Symbulation – Agent based modeling of symbiont ecology and evolution

Authors

Anya Vostinar and contributors.

GitHub

https://github.com/anyaevostinar/SymbulationEmp

This is a software model of symbiosis which allows for evolution of parasitism and mutualism.

Click here to try it out in your web browser!

Checkout our quick start guides for more information on getting started.

Search for any function, class or variable using the search feature in the top left!

Table of Contents

Projects using Symbulation

This is a running list of the projects that have used Symbulation! If you would like to have your project added to this list, please include a short description of you work, and a link to any git repository that you may have. You can complete a pull request to add your information to this list. See Getting Started with Symbulation Development for information on how to complete a pull request.

Quick Start Guides

Contents:

Overview

The goal of Symbulation is to provide an evolutionary agent-based framework for studying the evolution of symbiosis. It supports a population of hosts and a population of symbionts. The symbionts can live inside of hosts (endosymbionts) or outside of hosts (free-living and/or ectosymbionts). The hosts and symbionts can engage in a relationship anywhere between full antagonism/parasitism to mutualism.

A figure with an overview of the system

If you haven’t already, we recommend first taking a look at the browser-based GUI.

Then you can start with the Default Mode guide, which includes running Symbulation both from the command line and a local browser-based GUI.

Default Mode

Symbulation allows you to compile your C++ to either:

  • running at the command line (e.g., native machine code) and

  • running in the web browser (e.g., javascript assembly code).

This how-to aims to walk you through all the nitty gritty required to successfully compile a simple “default” executable for running at the command line.

Install: Native C++ Compiler

In the Unix-verse (e.g., Linux / MacOS) commonly used compilers include gcc and clang. From this point onwards, we assume that you’re working with gcc.
Unless you really know what you’re doing, you’ll want to have gcc installed. The good news is: you might already!

Bring up a terminal and try entering:

which gcc

If which spits out a path, then you have gcc installed! If which says “not found,” you’ll need to go ahead and install gcc. For Linux users, your package manager (e.g., yum, apt, etc.) is probably the way to go about this. For MacOS users, you’ll need to get Apple’s “Command Line Tools for Xcode.” Either way, give it a quick web search (e.g., “install gcc on [my operating system]”) and there should be plenty of how-to guides that walk you through step-by-step.

For Windows users, things are a bit more complicated. We recommend using Windows Subsystem for Linux and then following the steps above for gcc.

Compile & Run: Command Line

Assuming you haven’t already pulled down a clone of Symbulation, let’s get your working environment all set.

Using Cookiecutter

The easiest thing to do is use our Cookiecutter template.

  • Install the latest Cookiecutter:

    pip install -U cookiecutter

  • Generate a Symbulation project:

    cookiecutter https://github.com/anyaevostinar/SymbulationProjectTemplate.git

  • Change directory into your newly created project:

    cd SymbulationProject
Without Cookiecutter

If you have something against delicious cookies and want to do without Cookiecutter, here are the steps. (Note that these steps don’t include making Data and Analysis files, which is assumed for the rest of the guide. If you are doing it this way, we assume you have your own preference for organizing things.)

  1. Clone Symbulation:

    git clone https://github.com/anyaevostinar/SymbulationEmp

  2. In the same level as SymbulationEmp, you will need a recursive copy of Empirical:

    git clone --recursive https://github.com/devosoft/Empirical.git
Compiling

Regardless of how you got everything downloaded, it’s now time to compile!

cd SymbulationEmp
make

Which command you use to run the executable depends on your version. If you are using version 0.1:

./symbulation

If you are using a later version (or the refactor branch, which has the development version):

./symbulation_default

You can make changes to the file SymSettings.cfg to change the configuration options without needing to recompile. These can also be altered at the command line:

./<executable file> -<Option to change> <new value>

For example:

./symbulation_default -VERTICAL_TRANSMISSION 0.5

To see how to use our workflow and scripts to collect and analyze data, please proceed to the Collecting Data quickstart guide!

Install: Web GUI

These instructions are for if you want to make changes to the web GUI and run it locally. You don’t need to do this to be able to use Symbulation’s web browser; you can instead access it here: https://anyaevostinar.github.io/SymbulationEmp/web/symbulation.html.

First, you’ll need Emscripten. We recommend putting it in the same directory that you have SymbulationEmp and Empirical:

git clone https://github.com/emscripten-core/emsdk.git
cd emsdk
./emsdk install 3.1.2
./emsdk activate 3.1.2

Then every time that you want to build and run Symbulation’s web GUI, you’ll need to load Emscripten into your PATH for a given terminal session. If you’ve closed and opened a new terminal, you’ll need to do this again (this is what people usually forget to do after they’ve been away for a while):

cd emsdk
source ./emsdk_env.sh

Then navigate back to SymbulationEmp and build the web version:

cd SymbulationEmp
make web

./symbulation_default
Web

You don’t need to do this to be able to use Symbulation’s web browser since it is hosted here: https://anyaevostinar.github.io/SymbulationEmp/web/symbulation.html.

However, if you want to make changes to the web GUI and run it locally, this is how you do that.

First, you’ll need Emscripten, we recommend putting it in the same directory that you have SymbulationEmp and Empirical:

git clone https://github.com/emscripten-core/emsdk.git
cd emsdk
./emsdk install 2.0.5
./emsdk activate 2.0.5

Then every time that you want to build and run Symbulation’s web GUI, you’ll need to load Emscripten into your PATH for a given terminal session. If you’ve closed and opened a new terminal, you’ll need to do this again (this is what people usually forget to do after they’ve been away for a while):

cd emsdk
source ./emsdk_env.sh

Then navigate back to SymbulationEmp and build the web version:

cd SymbulationEmp
make web

Now you have the website all built and in the web folder, so just navigate into that and run a website from it using Python’s handy local webserver (you need Python 3.5 or above for this):

cd web
python3 -m http.server

You should then be able to go to http://localhost:8000/ to see you custom run Symbulation GUI!

Collecting Data with Symbulation

You are able to run Symbulation with whatever workflow you prefer to run many replicates. The following assumes that you used the Symbulation Cookiecutter to get setup.

We’ve provided a short script that can be used with screen to run several replicates and treatments.

We recommend (and have provided) a workflow where you have a Data folder that contains subfolders for each experiment and within each of those subfolders are:

  • simple_repeat.py

  • SymSettings.cfg

  • Your executable file

  • A README.md containing the date and the purpose of the experiment

Assuming that you are in the SymbulationEmp directory and have already compiled your symbulation or symbulation_default executable, copy your executable to your Data folder and change to that directory:

cp symbulation ../Data/sample_treatment
cd ../Data/sample_treatment

The simple_repeat.py script assumes that you already have a copy of the executable and SymSettings.cfg in the same directory. Within that directory, you can run simple_repeat.py:

python3 simple_repeat.py

By default, this will run 5 replicates of each treatment specified in simple_repeat.py and use the random seeds 21-25 (inclusive). You can specify the random seeds (and therefore also the number of replicates) using command line arguments, which are optional. The first command line argument is the start of the range of seeds (inclusive), and the second command line argument is the end of the range of seeds (exclusive).

For example, the input

python3 simple_repeat.py 10 15

will use seeds 10, 11, 12, 13, and 14.

Analyzing Data

We’ve also provided a basic analysis pipeline for visualizing your data. Once you have let simple_repeat.py run, you can change directory to the Analysis folder:

cd ../../Analysis/sample_treatment

and run our provided Python script:

python3 munge_data.py

These commands will output a file munged_basic.dat that contains the average interaction value of hosts and symbionts over time in each of your replicates and treatments.

You can then open the R script SampleAnalysis.R, set your working directory to the Analysis folder and run all of the lines to see a plot of the effect of vertical transmission on the evolved interaction value for hosts and symbionts.

Creating A New Mode

Note: this guide is only for versions greater than 0.1. If you’d like to check out this functionality sooner, it is on the refactor branch.

Once you have familiarized yourself with Symbulation and its default mode, you might be interested in designing your own experiment, adding functionality to the codebase, and collecting data. The existing modes include default (Host and Symbiont), efficient (Efficient Host and Efficient Symbiont), lysis (Bacterium and Phage), and public goods game or PGG (PGG Host and PGG Symbiont). There are several steps to creating your own world, including following conventions for file structure, adding your own organisms, designing tests, adding a WorldSetup file, adding targets to the makefile, and more.

ALIFE 2022 Symbulation Tutorial

We will be hosting a introduction to Symbulation tutorial at the ALIFE 2022 conferece!

Overview

Symbulation is an agent-based modeling platform that enables the study of symbiosis along the parasitism to mutualism spectrum and available at https://github.com/anyaevostinar/SymbulationEmp. It uses the Empirical platform and allows for a large amount of customization based on existing functionality, including allowing symbionts to live outside or inside of hosts, lysogenic and lytic life cycles, several different spatial structures, and enabling symbionts occupying the same host to engage in a public goods game. It also supports the creation of new modes and functionality for those with some C++ experience. There are 56 current configuration options, controlled by an easy-to-use configuration file and customizable data-tracking. It also includes a web-based graphical user interface that can be customized by those with C++ knowledge. Symbulation is already being used to study how spatial structure and multi-infection interact with the evolution of mutualistic symbiosis, the evolution of lysogeny, and the de novo evolution of endosymbiosis. It has also been used in classroom settings with advanced undergraduate computer science students.

