### Example Simulation Setup

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/docs-build/C++APIReference/rrRoadRunner.html

Demonstrates how to set up simulation options, including start time, end time, and number of steps, for a simulation using a stiff integrator.

```cpp
RoadRunner rr = RoadRunner("someFile.xml");
SimulateOptions opt = rr.getSimulateOptions();
opt.start = 0;
opt.end = 10;
opt.steps = 1000;
```

--------------------------------

### Install Executable

Source: https://github.com/sys-bio/roadrunner/blob/develop/examples/create_uuid/CMakeLists.txt

Installs the built target executable to the bin directory, categorized under the 'examples' component. This is used for deploying built examples.

```cmake
install(TARGETS ${target}
        DESTINATION bin
        COMPONENT examples)
```

--------------------------------

### Example: Gillespie Simulation Setup

Source: https://github.com/sys-bio/roadrunner/blob/develop/wrappers/C/html/group__stochastic.html

Example demonstrating how to set up parameters for the gillespieOnGridEx function. Ensure rrHandle is properly initialized before calling.

```c
RRCDataPtr m;
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
m = gillespieOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints);
```

--------------------------------

### Example: Gillespie Simulation Setup

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/group__stochastic.html

Example demonstrating how to set up parameters for the gillespieOnGridEx function. Ensure the RRCDataPtr structure is freed after use.

```c
[RRCDataPtr](struct_r_r_c_data.html) m;

double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;

m = [gillespieOnGridEx](group__stochastic.html#gabedfc117be6781c6caca54ecc74561ea) (rrHandle, timeStart, timeEnd, numberOfPoints);
```

--------------------------------

### Installation Folder

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/rrc__api_8h_source.html

Functions for setting and getting the installation folder.

```APIDOC
## setInstallFolder

### Description
Set the internal string containing the folder in where the RoadRunner C wrappers is installed.

### Method
POST

### Endpoint
/setInstallFolder

### Parameters
#### Path Parameters
- **folder** (const char *) - Required - The path to the installation folder.

### Response
#### Success Response (200)
- **success** (bool) - True if the folder was set successfully, false otherwise.

### Response Example
```json
{
  "success": true
}
```

## getInstallFolder

### Description
Returns the folder in which the RoadRunner wrappers is installed.

### Method
GET

### Endpoint
/getInstallFolder

### Parameters
None

### Response
#### Success Response (200)
- **folderPath** (char *) - The path to the installation folder.

### Response Example
```json
{
  "folderPath": "/usr/local/roadrunner"
}
```
```

--------------------------------

### Example: Simulate Model with Custom Options

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/C++APIReference/rrRoadRunner.html

Demonstrates how to set simulation options (start time, end time, number of steps) and then perform a simulation using a specific integrator.

```cpp
RoadRunner rr = RoadRunner("someFile.xml");
SimulateOptions opt = rr.getSimulateOptions();
opt.start = 0;
// opt.end = 10;
// opt.steps = 1000;
// rr.simulate(&opt);
```

--------------------------------

### Example Usage of Setting Get and GetAs

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/classrr_1_1Setting.html

Demonstrates the usage of get() and getAs() methods for retrieving and converting values from a Setting object. It shows successful retrieval, expected exceptions for type mismatches, and successful conversions between compatible types.

```cpp
[Setting](classrr_1_1Setting.html#a2f3f6beff36ad237ca6493dfaa19741f) setting(5);

ASSERT_EQ(setting.get<int>(), 5); // fails if setting is not int

ASSERT_THROW(setting.get<unsigned int>();, std::bad_variant_access); // bad, setting contains an int

ASSERT_EQ(setting.getAs<unsigned int>(), 5); // Okay, we can convert from int to unsigned (when int > 0)
```

--------------------------------

### Example: Simulate with Stiff Integrator

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/classrr_1_1_road_runner.html

Demonstrates setting simulation options for a stiff integrator, including start time, duration, steps, and enabling stiffness.

```cpp
[RoadRunner](classrr_1_1_road_runner.html#a04a6fd481cfacc2510d5d113520143ef) r = [RoadRunner](classrr_1_1_road_runner.html#a04a6fd481cfacc2510d5d113520143ef)("someFile.xml");

BasicDictionary opt;
opt.setItem("start", 0);
opt.setItem("duration", 10);
opt.setItem("steps", 1000);
opt.setItem("stiff", true);

const DoubleMatrix *result = r.simulate(&opt);
```

--------------------------------

### Minimal Hello RoadRunner Plugin Example

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/rrplugins/rrplugins_architecture.html

A minimal example demonstrating how to create a plugin for RoadRunner. This example serves as a starting point for developing more complex plugins.

```python
import roadrunner

# Example usage of roadrunner functionalities within a plugin context
# (Actual plugin code would be more complex and involve C++ or other language bindings)

# Placeholder for plugin logic
print("Hello RoadRunner Plugin!")

