Merge pull request #425 from sys-bio/develop

Pull to Develop
sys-bio · Jan 17, 2019 · 08705f3 · 08705f3
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diff --git a/.gitignore b/.gitignore
@@ -70,3 +70,5 @@ examples/tellurium-files/phrasedml/results/
 examples/tellurium-files/omex/results/
 tellurium/tests/testdata/sedml/sed-ml/results/
 
+# Mac .DS_store
+.DS_Store
diff --git a/README.md b/README.md
@@ -211,7 +211,7 @@ If you use Tellurium in your research, we would appreciate following citations i
 
 Medley et al. (2018) ["Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology"](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006220) PLoS Computational Biology 14(6) e1006220.
 
-Choi et al. (2018) ["Tellurium: An extensible python-based modeling environment for systems and synthetic biology"](https://www.sciencedirect.com/science/article/pii/S0303264718301254) Biosystems.
+Choi et al. (2018) ["Tellurium: An extensible python-based modeling environment for systems and synthetic biology"](https://www.sciencedirect.com/science/article/pii/S0303264718301254) Biosystems 171 74-79.
 
 ## Contact Us
 

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diff --git a/docs/_notebooks/core/antimonyExample.rst b/docs/_notebooks/core/antimonyExample.rst
@@ -79,7 +79,7 @@ simulation.
 
     --------------------------------------------------------------------------------
     tellurium : 2.1.0
-    roadrunner : 1.4.24
+    roadrunner : 1.5.1
     antimony : 2.9.4
     libsbml : 5.15.0
     libsedml : 0.4.3

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diff --git a/docs/_notebooks/core/combineExample.rst b/docs/_notebooks/core/combineExample.rst
@@ -55,7 +55,8 @@ stored as Combine Archive.
 
 .. parsed-literal::
 