This tutorial will guide new users in understanding the overall architecture of Symbulation, setting up a project (using our Cookiecutter template) to conduct an experiment using existing configuration options, customizing the browser-based graphical user interface, and creating new functionality for those comfortable with C++. The tutorial will build on the existing guides and documentation (available at https://symbulation.readthedocs.io/en/latest/) and a page for the tutorial will be created there. Attendees will also be able to shape the future directions of Symbulation by discussing new desirable features and contributing their new functionality back to the codebase if they so wish. Attendees will leave the tutorial with the start of a new research project and, ideally, lots of new ideas and potential collaborations.

All material will be hosted here, check back later for a schedule!

=============== Library

Library API

Class Hierarchy

Full API

Namespaces
Namespace Catch
Classes
Functions
Namespace Catch::Generators
Namespace Catch::Generators::pf

Contents

Namespace Catch::Matchers::Exception

Contents

Namespace Catch::Matchers::Floating

Contents

Namespace Catch::Matchers::Generic

Contents

Namespace Catch::Matchers::Generic::Detail

Contents

Namespace mpl_
Namespace std
Classes and Structs
Template Struct always_false
Inheritance Relationships
Base Type

  • public false_type

Struct Documentation
template<typename T>
struct always_false : public false_type
Struct AssertionInfo
Struct Documentation
struct Catch::AssertionInfo

Public Members

StringRef macroName
SourceLineInfo lineInfo
StringRef capturedExpression
ResultDisposition::Flags resultDisposition
Struct AssertionReaction
Struct Documentation
struct Catch::AssertionReaction

Public Members

bool shouldDebugBreak = false
bool shouldThrow = false
Struct AutoReg
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::AutoReg : public Catch::NonCopyable

Public Functions

AutoReg(ITestInvoker *invoker, SourceLineInfo const &lineInfo, StringRef const &classOrMethod, NameAndTags const &nameAndTags) noexcept
~AutoReg()
Struct CaseSensitive
Struct Documentation
struct Catch::CaseSensitive

Public Types

enum Choice

Values:

enumerator Yes
enumerator No
Struct Counts
Struct Documentation
struct Catch::Counts

Public Functions

Counts operator-(Counts const &other) const
Counts &operator+=(Counts const &other)
std::size_t total() const
bool allPassed() const
bool allOk() const

Public Members

std::size_t passed = 0
std::size_t failed = 0
std::size_t failedButOk = 0
Struct Decomposer
Struct Documentation
struct Catch::Decomposer

Public Functions

template<typename T>
auto operator<=(T const &lhs) -> ExprLhs<T const&>
auto operator<=(bool value) -> ExprLhs<bool>
Struct EnumInfo
Struct Documentation
struct Catch::Detail::EnumInfo

Public Functions

~EnumInfo()
StringRef lookup(int value) const

Public Members

StringRef m_name
std::vector<std::pair<int, StringRef>> m_values
Template Struct as
Struct Documentation
template<typename T>
struct as
Template Struct IGenerator
Inheritance Relationships
Base Type
Derived Types
Struct IConfig
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::IConfig : public Catch::NonCopyable

Public Functions

~IConfig()
bool allowThrows() const = 0
std::ostream &stream() const = 0
std::string name() const = 0
bool includeSuccessfulResults() const = 0
bool shouldDebugBreak() const = 0
bool warnAboutMissingAssertions() const = 0
bool warnAboutNoTests() const = 0
int abortAfter() const = 0
bool showInvisibles() const = 0
ShowDurations::OrNot showDurations() const = 0
TestSpec const &testSpec() const = 0
bool hasTestFilters() const = 0
std::vector<std::string> const &getTestsOrTags() const = 0
RunTests::InWhatOrder runOrder() const = 0
unsigned int rngSeed() const = 0
UseColour::YesOrNo useColour() const = 0
std::vector<std::string> const &getSectionsToRun() const = 0
Verbosity verbosity() const = 0
bool benchmarkNoAnalysis() const = 0
int benchmarkSamples() const = 0
double benchmarkConfidenceInterval() const = 0
unsigned int benchmarkResamples() const = 0
std::chrono::milliseconds benchmarkWarmupTime() const = 0
Struct IContext
Inheritance Relationships
Derived Type
Struct Documentation
struct Catch::IContext

Subclassed by Catch::IMutableContext

Public Functions

~IContext()
IResultCapture *getResultCapture() = 0
IRunner *getRunner() = 0
IConfigPtr const &getConfig() const = 0
Struct IExceptionTranslator
Struct Documentation
struct Catch::IExceptionTranslator

Public Functions

~IExceptionTranslator()
std::string translate(ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd) const = 0
Struct IExceptionTranslatorRegistry
Struct Documentation
struct Catch::IExceptionTranslatorRegistry

Public Functions

~IExceptionTranslatorRegistry()
std::string translateActiveException() const = 0
Struct IGeneratorTracker
Struct Documentation
struct Catch::IGeneratorTracker

Public Functions

~IGeneratorTracker()
auto hasGenerator() const -> bool = 0
auto getGenerator() const -> Generators::GeneratorBasePtr const& = 0
void setGenerator(Generators::GeneratorBasePtr &&generator) = 0
Struct IMutableContext
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::IMutableContext : public Catch::IContext

Public Functions

~IMutableContext()
void setResultCapture(IResultCapture *resultCapture) = 0
void setRunner(IRunner *runner) = 0
void setConfig(IConfigPtr const &config) = 0
Struct IMutableEnumValuesRegistry
Struct Documentation
struct Catch::IMutableEnumValuesRegistry

Public Functions

~IMutableEnumValuesRegistry()
Detail::EnumInfo const &registerEnum(StringRef enumName, StringRef allEnums, std::vector<int> const &values) = 0
template<typename E>
Detail::EnumInfo const &registerEnum(StringRef enumName, StringRef allEnums, std::initializer_list<E> values)
Struct IMutableRegistryHub
Struct Documentation
struct Catch::IMutableRegistryHub

Public Functions

~IMutableRegistryHub()
void registerReporter(std::string const &name, IReporterFactoryPtr const &factory) = 0
void registerListener(IReporterFactoryPtr const &factory) = 0
void registerTest(TestCase const &testInfo) = 0
void registerTranslator(const IExceptionTranslator *translator) = 0
void registerTagAlias(std::string const &alias, std::string const &tag, SourceLineInfo const &lineInfo) = 0
void registerStartupException() noexcept = 0
IMutableEnumValuesRegistry &getMutableEnumValuesRegistry() = 0
Struct IRegistryHub
Struct Documentation
struct Catch::IRegistryHub

Public Functions

~IRegistryHub()
IReporterRegistry const &getReporterRegistry() const = 0
ITestCaseRegistry const &getTestCaseRegistry() const = 0
ITagAliasRegistry const &getTagAliasRegistry() const = 0
IExceptionTranslatorRegistry const &getExceptionTranslatorRegistry() const = 0
StartupExceptionRegistry const &getStartupExceptionRegistry() const = 0
Struct IResultCapture
Struct Documentation
struct Catch::IResultCapture

Public Functions

~IResultCapture()
bool sectionStarted(SectionInfo const &sectionInfo, Counts &assertions) = 0
void sectionEnded(SectionEndInfo const &endInfo) = 0
void sectionEndedEarly(SectionEndInfo const &endInfo) = 0
auto acquireGeneratorTracker(SourceLineInfo const &lineInfo) -> IGeneratorTracker& = 0
void pushScopedMessage(MessageInfo const &message) = 0
void popScopedMessage(MessageInfo const &message) = 0
void emplaceUnscopedMessage(MessageBuilder const &builder) = 0
void handleFatalErrorCondition(StringRef message) = 0
void handleExpr(AssertionInfo const &info, ITransientExpression const &expr, AssertionReaction &reaction) = 0
void handleMessage(AssertionInfo const &info, ResultWas::OfType resultType, StringRef const &message, AssertionReaction &reaction) = 0
void handleUnexpectedExceptionNotThrown(AssertionInfo const &info, AssertionReaction &reaction) = 0
void handleUnexpectedInflightException(AssertionInfo const &info, std::string const &message, AssertionReaction &reaction) = 0
void handleIncomplete(AssertionInfo const &info) = 0
void handleNonExpr(AssertionInfo const &info, ResultWas::OfType resultType, AssertionReaction &reaction) = 0
bool lastAssertionPassed() = 0
void assertionPassed() = 0
std::string getCurrentTestName() const = 0
const AssertionResult *getLastResult() const = 0
void exceptionEarlyReported() = 0
Struct IRunner
Struct Documentation
struct Catch::IRunner

Public Functions

~IRunner()
bool aborting() const = 0
Template Struct is_callable
Struct Documentation
template<typename T>
struct is_callable
Template Struct is_callable< Fun(Args…)>
Inheritance Relationships
Base Type

  • public decltypeis_callable_tester::test< Fun, Args... >

Struct Documentation
template<typename Fun, typename ...Args>
struct is_callable<Fun(Args...)> : public decltypeis_callable_tester::test<Fun, Args...>
Struct is_callable_tester
Struct Documentation
struct Catch::is_callable_tester

Public Static Functions

template<typename Fun, typename... Args> true_given< decltype(std::declval< Fun >)(std::declval< Args >)...))> test (int)
template<typename...>
std::false_type test(...)
Template Struct is_range
Struct Documentation
template<typename T>
struct Catch::is_range

Public Static Attributes

const bool value = !std::is_same<decltype(begin(std::declval<T>())), not_this_one>::value && !std::is_same<decltype(end(std::declval<T>())), not_this_one>::value
Struct IStream
Struct Documentation
struct Catch::IStream

