[docs] def timespan(self, time_span):
"""
- Set the time span of simulation. StochKit does not support non-uniform
+ Set the time span of simulation. GillesPy2 does not support non-uniform
timespans.
:param time_span: Evenly-spaced list of times at which to sample the species populations
@@ -1461,7 +1461,7 @@ Source code for gillespy2.core.model
[docs]class StochMLDocument():
""" Serializiation and deserialization of a Model to/from
- the native StochKit2 XML format. """
+ the native XML format. """
def __init__(self):
# The root element
@@ -1471,7 +1471,7 @@ Source code for gillespy2.core.model
[docs] @classmethod
def from_model(cls, model):
"""
- Creates an StochKit XML document from an exisiting Model object.
+ Creates an XML document from an exisiting Model object.
This method assumes that all the parameters in the model are already
resolved to scalar floats (see Model.resolveParamters).
@@ -1546,7 +1546,7 @@ Source code for gillespy2.core.model
[docs] @classmethod
def from_file(cls, filepath):
- """ Intializes the document from an exisiting native StochKit XML
+ """ Intializes the document from an exisiting native XML
file read from disk. """
tree = eTree.parse(filepath)
root = tree.getroot()
@@ -1556,7 +1556,7 @@ Source code for gillespy2.core.model
[docs] @classmethod
def from_string(cls, string):
- """ Intializes the document from an exisiting native StochKit XML
+ """ Intializes the document from an exisiting native XML
file read from disk. """
root = eTree.fromString(string)
@@ -1706,8 +1706,8 @@ Source code for gillespy2.core.model
try:
kwargs['rate'] = model.listOfParameters[ratename]
except KeyError:
- # No paramter name is given. This is a valid use case
- # in StochKit. We generate a name for the paramter,
+ # No paramter name is given. This is a valid use case.
+ # We generate a name for the paramter,
# and create a new parameter instance. The parameter's
# value should now be found in 'ratename'.
generated_rate_name = "Reaction_" + name + \
@@ -1792,7 +1792,7 @@ Source code for gillespy2.core.model
description_element.text = self.annotation
sml_reac.append(description_element)
- # StochKit2 wants a rate for mass-action propensites
+ # Need a rate for mass-action propensites
if reaction.massaction and model_volume == 1.0:
rate_element = eTree.Element('Rate')
# A mass-action reactions should only have one parameter
diff --git a/docs/build/html/_modules/gillespy2/core/timespan.html b/docs/build/html/_modules/gillespy2/core/timespan.html
index fd76daa41..bdef62717 100644
--- a/docs/build/html/_modules/gillespy2/core/timespan.html
+++ b/docs/build/html/_modules/gillespy2/core/timespan.html
@@ -235,7 +235,7 @@ Source code for gillespy2.core.timespan
isuniform = np.isclose(other_diff, first_diff).all()
if not isuniform:
- raise TimespanError("StochKit only supports uniform timespans.")
+ raise TimespanError("GillesPy2 only supports uniform timespans.")
if first_diff == 0 or np.count_nonzero(other_diff) != len(other_diff):
raise TimespanError("Timespan can't contain a single repeating value.")
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
index a475391b4..f702f9d5f 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html
@@ -204,7 +204,8 @@ Source code for gillespy2.solvers.cpp.build.make
result = subprocess.run(make_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
except KeyboardInterrupt:
- log.warning(f"Makefile was interrupted during execution of target: '{target}', unexpected behavior may occur.")
