increased dependency versions for compatibility with depht-gui; fixed…

… bokeh bug according to issue #56 from DNAFeaturesViewer GitHub

requirements.txt

@@ -1,9 +1,10 @@
-bitarray~=2.0.0
-bokeh==2.2.2
-numpy~=1.20.2
-pandas~=1.2.4
+biopython~=1.78
+bitarray~=2.4.1
+bokeh~=2.4.2
+numpy~=1.22.3
+pandas~=1.4.2
 plotly~=5.1.0
 scipy~=1.7.0
-dna_features_viewer~=3.0.3
+dna_features_viewer~=3.1.0
 pretty_html_table~=0.9.14
-phamclust~=0.1.0
+phamclust~=0.1.2

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 license_file = LICENSE
 name = depht
-version = 1.1.2
+version = 1.1.3
 author = Christian Gauthier
 author_email = chg60@pitt.edu
 description = Discovery and Extraction of Phages Tool
@@ -28,16 +28,16 @@ package_dir =
     =src
 packages = find:
 install_requires =
-    biopython~=1.79
-    bitarray~=2.0.0
-    bokeh~=2.2.2
-    dna-features-viewer~=3.0.3
+    biopython~=1.78
+    bitarray~=2.4.1
+    bokeh~=2.4.2
+    dna-features-viewer~=3.1.0
     kaleido~=0.2.1
     matplotlib~=3.4.1
-    numpy~=1.20.2
-    pandas~=1.2.4
-    phamclust~=0.1.0
-    pretty-html-table~=0.9.10
+    numpy~=1.22.3
+    pandas~=1.4.2
+    phamclust~=0.1.2
+    pretty-html-table~=0.9.14
     plotly~=5.1.0
     scipy~=1.7.0
 

src/depht/functions/visualization.py

@@ -2,6 +2,7 @@
 import pretty_html_table
 import bokeh
 from bokeh import plotting
+from bokeh.core.properties import value
 from bokeh.embed import file_html
 from bokeh.models import HoverTool, Range1d, Title
 from bokeh.resources import CDN
@@ -364,7 +365,7 @@ def plot_with_bokeh(graphic_record, figure_width=100, figure_height="auto",
                                                     bokeh_floating_labels))
         plot.text(x="x", y="y", text="text", text_align="center",
                   text_font_size=label_text_font_size,
-                  text_font=label_text_font,
+                  text_font=value(label_text_font),
                   text_font_style=label_text_font_style,
                   source=labels_source)