Public Functions

~IStream()
std::ostream &stream() const = 0
Struct ITestCaseRegistry
Struct Documentation
struct Catch::ITestCaseRegistry

Public Functions

~ITestCaseRegistry()
std::vector<TestCase> const &getAllTests() const = 0
std::vector<TestCase> const &getAllTestsSorted(IConfig const &config) const = 0
Struct ITestInvoker
Inheritance Relationships
Derived Type
Struct Documentation
struct Catch::ITestInvoker

Subclassed by Catch::TestInvokerAsMethod< C >

Public Functions

void invoke() const = 0
~ITestInvoker()
Struct ITransientExpression
Inheritance Relationships
Derived Types
Struct Documentation
struct Catch::ITransientExpression

Subclassed by Catch::BinaryExpr< LhsT, RhsT >, Catch::MatchExpr< ArgT, MatcherT >, Catch::UnaryExpr< LhsT >

Public Functions

auto isBinaryExpression() const -> bool
auto getResult() const -> bool
void streamReconstructedExpression(std::ostream &os) const = 0
ITransientExpression(bool isBinaryExpression, bool result)
~ITransientExpression()

Public Members

bool m_isBinaryExpression
bool m_result
Struct WithinAbsMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::Floating::WithinAbsMatcher : public Catch::Matchers::Impl::MatcherBase<double>

Public Functions

WithinAbsMatcher(double target, double margin)
bool match(double const &matchee) const override
std::string describe() const override
Struct WithinRelMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::Floating::WithinRelMatcher : public Catch::Matchers::Impl::MatcherBase<double>

Public Functions

WithinRelMatcher(double target, double epsilon)
bool match(double const &matchee) const override
std::string describe() const override
Struct WithinUlpsMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::Floating::WithinUlpsMatcher : public Catch::Matchers::Impl::MatcherBase<double>

Public Functions

WithinUlpsMatcher(double target, uint64_t ulps, FloatingPointKind baseType)
bool match(double const &matchee) const override
std::string describe() const override
Template Struct MatchAllOf
Inheritance Relationships
Base Type
Struct Documentation
template<typename ArgT>
struct Catch::Matchers::Impl::MatchAllOf : public Catch::Matchers::Impl::MatcherBase<ArgT>

Public Functions

bool match(ArgT const &arg) const override
std::string describe() const override
MatchAllOf<ArgT> operator&&(MatcherBase<ArgT> const &other)

Public Members

std::vector<MatcherBase<ArgT> const*> m_matchers
Template Struct MatchAnyOf
Inheritance Relationships
Base Type
Struct Documentation
template<typename ArgT>
struct Catch::Matchers::Impl::MatchAnyOf : public Catch::Matchers::Impl::MatcherBase<ArgT>

Public Functions

bool match(ArgT const &arg) const override
std::string describe() const override
MatchAnyOf<ArgT> operator||(MatcherBase<ArgT> const &other)

Public Members

std::vector<MatcherBase<ArgT> const*> m_matchers
Template Struct MatcherBase
Inheritance Relationships
Base Types
Derived Types
Template Struct MatcherMethod
Struct Documentation
template<typename ObjectT>
struct Catch::Matchers::Impl::MatcherMethod

Public Functions

bool match(ObjectT const &arg) const = 0
Template Struct MatchNotOf
Inheritance Relationships
Base Type
Struct Documentation
template<typename ArgT>
struct Catch::Matchers::Impl::MatchNotOf : public Catch::Matchers::Impl::MatcherBase<ArgT>

Public Functions

MatchNotOf(MatcherBase<ArgT> const &underlyingMatcher)
bool match(ArgT const &arg) const override
std::string describe() const override

Public Members

MatcherBase<ArgT> const &m_underlyingMatcher
Struct CasedString
Struct Documentation
struct Catch::Matchers::StdString::CasedString

Public Functions

CasedString(std::string const &str, CaseSensitive::Choice caseSensitivity)
std::string adjustString(std::string const &str) const
std::string caseSensitivitySuffix() const

Public Members

CaseSensitive::Choice m_caseSensitivity
std::string m_str
Struct ContainsMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::StdString::ContainsMatcher : public Catch::Matchers::StdString::StringMatcherBase

Public Functions

ContainsMatcher(CasedString const &comparator)
bool match(std::string const &source) const override
Struct EndsWithMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::StdString::EndsWithMatcher : public Catch::Matchers::StdString::StringMatcherBase

Public Functions

EndsWithMatcher(CasedString const &comparator)
bool match(std::string const &source) const override
Struct EqualsMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::StdString::EqualsMatcher : public Catch::Matchers::StdString::StringMatcherBase

Public Functions

EqualsMatcher(CasedString const &comparator)
bool match(std::string const &source) const override
Struct RegexMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::StdString::RegexMatcher : public Catch::Matchers::Impl::MatcherBase<std::string>

Public Functions

RegexMatcher(std::string regex, CaseSensitive::Choice caseSensitivity)
bool match(std::string const &matchee) const override
std::string describe() const override
Struct StartsWithMatcher
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::Matchers::StdString::StartsWithMatcher : public Catch::Matchers::StdString::StringMatcherBase

Public Functions

StartsWithMatcher(CasedString const &comparator)
bool match(std::string const &source) const override
Struct StringMatcherBase
Inheritance Relationships
Base Type
Derived Types
Struct Documentation
struct Catch::Matchers::StdString::StringMatcherBase : public Catch::Matchers::Impl::MatcherBase<std::string>

Subclassed by Catch::Matchers::StdString::ContainsMatcher, Catch::Matchers::StdString::EndsWithMatcher, Catch::Matchers::StdString::EqualsMatcher, Catch::Matchers::StdString::StartsWithMatcher

Public Functions

StringMatcherBase(std::string const &operation, CasedString const &comparator)
std::string describe() const override

Public Members

CasedString m_comparator
std::string m_operation
Template Struct ApproxMatcher
Inheritance Relationships
Base Type
Struct Documentation
template<typename T>
struct Catch::Matchers::Vector::ApproxMatcher : public Catch::Matchers::Impl::MatcherBase<std::vector<T>>

Public Functions

ApproxMatcher(std::vector<T> const &comparator)
bool match(std::vector<T> const &v) const override
std::string describe() const override
template<typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
ApproxMatcher &epsilon(T const &newEpsilon)
template<typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
ApproxMatcher &margin(T const &newMargin)
template<typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
ApproxMatcher &scale(T const &newScale)

Public Members

std::vector<T> const &m_comparator
Catch::Detail::Approx approx = Catch::Detail::Approx::custom()
Template Struct ContainsElementMatcher
Inheritance Relationships
Base Type
Struct Documentation
template<typename T>
struct Catch::Matchers::Vector::ContainsElementMatcher : public Catch::Matchers::Impl::MatcherBase<std::vector<T>>

Public Functions

ContainsElementMatcher(T const &comparator)
bool match(std::vector<T> const &v) const override
std::string describe() const override

Public Members

T const &m_comparator
Template Struct ContainsMatcher
Inheritance Relationships
Base Type
Struct Documentation
template<typename T>
struct Catch::Matchers::Vector::ContainsMatcher : public Catch::Matchers::Impl::MatcherBase<std::vector<T>>

Public Functions

ContainsMatcher(std::vector<T> const &comparator)
bool match(std::vector<T> const &v) const override
std::string describe() const override

Public Members

std::vector<T> const &m_comparator
Template Struct EqualsMatcher
Inheritance Relationships
Base Type
Struct Documentation
template<typename T>
struct Catch::Matchers::Vector::EqualsMatcher : public Catch::Matchers::Impl::MatcherBase<std::vector<T>>

Public Functions

EqualsMatcher(std::vector<T> const &comparator)
bool match(std::vector<T> const &v) const override
std::string describe() const override

Public Members

std::vector<T> const &m_comparator
Template Struct UnorderedEqualsMatcher
Inheritance Relationships
Base Type
Struct Documentation
template<typename T>
struct Catch::Matchers::Vector::UnorderedEqualsMatcher : public Catch::Matchers::Impl::MatcherBase<std::vector<T>>

Public Functions

UnorderedEqualsMatcher(std::vector<T> const &target)
bool match(std::vector<T> const &vec) const override
std::string describe() const override
Struct MessageBuilder
Inheritance Relationships
Base Type
Struct Documentation
struct Catch::MessageBuilder : public Catch::MessageStream

Public Functions

MessageBuilder(StringRef const &macroName, SourceLineInfo const &lineInfo, ResultWas::OfType type)
template<typename T>
MessageBuilder &operator<<(T const &value)

Public Members

MessageInfo m_info
Struct MessageInfo
Struct Documentation
struct Catch::MessageInfo

Public Functions

MessageInfo(StringRef const &_macroName, SourceLineInfo const &_lineInfo, ResultWas::OfType _type)
bool operator==(MessageInfo const &other) const
bool operator<(MessageInfo const &other) const

Public Members

StringRef macroName
std::string message
SourceLineInfo lineInfo
ResultWas::OfType type
unsigned int sequence
Struct MessageStream
Inheritance Relationships
Derived Type
Struct Documentation
struct Catch::MessageStream

Subclassed by Catch::MessageBuilder

Public Functions

template<typename T>
MessageStream &operator<<(T const &value)

Public Members

ReusableStringStream m_stream
Struct NameAndTags
Struct Documentation
struct Catch::NameAndTags

Public Functions

NameAndTags(StringRef const &name_ = StringRef(), StringRef const &tags_ = StringRef()) noexcept