+ log.warning(
+ f"Makefile was interrupted during execution of target: '{target}', unexpected behavior may occur.")
if result.returncode == 0 and os.path.exists(self.output_file):
return
diff --git a/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html b/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
index 949dd69bc..4f24ee1ac 100644
--- a/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
+++ b/docs/build/html/_modules/gillespy2/solvers/cpp/build/template_gen.html
@@ -118,16 +118,15 @@ Source code for gillespy2.solvers.cpp.build.template_gen
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
+import math
from collections import OrderedDict
from typing import Optional
from gillespy2.core import Species, Reaction, Parameter, Model, RateRule
from gillespy2.solvers.cpp.build.expression import Expression
+from gillespy2.solvers.utilities.solverutils import species_parse
from gillespy2.core import log
from gillespy2.core.gillespyError import SimulationError
-import math
-
-
[docs]class SanitizedModel:
"""
Utility class for preparing a model to be passed to a C++ solver.
@@ -176,7 +175,7 @@ Source code for gillespy2.solvers.cpp.build.template_gen
# ORDER IS IMPORTANT HERE!
# All "system" namespace entries should always be first.
# Otherwise, user-defined identifiers (like, for example, "gamma") might get overwritten.
- **{name: name for name in math.__dict__.keys()},
+ **{name: name for name in math.__dict__},
**self.function_map,
**self.species_names,
**self.parameter_names,
@@ -193,6 +192,7 @@ Source code for gillespy2.solvers.cpp.build.template_gen
self.reactions: "OrderedDict[str, dict[str, int]]" = OrderedDict()
self.reaction_reactants: "OrderedDict[str, dict[str, int]]" = OrderedDict()
self.reaction_products: "OrderedDict[str, dict[str, int]]" = OrderedDict()
+ self.reaction_props_deps: "OrderedDict[str, [int]]" = OrderedDict()
# Rate Rules: maps sanitized species names to their corresponding rate rule expression.
self.rate_rules: "OrderedDict[str, str]" = OrderedDict()
# Options: custom definitions that can be supplied by the solver, maps macros to their definitions.
@@ -230,6 +230,7 @@ Source code for gillespy2.solvers.cpp.build.template_gen
self.reactions[reaction.name] = {spec: int(0) for spec in self.species_names.values()}
self.reaction_reactants[reaction.name] = {spec: int(0) for spec in self.species_names.values()}
self.reaction_products[reaction.name] = {spec: int(0) for spec in self.species_names.values()}
+ self.reaction_props_deps[reaction.name] = {spec: int(0) for spec in self.species_names.values()}
for reactant, stoich_value in reaction.reactants.items():
reactant = self.species_names[reactant.name]
self.reactions[reaction.name][reactant] -= int(stoich_value)
@@ -240,6 +241,10 @@ Source code for gillespy2.solvers.cpp.build.template_gen
self.reactions[reaction.name][product] += int(stoich_value)
self.reaction_products[reaction.name][product] = int(stoich_value)
+ parsed_species = [spec.name for spec in species_parse(self.model, reaction.propensity_function)]
+ for species, san_species in self.species_names.items():
+ if species in parsed_species:
+ self.reaction_props_deps[reaction.name][san_species] = 1
return self
[docs] def use_rate_rule(self, rate_rule: "RateRule") -> "SanitizedModel":
@@ -511,6 +516,7 @@ Source code for gillespy2.solvers.cpp.build.template_gen
reaction_set = OrderedDict()
reactants_set = OrderedDict()
products_set = OrderedDict()
+ props_deps_set = OrderedDict()
for rxn_name, reaction in model.reactions.items():
stoich = [str(int(reaction[species])) for species in model.species_names.values()]
@@ -521,11 +527,15 @@ Source code for gillespy2.solvers.cpp.build.template_gen
for rxn_name, reaction_products in model.reaction_products.items():
