Fixes #14

.gitignore

@@ -18,6 +18,7 @@ wheels/
 .specify/
 todo/
 *.ipynb
+.vscode/
 
 # Refactor planning
 REFACTOR_PLAN.md

examples/.gitignore

@@ -0,0 +1 @@
+*.png

pyproject.toml

@@ -14,18 +14,21 @@ classifiers = [
 ]
 dependencies = [
   "cython>=3.0.12",
+  "numba>=0.62.1",
   "numpy<2",
   "pandas",
   "pip>=25.2",
   "pydantic>=2.11.4",
   "pytest>=8.4",
   "rich>=14",
   "scanpy[leiden]>=1.11.2",
+  "scikit-misc>=0.5.2",
   "statsmodels==0.14.4",
   "tensorflow>=2.18.1",
   "torch",
   "torchdyn>=1.0.6",
   "torchvision",
+  "tqdm-joblib>=0.0.5",
   "umap-learn>=0.5.7",
 ]
 

src/scloop/__init__.py

@@ -1,4 +1,5 @@
 import warnings
+
 warnings.filterwarnings("ignore", category=FutureWarning, module="scanpy")
 warnings.filterwarnings("ignore", category=FutureWarning, module="anndata")
 

src/scloop/data/analysis_containers.py

@@ -16,6 +16,7 @@ class BootstrapAnalysis:
     loop_rank: pd.DataFrame = Field(default_factory=pd.DataFrame)
     parameters: dict = Field(default_factory=dict)
 
+
 @dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class HodgeAnalysis:
     loop_id: str
@@ -24,12 +25,14 @@ class HodgeAnalysis:
     loops_edges_embedding: list[np.ndarray] = Field(default_factory=list)
     parameters: dict = Field(default_factory=dict)
 
+
 @dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class PseudotimeAnalysis:
     edge_pseudotime_deltas: np.ndarray = Field(default_factory=lambda: np.array([]))
     pseudotime_source: str = ""
     parameters: dict = Field(default_factory=dict)
 
+
 @dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class VelocityAnalysis:
     edge_velocity_deltas: np.ndarray = Field(default_factory=lambda: np.array([]))

src/scloop/data/containers.py

@@ -6,9 +6,11 @@
 from anndata import AnnData
 import numpy as np
 
-'''
+"""
 store core homology data and associated analysis data
-'''
+"""
+
+
 @dataclass(config=ConfigDict(arbitrary_types_allowed=True))
 class HomologyData:
     meta: ScloopMeta

src/scloop/preprocessing/__init__.py

@@ -1 +1,2 @@
 from .prepare import prepare_adata
+from .delve import delve_fs

src/scloop/preprocessing/delve/__init__.py

@@ -0,0 +1 @@
+from .delve import *