Public Members

StringRef name
StringRef tags
Struct not_this_one
Struct Documentation
struct not_this_one
Struct pluralise
Struct Documentation
struct Catch::pluralise

Public Functions

pluralise(std::size_t count, std::string const &label)

Public Members

std::size_t m_count
std::string m_label

Friends

friend std::ostream &operator<<(std::ostream &os, pluralise const &pluraliser)
Struct RegistrarForTagAliases
Struct Documentation
struct Catch::RegistrarForTagAliases

Public Functions

RegistrarForTagAliases(char const *alias, char const *tag, SourceLineInfo const &lineInfo)
Struct ResultDisposition
Struct Documentation
struct Catch::ResultDisposition

Public Types

enum Flags

Values:

enumerator Normal
enumerator ContinueOnFailure
enumerator FalseTest
enumerator SuppressFail
Struct ResultWas
Struct Documentation
struct Catch::ResultWas

Public Types

enum OfType

Values:

enumerator Unknown
enumerator Ok
enumerator Info
enumerator Warning
enumerator FailureBit
enumerator ExpressionFailed
enumerator ExplicitFailure
enumerator Exception
enumerator ThrewException
enumerator DidntThrowException
enumerator FatalErrorCondition
Struct RunTests
Struct Documentation
struct Catch::RunTests

Public Types

enum InWhatOrder

Values:

enumerator InDeclarationOrder
enumerator InLexicographicalOrder
enumerator InRandomOrder
Struct SectionEndInfo
Struct Documentation
struct Catch::SectionEndInfo

Public Members

SectionInfo sectionInfo
Counts prevAssertions
double durationInSeconds
Struct SectionInfo
Struct Documentation
struct Catch::SectionInfo

Public Functions

SectionInfo(SourceLineInfo const &_lineInfo, std::string const &_name)
SectionInfo(SourceLineInfo const &_lineInfo, std::string const &_name, std::string const&)

Public Members

std::string name
std::string description
SourceLineInfo lineInfo
Struct ShowDurations
Struct Documentation
struct Catch::ShowDurations

Public Types

enum OrNot

Values:

enumerator DefaultForReporter
enumerator Always
enumerator Never
Struct SourceLineInfo
Struct Documentation
struct Catch::SourceLineInfo

Public Functions

SourceLineInfo() = delete
SourceLineInfo(char const *_file, std::size_t _line) noexcept
SourceLineInfo(SourceLineInfo const &other) = default
SourceLineInfo &operator=(SourceLineInfo const&) = default
SourceLineInfo(SourceLineInfo&&) noexcept = default
SourceLineInfo &operator=(SourceLineInfo&&) noexcept = default
bool empty() const noexcept
bool operator==(SourceLineInfo const &other) const noexcept
bool operator<(SourceLineInfo const &other) const noexcept

Public Members

char const *file
std::size_t line
Struct StreamEndStop
Struct Documentation
struct Catch::StreamEndStop

Public Functions

std::string operator+() const
Template Struct StringMaker
Struct Documentation
template<typename T, typename = void>
struct Catch::StringMaker

Public Static Functions

template<typename Fake = T>
std::enable_if<::Catch::Detail::IsStreamInsertable<Fake>::value, std::string>::type convert(const Fake &value)
template<typename Fake = T>
std::enable_if<!::Catch::Detail::IsStreamInsertable<Fake>::value, std::string>::type convert(const Fake &value)
Template Struct StringMaker< bool >
Struct Documentation
template<>
struct Catch::StringMaker<bool>

Public Static Functions

std::string convert(bool b)
Template Struct StringMaker< Catch::Detail::Approx >
Struct Documentation
template<>
struct Catch::StringMaker<Catch::Detail::Approx>

Public Static Functions

std::string convert(Catch::Detail::Approx const &value)
Template Struct StringMaker< char * >
Struct Documentation
template<>
struct Catch::StringMaker<char*>

Public Static Functions

std::string convert(char *str)
Template Struct StringMaker< char >
Struct Documentation
template<>
struct Catch::StringMaker<char>

Public Static Functions

std::string convert(char c)
Template Struct StringMaker< char const * >
Struct Documentation
template<>
struct Catch::StringMaker<char const*>

Public Static Functions

std::string convert(char const *str)
Template Struct StringMaker< char[SZ]>
Struct Documentation
template<int SZ>
struct Catch::StringMaker<char[SZ]>

Public Static Functions

std::string convert(char const *str)
Template Struct StringMaker< double >
Struct Documentation
template<>
struct Catch::StringMaker<double>

Public Static Functions

std::string convert(double value)

Public Static Attributes

int precision
Template Struct StringMaker< float >
Struct Documentation
template<>
struct Catch::StringMaker<float>

Public Static Functions

std::string convert(float value)

Public Static Attributes

int precision
Template Struct StringMaker< int >
Struct Documentation
template<>
struct Catch::StringMaker<int>

Public Static Functions

std::string convert(int value)
Template Struct StringMaker< long >
Struct Documentation
template<>
struct Catch::StringMaker<long>

Public Static Functions

std::string convert(long value)
Template Struct StringMaker< long long >
Struct Documentation
template<>
struct Catch::StringMaker<long long>

Public Static Functions

std::string convert(long long value)
Template Struct StringMaker< R C::* >
Struct Documentation
template<typename R, typename C>
struct Catch::StringMaker<R C::*>

Public Static Functions

std::string convert(R C::* p)
Template Struct StringMaker< R, typename std::enable_if< is_range< R >::value &&!::Catch::Detail::IsStreamInsertable< R >::value >::type >
Struct Documentation
template<typename R>
struct Catch::StringMaker<R, typename std::enable_if<is_range<R>::value && !::Catch::Detail::IsStreamInsertable<R>::value>::type>

Public Static Functions

std::string convert(R const &range)
Template Struct StringMaker< signed char >
Struct Documentation
template<>
struct Catch::StringMaker<signed char>

Public Static Functions

std::string convert(signed char c)
Template Struct StringMaker< signed char[SZ]>
Struct Documentation
template<int SZ>
struct Catch::StringMaker<signed char[SZ]>

Public Static Functions

std::string convert(signed char const *str)
Template Struct StringMaker< std::nullptr_t >
Struct Documentation
template<>
struct Catch::StringMaker<std::nullptr_t>

Public Static Functions

std::string convert(std::nullptr_t)
Template Struct StringMaker< std::string >
Struct Documentation
template<>
struct Catch::StringMaker<std::string>

Public Static Functions

std::string convert(const std::string &str)
Template Struct StringMaker< std::wstring >
Struct Documentation
template<>
struct Catch::StringMaker<std::wstring>

Public Static Functions

std::string convert(const std::wstring &wstr)
Template Struct StringMaker< T * >
Struct Documentation
template<typename T>
struct Catch::StringMaker<T*>

Public Static Functions

template<typename U>
std::string convert(U *p)
Template Struct StringMaker< T[SZ]>
Struct Documentation
template<typename T, int SZ>
struct Catch::StringMaker<T[SZ]>

Public Static Functions

std::string convert(T const (&arr)[SZ])
Template Struct StringMaker< unsigned char >
Struct Documentation
template<>
struct Catch::StringMaker<unsigned char>

Public Static Functions

std::string convert(unsigned char c)
Template Struct StringMaker< unsigned char[SZ]>
Struct Documentation
template<int SZ>
struct Catch::StringMaker<unsigned char[SZ]>

Public Static Functions

std::string convert(unsigned char const *str)
Template Struct StringMaker< unsigned int >
Struct Documentation
template<>
struct Catch::StringMaker<unsigned int>

Public Static Functions

std::string convert(unsigned int value)
Template Struct StringMaker< unsigned long >
Struct Documentation
template<>
struct Catch::StringMaker<unsigned long>

Public Static Functions

std::string convert(unsigned long value)
Template Struct StringMaker< unsigned long long >
Struct Documentation
template<>
struct Catch::StringMaker<unsigned long long>

Public Static Functions

std::string convert(unsigned long long value)
Template Struct StringMaker< wchar_t * >
Struct Documentation
template<>
struct Catch::StringMaker<wchar_t*>

Public Static Functions

std::string convert(wchar_t *str)
Template Struct StringMaker< wchar_t const * >
Struct Documentation
template<>
struct Catch::StringMaker<wchar_t const*>

Public Static Functions

std::string convert(wchar_t const *str)
Struct TestCaseInfo
Inheritance Relationships
Derived Type
Struct Documentation
struct Catch::TestCaseInfo

Subclassed by Catch::TestCase

Public Types

enum SpecialProperties

Values:

enumerator None
enumerator IsHidden
enumerator ShouldFail
enumerator MayFail
enumerator Throws
enumerator NonPortable
enumerator Benchmark

Public Functions

TestCaseInfo(std::string const &_name, std::string const &_className, std::string const &_description, std::vector<std::string> const &_tags, SourceLineInfo const &_lineInfo)
bool isHidden() const
bool throws() const
bool okToFail() const
bool expectedToFail() const
std::string tagsAsString() const

Public Members

std::string name
std::string className
std::string description
std::vector<std::string> tags
std::vector<std::string> lcaseTags
SourceLineInfo lineInfo
SpecialProperties properties

Friends

friend void setTags(TestCaseInfo &testCaseInfo, std::vector<std::string> tags)
Struct TestFailureException
Struct Documentation
struct TestFailureException
Struct Totals
Struct Documentation
struct Catch::Totals