products_count = [str(int(reaction_products[species])) for species in model.species_names.values()]
products_set[rxn_name] = f"{{{','.join(products_count)}}}"
+ for rxn_name, reaction_props_deps in model.reaction_props_deps.items():
+ props_deps_count = [str(int(reaction_props_deps[species])) for species in model.species_names.values()]
+ props_deps_set[rxn_name] = f"{{{','.join(props_deps_count)}}}"
reaction_names = " ".join([f"REACTION_NAME({rxn})" for rxn in reaction_set.keys()])
reaction_set = f"{{{','.join(reaction_set.values())}}}"
reactants_set = f"{{{','.join(reactants_set.values())}}}"
products_set = f"{{{','.join(products_set.values())}}}"
+ props_deps_set = f"{{{','.join(props_deps_set.values())}}}"
return {
"GPY_NUM_REACTIONS": num_reactions,
@@ -533,6 +543,7 @@ Source code for gillespy2.solvers.cpp.build.template_gen
"GPY_REACTIONS": reaction_set,
"GPY_REACTION_REACTANTS": reactants_set,
"GPY_REACTION_PRODUCTS": products_set,
+ "GPY_REACTION_PROPS_DEPS": props_deps_set
}
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
index 2c1d6d6fa..9b657c45d 100644
--- a/docs/build/html/_modules/index.html
+++ b/docs/build/html/_modules/index.html
@@ -133,7 +133,6 @@ All modules for which code is available
gillespy2.solvers.numpy.ssa_solver
gillespy2.solvers.numpy.tau_hybrid_solver
gillespy2.solvers.numpy.tau_leaping_solver
-gillespy2.solvers.stochkit.stochkit_solvers
gillespy2.solvers.utilities.Tau
gillespy2.solvers.utilities.cpp_support_test
gillespy2.solvers.utilities.solverutils
diff --git a/docs/build/html/_sources/classes/gillespy2.solvers.rst.txt b/docs/build/html/_sources/classes/gillespy2.solvers.rst.txt
index 6836f632a..73f75ea82 100644
--- a/docs/build/html/_sources/classes/gillespy2.solvers.rst.txt
+++ b/docs/build/html/_sources/classes/gillespy2.solvers.rst.txt
@@ -9,7 +9,6 @@ Subpackages
gillespy2.solvers.cpp
gillespy2.solvers.numpy
- gillespy2.solvers.stochkit
gillespy2.solvers.utilities
Module contents
diff --git a/docs/build/html/classes/gillespy2.core.html b/docs/build/html/classes/gillespy2.core.html
index 5af0abf3c..0c731a9e5 100644
--- a/docs/build/html/classes/gillespy2.core.html
+++ b/docs/build/html/classes/gillespy2.core.html
@@ -1797,7 +1797,7 @@ Submodules
timespan(time_span)[source]¶
-Set the time span of simulation. StochKit does not support non-uniform
+
Set the time span of simulation. GillesPy2 does not support non-uniform
timespans.
- Parameters:
@@ -1837,18 +1837,18 @@ Submodulesclass gillespy2.core.model.StochMLDocument[source]¶
Bases: object
Serializiation and deserialization of a Model to/from
-the native StochKit2 XML format.
+the native XML format.
-
classmethod from_file(filepath)[source]¶
-Intializes the document from an exisiting native StochKit XML
+
Intializes the document from an exisiting native XML
file read from disk.
-
classmethod from_model(model)[source]¶
-Creates an StochKit XML document from an exisiting Model object.
+
Creates an XML document from an exisiting Model object.
This method assumes that all the parameters in the model are already
resolved to scalar floats (see Model.resolveParamters).
Note, this method is intended to be used internally by the models
@@ -1868,7 +1868,7 @@
Submodules
-
classmethod from_string(string)[source]¶
-Intializes the document from an exisiting native StochKit XML
+
Intializes the document from an exisiting native XML
file read from disk.
@@ -3923,7 +3923,7 @@ Submodules
-
timespan(time_span)[source]¶
-Set the time span of simulation. StochKit does not support non-uniform
+
Set the time span of simulation. GillesPy2 does not support non-uniform
timespans.
- Parameters:
@@ -4691,18 +4691,18 @@ Submodulesclass gillespy2.core.StochMLDocument[source]¶
Bases: object
Serializiation and deserialization of a Model to/from
-the native StochKit2 XML format.
+the native XML format.
