Fix motif_data bugs

Author: xfchen0912

src/scmagnify/external/plotting/__init__.py

@@ -1,4 +1,4 @@
-from ._plot1cell import plot1cell
+# from ._plot1cell import plot1cell
 from .liana import LianaVisualizer
 
-__all__ = ["LianaVisualizer", "plot1cell"]
+__all__ = ["LianaVisualizer"]

src/scmagnify/tools/_func_enrich.py

@@ -12,16 +12,19 @@
 from rich.table import Table
 
 # Import your package to get its file path
-import scmagnify as scm
 from scmagnify import logging as logg
+from scmagnify.settings import settings
 
 if TYPE_CHECKING:
     from typing import Any
 
 __all__ = ["FuncEnrich"]
 
 # Define the default directory for gene sets within the package
-GENESET_DIR = os.path.join(os.path.dirname(scm.__file__), "data", "genesets")
+if os.path.exists(settings.scm_data):
+    GENESET_DIR = os.path.join(settings.scm_data, "genesets")
+else:
+    GENESET_DIR = None
 
 
 # ==============================================================================

src/scmagnify/tools/_motif_scan.py

@@ -40,7 +40,10 @@
 ]
 
 _BACKGROUND = Literal["subject", "genome", "even"]
-MOTIF_DIR = os.path.join(settings.scm_data, "motifs")
+if os.path.exists(settings.scm_data):
+    MOTIF_DIR = os.path.join(settings.scm_data, "motifs")
+else:
+    MOTIF_DIR = None
 
 
 def _add_peak_seq(

src/scmagnify/tools/_tensor_decomp.py

@@ -84,7 +84,7 @@ def __init__(
         self.filtered_network = self.network.copy()
         for attri in self.network.columns[2:-1]:
             self.filtered_network[attri] = filter_network(
-                self.network, attri=attri, method=filter[0], param=filter[1], binarize=filter[2], verbose=False
+                self.network, attri=attri, method=filter[0], param=filter[1], binarize=filter[2], verbose=True
             )[attri]
 
         logg.info(f"Filtering Network: \n Method: {filter[0]} \n Parameter: {filter[1]} \n Binarize: {filter[2]}")