Public Functions

Totals operator-(Totals const &other) const
Totals &operator+=(Totals const &other)
Totals delta(Totals const &prevTotals) const

Public Members

int error = 0
Counts assertions
Counts testCases
Template Struct true_given
Inheritance Relationships
Base Type

  • public true_type

Struct Documentation
template<typename>
struct true_given : public true_type
Struct UseColour
Struct Documentation
struct Catch::UseColour

Public Types

enum YesOrNo

Values:

enumerator Auto
enumerator Yes
enumerator No
Struct WaitForKeypress
Struct Documentation
struct Catch::WaitForKeypress

Public Types

enum When

Values:

enumerator Never
enumerator BeforeStart
enumerator BeforeExit
enumerator BeforeStartAndExit
Struct WarnAbout
Struct Documentation
struct Catch::WarnAbout

Public Types

enum What

Values:

enumerator Nothing
enumerator NoAssertions
enumerator NoTests
Struct Catch_global_namespace_dummy
Struct Documentation
struct Catch_global_namespace_dummy
Class Bacterium
Inheritance Relationships
Base Type
Class Documentation
class Bacterium : public Host

Public Functions

Bacterium(emp::Ptr<emp::Random> _random, emp::Ptr<LysisWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, emp::vector<emp::Ptr<Organism>> _syms = {}, emp::vector<emp::Ptr<Organism>> _repro_syms = {}, std::set<int> _set = std::set<int>(), double _points = 0.0)

The constructor for the bacterium class

Bacterium(const Bacterium&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

Bacterium(Bacterium&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

Bacterium() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

double GetIncVal()

Input: None

Output: The double representing a genome’s value.

Purpose: To determine a genome’s value.

void SetIncVal(double _in)

Input: The double to be set as the bacterium’s genome value

Output: None

Purpose: To set a bacterium’s genome value

emp::Ptr<Organism> makeNew()

Input: None.

Output: A new bacterium with same properties as this bacterium.

Purpose: To avoid creating an organism via constructor in other methods.

void mutate()

Input: None

Output: None

Purpose: To mutate a bacterium’s genome. The mutation will be based on a value chosen from a normal distribution centered at 0, with a standard deviation that is equal to the mutation size. Bacterium mutation can be turned on or off.

double ProcessLysogenResources(double phage_inc_val)

Protected Attributes

double host_incorporation_val = 0

Purpose: Represents the host’s genome. A double with a range from 0 to 1. The host’s genome gets compared against the phage’s incorporation value.

emp::Ptr<LysisWorld> my_world = NULL

Purpose: Represents the world that the hosts are living in.

Class AssertionHandler
Class Documentation
class Catch::AssertionHandler

Public Functions

AssertionHandler(StringRef const &macroName, SourceLineInfo const &lineInfo, StringRef capturedExpression, ResultDisposition::Flags resultDisposition)
~AssertionHandler()
template<typename T>
void handleExpr(ExprLhs<T> const &expr)
void handleExpr(ITransientExpression const &expr)
void handleMessage(ResultWas::OfType resultType, StringRef const &message)
void handleExceptionThrownAsExpected()
void handleUnexpectedExceptionNotThrown()
void handleExceptionNotThrownAsExpected()
void handleThrowingCallSkipped()
void handleUnexpectedInflightException()
void complete()
void setCompleted()
auto allowThrows() const -> bool
Template Class BinaryExpr
Inheritance Relationships
Base Type
Class Documentation
template<typename LhsT, typename RhsT>
class Catch::BinaryExpr : public Catch::ITransientExpression

Public Functions

BinaryExpr(bool comparisonResult, LhsT lhs, StringRef op, RhsT rhs)
template<typename T>
auto operator&&(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator||(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator==(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator!=(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator>(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator<(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator>=(T) const -> BinaryExpr<LhsT, RhsT const&> const
template<typename T>
auto operator<=(T) const -> BinaryExpr<LhsT, RhsT const&> const
Class Capturer
Class Documentation
class Catch::Capturer

Public Functions

Capturer(StringRef macroName, SourceLineInfo const &lineInfo, ResultWas::OfType resultType, StringRef names)
~Capturer()
void captureValue(size_t index, std::string const &value)
template<typename T>
void captureValues(size_t index, T const &value)
template<typename T, typename ...Ts>
void captureValues(size_t index, T const &value, Ts const&... values)
Class Approx
Class Documentation
class Catch::Detail::Approx

Public Functions

Approx(double value)
Approx operator-() const
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
Approx operator()(T const &value)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
Approx(T const &value)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
Approx &epsilon(T const &newEpsilon)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
Approx &margin(T const &newMargin)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
Approx &scale(T const &newScale)
std::string toString() const

Public Static Functions

Approx custom()

Friends

template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator==(const T &lhs, Approx const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator==(Approx const &lhs, const T &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator!=(T const &lhs, Approx const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator!=(Approx const &lhs, T const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator<=(T const &lhs, Approx const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator<=(Approx const &lhs, T const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator>=(T const &lhs, Approx const &rhs)
template<typename T, typename = typename std::enable_if<std::is_constructible<double, T>::value>::type>
friend bool operator>=(Approx const &lhs, T const &rhs)
Template Class IsStreamInsertable
Class Documentation
template<typename T>
class Catch::Detail::IsStreamInsertable

Public Static Attributes

const bool value = decltype(test<std::ostream, const T&>(0))::value
Class ExceptionTranslatorRegistrar
Class Documentation
class Catch::ExceptionTranslatorRegistrar

Public Functions

template<typename T>
ExceptionTranslatorRegistrar(std::string (*translateFunction)(T&))
Template Class ExceptionTranslatorRegistrar::ExceptionTranslator
Nested Relationships

This class is a nested type of Class ExceptionTranslatorRegistrar.

Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::ExceptionTranslatorRegistrar::ExceptionTranslator : public Catch::IExceptionTranslator

Public Functions

ExceptionTranslator(std::string (*translateFunction)(T&))
std::string translate(ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd) const override

Protected Attributes

std::string (*m_translateFunction)(T&)
Template Class ExprLhs
Class Documentation
template<typename LhsT>
class Catch::ExprLhs

Public Functions

ExprLhs(LhsT lhs)
template<typename RhsT>
auto operator==(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
auto operator==(bool rhs) -> BinaryExpr<LhsT, bool> const
template<typename RhsT>
auto operator!=(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
auto operator!=(bool rhs) -> BinaryExpr<LhsT, bool> const
template<typename RhsT>
auto operator>(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
template<typename RhsT>
auto operator<(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
template<typename RhsT>
auto operator>=(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
template<typename RhsT>
auto operator<=(RhsT const &rhs) -> BinaryExpr<LhsT, RhsT const&> const
template<typename RhsT>
auto operator&&(RhsT const&) -> BinaryExpr<LhsT, RhsT const&> const
template<typename RhsT>
auto operator||(RhsT const&) -> BinaryExpr<LhsT, RhsT const&> const
auto makeUnaryExpr() const -> UnaryExpr<LhsT>
Class GeneratorException
Inheritance Relationships
Base Type

  • public exception

Class Documentation
class Catch::GeneratorException : public exception

Public Functions

GeneratorException(const char *msg)
const char *what() const noexcept final override
Template Class ChunkGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::ChunkGenerator : public Catch::Generators::IGenerator<std::vector<T>>

Public Functions

ChunkGenerator(size_t size, GeneratorWrapper<T> generator)
std::vector<T> const &get() const override
bool next() override
Template Class FilterGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T, typename Predicate>
class Catch::Generators::FilterGenerator : public Catch::Generators::IGenerator<T>

Public Functions

template<typename P = Predicate>
FilterGenerator(P &&pred, GeneratorWrapper<T> &&generator)
T const &get() const override
bool next() override
Template Class FixedValuesGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::FixedValuesGenerator : public Catch::Generators::IGenerator<T>

Public Functions

FixedValuesGenerator(std::initializer_list<T> values)
T const &get() const override
bool next() override
Template Class Generators
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::Generators : public Catch::Generators::IGenerator<T>

Public Functions

template<typename ...Gs>
Generators(Gs&&... moreGenerators)
T const &get() const override
bool next() override
Class GeneratorUntypedBase
Inheritance Relationships
Derived Types
Class Documentation
class Catch::Generators::GeneratorUntypedBase

Subclassed by Catch::Generators::IGenerator< T >, Catch::Generators::IGenerator< Float >, Catch::Generators::IGenerator< Integer >, Catch::Generators::IGenerator< std::vector< T > >

Public Functions

GeneratorUntypedBase() = default
~GeneratorUntypedBase()
bool next() = 0
Template Class GeneratorWrapper
Class Documentation
template<typename T>
class Catch::Generators::GeneratorWrapper

Public Functions

GeneratorWrapper(std::unique_ptr<IGenerator<T>> generator)
T const &get() const
bool next()
Template Class IteratorGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::IteratorGenerator : public Catch::Generators::IGenerator<T>

Public Functions

template<typename InputIterator, typename InputSentinel>
IteratorGenerator(InputIterator first, InputSentinel last)
T const &get() const override
bool next() override
Template Class MapGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T, typename U, typename Func>
class Catch::Generators::MapGenerator : public Catch::Generators::IGenerator<T>

Public Functions

template<typename F2 = Func>
MapGenerator(F2 &&function, GeneratorWrapper<U> &&generator)
T const &get() const override
bool next() override
Template Class RandomFloatingGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename Float>
class Catch::Generators::RandomFloatingGenerator : public Catch::Generators::IGenerator<Float>