-    {'/tmp/tmpuso70njf/main.xml': {'code': 'r"""\n####################################################################################################\n                            tellurium 2.1.0\n-+++++++++++++++++-         Python Environment for Modeling and Simulating Biological Systems\n .+++++++++++++++.\n  .+++++++++++++.           Homepage:      http://tellurium.analogmachine.org/\n-//++++++++++++/.   -:/-`   Documentation: https://tellurium.readthedocs.io/en/latest/index.html\n.----:+++++++/.++  .++++/   Forum:         https://groups.google.com/forum/#!forum/tellurium-discuss\n      :+++++:  .+:` .--++   Bug reports:   https://github.com/sys-bio/tellurium/issues\n       -+++-    ./+:-://.   Repository:    https://github.com/sys-bio/tellurium\n        .+.       `...`\n\nSED-ML simulation experiments: http://www.sed-ml.org/\n    sedmlDoc: L1V2  \n    inputType:      \'SEDML_FILE\'\n    workingDir:     \'/tmp/tmpuso70njf\'\n    saveOutputs:    \'False\'\n    outputDir:      \'None\'\n    plottingEngine: \'<MatplotlibEngine>\'\n\nLinux-4.1.7-200.fc22.x86_64-x86_64-with-fedora-22-Twenty_Two\npython 3.6.3 (default, Oct 25 2017, 01:09:07) \n[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]\n####################################################################################################\n"""\nimport tellurium as te\nfrom roadrunner import Config\nfrom tellurium.sedml.mathml import *\nfrom tellurium.sedml.tesedml import process_trace, terminate_trace, fix_endpoints\n\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport mpl_toolkits.mplot3d\ntry:\n    import tesedml as libsedml\nexcept ImportError:\n    import libsedml\nimport pandas\nimport os.path\nConfig.LOADSBMLOPTIONS_RECOMPILE = True\n\nworkingDir = r\'/tmp/tmpuso70njf\'\n\n# --------------------------------------------------------\n# Models\n# --------------------------------------------------------\n# Model <model1>\nmodel1 = te.loadSBMLModel(os.path.join(workingDir, \'myModel.xml\'))\n\n\n\n\n# --------------------------------------------------------\n# Tasks\n# --------------------------------------------------------\n# Task <task1>\n# Task: <task1>\ntask1 = [None]\nmodel1.setIntegrator(\'cvode\')\nif model1.conservedMoietyAnalysis == True: model1.conservedMoietyAnalysis = False\nmodel1.timeCourseSelections = [\'time\', \'[S1]\', \'[S2]\']\nmodel1.reset()\ntask1[0] = model1.simulate(start=0.0, end=5.0, steps=100)\n\n# --------------------------------------------------------\n# DataGenerators\n# --------------------------------------------------------\n# DataGenerator <plot_0_0_0>\n__var__time = np.concatenate([sim[\'time\'] for sim in task1])\nif len(__var__time.shape) == 1:\n     __var__time.shape += (1,)\nplot_0_0_0 = __var__time\n# DataGenerator <plot_0_0_1>\n__var__S1 = np.concatenate([sim[\'[S1]\'] for sim in task1])\nif len(__var__S1.shape) == 1:\n     __var__S1.shape += (1,)\nplot_0_0_1 = __var__S1\n# DataGenerator <plot_0_1_1>\n__var__S2 = np.concatenate([sim[\'[S2]\'] for sim in task1])\nif len(__var__S2.shape) == 1:\n     __var__S2.shape += (1,)\nplot_0_1_1 = __var__S2\n\n# --------------------------------------------------------\n# Outputs\n# --------------------------------------------------------\n# Output <plot_0>\n_stacked = False\nif _stacked:\n    tefig = te.getPlottingEngine().newStackedFigure(title=\'Figure 1\', xtitle=\'time\')\nelse:\n    tefig = te.nextFigure(title=\'Figure 1\', xtitle=\'time\')\n\nfor k in range(plot_0_0_0.shape[1]):\n    extra_args = {}\n    if k == 0:\n        extra_args[\'name\'] = \'S1\'\n    tefig.addXYDataset(plot_0_0_0[:,k], plot_0_0_1[:,k], color=\'C0\', tag=\'tag0\', logx=False, logy=False, **extra_args)\nfor k in range(plot_0_0_0.shape[1]):\n    extra_args = {}\n    if k == 0:\n        extra_args[\'name\'] = \'S2\'\n    tefig.addXYDataset(plot_0_0_0[:,k], plot_0_1_1[:,k], color=\'C1\', tag=\'tag1\', logx=False, logy=False, **extra_args)\nif te.tiledFigure():\n\n    if te.tiledFigure().renderIfExhausted():\n\n        te.clearTiledFigure()\n\nelse:\n\n    fig = tefig.render()\n\n####################################################################################################',
+    {'/tmp/tmp2clb19gp/main.xml': {'code': 'r"""\n####################################################################################################\n                            tellurium 2.1.0\n-+++++++++++++++++-         Python Environment for Modeling and Simulating Biological Systems\n .+++++++++++++++.\n  .+++++++++++++.           Homepage:      http://tellurium.analogmachine.org/\n-//++++++++++++/.   -:/-`   Documentation: https://tellurium.readthedocs.io/en/latest/index.html\n.----:+++++++/.++  .++++/   Forum:         https://groups.google.com/forum/#!forum/tellurium-discuss\n      :+++++:  .+:` .--++   Bug reports:   https://github.com/sys-bio/tellurium/issues\n       -+++-    ./+:-://.   Repository:    https://github.com/sys-bio/tellurium\n        .+.       `...`\n\nSED-ML simulation experiments: http://www.sed-ml.org/\n    sedmlDoc: L1V2  \n    inputType:      \'SEDML_FILE\'\n    workingDir:     \'/tmp/tmp2clb19gp\'\n    saveOutputs:    \'False\'\n    outputDir:      \'None\'\n    plottingEngine: \'<MatplotlibEngine>\'\n\nLinux-4.15.0-29-generic-x86_64-with-debian-buster-sid\npython 3.6.5 |Anaconda, Inc.| (default, Apr 29 2018, 16:14:56) \n[GCC 7.2.0]\n####################################################################################################\n"""\nimport tellurium as te\nfrom roadrunner import Config\nfrom tellurium.sedml.mathml import *\nfrom tellurium.sedml.tesedml import process_trace, terminate_trace, fix_endpoints\n\nimport numpy as np\nimport matplotlib.pyplot as plt\nimport mpl_toolkits.mplot3d\ntry:\n    import tesedml as libsedml\nexcept ImportError:\n    import libsedml\nimport pandas\nimport os.path\nConfig.LOADSBMLOPTIONS_RECOMPILE = True\n\nworkingDir = r\'/tmp/tmp2clb19gp\'\n\n# --------------------------------------------------------\n# Models\n# --------------------------------------------------------\n# Model <model1>\nmodel1 = te.loadSBMLModel(os.path.join(workingDir, \'myModel.xml\'))\n\n\n\n\n# --------------------------------------------------------\n# Tasks\n# --------------------------------------------------------\n# Task <task1>\n# Task: <task1>\ntask1 = [None]\nmodel1.setIntegrator(\'cvode\')\nif model1.conservedMoietyAnalysis == True: model1.conservedMoietyAnalysis = False\nmodel1.timeCourseSelections = [\'[S2]\', \'[S1]\', \'time\']\nmodel1.reset()\ntask1[0] = model1.simulate(start=0.0, end=5.0, steps=100)\n\n# --------------------------------------------------------\n# DataGenerators\n# --------------------------------------------------------\n# DataGenerator <plot_0_0_0>\n__var__time = np.concatenate([sim[\'time\'] for sim in task1])\nif len(__var__time.shape) == 1:\n     __var__time.shape += (1,)\nplot_0_0_0 = __var__time\n# DataGenerator <plot_0_0_1>\n__var__S1 = np.concatenate([sim[\'[S1]\'] for sim in task1])\nif len(__var__S1.shape) == 1:\n     __var__S1.shape += (1,)\nplot_0_0_1 = __var__S1\n# DataGenerator <plot_0_1_1>\n__var__S2 = np.concatenate([sim[\'[S2]\'] for sim in task1])\nif len(__var__S2.shape) == 1:\n     __var__S2.shape += (1,)\nplot_0_1_1 = __var__S2\n\n# --------------------------------------------------------\n# Outputs\n# --------------------------------------------------------\n# Output <plot_0>\n_stacked = False\nif _stacked:\n    tefig = te.getPlottingEngine().newStackedFigure(title=\'Figure 1\', xtitle=\'time\')\nelse:\n    tefig = te.nextFigure(title=\'Figure 1\', xtitle=\'time\')\n\nfor k in range(plot_0_0_0.shape[1]):\n    extra_args = {}\n    if k == 0:\n        extra_args[\'name\'] = \'S1\'\n    tefig.addXYDataset(plot_0_0_0[:,k], plot_0_0_1[:,k], color=\'C0\', tag=\'tag0\', logx=False, logy=False, **extra_args)\nfor k in range(plot_0_0_0.shape[1]):\n    extra_args = {}\n    if k == 0:\n        extra_args[\'name\'] = \'S2\'\n    tefig.addXYDataset(plot_0_0_0[:,k], plot_0_1_1[:,k], color=\'C1\', tag=\'tag1\', logx=False, logy=False, **extra_args)\nif te.tiledFigure():\n\n    if te.tiledFigure().renderIfExhausted():\n\n        te.clearTiledFigure()\n\nelse:\n\n    fig = tefig.render()\n\n####################################################################################################',
+      'platform': 'Linux-4.15.0-29-generic-x86_64-with-debian-buster-sid',
       'dataGenerators': {'plot_0_0_0': array([[0.  ],
               [0.05],
               [0.1 ],
@@ -356,7 +357,6 @@ stored as Combine Archive.
               [9.92171419],
               [9.92553221],
               [9.92916402],
-              [9.9326187 ]])},
-      'platform': 'Linux-4.1.7-200.fc22.x86_64-x86_64-with-fedora-22-Twenty_Two'}}
+              [9.9326187 ]])}}}
 
