Merge pull request #385 from sys-bio/develop

Pull to HEAD

README.md

@@ -116,8 +116,6 @@ The notebook viewer comes with Python 3.6 (64-bit).
 
 -------
 
--------
-
 ### Front-end 2: Tellurium Spyder IDE
 The Spyder IDE installers are tested with Windows 7+ and Mac OS X 10.9+. Some older Macs cannot run Spyder, regardless of 
 whether the operating system is up-to-date. 

docs/_notebooks/core/introduction.rst

@@ -31,7 +31,7 @@ below.
 
 
 
-.. image:: _notebooks/core/introduction_files/introduction_2_1.png
+.. image:: introduction_files/introduction_2_1.png
 
 
 More Complex Example
@@ -83,5 +83,5 @@ model.
 
 
 
-.. image:: _notebooks/core/introduction_files/introduction_4_0.png
+.. image:: introduction_files/introduction_4_0.png
 

docs/_notebooks/core/tellurium_stochastic.rst

@@ -32,7 +32,7 @@ type to 'gillespie' or by using the ``r.gillespie`` function.
 
 
 
-.. image:: _notebooks/core/tellurium_stochastic_files/tellurium_stochastic_2_1.png
+.. image:: tellurium_stochastic_files/tellurium_stochastic_2_1.png
 
 
 Seed
@@ -54,7 +54,7 @@ in each simulation.
 
 
 
-.. image:: _notebooks/core/tellurium_stochastic_files/tellurium_stochastic_4_0.png
+.. image:: tellurium_stochastic_files/tellurium_stochastic_4_0.png
 
 
 Combining Simulations
@@ -89,5 +89,5 @@ be drawn with the same color.
 
 
 
-.. image:: _notebooks/core/tellurium_stochastic_files/tellurium_stochastic_6_0.png
+.. image:: tellurium_stochastic_files/tellurium_stochastic_6_0.png
 

docs/_notebooks/core/widgets_lorenz.rst

@@ -100,7 +100,7 @@ attractors.
 
 
 
-.. image:: _notebooks/core/widgets_lorenz_files/widgets_lorenz_11_0.png
+.. image:: widgets_lorenz_files/widgets_lorenz_11_0.png
 
 
 Using IPython's ``interactive`` function, we can explore how the
@@ -113,7 +113,7 @@ trajectories behave as we change the various parameters.
 
 
 
-.. image:: _notebooks/core/widgets_lorenz_files/widgets_lorenz_13_0.png
+.. image:: widgets_lorenz_files/widgets_lorenz_13_0.png
 
 
 
@@ -434,7 +434,7 @@ attractors.
 
 
 
-.. image:: _notebooks/core/widgets_lorenz_files/widgets_lorenz_21_1.png
+.. image:: widgets_lorenz_files/widgets_lorenz_21_1.png
 
 
 .. code:: python
@@ -452,6 +452,6 @@ attractors.
 
 
 
-.. image:: _notebooks/core/widgets_lorenz_files/widgets_lorenz_22_1.png
+.. image:: widgets_lorenz_files/widgets_lorenz_22_1.png
 
 

requirements.txt

@@ -1,11 +1,11 @@
 # general
-numpy>=1.11.0  # 0.13.1
+numpy>=1.15.0 
 scipy>=0.19.0  # 0.19.1
 matplotlib>=2.0.2
 pandas>=0.20.2
 
 # SBW-derived
-libroadrunner==1.4.24
+libroadrunner>=1.4.24
 phrasedml>=1.0.9
 antimony>=2.9.4
 rrplugins>=1.1.10

tellurium/sedml/tesedml.py

@@ -1044,6 +1044,7 @@ def simpleTaskToPython(doc, node):
         # <STEADY STATE>
         # -------------------------------------------------------------------------
         elif simType == libsedml.SEDML_SIMULATION_STEADYSTATE:
+            lines.append("{}.steadyStateSolver.setValue('{}', {})".format(mid, 'allow_presimulation', False))
             lines.append("{}.steadyStateSelections = {}".format(mid, list(selections)))
             lines.append("{}.simulate()".format(mid))  # for stability of the steady state solver
             lines.append("{} = {}.steadyStateNamedArray()".format(resultVariable, mid))
@@ -1251,7 +1252,7 @@ def getIntegratorNameForKisaoID(kid):
         :rtype: str
         """
         if kid in KISAOS_NLEQ:
-            return 'nleq'
+            return 'nleq2'
         if kid in KISAOS_CVODE:
             return 'cvode'
         if kid in KISAOS_GILLESPIE: