Update render_network_bokeh to use Scatter instead of Square + other …

…small fixes (#281)

* change some docstrings using math to use raw strings

* ignore files created by Emacs

* update networkx plots to not use Square + unit test

* update specialized tutorials to run with latest versions

.gitignore

@@ -24,7 +24,6 @@ Tests/bioscrape_test.xml
 Tests/dcas9_repression_test.xml
 Tests/sbml_test_file.xml
 
-
 # Sphinx documentation
 docs/build/
 
@@ -74,3 +73,6 @@ docs/build/
 ### BioCRNPlyer
 # Ignore xml files generated by this toolbox
 *.xml
+
+### Emacs backup files
+*~

Tests/Unit/test_plotting.py

@@ -1,13 +1,16 @@
-
 #  Copyright (c) 2020, Build-A-Cell. All rights reserved.
 #  See LICENSE file in the project root directory for details.
 
-from biocrnpyler.dna_construct import RNA_construct
+import copy
+import re
+import warnings
+
 import pytest
-#from unittest import TestCase
+
+import biocrnpyler as bcp
 from biocrnpyler import CRNPlotter, DNA_construct, Promoter,IntegraseSite,\
-                        RBS,CDS,Terminator, Complex, Species, DNA_part, RegulatedPromoter
-import copy
+    RBS,CDS,Terminator, Complex, Species, DNA_part, RegulatedPromoter
+from biocrnpyler.dna_construct import RNA_construct
 
 def test_CRNPlotter():
     class dummy_renderer:
@@ -25,7 +28,7 @@ def renderDNA(self,ax,designs,renderers,**keywords):
             ax.plot([0],[1])
 
             return(0,100)
-    
+
     d_r = dummy_renderer()
     test_plotter = CRNPlotter(dna_renderer=dummy_renderer(),rna_renderer=dummy_renderer(),cmap=[0,1,2,3,4,5,6])
 
@@ -77,7 +80,7 @@ def renderDNA(self,ax,designs,renderers,**keywords):
     boundspec = test_plotter.make_dpl_from_species(Species("ooga",material_type="booga")) #make a species to be bound to the promoter
     revpart = test_plotter.part_dpl_dict[RegulatedPromoter("p1",regulators=["r1","r2"])].get_directed("reverse",bound=[boundspec]) #return reverse promoter with things bound
     assert(revpart.get_dpl()[0]["type"]=="Operator") #reverse promoter has operators on the left
-    
+
 
     test_plotter.colordict = {"Promoter":"purple"}
     prom_dpl = test_plotter.make_dpl_from_part(Promoter("pconst")) #make a promoter part
@@ -94,7 +97,7 @@ def renderDNA(self,ax,designs,renderers,**keywords):
     test_construct4 = DNA_construct([RegulatedPromoter("p1",regulators=["r1","r2"]),DNA_part("test")])
     test_plotter.make_dpl_from_species(test_construct4.get_species())
     assert(test_construct4.get_species() in test_plotter.species_dpl_dict) #construct is in the dictionary
-    
+
     rna_construct = RNA_construct([RBS("ooga"),CDS("booga")])
     condpl1 = test_plotter.make_dpls_from_construct(rna_construct)
     assert(condpl1.material_type == "rna") #material type is set correctly
@@ -103,7 +106,7 @@ def renderDNA(self,ax,designs,renderers,**keywords):
     condpl2 = test_plotter.make_dpls_from_construct(rna_construct2)
     assert(condpl2==condpl1) #this construct is already in the dictionary! Just return it
 
-    
+
 
     bound_construct = Complex([test_construct4.get_species()[1],Species("integrase",material_type="protein")]).parent
     #making a construct that is bound to something
@@ -118,5 +121,33 @@ def renderDNA(self,ax,designs,renderers,**keywords):
     #make sure the part inside the construct made it into the species dict
     assert(Species("mydna",material_type="dna") in test_plotter.species_dpl_dict)
 
-
 
+def test_render_network_bokeh():
+    # Create a simple reaction
+    parameters = {
+        (None, None, "ktx"): 0.05,
+        (None, None, "kb"): 100,
+        (None, None, "ku"): 10,
+        (None, None, "ktl"): 0.05,
+        ("rna_degredation_mm", None, "kdeg"): 0.001,
+        (None, None, "cooperativity"): 2}
+    txtl = bcp.TxTlExtract('mixture1', parameters=parameters)
+    dna = bcp.DNAassembly(
+        'mydna', promoter=bcp.RegulatedPromoter('plac', ['laci']),
+        rbs='UTR1', protein='GFP', initial_concentration=10)
+    txtl.add_component(dna)
+    crn1 = txtl.compile_crn()
+    crn1.add_reactions([
+        bcp.Reaction.from_massaction(
+            [bcp.Species('mydna', material_type='rna')], [], k_forward=0.1)])
+
+    # Generate a graph and make sure it is created
+    with warnings.catch_warnings(record=True) as records:
+        plot = bcp.render_network_bokeh(crn1)
+
+    for w in records:
+        if re.search("plotting disabled", w.message.args[0]):
+            pytest.fail("plotting library import error")
+        else:
+            warnings.showwarning(
+                w.message.args[0], w.category, w.filename, w.lineno)