 
diff --git a/docs/_notebooks/core/combineExample_files/combineExample_2_0.png b/docs/_notebooks/core/combineExample_files/combineExample_2_0.png
diff --git a/docs/_notebooks/core/combineExample_files/combineExample_3_0.png b/docs/_notebooks/core/combineExample_files/combineExample_3_0.png
diff --git a/docs/_notebooks/core/computeSteadyState.rst b/docs/_notebooks/core/computeSteadyState.rst
@@ -10,8 +10,6 @@ Steady states can be calculated using ``r.getSteadyStateValues``
     import tellurium as te
     from roadrunner import Config
     
-    Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True) 
-    
     r = te.loada('''
       model pathway()
          $Xo -> S1; k1*Xo - k2*S1
@@ -29,11 +27,10 @@ Steady states can be calculated using ``r.getSteadyStateValues``
     values = r.getSteadyStateValues()
     for sid, value in zip(r.steadyStateSelections, r.getSteadyStateValues()):
         print(sid, "=", value)
-    Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, False)
 
 
 .. parsed-literal::
 
     [S1] = 0.17857142857142858
-    [S2] = 0.0
+    [S2] = 4.5150957559317066e-35
 
diff --git a/docs/_notebooks/core/introduction_files/introduction_2_0.png b/docs/_notebooks/core/introduction_files/introduction_2_0.png
diff --git a/docs/_notebooks/core/introduction_files/introduction_4_0.png b/docs/_notebooks/core/introduction_files/introduction_4_0.png
diff --git a/docs/_notebooks/core/methods_installing_packages.rst b/docs/_notebooks/core/methods_installing_packages.rst
@@ -1,4 +1,13 @@
 