```

--------------------------------

### CMake Project Setup and Installation

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/examples/python/parameter_minimization/one_parameter/CMakeLists.txt

Configures the minimum required CMake version, names the project, and specifies files to be installed. Ensure the DESTINATION path is correctly set for your project structure.

```cmake
CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3 FATAL_ERROR)
PROJECT(TEL_PYTHON_EXAMPLES)

set(plugin_examples
)
install (
FILES
README.txt
${plugin_examples}
DESTINATION examples/python/parameter_minimization/one_parameter
COMPONENT examples
)
```

--------------------------------

### main.cpp Example for RoadRunner C++ Simulation

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/docs-build/_sources/UsingRoadRunnerFromCxx/using_roadrunner_from_cxx.rst.txt

This C++ code demonstrates how to initialize RoadRunner, load a model, create a simulation, and run it. Ensure RoadRunner is installed and CMakeLists.txt is correctly configured.

```C++
#include <roadrunner.h>
#include <iostream>

int main() {
    // Create a RoadRunner instance
    rr::RoadRunner rr;

    // Load a model (replace with your model file path)
    rr.loadModel("path/to/your/model.xml");

    // Create a simulation
    rr.setSimulateOptions(0.0, 10.0); // Start time, end time

    // Run the simulation
    rr.simulate();

    // Get results (example: get the value of the first variable)
    rr::RVCollection* results = rr.getFloatingSpeciesCongruentValues();
    if (results && results->size() > 0) {
        std::cout << "First floating species value: " << (*results)[0] << std::endl;
    }

    // Clean up
    delete results;

    return 0;
}
```

--------------------------------

### Example: Add Plugin Usage

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/_sources/rrplugins/introduction.rst.txt

Demonstrates a complete workflow: instantiating an 'add' plugin, setting input properties, executing, and retrieving the result.

```python
p = Plugin("add")
p.x = 3.4
p.y = 5.6
p.execute()
print(p.result)
```

--------------------------------

### Install Python Setup Script with CMake

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/wrappers/python/CMakeLists.txt

Installs the Python setup script for the Roadrunner plugins to the root of the installation directory. This script is essential for package management.

```cmake
install(
  FILES
  ${CMAKE_CURRENT_SOURCE_DIR}/setup_rrplugins.py
  DESTINATION .
  COMPONENT rrplugins
)
```

--------------------------------

### Conditional Python Build and Example Installation

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/plugins/monte_carlo_bs/CMakeLists.txt

Installs the target library to a Python-specific location and copies example files if the BUILD_PYTHON flag is enabled.

```cmake
if(BUILD_PYTHON)
    install (TARGETS ${target}
    DESTINATION ${RR_PLUGINS_PYLIB_INSTALL_PREFIX}
    COMPONENT plugins
    )
    file(GLOB EXAMPLES docs/Examples/*)
    install(FILES ${EXAMPLES} DESTINATION "${RR_PLUGINS_PYTHON_INSTALL_PREFIX}" COMPONENT plugins)
    unset(EXAMPLES)
endif()
```

--------------------------------

### Create Project Directory

Source: https://github.com/sys-bio/roadrunner/blob/develop/test/googletest-master/docs/quickstart-cmake.md

Initializes a new project directory and navigates into it. This is the first step in setting up a new project.

```bash
$ mkdir my_project && cd my_project
```