biocrnpyler/chemical_reaction_network.py

@@ -18,7 +18,7 @@
 
 
 class ChemicalReactionNetwork(object):
-    """A chemical reaction network is a container of species and reactions
+    r"""A chemical reaction network is a container of species and reactions
     chemical reaction networks can be compiled into SBML.
 
     reaction types:

biocrnpyler/plotting.py

@@ -47,15 +47,14 @@
 PLOT_NETWORK = False
 try:
     import networkx as nx
-    from bokeh.models import (BoxSelectTool, Circle, EdgesAndLinkedNodes,
+    from bokeh.models import (BoxSelectTool, EdgesAndLinkedNodes,
                               HoverTool, MultiLine, NodesAndLinkedEdges,
-                              PanTool, Plot, Range1d, TapTool,
+                              PanTool, Plot, Range1d, Scatter, TapTool,
                               WheelZoomTool)
-    from bokeh.models.markers import Square
     from bokeh.plotting import from_networkx
     from bokeh.palettes import Spectral4
     from bokeh.io import export_svgs, output_notebook
-    from fa2 import ForceAtlas2
+    from fa2_modified import ForceAtlas2
     PLOT_NETWORK = True
 except ModuleNotFoundError:
     pass
@@ -184,8 +183,9 @@ def graphPlot(DG,DGspecies,DGreactions,plot,layout="force",positions=None,plot_s
     ybounds[1] += max_glyph
 
     # edges
-    edges_renderer.node_renderer.glyph = Circle(
-        size=species_glyph_size, line_alpha=0, fill_alpha=0, fill_color="color")
+    edges_renderer.node_renderer.glyph = Scatter(
+        marker="circle", size=species_glyph_size, line_alpha=0,
+        fill_alpha=0, fill_color="color")
     edges_renderer.edge_renderer.glyph = MultiLine(
         line_alpha=0.2, line_width=4, line_join="round", line_color="color")
     edges_renderer.edge_renderer.selection_glyph = MultiLine(
@@ -217,17 +217,20 @@ def graphPlot(DG,DGspecies,DGreactions,plot,layout="force",positions=None,plot_s
     plot.y_range = Range1d(ylim[0], ylim[1])
 
     # reactions
-    reaction_renderer.node_renderer.glyph = Square(
-        size=reaction_glyph_size, fill_color="color")
-    reaction_renderer.node_renderer.selection_glyph = Square(
-        size=reaction_glyph_size, fill_color=Spectral4[2])
-    reaction_renderer.node_renderer.hover_glyph = Square(
-        size=reaction_glyph_size, fill_color=Spectral4[1])
+    reaction_renderer.node_renderer.glyph = Scatter(
+        marker="square", size=reaction_glyph_size, fill_color="color")
+    reaction_renderer.node_renderer.selection_glyph = Scatter(
+        marker="square", size=reaction_glyph_size, fill_color=Spectral4[2])
+    reaction_renderer.node_renderer.hover_glyph = Scatter(
+        marker="square", size=reaction_glyph_size, fill_color=Spectral4[1])
 
     # nodes
-    species_renderer.node_renderer.glyph = Circle(size=12, fill_color="color")
-    species_renderer.node_renderer.selection_glyph = Circle(size=15, fill_color=Spectral4[2])
-    species_renderer.node_renderer.hover_glyph = Circle(size=15, fill_color=Spectral4[1])
+    species_renderer.node_renderer.glyph = Scatter(
+        marker="circle", size=12, fill_color="color")
+    species_renderer.node_renderer.selection_glyph = Scatter(
+        marker="circle", size=15, fill_color=Spectral4[2])
+    species_renderer.node_renderer.hover_glyph = Scatter(
+        marker="circle", size=15, fill_color=Spectral4[1])
 
     #this part adds the interactive elements that make it so that the lines are highlighted 
     #when you mouse over and click

biocrnpyler/reaction.py

@@ -15,7 +15,7 @@
 
 
 class Reaction(object):
-    """An abstract representation of a chemical reaction in a CRN.
+    r"""An abstract representation of a chemical reaction in a CRN.
 
     A reaction has the form:
     .. math::