+How to install additional packages
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you are using Tellurium notebook or Tellurium Spyder, you can install
+additional package using ``installPackage`` function. In Tellurium
+Spyder, you can also install packages using included command Prompt. For
+more information, see `Running Command Prompt for Tellurium
+Spyder <https://tellurium.readthedocs.io/en/latest/walkthrough.html#running-command-prompt-for-tellurium-spyder>`__.
+
 .. code-block:: python
 
     import tellurium as te

diff --git a/...model_consecutiveUniUniReactions_files/model_consecutiveUniUniReactions_2_0.png b/...model_consecutiveUniUniReactions_files/model_consecutiveUniUniReactions_2_0.png
diff --git a/...ooks/core/model_feedback_oscillations_files/model_feedback_oscillations_2_0.png b/...ooks/core/model_feedback_oscillations_files/model_feedback_oscillations_2_0.png
diff --git a/...ooks/core/model_feedback_oscillations_files/model_feedback_oscillations_2_1.png b/...ooks/core/model_feedback_oscillations_files/model_feedback_oscillations_2_1.png
diff --git a/...l_generatingDifferentWaveforms_files/model_generatingDifferentWaveforms_2_0.png b/...l_generatingDifferentWaveforms_files/model_generatingDifferentWaveforms_2_0.png
diff --git a/docs/_notebooks/core/model_modelFromBioModels.rst b/docs/_notebooks/core/model_modelFromBioModels.rst
@@ -12,57 +12,11 @@ URL to directly load ``BIOMD0000000010``.
     import tellurium as te
     
     # Load model from biomodels (may not work with https).
-    r = te.loadSBMLModel("http://biomodels.caltech.edu/download?mid=BIOMD0000000010")
+    r = te.loadSBMLModel("https://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000010")
     result = r.simulate(0, 3000, 5000)
     r.plot(result)
 
 
-::
 
-
-    ---------------------------------------------------------------------------
-
-    RuntimeError                              Traceback (most recent call last)
-
-    <ipython-input-1-8a25f612667b> in <module>()
-          5 
-          6 # Load model from biomodels (may not work with https).
-    ----> 7 r = te.loadSBMLModel("http://biomodels.caltech.edu/download?mid=BIOMD0000000010")
-          8 result = r.simulate(0, 3000, 5000)
-          9 r.plot(result)
-
-
-    /extra/devel/src/tellurium/tellurium/tellurium.py in loadSBMLModel(sbml)
-        557     :rtype: roadrunner.ExtendedRoadRunner
-        558     """
-    --> 559     return roadrunner.RoadRunner(sbml)
-        560 
-        561 
-
-
-    /extra/devel/src/tellurium/tellurium/roadrunner/extended_roadrunner.py in __init__(self, *args, **kwargs)
-         14 
-         15     def __init__(self, *args, **kwargs):
-    ---> 16         super(ExtendedRoadRunner, self).__init__(*args, **kwargs)
-         17 
-         18     # ---------------------------------------------------------------------
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/roadrunner/roadrunner.py in _new_init(self, *args)
-       3513                 return
-       3514     # Otherwise, use regular init
-    -> 3515         RoadRunner._swig_init(self, *args)
-       3516         RoadRunner._makeProperties(self)
-       3517 
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/roadrunner/roadrunner.py in __init__(self, *args)
-       2520 
-       2521     def __init__(self, *args):
-    -> 2522         this = _roadrunner.new_RoadRunner(*args)
-       2523         try:
-       2524             self.this.append(this)
-
-
-    RuntimeError: static std::string rr::SBMLReader::read(const string&), could not open http://biomodels.caltech.edu/download?mid=BIOMD0000000010 as a file or uri
+.. image:: _notebooks/core/model_modelFromBioModels_files/model_modelFromBioModels_2_0.png
 
diff --git a/..._notebooks/core/model_modelFromBioModels_files/model_modelFromBioModels_2_0.png b/..._notebooks/core/model_modelFromBioModels_files/model_modelFromBioModels_2_0.png
diff --git a/docs/_notebooks/core/model_normalizedSpecies_files/model_normalizedSpecies_3_0.png b/docs/_notebooks/core/model_normalizedSpecies_files/model_normalizedSpecies_3_0.png
diff --git a/docs/_notebooks/core/parameter_scan.rst b/docs/_notebooks/core/parameter_scan.rst
@@ -1,11 +1,9 @@
+Perform Parameter Scan
+~~~~~~~~~~~~~~~~~~~~~~
 
