diff --git a/docs/build/html/.doctrees/classes/gillespy2.core.doctree b/docs/build/html/.doctrees/classes/gillespy2.core.doctree index d2ea30454..bd088d255 100644 Binary files a/docs/build/html/.doctrees/classes/gillespy2.core.doctree and b/docs/build/html/.doctrees/classes/gillespy2.core.doctree differ diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle index 072883dfd..9c951c38e 100644 Binary files a/docs/build/html/.doctrees/environment.pickle and b/docs/build/html/.doctrees/environment.pickle differ diff --git a/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree b/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree index 9d41ba84b..6a76c3e99 100644 Binary files a/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree and b/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree differ diff --git a/docs/build/html/_modules/gillespy2/core/model.html b/docs/build/html/_modules/gillespy2/core/model.html index 0273d918d..4e049436d 100644 --- a/docs/build/html/_modules/gillespy2/core/model.html +++ b/docs/build/html/_modules/gillespy2/core/model.html @@ -1768,8 +1768,8 @@

Source code for gillespy2.core.model

             doc = eTree.tostring(self.document)
             xmldoc = xml.dom.minidom.parseString(doc)
             ugly_xml = xmldoc.toprettyxml(indent='  ')
-            text_re = re.compile(">\n\s+([^<>\s].*?)\n\s+</", re.DOTALL)
-            pretty_xml = text_re.sub(">\g<1></", ugly_xml)
+            text_re = re.compile(r">\n\s+([^<>\s].*?)\n\s+</", re.DOTALL)
+            pretty_xml = text_re.sub(r">\g<1></", ugly_xml)
             return pretty_xml
def __species_to_element(self, species): diff --git a/docs/build/html/_modules/gillespy2/core/results.html b/docs/build/html/_modules/gillespy2/core/results.html index d33d3d7a5..d04691ab0 100644 --- a/docs/build/html/_modules/gillespy2/core/results.html +++ b/docs/build/html/_modules/gillespy2/core/results.html @@ -387,7 +387,7 @@

Source code for gillespy2.core.results

             return results
         raise ValueError("number_of_trajectories must be non-negative and non-zero")
-
[docs] def to_csv(self, path=".", nametag=None, stamp=None, postfix=".odf", verbose=False): +
[docs] def to_csv(self, path=".", nametag=None, stamp=None, suffix=".odf", verbose=False): """ Outputs the Results to one or more .csv files in a new directory. @@ -415,7 +415,7 @@

Source code for gillespy2.core.results

         else:
             identifier = nametag
 
-        directory = os.path.join(path, f"{identifier}-{stamp}{postfix}")
+        directory = os.path.join(path, f"{identifier}-{stamp}{suffix}")
         if verbose:
             print(f"Writing data to: {directory}")
         # multiple trajectories
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
index 7ce016f82..e75b674ff 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
@@ -163,7 +163,7 @@ 
Source code for gillespy2.solvers.numpy.CLE_solver
self.is_instantiated = True
 
     def __get_reactions(self, step, curr_state, curr_time, save_time, propensities, reactions):
-        """
+        r"""
         Helper Function to get reactions fired from t to t+tau.  
         
         In the equation:
diff --git a/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt b/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
index e9550fbfe..e68601760 100644
--- a/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
+++ b/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
@@ -8,7 +8,7 @@ First, in a Python script that uses GillesPy2 to perform model simulation, we be
 .. code-block:: python
 
  import gillespy2
- 
+
 
 Next, we define a model. This is a model based on a publication by Gardner et al. in Nature, 1999, and represents a genetic toggle switch in Escherichia coli.  In GillesPy2, a model is expressed as an object having the parent class ``Model``.  Components of the model, such as the reactions, molecular species, and characteristics such as the time span for simulation, are all defined within the subclass definition.  The following Python code represents our model using GillesPy2's facility:
 
@@ -77,7 +77,7 @@ And here is a plot of the deterministic simulation results:
 
 .. code-block:: python
 
- d_results.plot(title="Stochastic Switch")
+ d_results.plot(title="Deterministic Switch")
 
 
 .. image:: ode.png
diff --git a/docs/build/html/classes/gillespy2.core.html b/docs/build/html/classes/gillespy2.core.html
index d9cd66ead..721e2e338 100644
--- a/docs/build/html/classes/gillespy2.core.html
+++ b/docs/build/html/classes/gillespy2.core.html
@@ -2449,7 +2449,7 @@ 
Submodules
 

-to_csv(path='.', nametag=None, stamp=None, postfix='.odf', verbose=False)[source]

+to_csv(path='.', nametag=None, stamp=None, suffix='.odf', verbose=False)[source]
 
Outputs the Results to one or more .csv files in a new directory.

 

 
Parameters:

@@ -4567,7 +4567,7 @@ 
Submodules
 

-to_csv(path='.', nametag=None, stamp=None, postfix='.odf', verbose=False)[source]

+to_csv(path='.', nametag=None, stamp=None, suffix='.odf', verbose=False)[source]
 
Outputs the Results to one or more .csv files in a new directory.

 

 
Parameters:

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index df0d171d1..328559b6d 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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gillespy2.solvers.utilities.solverutils)": [[10, "gillespy2.solvers.utilities.solverutils.species_parse"]], "update_species_init_values() (in module gillespy2.solvers.utilities.solverutils)": [[10, "gillespy2.solvers.utilities.solverutils.update_species_init_values"]], "export() (in module gillespy2.stochss.stochssexport)": [[11, "gillespy2.stochss.StochSSexport.export"]], "gillespy2.stochss": [[11, "module-gillespy2.stochss"]], "gillespy2.stochss.stochssexport": [[11, "module-gillespy2.stochss.StochSSexport"]]}})
\ No newline at end of file
diff --git a/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html b/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
index 1c62b485b..a2af6b15c 100644
--- a/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
+++ b/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
@@ -160,7 +160,7 @@ 
Tutorial: ODE vs. SSA
 ../../_images/stochastic.png
 
And here is a plot of the deterministic simulation results:

-
d_results.plot(title="Stochastic Switch")
+
d_results.plot(title="Deterministic Switch")
 

 

 ../../_images/ode.png