-
classmethod from_file(filepath)[source]¶
-Intializes the document from an exisiting native StochKit XML
+
Intializes the document from an exisiting native XML
file read from disk.
-
classmethod from_model(model)[source]¶
-Creates an StochKit XML document from an exisiting Model object.
+
Creates an XML document from an exisiting Model object.
This method assumes that all the parameters in the model are already
resolved to scalar floats (see Model.resolveParamters).
Note, this method is intended to be used internally by the models
@@ -4722,7 +4722,7 @@
Submodules
-
classmethod from_string(string)[source]¶
-Intializes the document from an exisiting native StochKit XML
+
Intializes the document from an exisiting native XML
file read from disk.
diff --git a/docs/build/html/classes/gillespy2.html b/docs/build/html/classes/gillespy2.html
index 4cb504aba..6f12d3b94 100644
--- a/docs/build/html/classes/gillespy2.html
+++ b/docs/build/html/classes/gillespy2.html
@@ -714,12 +714,6 @@ SubpackagesModule contents
-
- gillespy2.solvers.stochkit package
-
- gillespy2.solvers.utilities package
- Submodules
- gillespy2.solvers.utilities.Tau module
diff --git a/docs/build/html/classes/gillespy2.solvers.html b/docs/build/html/classes/gillespy2.solvers.html
index 5e6ccc731..0c81ac695 100644
--- a/docs/build/html/classes/gillespy2.solvers.html
+++ b/docs/build/html/classes/gillespy2.solvers.html
@@ -380,49 +380,6 @@ Subpackagesgillespy2.solvers.stochkit package
-
- gillespy2.solvers.utilities package
- Submodules
- gillespy2.solvers.utilities.Tau module
diff --git a/docs/build/html/classes/gillespy2.solvers.numpy.html b/docs/build/html/classes/gillespy2.solvers.numpy.html
index a1ba834e0..062ddd6ef 100644
--- a/docs/build/html/classes/gillespy2.solvers.numpy.html
+++ b/docs/build/html/classes/gillespy2.solvers.numpy.html
@@ -18,7 +18,7 @@
-
+
@@ -86,7 +86,7 @@ Related Topics
- gillespy2 package
@@ -1023,7 +1023,7 @@ Submodulesgillespy2.solvers.cpp.build package
-
- gillespy2.solvers.stochkit package
+ gillespy2.solvers.utilities package
→
diff --git a/docs/build/html/classes/gillespy2.solvers.stochkit.html b/docs/build/html/classes/gillespy2.solvers.stochkit.html
index 419746dbf..12003fd98 100644
--- a/docs/build/html/classes/gillespy2.solvers.stochkit.html
+++ b/docs/build/html/classes/gillespy2.solvers.stochkit.html
@@ -18,8 +18,6 @@
-
-
@@ -65,30 +63,14 @@ Navigation
- Tutorial: ODE vs. SSA
API reference
-
-- gillespy2 package
-
+
Related Topics
@@ -123,387 +105,11 @@ gillespy2.solvers.stochkit package
Submodules¶
-
-gillespy2.solvers.stochkit.stochkit_solvers module¶
-
--
-class gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver[source]¶
-Bases: GillesPySolver
-
-
-
-
-
--
-name = 'StochKitBaseSolver'¶
-
-
-
-
-
--
-rc = 0¶
-Abstract class for a StochKit solver. This is generally called from within a
-GillesPy Model through the Model.run function. Returns simulation
-trajectories.
-
-- Parameters:
-
-model (GillesPy2.model) – The model on which the solver will operate
t (float) – The end time of the solver
number_of_trajectories – The number of times to sample the chemical master equation. Each
-
-trajectory will be returned at the end of the simulation.
-:type number_of_trajectories: int
-
-- Parameters:
-
-increment (float) – The time step of the solution
seed (int) – The random seed for the simulation. Defaults to None.
stochkit_home – Path to stochkit. This is set automatically upon installation, but
-
-may be overwritten if desired.
