs"
 Requires-Dist: sphinx_design>=0.3.0; extra == "docs"
+Dynamic: license-file
 
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