Now added an exception so that the suite runs in a docker container w…

…ithout raising an error if trying to plot

Aerosol/Property_calculation.py

@@ -27,7 +27,7 @@
 
 import sys
 import numpy 
-sys.path.append('/Code/Git_repos/UManSysProp_public/')
+sys.path.append('/Users/davidtopping/Code/Git_repos/UManSysProp_public/')
 from umansysprop import boiling_points
 from umansysprop import vapour_pressures
 from umansysprop import critical_properties

Aerosol/f2py/Fixed_yield/ODE_solver_fixedyield.py

@@ -291,6 +291,8 @@ def dydt_func(t,y):
     #Plot the change in concentration over time for a given specie. For the user to change / remove
     #In a future release I will add this as a seperate module
     if with_plots:
-
-        Plotting.stacked_bar(t_array,y_matrix,num_species_condensed,num_bins,numpy.array(y_mw[include_index]),NA)
+        try:
+            Plotting.stacked_bar(t_array,y_matrix,num_species_condensed,num_bins,numpy.array(y_mw[include_index]),NA)
+        except:
+            print("There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI ")
 

Aerosol/f2py/ODE_solver.py

@@ -315,10 +315,13 @@ def dydt_func(t,y):
     #Plot the change in concentration over time for a given specie. For the user to change / remove
     #In a future release I will add this as a seperate module
     if plot_mass is True:
-        P.plot(t_array,SOA_matrix[:,0], marker='o')
-        P.title(exp_mod.name)
-        P.ylabel("SOA mass [micrograms/m3]")
-        P.xlabel("Time [seconds] since start of simulation")
-        P.show()
+        try:
+            P.plot(t_array,SOA_matrix[:,0], marker='o')
+            P.title(exp_mod.name)
+            P.ylabel("SOA mass [micrograms/m3]")
+            P.xlabel("Time [seconds] since start of simulation")
+            P.show()
+        except:
+            print("There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI ")
 
 

ODE_solver.py

@@ -253,12 +253,15 @@ def dydt_func(t,y):
     #Plot the change in concentration over time for a given specie. For the user to change / remove
     #In a future release I will add this as a seperate module
     if with_plots:
-        P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['APINENE']]), marker='o',label="APINENE")
-        P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['PINONIC']]), marker='o',label="PINONIC")
-        P.title(exp_mod.name)
-        P.legend(loc='upper left')
-        P.ylabel("Concetration log10[molecules/cc]")
-        P.xlabel("Time [seconds] since start of simulation")
-        P.show()
+        try:
+            P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['APINENE']]), marker='o',label="APINENE")
+            P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['PINONIC']]), marker='o',label="PINONIC")
+            P.title(exp_mod.name)
+            P.legend(loc='upper left')
+            P.ylabel("Concetration log10[molecules/cc]")
+            P.xlabel("Time [seconds] since start of simulation")
+            P.show()
+        except:
+            print("There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI ")
 
 

f2py/ODE_solver.py

@@ -231,12 +231,16 @@ def jacobian(t,y):
     #Plot the change in concentration over time for a given specie. For the user to change / remove
     #In a future release I will add this as a seperate module
     if with_plots:
-        P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['APINENE']]), marker='o',label="APINENE")
-        P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['PINONIC']]), marker='o',label="PINONIC")
-        P.title(exp_mod.name)
-        P.legend(loc='upper left')
-        P.ylabel("Concetration log10[molecules/cc]")
-        P.xlabel("Time [seconds] since start of simulation")
-        P.show()
+
+        try:
+            P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['APINENE']]), marker='o',label="APINENE")
+            P.plot(t_array,numpy.log10(y_matrix[:,species_dict2array['PINONIC']]), marker='o',label="PINONIC")
+            P.title(exp_mod.name)
+            P.legend(loc='upper left')
+            P.ylabel("Concetration log10[molecules/cc]")
+            P.xlabel("Time [seconds] since start of simulation")
+            P.show()
+        except:
+            print("There is a problem using Matplotlib in your environment. If using this within a docker container, you will need to transfer the data to the host or configure your container to enable graphical displays. More information can be found at http://wiki.ros.org/docker/Tutorials/GUI ")