--------------------------------

### Installation Folder

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__initialization.html

Functions to get and set the RoadRunner installation folder.

```APIDOC
## getInstallFolder()

### Description
Returns the folder in which the RoadRunner wrappers are installed.

### Method
N/A (C function)

### Endpoint
N/A

### Parameters
None

### Request Example
```c
char* install_dir = getInstallFolder();
```

### Response
#### Success Response
- **char*** - Pointer to a string holding the install folder path.

#### Response Example
```c
char* install_dir = getInstallFolder();
printf("RoadRunner installed in: %s\n", install_dir);
```

## setInstallFolder(const char *folder)

### Description
Set the internal string containing the folder where the RoadRunner C wrappers are installed.

### Method
N/A (C function)

### Endpoint
N/A

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```c
setInstallFolder("/opt/roadrunner/lib");
```

### Response
#### Success Response
- **bool** - Boolean indicating success.

#### Response Example
```c
bool success = setInstallFolder("/usr/local/roadrunner");
```
```

--------------------------------

### Simulate Model with Custom Options (Example 1)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/classrr_1_1RoadRunner.html

Example demonstrating how to set simulation options for time, duration, and steps, and specifying a stiff integrator.

```cpp
[RoadRunner](classrr_1_1RoadRunner.html#a04a6fd481cfacc2510d5d113520143ef) rr = [RoadRunner](classrr_1_1RoadRunner.html#a04a6fd481cfacc2510d5d113520143ef)("someFile.xml");
SimulateOptions opt = rr.getSimulateOptions();
opt.start = 0;
opt.duration = 10;
opt.steps = 1000;
const DoubleMatrix *result = rr.simulate(&opt);
```

--------------------------------

### Get Time Start

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__simulation.html

Retrieves the current start time for the simulation.

```APIDOC
## GET /sys-bio/roadrunner/timeStart

### Description
Get the value of the current time start.

### Method
GET

### Endpoint
/sys-bio/roadrunner/timeStart

### Parameters
#### Query Parameters
- **handle** (RRHandle) - Required - Handle to a RoadRunner instance

### Response
#### Success Response (200)
- **timeStart** (double) - The current value for the time start.

#### Response Example
```json
{
  "timeStart": 0.0
}
```
```

--------------------------------

### getTimeStart() - Get Simulation Start Time

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/group__simulation.html

Retrieves the current start time of the simulation.

```APIDOC
## GET /sys-bio/roadrunner/getTimeStart

### Description
Get the value of the current time start.

### Method
GET

### Endpoint
/sys-bio/roadrunner/getTimeStart

### Parameters
#### Path Parameters
- **handle** (RRHandle) - Required - Handle to a RoadRunner instance

#### Query Parameters
- **timeStart** (double*) - Required - Pointer to store the current value for the time start

### Response
#### Success Response (200)
- **success** (bool) - Returns true if successful

#### Response Example
```json
{
  "success": true,
  "timeStart": 0.0
}
```
```

--------------------------------

### Basic Plugin Usage Example

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/_sources/rrplugins/introduction.rst.txt

A simple example demonstrating loading a 'test' plugin, setting its 'x' and 'y' properties, executing it, and printing the result from property 'z'.

```python
import rrplugins as tel
p = tel.Plugin("test")
p.x = 1.2
p.y = 4.5
p.execute()
print(p.z)
```

--------------------------------

### Get Simulation Start Time

Source: https://github.com/sys-bio/roadrunner/blob/develop/wrappers/C/html/group__simulation.html

Retrieves the current start time of the simulation. Requires a valid RRHandle.

```c
bool rrcCallConv getTimeStart(RRHandle handle, double *timeStart)
```

--------------------------------

### Get Start Time of Simulation

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__simulation.html

Retrieves the current start time for the simulation. Requires a handle to a RoadRunner instance.

```c
bool rrcCallConv getTimeStart(RRHandle handle, double *timeStart)
```

```c
status = getTimeStart (rrHandle, &timeStart);
```

--------------------------------

### Get Installation Folder

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__initialization.html

Retrieves the installation directory of the RoadRunner C wrappers. Useful for locating necessary files or configurations.

```c
char * 
getInstallFolder(void)
```

--------------------------------

### Model Initialization and Setup

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/classrr_1_1CompiledExecutableModel-members.html

Methods for initializing and setting up the simulation model.