Public Functions

RandomFloatingGenerator(Float a, Float b)
Float const &get() const override
bool next() override
Template Class RandomIntegerGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename Integer>
class Catch::Generators::RandomIntegerGenerator : public Catch::Generators::IGenerator<Integer>

Public Functions

RandomIntegerGenerator(Integer a, Integer b)
Integer const &get() const override
bool next() override
Template Class RangeGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::RangeGenerator : public Catch::Generators::IGenerator<T>

Public Functions

RangeGenerator(T const &start, T const &end, T const &step)
RangeGenerator(T const &start, T const &end)
T const &get() const override
bool next() override
Template Class RepeatGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::RepeatGenerator : public Catch::Generators::IGenerator<T>

Public Functions

RepeatGenerator(size_t repeats, GeneratorWrapper<T> &&generator)
T const &get() const override
bool next() override
Template Class SingleValueGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::SingleValueGenerator : public Catch::Generators::IGenerator<T>

Public Functions

SingleValueGenerator(T &&value)
T const &get() const override
bool next() override
Template Class TakeGenerator
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Generators::TakeGenerator : public Catch::Generators::IGenerator<T>

Public Functions

TakeGenerator(size_t target, GeneratorWrapper<T> &&generator)
T const &get() const override
bool next() override
Class LazyExpression
Class Documentation
class Catch::LazyExpression

Public Functions

LazyExpression(bool isNegated)
LazyExpression(LazyExpression const &other)
LazyExpression &operator=(LazyExpression const&) = delete
operator bool() const

Friends

friend auto operator<<(std::ostream &os, LazyExpression const &lazyExpr) -> std::ostream&
Class ExceptionMessageMatcher
Inheritance Relationships
Base Type
Class Documentation
class Catch::Matchers::Exception::ExceptionMessageMatcher : public Catch::Matchers::Impl::MatcherBase<std::exception>

Public Functions

ExceptionMessageMatcher(std::string const &message)
bool match(std::exception const &ex) const override
std::string describe() const override
Template Class PredicateMatcher
Inheritance Relationships
Base Type
Class Documentation
template<typename T>
class Catch::Matchers::Generic::PredicateMatcher : public Catch::Matchers::Impl::MatcherBase<T>

Public Functions

PredicateMatcher(std::function<bool(T const&)> const &elem, std::string const &descr, )
bool match(T const &item) const override
std::string describe() const override
Class MatcherUntypedBase
Inheritance Relationships
Derived Types
Class Documentation
class Catch::Matchers::Impl::MatcherUntypedBase

Subclassed by Catch::Matchers::Impl::MatcherBase< T >, Catch::Matchers::Impl::MatcherBase< ArgT >, Catch::Matchers::Impl::MatcherBase< double >, Catch::Matchers::Impl::MatcherBase< std::exception >, Catch::Matchers::Impl::MatcherBase< std::string >, Catch::Matchers::Impl::MatcherBase< std::vector< T > >

Public Functions

MatcherUntypedBase() = default
MatcherUntypedBase(MatcherUntypedBase const&) = default
MatcherUntypedBase &operator=(MatcherUntypedBase const&) = delete
std::string toString() const

Protected Functions

~MatcherUntypedBase()
std::string describe() const = 0

Protected Attributes

std::string m_cachedToString
Template Class MatchExpr
Inheritance Relationships
Base Type
Class Documentation
template<typename ArgT, typename MatcherT>
class Catch::MatchExpr : public Catch::ITransientExpression

Public Functions

MatchExpr(ArgT const &arg, MatcherT const &matcher, StringRef const &matcherString)
void streamReconstructedExpression(std::ostream &os) const override
Class NonCopyable
Inheritance Relationships
Derived Types
Class Documentation
class Catch::NonCopyable

Subclassed by Catch::AutoReg, Catch::IConfig, Catch::ReusableStringStream, Catch::Section

Protected Functions

NonCopyable()
~NonCopyable()
Template Class Option
Class Documentation
template<typename T>
class Catch::Option

Public Functions

Option()
Option(T const &_value)
Option(Option const &_other)
~Option()
Option &operator=(Option const &_other)
Option &operator=(T const &_value)
void reset()
T &operator*()
T const &operator*() const
T *operator->()
const T *operator->() const
T valueOr(T const &defaultValue) const
bool some() const
bool none() const
bool operator!() const
operator bool() const
Class ReusableStringStream
Inheritance Relationships
Base Type
Class Documentation
class Catch::ReusableStringStream : private Catch::NonCopyable

Public Functions

ReusableStringStream()
~ReusableStringStream()
auto str() const -> std::string
template<typename T>
auto operator<<(T const &value) -> ReusableStringStream&
auto get() -> std::ostream&
Class ScopedMessage
Class Documentation
class Catch::ScopedMessage

Public Functions

ScopedMessage(MessageBuilder const &builder)
ScopedMessage(ScopedMessage &duplicate) = delete
ScopedMessage(ScopedMessage &&old)
~ScopedMessage()

Public Members

MessageInfo m_info
bool m_moved
Class Section
Inheritance Relationships
Base Type
Class Documentation
class Catch::Section : private Catch::NonCopyable

Public Functions

Section(SectionInfo const &info)
~Section()
operator bool() const
Class SimplePcg32
Class Documentation
class Catch::SimplePcg32

Public Types

using result_type = std::uint32_t

Public Functions

SimplePcg32()
SimplePcg32(result_type seed_)
void seed(result_type seed_)
void discard(uint64_t skip)
result_type operator()()

Public Static Functions

constexpr result_type() min ()
constexpr result_type() max ()
Class StringRef
Class Documentation
class Catch::StringRef

A non-owning string class (similar to the forthcoming std::string_view) Note that, because a StringRef may be a substring of another string, it may not be null terminated.

Public Types

using size_type = std::size_t
using const_iterator = const char*

Public Functions

constexpr StringRef() noexcept = default
StringRef(char const *rawChars) noexcept
constexpr StringRef(char const *rawChars, size_type size) noexcept
StringRef(std::string const &stdString) noexcept
operator std::string() const
auto operator==(StringRef const &other) const noexcept -> bool
auto operator!=(StringRef const &other) const noexcept -> bool
auto operator[](size_type index) const noexcept -> char
constexpr auto empty() const noexcept -> bool
constexpr auto size() const noexcept -> size_type
auto c_str() const -> char const*
auto substr(size_type start, size_type length) const noexcept -> StringRef
auto data() const noexcept -> char const*
constexpr auto isNullTerminated() const noexcept -> bool
constexpr const_iterator begin() const
constexpr const_iterator end() const
Class TestCase
Inheritance Relationships
Base Type
Class Documentation
class Catch::TestCase : public Catch::TestCaseInfo

Public Functions

TestCase(ITestInvoker *testCase, TestCaseInfo &&info)
TestCase withName(std::string const &_newName) const
void invoke() const
TestCaseInfo const &getTestCaseInfo() const
bool operator==(TestCase const &other) const
bool operator<(TestCase const &other) const
Template Class TestInvokerAsMethod
Inheritance Relationships
Base Type
Class Documentation
template<typename C>
class Catch::TestInvokerAsMethod : public Catch::ITestInvoker

Public Functions

TestInvokerAsMethod(void (C::* testAsMethod)()) noexcept
void invoke() const override
Class Timer
Class Documentation
class Catch::Timer

Public Functions

void start()
auto getElapsedNanoseconds() const -> uint64_t
auto getElapsedMicroseconds() const -> uint64_t
auto getElapsedMilliseconds() const -> unsigned int
auto getElapsedSeconds() const -> double
Template Class UnaryExpr
Inheritance Relationships
Base Type
Class Documentation
template<typename LhsT>
class Catch::UnaryExpr : public Catch::ITransientExpression

Public Functions

UnaryExpr(LhsT lhs)
Class EfficientHost
Inheritance Relationships
Base Type
Class Documentation
class EfficientHost : public Host

Public Functions

EfficientHost(emp::Ptr<emp::Random> _random, emp::Ptr<EfficientWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, emp::vector<emp::Ptr<Organism>> _syms = {}, emp::vector<emp::Ptr<Organism>> _repro_syms = {}, std::set<int> _set = std::set<int>(), double _points = 0.0, double _efficient = 0.1)

The constructor for efficient host

EfficientHost(const EfficientHost&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

EfficientHost(EfficientHost&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

EfficientHost() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

void SetEfficiency(double _in)

Input: Efficiency value

Output: None

Purpose: Setting an efficient symbiont’s efficiency value.

double GetEfficiency()

Input: None

Output: A double representing the symbiont’s efficiency.

Purpose: Getting an efficient symbiont’s efficiency value.

emp::Ptr<Organism> makeNew()

Input: None.

Output: A new host with same properties as this host.

Purpose: To avoid creating an organism via constructor in other methods.

Protected Attributes

double efficiency

Purpose: Represents the efficiency of a host.

emp::Ptr<EfficientWorld> my_world = NULL

Purpose: Represents the world that the efficient hosts are living in.

Class EfficientSymbiont
Inheritance Relationships
Base Type
Class Documentation
class EfficientSymbiont : public Symbiont

Public Functions

EfficientSymbiont(emp::Ptr<emp::Random> _random, emp::Ptr<EfficientWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, double _points = 0.0, double _efficient = 0.1)

The constructor for efficient symbiont

EfficientSymbiont(const EfficientSymbiont&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

EfficientSymbiont(EfficientSymbiont&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

EfficientSymbiont() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

void SetEfficiency(double _in)

Input: Efficiency value

Output: None

Purpose: Setting an efficient symbiont’s efficiency value.

double GetEfficiency()

Input: None

Output: A double representing the symbiont’s efficiency.

