Welcome to the Pulse Wiki
We use this space to talk about various features and possibilities you may not know Pulse supports, demonstrate best practices, and provide detailed explanations for any questions or problems anyone brings to our attention.
If you would like us to expand upon anything feel free to bring it up in our discourse channel.
We also assume you have build the source code per instruction from our repository.
- We will refer to the source code directory as
- The build directory you set where you ran CMake, will be refereed to as
- All commands will be run from a terminal in the
<pulse/build>/install/bin, which we will refer to as
The script to run all of our tests, utilities, and tools is written in CMake to ensure cross platform compatibility. CMake should be available on your path to use these tools. We also provide a simple
run batch/shell script wrapper around the CMake calling format to be run as follows :
# The CMake invocation cmake -DTYPE:STRING=[command] -P run.cmake # On Windows > run [command] # On Linux/Max $ ./run.sh [command] # Note you may need to do a $ chmod +x run.sh # To run this script on your machine
Where [command] can be one of the following values:
- genData - Generate pba files from data in the
<pulse/source>/data/Data.xlxsfile (Patients, Substances, etc.)
- genStates - Generate a state file for every patient at the point where the patient completed stabilization (Simulation time 0s)to
- SystemValidation - Will use
<pulse/source>/test/config/ValidationSystems.configto create system validation tables in the
- PatientValidation - Will use
<pulse/source>/test/config/ValidationPatients.configto create patient validation tables in the
- The names of the other config files in the
<pulse/source>/test/config/directory without the suffix
- For Example : DebugRun, CDMUnitTests, ValidationSystems, VerificationScenarios, etc.
- With exception of the Characterize.config, this is a legacy testing configuration that will not work
Lastly, to follow along and both execute and debug the engine, you will need to pull all of our baseline scenarios. If you chose not to pull the baselines in your build process (you do not have a <pulse/bin>/verification folder), you will need to pull them. From a command/terminal running in the <pulse/bin>, execute the following command :
# Windows > run updateBaselines # On Mac/Linux $ ./run.sh updateBaselines
This baseline collection will be create the following folder :
<pulse/bin>/verification. It will contain both Scenario files, and baseline results files. We will discuss the baseline results in the test suite section.
Being a C++ library, Pulse requires a separate application to instantiate and execute the engine. We will explore various execution mechanisms in our repository in the sections below :
Setting up an IDE
Pulse provides an API for many different languages. To learn more about working with the Pulse API, you can find HowTo folders in many of the language folders in src Pulse provides an API for each of these languages, and they are designed to be very consistent with each other. So if you are looking for how to use a particular feature in Pulse and the language you are using does not provide an example, look around in the other languages and it should be trivial to translate to the language of your application.
Where to start
How to modify a system
How to create a new action
How to create a new condition
How to add a new patient parameter
How to create a scenario
How to create a unit test
How to update the documentation
How to generate the documentation
How to perform verification and validation
How to rebase the verification baselines