```APIDOC
## setupDLLFunctions

### Description
Sets up the necessary functions from the loaded DLL.

### Method
POST

### Endpoint
/api/model/setupDLLFunctions

### Response
#### Success Response (200)
- **status** (string) - Indicates success.

#### Response Example
```json
{
  "status": "success"
}
```
```

```APIDOC
## setupModelData

### Description
Initializes and sets up the internal data structures for the model.

### Method
POST

### Endpoint
/api/model/setupModelData

### Response
#### Success Response (200)
- **status** (string) - Indicates success.

#### Response Example
```json
{
  "status": "success"
}
```
```

--------------------------------

### Installation

Source: https://github.com/sys-bio/roadrunner/blob/develop/source/thread-pool/README.md

Instructions for installing the thread pool library using different methods.

```APIDOC
## Installation

### Including the Library

Download the `thread_pool.hpp` header file and include it in your project:

```cpp
#include "thread_pool.hpp"
```

### Installing using vcpkg

**Linux/macOS:**
```none
./vcpkg install bshoshany-thread-pool
```

**Windows:**
```none
.\vcpkg install bshoshany-thread-pool:x86-windows bshoshany-thread-pool:x64-windows
```

After installation with vcpkg, include `thread_pool.hpp` directly in your project.
```

--------------------------------

### Basic Simulation with Options

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/C++APIReference/rrRoadRunner.html

A basic example of setting simulation duration and steps using `SimulateOptions` before calling the simulate function.

```cpp
opt.duration = 10;
opt.steps = 1000;
const DoubleMatrix *result = rr.simulate(&opt);
```

--------------------------------

### Project and Include Directories Setup

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/plugins/CMakeLists.txt

Sets up the project name and includes directories for common plugin headers. Ensure RR_PLUGINS_ROOT is defined in your environment.

```cmake
project(plugins)

#Give all plugins access to headers in the following folders
include_directories(
  ${RR_PLUGINS_ROOT}/rrplugins/core
  ${RR_PLUGINS_ROOT}/rrplugins/common
  ${RR_PLUGINS_ROOT}/rrplugins/math
  ${RR_PLUGINS_ROOT}/wrappers/C
)
```

--------------------------------

### Install Roadrunner Library Components

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/plugins/test_model/CMakeLists.txt

Configures the installation of the Roadrunner library targets for runtime, archive, and library components. Includes conditional installation for Python components and example files if BUILD_PYTHON is enabled.

```cmake
install(
        TARGETS ${target}
        RUNTIME DESTINATION bin COMPONENT rrplugins
        ARCHIVE DESTINATION lib COMPONENT rrplugins
        LIBRARY DESTINATION lib COMPONENT rrplugins
)

if(BUILD_PYTHON)
    install(TARGETS ${target} DESTINATION ${RR_PLUGINS_PYLIB_INSTALL_PREFIX} COMPONENT plugins)
    file(GLOB EXAMPLES docs/Examples/*)
    install(FILES ${EXAMPLES} DESTINATION "${RR_PLUGINS_PYTHON_INSTALL_PREFIX}" COMPONENT plugins)
    unset(EXAMPLES)
endif()
```

--------------------------------

### Simulate Model with Custom Options (Example 2)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/classrr_1_1RoadRunner.html

Example showing how to set integrator, simulation time, duration, steps, and integrator-specific options like 'seed' for the Gillespie integrator.

```cpp
[RoadRunner](classrr_1_1RoadRunner.html#a04a6fd481cfacc2510d5d113520143ef) rr = [RoadRunner](classrr_1_1RoadRunner.html#a04a6fd481cfacc2510d5d113520143ef)("someFile.xml");
rr.setIntegrator("gillespie");
SimulateOptions opt;
opt.start = 0;
opt.duration = 10;
opt.steps = 1000;
opt.setItem("stiff", true);
opt.setItem("seed", 12345);
const DoubleMatrix *result = rr.simulate(&opt);
```

--------------------------------

### Get Floating Species Initial Concentrations (Example)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__initialConditions.html

Example usage for retrieving initial floating species concentrations. Requires a valid RRHandle.

```c
vec = [getFloatingSpeciesInitialConcentrations](group__initialConditions.html#ga69c0a516f028a0608d8b9167ff56111f) ([RRHandle](rrc__types_8h.html#a1d68f0592372208fa5a5f2799ea4b3ae) handle);
```

--------------------------------

### Setup and Execute Minimization

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/source/rrplugins/rrplugins_LM_plugin.md

This snippet loads necessary plugins, sets up a progress event handler, executes a model to generate data, configures the Levenberg-Marquardt minimizer with model data and parameters, and initiates the minimization process.