+``plotPolyArray()`` example
 
-Parameter scan
-~~~~~~~~~~~~~~
-
-Perform a parameter scan.
-
-.. code:: ipython2
+.. code-block:: python
 
     import tellurium as te
     
@@ -37,91 +35,11 @@ Perform a parameter scan.
     p.plotPolyArray()
 
 
-::
-
-
-    ---------------------------------------------------------------------------
-
-    TypeError                                 Traceback (most recent call last)
-
-    <ipython-input-1-f092f852a16c> in <module>()
-         28 )
-         29 # plot
-    ---> 30 p.plotPolyArray()
-    
-
-    /extra/devel/src/tellurium/tellurium/analysis/parameterscan.py in plotPolyArray(self)
-        349 
-        350         if not IPYTHON:
-    --> 351             self.plotPolyArrayFunction(result)
-        352             return result
-        353         else:
-
-
-    /extra/devel/src/tellurium/tellurium/analysis/parameterscan.py in plotPolyArrayFunction(self, result)
-        301             if len(self.color) != self.polyNumber:
-        302                 self.color = self.colorCycle()
-    --> 303             poly = PolyCollection(result, facecolors=self.color, closed=False)
-        304 
-        305         poly.set_alpha(self.alpha)
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/collections.py in __init__(self, verts, sizes, closed, **kwargs)
-        961         Collection.__init__(self, **kwargs)
-        962         self.set_sizes(sizes)
-    --> 963         self.set_verts(verts, closed)
-        964         self.stale = True
-        965 
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/collections.py in set_verts(self, verts, closed)
-        986                     self._paths.append(mpath.Path(xy))
-        987         else:
-    --> 988             self._paths = [mpath.Path(xy) for xy in verts]
-        989         self.stale = True
-        990 
-
+.. image:: _notebooks/core/parameter_scan_files/parameter_scan_2_0.png
 
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/collections.py in <listcomp>(.0)
-        986                     self._paths.append(mpath.Path(xy))
-        987         else:
-    --> 988             self._paths = [mpath.Path(xy) for xy in verts]
-        989         self.stale = True
-        990 
+``plotSurface()`` example
 
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/path.py in __init__(self, vertices, codes, _interpolation_steps, closed, readonly)
-        130             and codes as read-only arrays.
-        131         """
-    --> 132         vertices = _to_unmasked_float_array(vertices)
-        133         if (vertices.ndim != 2) or (vertices.shape[1] != 2):
-        134             raise ValueError(
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/cbook/__init__.py in _to_unmasked_float_array(x)
-       2048         return np.ma.asarray(x, float).filled(np.nan)
-       2049     else:
-    -> 2050         return np.asarray(x, float)
-       2051 
-       2052 
-
-
-    ~/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/numpy/core/numeric.py in asarray(a, dtype, order)
-        490 
-        491     """
-    --> 492     return array(a, dtype, copy=False, order=order)
-        493 
-        494 
-
-
-    TypeError: float() argument must be a string or a number, not 'zip'
-
-
-
-.. image:: _notebooks/core/parameter_scan_files/parameter_scan_2_1.png
-
-
-.. code:: ipython2
+.. code-block:: python
 
     r = te.loada('''
         $Xo -> S1; vo;
@@ -150,7 +68,5 @@ Perform a parameter scan.
     # plot
     p.plotSurface()
 
-
-
 .. image:: _notebooks/core/parameter_scan_files/parameter_scan_3_0.png
 
diff --git a/docs/_notebooks/core/parameter_scan_files/parameter_scan_2_0.png b/docs/_notebooks/core/parameter_scan_files/parameter_scan_2_0.png
diff --git a/docs/_notebooks/core/parameter_scan_files/parameter_scan_2_1.png b/docs/_notebooks/core/parameter_scan_files/parameter_scan_2_1.png
diff --git a/docs/_notebooks/core/parameter_scan_files/parameter_scan_3_0.png b/docs/_notebooks/core/parameter_scan_files/parameter_scan_3_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_10_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_10_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_10_1.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_10_1.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_12_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_12_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_12_1.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_12_1.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_14_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_14_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_2_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_2_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_4_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_4_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_4_1.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_4_1.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_6_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_6_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_8_0.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_8_0.png
diff --git a/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_8_1.png b/docs/_notebooks/core/phrasedmlExample_files/phrasedmlExample_8_1.png
diff --git a/docs/_notebooks/core/plot2DParameterScan.rst b/docs/_notebooks/core/plot2DParameterScan.rst
@@ -1,6 +1,9 @@
 
