fix: pydantic type check

Author: stanfish06

mise.toml

@@ -7,6 +7,17 @@ CPLUS_INCLUDE_PATH = "{{config_root}}/src/scloop/data"
 [settings]
 python.uv_venv_auto = true
 
+[tasks.clean]
+run = [
+	"uv cache clean",
+	"uv cache prune",
+	"rm -rf .venv",
+	"rm -rf dist",
+	"rm -rf ./src/scloop.egg-info",
+	"rm -f uv.lock",
+	"find ./src -name '*.so'  -type f -delete",
+]
+
 [tasks.sync_full]
 run = [
 	"uv cache clean",

src/scloop/data/analysis_containers.py

@@ -3,34 +3,35 @@
 
 import numpy as np
 import pandas as pd
-from pydantic.dataclasses import dataclass, field
+from pydantic.dataclasses import dataclass
+from pydantic import Field, ConfigDict
 
 
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class BootstrapAnalysis:
-    loops_eidx_boot: list[list[list[np.ndarray]]] = field(default_factory=list)
-    persistence_diagram_boot: list[np.ndarray] = field(default_factory=list)
-    matching_df: list[pd.DataFrame] = field(default_factory=list)
+    loops_eidx_boot: list[list[list[np.ndarray]]] = Field(default_factory=list)
+    persistence_diagram_boot: list[np.ndarray] = Field(default_factory=list)
+    matching_df: list[pd.DataFrame] = Field(default_factory=list)
     n_booted: int = 0
-    loop_rank: pd.DataFrame = field(default_factory=pd.DataFrame)
-    parameters: dict = field(default_factory=dict)
+    loop_rank: pd.DataFrame = Field(default_factory=pd.DataFrame)
+    parameters: dict = Field(default_factory=dict)
 
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class HodgeAnalysis:
     loop_id: str
-    eigenvalues: np.ndarray = field(default_factory=lambda: np.array([]))
-    eigenvectors: np.ndarray = field(default_factory=lambda: np.array([]))
-    loops_edges_embedding: list[np.ndarray] = field(default_factory=list)
-    parameters: dict = field(default_factory=dict)
+    eigenvalues: np.ndarray = Field(default_factory=lambda: np.array([]))
+    eigenvectors: np.ndarray = Field(default_factory=lambda: np.array([]))
+    loops_edges_embedding: list[np.ndarray] = Field(default_factory=list)
+    parameters: dict = Field(default_factory=dict)
 
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class PseudotimeAnalysis:
-    edge_pseudotime_deltas: np.ndarray = field(default_factory=lambda: np.array([]))
+    edge_pseudotime_deltas: np.ndarray = Field(default_factory=lambda: np.array([]))
     pseudotime_source: str = ""
-    parameters: dict = field(default_factory=dict)
+    parameters: dict = Field(default_factory=dict)
 
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class VelocityAnalysis:
-    edge_velocity_deltas: np.ndarray = field(default_factory=lambda: np.array([]))
+    edge_velocity_deltas: np.ndarray = Field(default_factory=lambda: np.array([]))
     velocity_source: str = ""
-    parameters: dict = field(default_factory=dict)
+    parameters: dict = Field(default_factory=dict)

src/scloop/data/containers.py

@@ -1,14 +1,15 @@
 # Copyright 2025 Zhiyuan Yu (Heemskerk's lab, University of Michigan)
 from pydantic.dataclasses import dataclass
+from pydantic import ConfigDict
 from .metadata import ScloopMeta
 from .analysis_containers import BootstrapAnalysis, HodgeAnalysis
-from anndata import Anndata
+from anndata import AnnData
 import numpy as np
 
 '''
 store core homology data and associated analysis data
 '''
-@dataclass
+@dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class HomologyData:
     meta: ScloopMeta
     persistence_diagram: np.ndarray | None = None
@@ -17,7 +18,7 @@ class HomologyData:
     bootstrap_data: BootstrapAnalysis | None = None
     hodge_data: HodgeAnalysis | None = None
 
-    def _compute_homology(self, adata: Anndata, thresh=None):
+    def _compute_homology(self, adata: AnnData, thresh=None):
         pass
 
     def _compute_boundary_matrix(self, thresh=None):