gengeneeval 0.1.0__tar.gz → 0.1.1__tar.gz

{gengeneeval-0.1.0 → gengeneeval-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gengeneeval
-Version: 0.1.0
+Version: 0.1.1
 Summary: Comprehensive evaluation of generated gene expression data. Computes metrics between real and generated datasets with support for condition matching, train/test splits, and publication-quality visualizations.
 License: MIT
 License-File: LICENSE

{gengeneeval-0.1.0 → gengeneeval-0.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "gengeneeval"
-version = "0.1.0"
+version = "0.1.1"
 description = "Comprehensive evaluation of generated gene expression data. Computes metrics between real and generated datasets with support for condition matching, train/test splits, and publication-quality visualizations."
 authors = ["GenEval Team <geneval@example.com>"]
 license = "MIT"

{gengeneeval-0.1.0 → gengeneeval-0.1.1}/src/geneval/__init__.py

@@ -25,7 +25,7 @@ CLI Usage:
               --conditions perturbation cell_type --output results/
 """
 
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 __author__ = "GenEval Team"
 
 # Main evaluation interface

{gengeneeval-0.1.0 → gengeneeval-0.1.1}/src/geneval/metrics/metrics.py

@@ -7,6 +7,24 @@ from scipy.stats import pearsonr, spearmanr
 import torch
 from . import metric_MMD
 
+
+def scanpy_preprocessing(adata: ad.AnnData) -> ad.AnnData:
+    """Apply standard scanpy preprocessing."""
+    adata = adata.copy()
+    sc.pp.normalize_total(adata, target_sum=1e4)
+    sc.pp.log1p(adata)
+    return adata
+
+
+def scanpy_pca(adata: ad.AnnData, n_comps: int = 50) -> ad.AnnData:
+    """Compute PCA on AnnData object."""
+    adata = adata.copy()
+    if adata.n_vars > 2000:
+        sc.pp.highly_variable_genes(adata, n_top_genes=2000, flavor='seurat_v3', subset=True)
+    sc.tl.pca(adata, n_comps=min(n_comps, adata.n_vars - 1, adata.n_obs - 1))
+    return adata
+
+
 class Metric():
     def __init__(self, name: str, fn):
         self.name = name

{gengeneeval-0.1.0 → gengeneeval-0.1.1}/src/geneval/visualization/visualizer.py

@@ -10,12 +10,16 @@ Provides publication-quality plots for evaluation results:
 """
 from __future__ import annotations
 
-from typing import Dict, List, Optional, Tuple, Union, Any
+from typing import Dict, List, Optional, Tuple, Union, Any, TYPE_CHECKING
 from pathlib import Path
 import numpy as np
 import pandas as pd
 import warnings
 
+if TYPE_CHECKING:
+    from geneval.results import EvaluationResult
+    from geneval.data.loader import GeneExpressionDataLoader
+
 try:
     import matplotlib.pyplot as plt
     import matplotlib.patches as mpatches