gengeneeval 0.1.0__py3-none-any.whl → 0.1.1__py3-none-any.whl

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

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

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

{gengeneeval-0.1.0.dist-info → gengeneeval-0.1.1.dist-info}/METADATA

@@ -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.dist-info → gengeneeval-0.1.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-geneval/__init__.py,sha256=6aSk50coEvm8rqwxGvuCyCaN_Dqj1VfuSqvOSTLEgqY,2872
+geneval/__init__.py,sha256=8D8KN9PSLbux6LMc6Ap1nz_WlQ4Jc6YNylPy_0udJ-Q,2872
 geneval/cli.py,sha256=0ai0IGyn3SSmEnfLRJhcr0brvUxuNZHE4IXod7jvosU,9977
 geneval/config.py,sha256=gkCjs_gzPWgUZNcmSR3Y70XQCAZ1m9AKLueaM-x8bvw,3729
 geneval/core.py,sha256=No0DP8bNR6LedfCWEedY9C5r_c4M14rvSPaGZqbxc94,1155
@@ -13,7 +13,7 @@ geneval/metrics/__init__.py,sha256=wk0CdFXvipfPqXWUMsRRz9CPiSVPG40Id4lyoSaLIkY,1
 geneval/metrics/base_metric.py,sha256=prbnB-Ap-P64m-2_TUrHxO3NFQaw-obVg1Tw4pjC5EY,6961
 geneval/metrics/correlation.py,sha256=jpYmaihWK89J1E5yQinGUJeB6pTZ21xPNHJi3XYyXJE,6987
 geneval/metrics/distances.py,sha256=9mWzbMbIBY1ckOd2a0l3by3aEFMQZL9bVMSeP44xzUg,16155
-geneval/metrics/metrics.py,sha256=RPRUkgaDeL3cmJDEN7b3sUuPZdvrWXI3YRWwdsTTjL0,4171
+geneval/metrics/metrics.py,sha256=s3ONmYTOk1ou6DUqCDOREQaqk3ajgpW_lZbZp1WW4aY,4747
 geneval/models/__init__.py,sha256=vJHXIhwzykjoqZ-vHQJnPwwjSUu9nnMyo7jGnWlTd94,42
 geneval/models/base_model.py,sha256=2QDtweYTgiovnksaRPBjNbIDu1l9l_WQMMFfeIX3GB8,1345
 geneval/results.py,sha256=iXSB0o0f1jQrCKjc-lbRfwBFGhspTDDJpQ2K2tM-XR4,11362
@@ -23,9 +23,9 @@ geneval/utils/io.py,sha256=LrRhIRlx_wlCs5Mayaq8hyVIp9uduHHohXuv8zQMwyI,888
 geneval/utils/preprocessing.py,sha256=1Cij1O2dwDR6_zh5IEgLPq3jEmV8VfIRjfQrHiKe3Mw,2612
 geneval/visualization/__init__.py,sha256=LN19jl5xV4WVJTePaOUHWvKZ_pgDFp1chhcklGkNtm8,792
 geneval/visualization/plots.py,sha256=3K94r3x5NjIUZ-hYVQIivO63VkLOvDWl-BLB_qL2pSY,15008
-geneval/visualization/visualizer.py,sha256=dwx1oc0C3dXlJguvIx1pLAOeHcGE5v85OctHOsRE2Yo,36526
-gengeneeval-0.1.0.dist-info/METADATA,sha256=KaYsfE44TMNNBVrfCEFvk4sBczDR5IYy1fzfY8C1nEI,6041
-gengeneeval-0.1.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-gengeneeval-0.1.0.dist-info/entry_points.txt,sha256=xTkwnNa2fP0w1uGVsafzRTaCeuBSWLlNO-1CN8uBSK0,43
-gengeneeval-0.1.0.dist-info/licenses/LICENSE,sha256=RDHgHDI4rSDq35R4CAC3npy86YUnmZ81ecO7aHfmmGA,1073
-gengeneeval-0.1.0.dist-info/RECORD,,
+geneval/visualization/visualizer.py,sha256=lX7K0j20nAsgdtOOdbxLdLKYAfovEp3hNAnZOjFTCq0,36670
+gengeneeval-0.1.1.dist-info/METADATA,sha256=4WJtqiCK88ZIKGObjIXQ-Fp0PvmF6D5-YGpm0WciUNc,6041
+gengeneeval-0.1.1.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+gengeneeval-0.1.1.dist-info/entry_points.txt,sha256=xTkwnNa2fP0w1uGVsafzRTaCeuBSWLlNO-1CN8uBSK0,43
+gengeneeval-0.1.1.dist-info/licenses/LICENSE,sha256=RDHgHDI4rSDq35R4CAC3npy86YUnmZ81ecO7aHfmmGA,1073
+gengeneeval-0.1.1.dist-info/RECORD,,