Purpose: Getting an efficient symbiont’s efficiency value.

void AddPoints(double _in)

Input: A double representing the amount to be incremented to a symbiont’s points.

Output: None

Purpose: Incrementing an efficient symbiont’s points. The points are adjusted by the efficiency of the symbiont.

void mutate(std::string mode)

Input: String indicating mode, either “vertical” or “horizontal”

Output: None

Purpose: Mutating the efficiency of an efficient symbiont based upon the config setting for mutation size.

emp::Ptr<Organism> makeNew()

Input: None.

Output: A new bacterium with same properties as this bacterium.

Purpose: To avoid creating an organism via constructor in other methods.

emp::Ptr<Organism> reproduce(std::string mode)

Input: String to indicate the mode of transmission, either vertical or horizontal

Output: The pointer to the newly created organism

Purpose: To produce a new symbiont

void VerticalTransmission(emp::Ptr<Organism> host_baby)

Input: The pointer to the organism that is the new host baby

Output: None

Purpose: To allow for vertical transmission to occur

void HorizontalTransmission(emp::WorldPosition location)

Input: The location of the organism as a WorldPosition

Output: None

Purpose: To check and allow for horizontal transmission to occur

Protected Attributes

double efficiency

Purpose: Represents the efficiency of a symbiont. This has a multiplicable impact on a symbiont’s resource collection.

double ht_mut_size = 0.002

Purpose: Represents the standard deviation of the values chosen as mutations of a symbiont’s interaction value when horizontal transmission is occuring. .

double ht_mut_rate = 0

Purpose: Represents the probability (0-1) of mutation occurring during horizontal transmission.

double eff_mut_rate = 0

Purpose: Represents the probability (0-1) of mutation occurring during horizontal transmission for the efficiency trait.

emp::Ptr<EfficientWorld> my_world = NULL

Purpose: Represents the world that the efficient symbionts are living in.

Class EfficientWorld
Inheritance Relationships
Base Type
Class Documentation
class EfficientWorld : public SymWorld

Public Functions

~EfficientWorld()

Input: None

Output: None

Purpose: To destruct the data nodes belonging to EfficientWorld to conserve memory.

emp::DataFile &SetupEfficiencyFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track mean efficiency

emp::DataMonitor<double> &GetEfficiencyDataNode()

Input: None

Output: The DataMonitor<double>& that has the information representing the symbiont’s efficiency.

Purpose: To collect data on the lysis burst size to be saved to the data file that is tracking lysis burst size.

Class Host
Inheritance Relationships
Base Type
Derived Types
Class Documentation
class Host : public Organism

Subclassed by Bacterium, EfficientHost, PggHost

Public Functions

Host(emp::Ptr<emp::Random> _random, emp::Ptr<SymWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, emp::vector<emp::Ptr<Organism>> _syms = {}, emp::vector<emp::Ptr<Organism>> _repro_syms = {}, std::set<int> _set = std::set<int>(), double _points = 0.0)

The constructor for the host class

~Host()

Input: None

Output: None

Purpose: To delete the memory used by a host’s symbionts when the host is deleted.

Host(const Host&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

Host(Host&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

Host() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

Host &operator=(const Host&) = default

Input: None

Output: None

Purpose: To force a copy assignment operator to be generated by the compiler.

Host &operator=(Host&&) = default

Input: None

Output: None

Purpose: To force a move assignment operator to be generated by the compiler.

bool operator==(const Host &other) const

Input: An object of host to be compared to the current host.

Output: To boolean representing if thing1 == &thing2

Purpose: To override the bool operator == to return (thing1 == &thing2)

bool operator!=(const Host &other) const

Input: An object of host, and the address of the thing it is being compared to.

Output: To boolean representing if *thing1 == thing2

Purpose: To override the bool operator != to return !(*thing1 == thing2)

double GetIntVal() const

Input: None

Output: The double representing host’s interaction value

Purpose: To get the double representing host’s interaction value

emp::vector<emp::Ptr<Organism>> &GetSymbionts()

Input: None

Output: A vector of pointers to the organisms that are the host’s syms.

Purpose: To get the vector containing pointers to the host’s symbionts.

emp::vector<emp::Ptr<Organism>> &GetReproSymbionts()

Input: None

Output: A vector of pointers to the organisms that are the host’s repro syms.

Purpose: To get the vector containing pointers to the host’s repro syms.

std::set<int> GetResTypes() const

Input: None

Output: The set of ints representing a host’s res type.

Purpose: To get the set of ints representing the host’s res type.

double GetPoints()

Input: None

Output: The double representing a host’s points.

Purpose: To get the host’s points.

double GetResInProcess()

Input: None

Output: The double representing res_in_process

Purpose: To get the value of res_in_process

bool IsHost()

Input: None

Output: The bool representing if an organism is a host.

Purpose: To determine if an organism is a host.

void SetIntVal(double _in)

Input: A double representing the host’s new interaction value.

Output: None

Purpose: To set a host’s interaction value.

void SetSymbionts(emp::vector<emp::Ptr<Organism>> _in)

Input: A vector of pointers to organisms that will become a host’s symbionts.

Output: None

Purpose: To set a host’s symbionts to the input vector of organisms.

void SetResTypes(std::set<int> _in)

Input: A set of ints representing a host’s resource type.

Output: None

Purpose: To set a host’s resource types to the input.

void SetPoints(double _in)

Input: A double representing a host’s new point value.

Output: None

Purpose: To set a host’s points.

void ClearSyms()

Input: None

Output: None

Purpose: To clear a host’s symbionts.

void ClearReproSyms()

Input: None

Output: None

Purpose: To clear a host’s repro symbionts.

void SetDead()

Input: None

Output: None

Purpose: To kill a host.

void SetResInProcess(double _in)

Input: The double to be set as res_in_process

Output: None

Purpose: To set the value of res_in_process

bool GetDead()

Input: None

Output: boolean

Purpose: To determine if a host is dead.

int GetAge()

Input: None

Output: an int representing the current age of the Host

Purpose: To get the Host’s age.

void SetAge(int _in)

Input: An int of what age the Host should be set to

Output: None

Purpose: To set the Host’s age for testing purposes.

void GrowOlder()

Input: None

Output: None

Purpose: Increments age by one and kills it if too old.

double StealResources(double _intval)

Input: The interaction value of the symbiont that is eligible to steal resources from the host.

Output: The double representing the amount of resources that are actually stolen from the host.

Purpose: To determine if a host’s symbiont is eligible to steal resources from the host.

void AddPoints(double _in)

Input: The double representing the number of points to be incremented onto a host’s points.

Output: None

Purpose: To increment a host’s points by the input value.

void AddSymbiont(emp::Ptr<Organism> _in)

Input: The pointer to the organism that is to be added to the host’s symbionts.

Output: None

Purpose: To add a symbionts to a host’s symbionts

bool SymAllowedIn()

Input: None

Output: A bool representing if a symbiont will be allowed to enter a host.

Purpose: To determine if a symbiont will be allowed into a host. If phage exclusion is off, this function will always return true. If phage exclusion is on, then there is a 1/2^n chance of a new phage being allowed in, where n is the number of existing phage.

void AddReproSym(emp::Ptr<Organism> _in)

Input: A pointer to the organism to be added to the host’s symbionts.

Output: None

Purpose: To add a repro sym to the host’s symbionts.

bool HasSym()

Input: None

Output: A bool representing if a host has any symbionts.

Purpose: To determine if a host has any symbionts, though they might be corpses that haven’t been removed yet.

emp::Ptr<Organism> makeNew()

Input: None.

Output: A new host with same properties as this host.

Purpose: To avoid creating an organism via constructor in other methods.

emp::Ptr<Organism> reproduce()

Input: None.

Output: A new host baby of the current host, mutated.

Purpose: To create a new baby host and reset this host’s points to 0.

void mutate()

Input: None

Output: None

Purpose: To mutate a host’s interaction value. This is called on newly generated hosts to allow for evolution to occur.

void DistribResources(double resources)

Input: The double representing the number of resources to be distributed to the host and its symbionts and the position of the host in the world.

Output: None

Purpose: To distribute resources to a host and its symbionts. In the event that the host has no symbionts, the host gets all resources not allocated to defense or given to absent partner. Otherwise, the resource is split into equal chunks for each symbiont

double HandleEctosymbiosis(double resources, size_t location)

Input: The total resources recieved by the host and its location in the world.

Output: The resources remaining after the host maybe does ectosymbiosis.

Purpose: To handle ectosymbiosis.

bool GetDoEctosymbiosis(size_t location)

Input: The location of this host in the world.

Output: A bool value representing whether this host should interact with a parallel sym

Purpose: To determine whether a host should interact with a parallel sym

void DistribResToSym(emp::Ptr<Organism> sym, double sym_piece)

Input: The sym to whom resources are distributed and the resources it might recieve.

Output: None

Purpose: To distribute resources between sym and host depending on their interaction values.

void Process(emp::WorldPosition pos)

Input: The size_t value representing the location of the host.

Output: None

Purpose: To process the host, meaning determining eligibility for reproduction, checking for vertical transmission, removing dead syms, and processing alive syms.