-.. code:: ipython2
+.. code-block:: python
 
+    import warnings
+    warnings.filterwarnings("ignore")
+    
     import tellurium as te
     from tellurium.analysis.parameterscan import plot2DParameterScan
     
@@ -26,14 +29,6 @@
 .. image:: _notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_0.png
 
 
-.. parsed-literal::
-
-    /home/poltergeist/.config/Tellurium/telocal/python-3.6.3/lib/python3.6/site-packages/matplotlib/figure.py:459: UserWarning:
-    
-    matplotlib is currently using a non-GUI backend, so cannot show the figure
-    
-
-
 
-.. image:: _notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_2.png
+.. image:: _notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_1.png
 
diff --git a/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_0.png b/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_0.png
diff --git a/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_1.png b/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_1.png
diff --git a/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_2.png b/docs/_notebooks/core/plot2DParameterScan_files/plot2DParameterScan_0_2.png
diff --git a/docs/_notebooks/core/roadrunnerBasics.rst b/docs/_notebooks/core/roadrunnerBasics.rst
@@ -237,8 +237,7 @@ Selections
 
 The selections list can be used to set which state variables will appear
 in the output array. By default, it includes all SBML species and the
-``time`` variable. Selections can be either given as argument to
-``r.simulate``.
+``time`` variable. Selections can be given as an argument to ``r.simulate``.
 
 .. code-block:: python
 

diff --git a/docs/_notebooks/core/roadrunnerBasics_files/roadrunnerBasics_4_0.png b/docs/_notebooks/core/roadrunnerBasics_files/roadrunnerBasics_4_0.png
diff --git a/docs/_notebooks/core/roadrunnerBasics_files/roadrunnerBasics_6_1.png b/docs/_notebooks/core/roadrunnerBasics_files/roadrunnerBasics_6_1.png
diff --git a/docs/_notebooks/core/steadystate_scan.rst b/docs/_notebooks/core/steadystate_scan.rst
@@ -6,16 +6,14 @@ Steady state scan
 Using ``te.ParameterScan.SteadyStateScan`` for scanning the steady
 state.
 
-.. code:: ipython2
+.. code-block:: python
 
     import tellurium as te
     import matplotlib.pyplot as plt
     import tellurium as te
     import numpy as np
     from roadrunner import Config
     
-    Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, True) 
-    
     r = te.loada('''
         $Xo -> S1; vo;
         S1 -> S2; k1*S1 - k2*S2;
@@ -33,10 +31,35 @@ state.
         selection = ['S1', 'S2']                      
     )
     p.plotArray()
-    
-    Config.setValue(Config.LOADSBMLOPTIONS_CONSERVED_MOIETIES, False) 
 
 
 
 .. image:: _notebooks/core/steadystate_scan_files/steadystate_scan_2_0.png
 
+
+
+
+.. parsed-literal::
+
+    array([[2.05263158, 0.5       , 0.48717949],
+           [2.10526316, 0.5       , 0.475     ],
+           [2.15789474, 0.5       , 0.46341463],
+           [2.21052632, 0.5       , 0.45238095],
+           [2.26315789, 0.5       , 0.44186047],
+           [2.31578947, 0.5       , 0.43181818],
+           [2.36842105, 0.5       , 0.42222222],
+           [2.42105263, 0.5       , 0.41304348],
+           [2.47368421, 0.5       , 0.40425532],
+           [2.52631579, 0.5       , 0.39583333],
+           [2.57894737, 0.5       , 0.3877551 ],
+           [2.63157895, 0.5       , 0.38      ],
+           [2.68421053, 0.5       , 0.37254902],
+           [2.73684211, 0.5       , 0.36538462],
+           [2.78947368, 0.5       , 0.35849057],
+           [2.84210526, 0.5       , 0.35185185],
+           [2.89473684, 0.5       , 0.34545455],
+           [2.94736842, 0.5       , 0.33928571],
+           [3.        , 0.5       , 0.33333333],
+           [3.05263158, 0.5       , 0.32758621]])
+
+
diff --git a/docs/_notebooks/core/steadystate_scan_files/steadystate_scan_2_0.png b/docs/_notebooks/core/steadystate_scan_files/steadystate_scan_2_0.png