```python
chiPlugin       = Plugin("tel_chisquare")
lm              = Plugin("tel_levenberg_marquardt")
modelPlugin     = Plugin("tel_test_model")
addNoisePlugin  = Plugin("tel_add_noise")

try:
    #========== EVENT FUNCTION SETUP ===========================
    def myEvent(dummy): #We are not capturing any data from the plugin, so just pass a dummy
        print('Iteration, Norm = ' + `lm.getProperty("NrOfIter")`  + ', ' + `lm.getProperty("Norm")`)

    #Setup progress event function
    progressEvent =  NotifyEventEx(myEvent)
    assignOnProgressEvent(lm.plugin, progressEvent)
    #============================================================

    #Create model data, with and without noise using the test_model plugin
    modelPlugin.execute()

    #Setup lmfit properties.
    lm.SBML             = modelPlugin.Model
    lm.ExperimentalData = modelPlugin.TestDataWithNoise

    # Add the parameters that we're going to fit and an initial 'start' value
    lm.setProperty("InputParameterList", ["k1", .3])
    lm.setProperty("FittedDataSelectionList", "[S1] [S2]")
    lm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")

    # Start minimization
    lm.execute()

    print('Minimization finished. 
==== Result ====')
    print('Fit engine status: ' + `lm.getProperty('StatusMessage')`)

    print('Hessian Matrix')
    print(lm.getProperty("Hessian"))

    print('Covariance  Matrix')
    print(lm.getProperty("CovarianceMatrix"))

    print('ChiSquare = '            + `lm.getProperty("ChiSquare")`)
    print('Reduced ChiSquare = '    + `lm.getProperty("ReducedChiSquare")`)

    #This is a list of parameters
    parameters = tpc.getPluginProperty (lm.plugin, "OutputParameterList")
    confLimits = tpc.getPluginProperty (lm.plugin, "ConfidenceLimits")

    #Iterate trough list of parameters and confidence limits
    para  = getFirstProperty(parameters)
    limit = getFirstProperty(confLimits)
    while para and limit:
        print(getPropertyName(para) + ' = ' + `getPropertyValue(para)` + ' +/- ' + `getPropertyValue(limit)`)
        para  = getNextProperty(parameters)
        limit = getNextProperty(confLimits)


    # Get the fitted and residual data
    fittedData = lm.getProperty ("FittedData").toNumpy
    residuals  = lm.getProperty ("Residuals").toNumpy

    # Get the experimental data as a numpy array
    experimentalData = modelPlugin.TestDataWithNoise.toNumpy

    telplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
    telplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
    telplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
    telplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
    telplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
    telplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
    telplugins.plt.show()

except Exception as e:
    print('Problem.. ' + `e`)
```

--------------------------------

### Get Simulation Time Start - C

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/group__simulation.html

Retrieves the current start time of the simulation. Requires a valid RRHandle and a pointer to a double to store the result.

```c
C_DECL_SPEC bool rrcCallConv getTimeStart
(
[RRHandle](rrc__types_8h.html#a1d68f0592372208fa5a5f2799ea4b3ae) 
_handle_,
double * 
_timeStart_ 
)

```

```c
status = [getTimeStart](group__simulation.html#ga0d05bdfec6dd9387c64dd196ec3d880d) (rrHandle, &timeStart);
```

```c
C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double *timeStart)

```

--------------------------------

### Run Monte Carlo Simulation

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/_sources/rrplugins/rrplugins_monte_carlo_plugin.rst.txt

This snippet demonstrates the setup and execution of a Monte Carlo simulation. It includes configuring experimental data, selecting a minimization plugin, setting the number of runs, and defining input parameters and data selection lists. Use this to perform parameter fitting and uncertainty analysis.

```python
myEvent =  NotifyEventEx(myEventFunction)
        
        #Uncomment the event assignment below to plot each monte carlo data set
        #assignOnFinishedEvent(lmP.plugin, myEvent, None)                    
        
        #This will create test data with noise. We will use that as 'experimental' data
        modelP.execute() 
               
        #Setup Monte Carlo properties.
        mcP.SBML                             = modelP.Model
        mcP.ExperimentalData                 = modelP.TestDataWithNoise
        
        #Select what minimization plugin to use                     
        #mcP.MinimizerPlugin                  = "Nelder-Mead"
        mcP.MinimizerPlugin                  = "Levenberg-Marquardt"
        mcP.NrOfMCRuns                       = 100
        mcP.InputParameterList               = ["k1", 1.5]
        mcP.FittedDataSelectionList          = "[S1] [S2]"
        mcP.ExperimentalDataSelectionList    = "[S1] [S2]"
        
        # Start Monte Carlo
        mcP.execute()
```

--------------------------------

### Get Floating Species Initial Concentration IDs (Example)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/group__initialConditions.html

Example usage for retrieving initial floating species IDs. Requires a valid RRHandle.

