fixed small bug when importing the sif file, fixed tissue mapping, up…

…dated pyproject.toml

.github/workflows/sphinx_autodoc.yaml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v2
 

neko/_visual/visualize_network.py

@@ -75,11 +75,11 @@ def __init__(self, network, predefined_node=None, color_by="Effect", noi=False):
         self.__add_edges_to_graph()
         self.__add_nodes_to_graph()
 
-    def __set_custom_edge_colors(self, custom_edge_colors):
+    def set_custom_edge_colors(self, custom_edge_colors):
         # Update the edge_colors dictionary with custom mappings
         self.__edge_colors.update(custom_edge_colors)
 
-    def __set_node_colors(self, node_colors):
+    def set_node_colors(self, node_colors):
         # Update the node_colors dictionary with custom node colorsdataframe_nodes
         self.__node_colors.update(node_colors)
 
@@ -161,6 +161,12 @@ def render(self, output_file='network', view=False, highlight_nodes=None, highli
             highlight_nodes (list): List of nodes to highlight.
             highlight_color (str): Color to use for highlighting nodes.
         """
+        # Apply colors from __node_colors if available
+        if self.__node_colors:
+            for node, color in self.__node_colors.items():
+                if node in self.__dataframe_nodes['Genesymbol'].values:
+                    self.graph.node(node, style='filled', fillcolor=color)
+
         # If highlight_nodes is provided, set the color for each node in the list
         if highlight_nodes is not None:
             for node in highlight_nodes:

neko/core/network.py

@@ -277,7 +277,7 @@ def _populate(self):
             self.__drop_missing_nodes()
             self.nodes.reset_index(inplace=True, drop=True)
 
-        elif sif_files := self._init_args['sif_file']:
+        elif sif_file := self._init_args['sif_file']:
             self.initial_nodes = []
             self.__load_network_from_sif(sif_file)
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "nekomata"
-version = "0.9.5"
+version = "0.9.6"
 description = "Package to extract, visualize, convert and study interactions from database into executable activity flow based model"
 license = "GNU General Public License Version 3"
 authors = [
@@ -40,7 +40,7 @@ unipressed = "*"
 jupyterlab = "*"
 pycurl = "*"
 graphviz = "*"
-pandas = "*"
+pandas = "2.2.2"
 
 [tool.poetry.dev-dependencies]
 pandoc = "*"