-:type stochkit_home: str
-
-- Parameters:
-algorithm – The solver by which to simulate the model. ‘ssa’ or ‘tau_leaping’
-
-are the available options. If ‘ssa’ is chosen, StochKit will choose
-from the available ssa options.
-:type algorithm: str
-
-- Parameters:
-
-job_id (str) – If given, this will be the name of the solver run. Usually not set.
extra_args – Any extra arguments for the stochkit solver. See StochKit2
-
-documentation for details.
-:type extra_args: str
-
-- Parameters:
-
-debug (bool) – Set to True to provide additional debug information about the simulation.
show_labels (str) – Use names of species as index of result object rather than position numbers.
-
-
-
-
-
-
-
-
--
-class gillespy2.solvers.stochkit.stochkit_solvers.StochKitODESolver[source]¶
-Bases: StochKitBaseSolver
-
-
-
--
-name = 'StochKitODESolver'¶
-Abstract class for StochKit solver derived from the GillesPySolver class.
-This is generally used to set up the solver.
-
-- Parameters:
-
-model (GillesPy2.model) – The model on which the solver will operate
t (float) – The end time of the solver
number_of_trajectories – The number of times to sample the chemical master equation. Each
-
-trajectory will be returned at the end of the simulation.
-:type number_of_trajectories: int
-
-- Parameters:
-
-increment (float) – The time step of the solution
seed (int) – The random seed for the simulation. Defaults to None.
stochkit_home – Path to stochkit. This is set automatically upon installation, but
-
-may be overwritten if desired.
-:type stochkit_home: str
-
-- Parameters:
-algorithm – The solver by which to simulate the model. ‘ssa’ or ‘tau_leaping’
-
-are the available options. If ‘ssa’ is chosen, StochKit will choose
-from the available ssa options.
-:type algorithm: str
-
-- Parameters:
-
-job_id (str) – If given, this will be the name of the solver run. Usually not set.
extra_args – Any extra arguments for the stochkit solver. See StochKit2
-
-documentation for details.
-:type extra_args: str
-
-- Parameters:
-
-debug (bool) – Set to True to provide additional debug information about the simulation.
show_labels (str) – Use names of species as index of result object rather than position numbers.
-
-
-
-
-
-
-
-
--
-class gillespy2.solvers.stochkit.stochkit_solvers.StochKitSolver[source]¶
-Bases: StochKitBaseSolver
-
-
-
--
-name = 'StochKitSolver'¶
-Abstract class for StochKit solver derived from the GillesPySolver class.
-This is generally used to set up the solver.
-
-- Parameters:
-
-model (GillesPy2.model) – The model on which the solver will operate
t (float) – The end time of the solver
number_of_trajectories – The number of times to sample the chemical master equation. Each
-
-trajectory will be returned at the end of the simulation.
-:type number_of_trajectories: int
-
-- Parameters:
-
-increment (float) – The time step of the solution
seed (int) – The random seed for the simulation. Defaults to None.
stochkit_home – Path to stochkit. This is set automatically upon installation, but
-
-may be overwritten if desired.
-:type stochkit_home: str
-
-- Parameters:
-algorithm – The solver by which to simulate the model. ‘ssa’ or ‘tau_leaping’
-
-are the available options. If ‘ssa’ is chosen, StochKit will choose
-from the available ssa options.
-:type algorithm: str
-
-- Parameters:
-
-job_id (str) – If given, this will be the name of the solver run. Usually not set.
extra_args – Any extra arguments for the stochkit solver. See StochKit2
-
-documentation for details.
-:type extra_args: str
-
-- Parameters:
-
-debug (bool) – Set to True to provide additional debug information about the simulation.
show_labels (str) – Use names of species as index of result object rather than position numbers.
