constructs a CellModel struct for the CellML model defined in path

ODEProblem constructs an ODEProblem from a CellModel

classify_variables divides all the variables in the doc document into
two categorizes and returns a Dict from Var to Bool:
    true: Var is a left-hand-side variable
    false: Var is not a left-hand-side variable (should be a parameter)

components_of converts the output of get_connection_component to a pair
of strings (the names of the components)

list_alg_names returns the names of variables that occur on the left-hand-side
of a non-ODE equation; hence are *algebraic* variables
comp is an Ezxml(doc) as returned by list_components

find_closure finds the transitive closure of a list of components (l) minus
the list itself, i.e., it returns the list of components in doc which are
reachable through a chain of connections starting from any component in l.

find_component finds a component by name

find_equivalence_groups categorizes all the variables in the doc document
based on the connections into equivalence groups
it returns a Dictionary of Var to groups (Set of Vars)

find_iv finds the unique independent variable

list_state_names returns the names of variables that occur on the left-hand-side
of an ODE; hence are *state* variables
comp is an Ezxml(doc) as returned by list_components

get_connection_variables returns the pair of components for the given connection
conn is an Ezxml(doc) node as returned by list_connections

get_model returns the single <model> element of a CellML file

list_component_lhs returns a set of Var composed of all variables anywhere in
the doc document that occur on the left-hand-side of an ODE or algebraic equation

list_component_lhs returns a set of Var composed of all variables in component
comp that occur on the left-hand-side of an ODE or algebraic equation

list_component_math returns a list of the math elements in the
given component

get_component_variables returns the list of the variables of a component
comp is an Ezxml(doc) as returned by list_components

list_components returns the list of CellML <Component>s

list_connection_variables returns a list composed of pairs of variable
for the given connection
conn is an Ezxml(doc) node as returned by list_connections

list_connections returns the list of <connection> nodes in the CellML document

list_import_components returns the list of component nodes of the given
import element
node: an import node as returned by list_imports

list_imports returns the list of <import> nodes in the CellML document

Given a path to a directory containing multiple CellML files.

Returns the top level files.

Used as a helper function with the CellML Physiome Model repositories.

load_cellml loads a CellML file and populates a Document structures with
the components and connections.

If resolve = true, load_cellml also resolve the imported components.

post_substitution generates the substitution rules to be applied to
the merged system after structural_simplify is applied

if changes the names of the independent variable (iv) in each system
to the global iv name

TODO: this function assumes the basic iv name is the same among all systems

pre_substitution generates the substitution rules to be applied to
individual systems before structural_simplify merges them together

it morphes variables and parameters to their correct form for ModelingToolkit
based on the global CellML doc information

process_component converts a single CellML component to an ODESystem

comp in the name of the component
class is the output of classify_variables

process_components is the main entry point
it processes an doc document and returns a merged ODESystem

use simplify=false only for debugging purposes!

resolve_imports recursively resolves the imported components of doc.

subsystems returns a Dict of the subsystems (keys are Symbols), each one
based on one CellML component of the doc document.

class is the output of classify_variables

translate_connections translates the list of MathML connections to
a list of ModelingToolkit equations

components_of converts the output of list_connection_variables to a pair
of strings (the names of the variables)