```c
vec = [getFloatingSpeciesInitialConcentrationIds](group__initialConditions.html#ga205905d483bb876f0557d8b40cba2213) ([RRHandle](rrc__types_8h.html#a1d68f0592372208fa5a5f2799ea4b3ae) handle);
```

--------------------------------

### Write a Basic GoogleTest Example

Source: https://github.com/sys-bio/roadrunner/blob/develop/test/googletest-master/docs/quickstart-cmake.md

Includes the GoogleTest header and demonstrates basic assertions like EXPECT_STRNE and EXPECT_EQ. This file should be placed in your project directory.

```cpp
#include <gtest/gtest.h>

// Demonstrate some basic assertions.
TEST(HelloTest, BasicAssertions) {
  // Expect two strings not to be equal.
  EXPECT_STRNE("hello", "world");
  // Expect equality.
  EXPECT_EQ(7 * 6, 42);
}
```

--------------------------------

### Minimal Plugin Example (Python)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/docs-build/rrplugins/rrplugins_architecture.html

A basic example demonstrating how to create a plugin for RoadRunner. This serves as a starting point for developing custom plugin functionalities.

```python
import rrplugins

class HelloRoadRunner(rrplugins.Plugin):
    def __init__(self):
        super(HelloRoadRunner, self).__init__()

    def __del__(self):
        super(HelloRoadRunner, self).__del__()

    def getName(self):
        return "HelloRoadRunner"

    def getVersion(self):
        return "1.0.0"

    def getRRInfo(self):
        return "Hello RoadRunner Plugin"

    def execute(self, input):
        print("Hello RoadRunner!")
        return "Hello RoadRunner!"

```

--------------------------------

### Get Simulation Time Range

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/globals_func_g.html

Retrieves the start and end times for the simulation.

```APIDOC
## GET /api/simulation/time

### Description
Retrieves the start and end times for the simulation.

### Method
GET

### Endpoint
/api/simulation/time

### Response
#### Success Response (200)
- **timeStart** (number) - The start time of the simulation.
- **timeEnd** (number) - The end time of the simulation.

#### Response Example
{
  "timeStart": 0.0,
  "timeEnd": 100.0
}
```

--------------------------------

### Install Library Components

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/plugins/monte_carlo_bs/CMakeLists.txt

Defines installation rules for the target library, specifying runtime, archive, and library destinations and components.

```cmake
install(
        TARGETS ${target}
        RUNTIME DESTINATION bin COMPONENT rrplugins
        ARCHIVE DESTINATION lib COMPONENT rrplugins
        LIBRARY DESTINATION lib COMPONENT rrplugins
)
```

--------------------------------

### Conditional Python Plugin Installation

Source: https://github.com/sys-bio/roadrunner/blob/develop/rrplugins/plugins/add_noise/CMakeLists.txt

Conditionally installs the 'add_noise' library and associated example files into Python-specific directories if the BUILD_PYTHON flag is enabled. This facilitates Python integration.

```cmake
if(BUILD_PYTHON)
    install (TARGETS ${target}
        DESTINATION ${RR_PLUGINS_PYLIB_INSTALL_PREFIX}
        COMPONENT plugins
        )
    file(GLOB EXAMPLES docs/*)
    install(FILES ${EXAMPLES} DESTINATION "${RR_PLUGINS_PYTHON_INSTALL_PREFIX}" COMPONENT plugins)
    unset(EXAMPLES)
endif()
```

--------------------------------

### Get Floating Species Initial Condition IDs (Example)

Source: https://github.com/sys-bio/roadrunner/blob/develop/wrappers/C/html/group__initial_conditions.html

Example usage for retrieving floating species initial condition IDs. This function requires a handle to a RoadRunner instance.

