14e691e38eb579109dbc1df7b7077a3e2ec5d272
max
  Fri Jun 6 08:42:22 2025 -0700
suppressing perf warnings in numpy

diff --git src/cbPyLib/cellbrowser/cellbrowser.py src/cbPyLib/cellbrowser/cellbrowser.py
index b488cc5..7934127 100755
--- src/cbPyLib/cellbrowser/cellbrowser.py
+++ src/cbPyLib/cellbrowser/cellbrowser.py
@@ -5278,30 +5278,34 @@
     """
     outDir = path
 
     if doDebug is not None:
         setDebug(doDebug)
 
     if not isdir(outDir):
         makeDir(outDir)
 
     confName = join(outDir, "cellbrowser.conf")
     if isfile(confName):
         logging.warn("%s already exists. Overwriting existing files." % confName)
 
     import numpy as np
     import pandas as pd
+
+    from warnings import simplefilter
+    simplefilter(action="ignore", category=pd.errors.PerformanceWarning)
+
     import anndata
 
     configData = {} # dict that can override the default arguments in the generated cellbrowser.conf file
 
     # layers are the new thing to store multiple matrixces. In the old days, there only was the adata.raw matrix
     # in addition to ad.X. So if a layer was specified, we use that. Only when a layer was not specified do we respect 
     # the useRaw option
     if layer:
         if layer not in adata.layers:
             raise ValueError("The layer '%s' does not exist. Available layers are: %s" % (layer, adata.layers.keys()))
         logging.info("Using layer '%s' of anndata object (not using .raw)" % layer)
         adata.X = adata.layers[layer]
     else:
         if useRaw:
             if adata.raw is None: