🚚 move viz.py changes from phospho project version, lint w/ ruff

Author: enryH

.github/workflows/cdci.yml

@@ -14,22 +14,21 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
-  # lint:
-  #   name: Lint with ruff
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
+  lint:
+    name: Lint with ruff
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
 
-  #     - uses: actions/setup-python@v5
-  #       with:
-  #         python-version: "3.11"
-  #     - name: Install ruff
-  #       run: | 
-  #         pip install ruff
-  #     - name: Lint with ruff  
-  #       run: |
-  #         # stop the build if there are Python syntax errors or undefined names
-  #         ruff check .
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install ruff
+        run: | 
+          pip install ruff
+      - name: Lint with ruff  
+        run: |
+          ruff check .
   test:
     name: Test
     runs-on: ubuntu-latest

src/vuecore/Dendrogram.py

@@ -1,7 +1,7 @@
+from collections import OrderedDict
+
 import numpy as np
 import scipy as scp
-from collections import OrderedDict
-import plotly.graph_objs as go
 
 
 def plot_dendrogram(
@@ -58,7 +58,7 @@ def plot_dendrogram(
         color_threshold=color_threshold,
     )
 
-    if cutoff_line == True:
+    if cutoff_line:
         dendrogram.layout.update(
             {
                 "shapes": [
@@ -221,7 +221,7 @@ def set_axis_layout(self, axis_key, hide_labels):
 
         self.layout[axis_key].update(axis_defaults)
 
-        if hide_labels == True:
+        if hide_labels:
             self.layout[axis_key].update({"showticklabels": False})
         else:
             pass
@@ -280,8 +280,8 @@ def get_dendrogram_traces(
         icoord = scp.array(Z_dendrogram["icoord"])
         dcoord = scp.array(Z_dendrogram["dcoord"])
         ordered_labels = scp.array(Z_dendrogram["ivl"])
-        color_list = scp.array(Z_dendrogram["color_list"])
-        colors = self.get_color_dict(colorscale)
+        # color_list = scp.array(Z_dendrogram["color_list"])
+        # colors = self.get_color_dict(colorscale)
 
         trace_list = []
 
@@ -295,7 +295,7 @@ def get_dendrogram_traces(
                 ys = dcoord[i]
             else:
                 ys = icoord[i]
-            color_key = color_list[i]
+            # color_key = color_list[i] # not used
             hovertext_label = None
             if hovertext:
                 hovertext_label = hovertext[i]

src/vuecore/utils.py

@@ -151,7 +151,7 @@ def networkx_to_neo4j_document(graph):
                 rel_type = edge["type"]
                 if "type" in graph.nodes()[r]:
                     edge["type"] = graph.nodes()[r]["type"]
-                if not (n, r, edge["type"]) in seen_rels:
+                if (n, r, edge["type"]) not in seen_rels:
                     rels[rel_type].append(edge)
                     seen_rels.update({(n, r, edge["type"]), (r, n, edge["type"])})
                     attr.update(rels)
@@ -268,9 +268,9 @@ def __extract_style(el):
             for k, v in [x.split(": ") for x in el.attrs["style"].split(";") if x != ""]
         }
 
-    if type(el) is str:
+    if isinstance(el, str):
         return convert_html_to_dash(parse_html(el))
-    if type(el) == bs.element.NavigableString:
+    if isinstance(el, bs.element.NavigableString):
         return str(el)
     else:
         name = el.name