```c
vec = getFloatingSpeciesInitialConcentrationIds(handle);
```

--------------------------------

### Example Usage of simulateEx

Source: https://github.com/sys-bio/roadrunner/blob/develop/wrappers/C/html/group__simulation.html

An example demonstrating how to call the simulateEx function with specific simulation parameters.

```c
RRCDataPtr m;
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
m = simulateEx(rrHandle, timeStart, timeEnd, numberOfPoints);
```

--------------------------------

### Simulation Time Control API

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/rrRoadRunnerData_8h_source.html

Functions to get the start and end times of the simulation.

```APIDOC
## GET /simulation/time/start

### Description
Get the value of the current time start.

### Method
GET

### Endpoint
/simulation/time/start

### Parameters
#### Query Parameters
- **handle** (RRHandle) - Required - Handle to the RoadRunner instance.

### Response
#### Success Response (200)
- **timeStart** (double *) - Pointer to a double that will store the time start value.

## GET /simulation/time/end

### Description
Get the value of the current time end.

### Method
GET

### Endpoint
/simulation/time/end

### Parameters
#### Query Parameters
- **handle** (RRHandle) - Required - Handle to the RoadRunner instance.

### Response
#### Success Response (200)
- **timeEnd** (double *) - Pointer to a double that will store the time end value.
```

--------------------------------

### Create JIT Engine with LLVM Backend Options

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/doxygen-output/html/_2home_2vsts_2work_21_2s_2source_2llvm_2JitFactory_8h-example.html

Instantiate a JIT engine using LoadSBMLOptions, specifying the LLVM backend. Options include MCJIT or LLJit.

```cpp
LoadSBMLOptions opt;

opt.setLLVMBackend(LoadSBMLOptions::MCJIT); // or LoadSBMLOptions::LLJit;

std::unique_ptr<Jit> j = JitFactory::makeJitEngine(opt.modelGeneratorOpt);
```

--------------------------------

### Load and Setup Plugins

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/rrplugins/rrplugins_LM_plugin.html

Loads necessary plugins for chi-square, Levenberg-Marquardt optimization, model testing, and noise addition. It also sets up a progress event function to monitor the minimization process.

```python
chiPlugin       = Plugin("tel_chisquare")
lm              = Plugin("tel_levenberg_marquardt")
modelPlugin     = Plugin("tel_test_model")
addNoisePlugin  = Plugin("tel_add_noise")

try:
    #========== EVENT FUNCTION SETUP ===========================
    def myEvent(dummy): #We are not capturing any data from the plugin, so just pass a dummy
        print('Iteration, Norm = ' + `lm.getProperty("NrOfIter")`  + ', ' + `lm.getProperty("Norm")`)

    #Setup progress event function
    progressEvent =  NotifyEventEx(myEvent)
    assignOnProgressEvent(lm.plugin, progressEvent)
    #============================================================

    #Create model data, with and without noise using the test_model plugin
    modelPlugin.execute()

    #Setup lmfit properties.
    lm.SBML             = modelPlugin.Model
    lm.ExperimentalData = modelPlugin.TestDataWithNoise

    # Add the parameters that we're going to fit and an initial 'start' value
    lm.setProperty("InputParameterList", ["k1", .3])
    lm.setProperty("FittedDataSelectionList", "[S1] [S2]")
    lm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")

    # Start minimization
    lm.execute()

    print('Minimization finished. \n==== Result ====')
    print('Fit engine status: ' + `lm.getProperty('StatusMessage')`)

    print('Hessian Matrix')
    print(lm.getProperty("Hessian"))

    print('Covariance  Matrix')
    print(lm.getProperty("CovarianceMatrix"))

    print('ChiSquare = '            + `lm.getProperty("ChiSquare")`)
    print('Reduced ChiSquare = '    + `lm.getProperty("ReducedChiSquare")`)

    #This is a list of parameters
    parameters = tpc.getPluginProperty (lm.plugin, "OutputParameterList")
    confLimits = tpc.getPluginProperty (lm.plugin, "ConfidenceLimits")

    #Iterate trough list of parameters and confidence limits
    para  = getFirstProperty(parameters)
    limit = getFirstProperty(confLimits)
    while para and limit:
        print(getPropertyName(para) + ' = ' + `getPropertyValue(para)` + ' +/- ' + `getPropertyValue(limit)`)
        para  = getNextProperty(parameters)
        limit = getNextProperty(confLimits)