-
-
-
-
-
-
-
+
+gillespy2.solvers.stochkit.stochkit_solvers module¶
-
-Module contents¶
-
--
-class gillespy2.solvers.stochkit.StochKitODESolver[source]¶
-Bases: StochKitBaseSolver
-
-
-
--
-name = 'StochKitODESolver'¶
-Abstract class for StochKit solver derived from the GillesPySolver class.
-This is generally used to set up the solver.
-
-- Parameters:
-
-model (GillesPy2.model) – The model on which the solver will operate
t (float) – The end time of the solver
number_of_trajectories – The number of times to sample the chemical master equation. Each
-
-trajectory will be returned at the end of the simulation.
-:type number_of_trajectories: int
-
-- Parameters:
-
-increment (float) – The time step of the solution
seed (int) – The random seed for the simulation. Defaults to None.
stochkit_home – Path to stochkit. This is set automatically upon installation, but
-
-may be overwritten if desired.
-:type stochkit_home: str
-
-- Parameters:
-algorithm – The solver by which to simulate the model. ‘ssa’ or ‘tau_leaping’
-
-are the available options. If ‘ssa’ is chosen, StochKit will choose
-from the available ssa options.
-:type algorithm: str
-
-- Parameters:
-
-job_id (str) – If given, this will be the name of the solver run. Usually not set.
extra_args – Any extra arguments for the stochkit solver. See StochKit2
-
-documentation for details.
-:type extra_args: str
-
-- Parameters:
-
-debug (bool) – Set to True to provide additional debug information about the simulation.
show_labels (str) – Use names of species as index of result object rather than position numbers.
-
-
-
-
-
-
-
-
--
-class gillespy2.solvers.stochkit.StochKitSolver[source]¶
-Bases: StochKitBaseSolver
-
-
-
--
-name = 'StochKitSolver'¶
-Abstract class for StochKit solver derived from the GillesPySolver class.
-This is generally used to set up the solver.
-
-- Parameters:
-
-model (GillesPy2.model) – The model on which the solver will operate
t (float) – The end time of the solver
number_of_trajectories – The number of times to sample the chemical master equation. Each
-
-trajectory will be returned at the end of the simulation.
-:type number_of_trajectories: int
-
-- Parameters:
-
-increment (float) – The time step of the solution
seed (int) – The random seed for the simulation. Defaults to None.
stochkit_home – Path to stochkit. This is set automatically upon installation, but
-
-may be overwritten if desired.
-:type stochkit_home: str
-
-- Parameters:
-algorithm – The solver by which to simulate the model. ‘ssa’ or ‘tau_leaping’
-
-are the available options. If ‘ssa’ is chosen, StochKit will choose
-from the available ssa options.
-:type algorithm: str
-
-- Parameters:
-
-job_id (str) – If given, this will be the name of the solver run. Usually not set.
extra_args – Any extra arguments for the stochkit solver. See StochKit2
-
-documentation for details.
-:type extra_args: str
-
-- Parameters:
-
-debug (bool) – Set to True to provide additional debug information about the simulation.
show_labels (str) – Use names of species as index of result object rather than position numbers.
-
-
-
-
-
-
-
+
+Module contents¶
@@ -513,14 +119,6 @@ Submodules
- -
- ←
- gillespy2.solvers.numpy package
-
- -
- gillespy2.solvers.utilities package
- →
-
diff --git a/docs/build/html/classes/gillespy2.solvers.utilities.html b/docs/build/html/classes/gillespy2.solvers.utilities.html
index 7240672d4..895ae6434 100644
--- a/docs/build/html/classes/gillespy2.solvers.utilities.html
+++ b/docs/build/html/classes/gillespy2.solvers.utilities.html
@@ -19,7 +19,7 @@
-
+
@@ -85,7 +85,7 @@ Related Topics
Documentation overview
- gillespy2 package
- gillespy2.solvers package
- - Previous: gillespy2.solvers.stochkit package
+ - Previous: gillespy2.solvers.numpy package
- Next: gillespy2.stochss package
@@ -246,7 +246,7 @@ Submodulesgillespy2.solvers.stochkit package
+ gillespy2.solvers.numpy package
gillespy2.stochss package
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index 4eb7bd570..82430ab09 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -860,22 +860,12 @@ G
(gillespy2.solvers.ODECSolver static method)
(gillespy2.solvers.TauHybridCSolver class method)
-
-
- get_template() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method)
-
- get_trajectories() (gillespy2.solvers.stochkit.stochkit_solvers.StochKitODESolver class method)
-
-
+ - get_template() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method)
+
- get_translation_table() (gillespy2.core.Jsonify method)
@@ -1150,20 +1140,6 @@ G
- module
-
-
- -
- gillespy2.solvers.stochkit
-
-
- - module
-
-
- -
- gillespy2.solvers.stochkit.stochkit_solvers
-
-
- - module
-
@@ -1298,8 +1274,6 @@
K
L
- - locate_executable() (gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver static method)
-
- LOOP_OVER_INTEGRATE (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute)
@@ -1435,10 +1407,6 @@ M
- gillespy2.solvers.numpy.tau_hybrid_solver
- gillespy2.solvers.numpy.tau_leaping_solver
-
- - gillespy2.solvers.stochkit
-
- - gillespy2.solvers.stochkit.stochkit_solvers
- gillespy2.solvers.utilities
@@ -1513,16 +1481,6 @@ N
- (gillespy2.solvers.ODESolver attribute)
- (gillespy2.solvers.SSACSolver attribute)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver attribute)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitODESolver attribute)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitSolver attribute)
-
- - (gillespy2.solvers.stochkit.StochKitODESolver attribute)
-
- - (gillespy2.solvers.stochkit.StochKitSolver attribute)
- (gillespy2.solvers.TauHybridCSolver attribute)
@@ -1731,8 +1689,6 @@ P
- (gillespy2.core.model.Model method)
- - process_seed() (gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver static method)
-
- public_vars() (gillespy2.core.Jsonify method)
@@ -1783,8 +1739,6 @@ R
- (gillespy2.solvers.NumPySSASolver attribute)
- (gillespy2.solvers.ODESolver attribute)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver attribute)
- (gillespy2.solvers.TauHybridSolver attribute)
@@ -1931,16 +1885,6 @@ R
- (gillespy2.solvers.ODESolver method)
- (gillespy2.solvers.SSACSolver method)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitBaseSolver class method)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitODESolver class method)
-
- - (gillespy2.solvers.stochkit.stochkit_solvers.StochKitSolver class method)
-
- - (gillespy2.solvers.stochkit.StochKitODESolver class method)
-
- - (gillespy2.solvers.stochkit.StochKitSolver class method)
- (gillespy2.solvers.TauHybridCSolver method)
@@ -2061,12 +2005,12 @@ S
- (gillespy2.core.reaction.Reaction method)
+
- SimulationReturnCode (class in gillespy2.solvers.cpp.c_solver)
- SimulationTimeoutError, [1]
@@ -2109,20 +2053,6 @@
S
- - StochKitBaseSolver (class in gillespy2.solvers.stochkit.stochkit_solvers)
-
- - StochKitODESolver (class in gillespy2.solvers.stochkit)
-
-
- - StochKitSolver (class in gillespy2.solvers.stochkit)
-
-
- StochMLDocument (class in gillespy2.core)
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index 6294c764b..e1f453ee3 100644
Binary files a/docs/build/html/objects.inv and b/docs/build/html/objects.inv differ
diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 796ef6824..2a087ec1a 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -304,16 +304,6 @@
Python Module Index
gillespy2.solvers.numpy.tau_leaping_solver
-
-
- gillespy2.solvers.stochkit
-
-
-
- gillespy2.solvers.stochkit.stochkit_solvers
-
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 1ef644db1..f36560790 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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