    # Get the fitted and residual data
    fittedData = lm.getProperty ("FittedData").toNumpy
    residuals  = lm.getProperty ("Residuals").toNumpy

    # Get the experimental data as a numpy array
    experimentalData = modelPlugin.TestDataWithNoise.toNumpy

    telplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
    telplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
    telplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
    telplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
    telplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
    telplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
    telplugins.plt.show()

except Exception as e:
    print('Problem.. ' + `e`)
```

--------------------------------

### Time Parameters

Source: https://github.com/sys-bio/roadrunner/blob/develop/wrappers/C/html/rrc__api_8h_source.html

Functions to get the start time, end time, and number of points for simulations.

```APIDOC
## GET /api/simulation/timestart

### Description
Retrieves the start time of the simulation.

### Method
GET

### Endpoint
/api/simulation/timestart

### Parameters
#### Path Parameters
None

#### Query Parameters
- **handle** (RRHandle) - Required - Handle to the simulation model.

### Request Example
```json
{
  "handle": "your_model_handle"
}
```

### Response
#### Success Response (200)
- **timeStart** (double) - The start time of the simulation.

#### Response Example
```json
{
  "timeStart": 0.0
}
```
```

```APIDOC
## GET /api/simulation/timeend

### Description
Retrieves the end time of the simulation.

### Method
GET

### Endpoint
/api/simulation/timeend

### Parameters
#### Path Parameters
None

#### Query Parameters
- **handle** (RRHandle) - Required - Handle to the simulation model.

### Request Example
```json
{
  "handle": "your_model_handle"
}
```

### Response
#### Success Response (200)
- **timeEnd** (double) - The end time of the simulation.

#### Response Example
```json
{
  "timeEnd": 10.0
}
```
```

```APIDOC
## GET /api/simulation/numpoints

### Description
Retrieves the number of data points for the simulation.

### Method
GET

### Endpoint
/api/simulation/numpoints

### Parameters
#### Path Parameters
None

#### Query Parameters
- **handle** (RRHandle) - Required - Handle to the simulation model.

### Request Example
```json
{
  "handle": "your_model_handle"
}
```

### Response
#### Success Response (200)
- **numPoints** (int) - The number of data points.

#### Response Example
```json
{
  "numPoints": 100
}
```
```

--------------------------------

### Simulation Time Control API

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/OriginalDoxygenStyleDocs/html/rr_road_runner_data_8h_source.html

Functions to get the start and end times of the current simulation.

```APIDOC
## Simulation Time Control

### GET /simulation/time/start

#### Description
Retrieves the start time of the current simulation.

#### Method
GET

#### Endpoint
/simulation/time/start

#### Parameters
##### Query Parameters
- **handle** (RRHandle) - Required - Handle to the RoadRunner instance.

#### Response
##### Success Response (200)
- **timeStart** (double*) - Pointer to a double that will store the start time.

### GET /simulation/time/end

#### Description
Retrieves the end time of the current simulation.

#### Method
GET

#### Endpoint
/simulation/time/end

#### Parameters
##### Query Parameters
- **handle** (RRHandle) - Required - Handle to the RoadRunner instance.

#### Response
##### Success Response (200)
- **timeEnd** (double*) - Pointer to a double that will store the end time.
```

--------------------------------

### Enable Test and Example Builds

Source: https://github.com/sys-bio/roadrunner/blob/develop/source/parallel-hashmap/CMakeLists.txt

Configures options to enable building tests and examples. These options are typically controlled by the master project.

```cmake
option(PHMAP_BUILD_TESTS    "Whether or not to build the tests"    ${PHMAP_MASTER_PROJECT})
option(PHMAP_BUILD_EXAMPLES "Whether or not to build the examples" ${PHMAP_MASTER_PROJECT})
```

--------------------------------

### Install CPython Debug Build (Windows)

Source: https://github.com/sys-bio/roadrunner/blob/develop/docs/docs-build/developers_docs/build_with_python_debug.html

This command installs the CPython debug build into the specified directory. Ensure the paths for `-d`, `-s`, `-b`, and `--copy install-cpython/x64/dbg` are correct for your setup.

```batch
.\python.bat .\PC\layout\ -d -s . -b .\PCbuild\amd64\ --copy install-cpython/x64/dbg --preset-default
```