Protected Attributes

double interaction_val = 0

Purpose: Represents the interaction value between the host and symbiont. A negative interaction value represent antagonism, while a positive one represents mutualism. Zero is a neutral value.

int age = 0

Purpose: Represents the number of updates the host has lived through; at birth is set to 0.

emp::vector<emp::Ptr<Organism>> syms = {}

Purpose: Represents the set of symbionts belonging to a host. This can be set with SetSymbionts(), and symbionts can be added with AddSymbiont(). This can be cleared with ClearSyms()

emp::vector<emp::Ptr<Organism>> repro_syms = {}

Purpose: Represents the set of repro symbionts belonging to a host. Symbionts can be added with AddReproSymb(). This can be cleared with ClearSyms()

std::set<int> res_types = {}

Purpose: Represents the resource type available to hosts. This is currently not implemented fully.

double points = 0

Purpose: Represents the resource points possessed by a host. This is what hosts must collect to reproduce.

double res_in_process = 0

Purpose: Represents the resources that could be in the process of being stolen.

emp::Ptr<emp::Random> random = NULL

Purpose: Represents an instance of random.

emp::Ptr<SymWorld> my_world = NULL

Purpose: Represents the world that the hosts are living in.

emp::Ptr<SymConfigBase> my_config = NULL

Purpose: Represents the configuration settings for a particular run.

bool dead = false

Purpose: Represents if a host is alive. This is set to true when a host is killed.

Class LysisWorld
Inheritance Relationships
Base Type
Class Documentation
class LysisWorld : public SymWorld

Public Functions

~LysisWorld()

Input: None

Output: None

Purpose: To destruct the data nodes belonging to LysisWorld to conserve memory.

emp::DataFile &SetupLysisChanceFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track mean lysis chance, the number of symbionts, and the histogram of the mean lysis chance.

emp::DataFile &SetupInductionChanceFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track mean induction chance, the number of symbionts, and the histogram of the mean induction chance.

emp::DataFile &SetupIncorporationDifferenceFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track the difference between bacterium and phage incorporation values and the histogram of the difference between the incorporation vals.

emp::DataMonitor<double, emp::data::Histogram> &GetLysisChanceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the chance of lysis for each symbiont.

Purpose: To collect data on the chance of lysis for each symbiont to be saved to the data file that is tracking the chance of lysis for each symbiont.

emp::DataMonitor<double> &GetBurstSizeDataNode()

Input: None

Output: The DataMonitor<double>& that has the information representing the lysis burst size.

Purpose: To collect data on the lysis burst size to be saved to the data file that is tracking lysis burst size.

emp::DataMonitor<int> &GetBurstCountDataNode()

Input: None

Output: The DataMonitor<int>& that has the information representing the lysis burst count.

Purpose: To collect data on the lysis burst count to be saved to the data file that is tracking lysis burst count.

emp::DataMonitor<double, emp::data::Histogram> &GetInductionChanceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the chance of induction for each symbionts.

Purpose: To collect data on the chance of induction for each symbiont to be saved to the data file that is tracking chance of induction for each symbiont.

emp::DataMonitor<double, emp::data::Histogram> &GetIncorporationDifferenceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the difference between incorporation vals for bacteriums and their phage

Purpose: To collect data on the difference between incorporation vals for each bacteria and their phage to be saved to the data file that is tracking incorporation val differences.

Class Organism
Inheritance Relationships
Derived Types
Class Documentation
class Organism

Subclassed by Host, Symbiont

Public Functions

Organism() = default
Organism(const Organism&) = default
Organism(Organism&&) = default
~Organism()
Organism &operator=(const Organism&) = default
Organism &operator=(Organism&&) = default
bool operator==(const Organism &other) const
bool operator!=(const Organism &other) const
double GetIntVal() const
double GetPoints()
void SetIntVal(double _in)
void SetPoints(double _in)
void AddPoints(double _in)
void SetHost(emp::Ptr<Organism> _in)
void SetDead()
bool GetDead()
void Process(emp::WorldPosition location)
double GetIncVal()
void SetIncVal(double _in)
int GetAge()
void SetAge(int _in)
emp::Ptr<Organism> makeNew()
void mutate()
emp::Ptr<Organism> reproduce()
void VerticalTransmission(emp::Ptr<Organism> host_baby)
void HorizontalTransmission(emp::WorldPosition location)
double ProcessResources(double sym_piece)
double ProcessResources(double sym_piece, emp::Ptr<Organism> host)
bool IsPhage()
emp::Ptr<Organism> GetHost()
bool WantsToInfect()
double GetInfectionChance()
void SetInfectionChance(double _in)
bool InfectionFails()
emp::Ptr<emp::Taxon<int>> GetTaxon()
void SetTaxon(emp::Ptr<emp::Taxon<int>> _in)
double GetEfficiency()
void SetEfficiency(double _in)
emp::Ptr<Organism> reproduce(std::string mode)
void mutate(std::string mode)
emp::vector<emp::Ptr<Organism>> &GetSymbionts()
emp::vector<emp::Ptr<Organism>> &GetReproSymbionts()
std::set<int> GetResTypes() const
void SetResInProcess(double _in)
double GetResInProcess()
double StealResources(double _intval)
void SetSymbionts(emp::vector<emp::Ptr<Organism>> _in)
void SetResTypes(std::set<int> _in)
void AddSymbiont(emp::Ptr<Organism> _in)
void AddReproSym(emp::Ptr<Organism> _in)
bool HasSym()
bool IsHost()
void DistribResources(double resources)
void ClearSyms()
void ClearReproSyms()
double ProcessLysogenResources(double phage_inc_val)
double GetBurstTimer()
void IncBurstTimer()
void SetBurstTimer(int _in)
double GetLysisChance()
double GetInductionChance()
void SetLysisChance(double _in)
void SetInductionChance(double _in)
void uponInjection()
void LysisBurst(emp::WorldPosition location)
void LysisStep()
bool GetLysogeny()
void SetPool()
void AddPool()
void DistribPool()
double GetDonation()
void Setdonation()
double ProcessPool()
Class PggHost
Inheritance Relationships
Base Type
Class Documentation
class PggHost : public Host

Public Functions

PggHost(emp::Ptr<emp::Random> _random, emp::Ptr<PggWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, emp::vector<emp::Ptr<Organism>> _syms = {}, emp::vector<emp::Ptr<Organism>> _repro_syms = {}, std::set<int> _set = std::set<int>(), double _points = 0.0)
PggHost(const PggHost&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

PggHost(PggHost&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

PggHost() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

double GetPool()

Input: None

Output: #

Purpose:

void SetPool(double _in)

Input: #

Output: None

Purpose:

void AddPool(double _in)

Input: #

Output: None

Purpose:

void DistribResources(double resources)

Input: #

Output: None

Purpose:

void DistribPool()

Input: None

Output: #

Purpose:

emp::Ptr<Organism> makeNew()

Input: None.

Output: A new pgghost with same properties as this pgghost.

Purpose: To avoid creating an organism via constructor in other methods.

Protected Attributes

double sourcepool = 0

Purpose:#

emp::Ptr<PggWorld> my_world = NULL

Purpose: Represents the world that the pgg hosts are living in.

Class PGGSymbiont
Inheritance Relationships
Base Type
Class Documentation
class PGGSymbiont : public Symbiont

Public Functions

PGGSymbiont(emp::Ptr<emp::Random> _random, emp::Ptr<PggWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, double _donation = 0.0, double _points = 0.0)
PGGSymbiont(const PGGSymbiont&) = default

Input: #

Output:

Purpose:

PGGSymbiont(PGGSymbiont&&) = default

Input: #

Output:

Purpose:

PGGSymbiont() = default

Input: #

Output:

Purpose:

PGGSymbiont &operator=(const PGGSymbiont&) = default

Input: #

Output:

Purpose:

PGGSymbiont &operator=(PGGSymbiont&&) = default

Input: #

Output:

Purpose:

double GetDonation()

Input: #

Output:

Purpose:

void Setdonation(double _in)

Input: #

Output:

Purpose:

void mutate()

Input: #

Output:

Purpose:

double ProcessPool()

Input: #

Output:

Purpose:

emp::Ptr<Organism> makeNew()

Input: None

Output: The pointer to the newly created organism

Purpose: To produce a new phage, identical to the original

std::string PrintSym(emp::Ptr<PGGSymbiont> org)

Input: #

Output:

Purpose:

Protected Attributes

double Pgg_donate = 0

Purpose: #

emp::Ptr<PggWorld> my_world = NULL

Purpose: Represents the world that the pgg symbionts are living in.

Class PggWorld
Inheritance Relationships
Base Type
Class Documentation
class PggWorld : public SymWorld

Public Functions

~PggWorld()

Input: None

Output: None

Purpose: To destruct the data nodes belonging to PggWorld to conserve memory.

emp::DataFile &SetupPGGSymIntValFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track information about the PGG symbiont’s interaction values

emp::DataMonitor<double, emp::data::Histogram> &GetPGGDataNode()

Input: The double representing the number of resources each host gets in each update.

Output: None

Purpose: To set the resources that each host gets per update.

Class Phage
Inheritance Relationships
Base Type
Class Documentation
class Phage : public Symbiont

Public Functions

Phage(emp::Ptr<emp::Random> _random, emp::Ptr<LysisWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, double _points = 0.0)

The constructor for phage

Phage(const Phage&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

Phage(Phage&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

Phage() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

double GetBurstTimer()

Input: None

Output: The double representing the phage’s burst timer.

Purpose: To get a phage’s burst timer.

void IncBurstTimer()

Input: None

Output: None

Purpose: To increment a phage’s burst timer.

void SetBurstTimer(double _in)

Input: The double to be set as the phage’s burst timer

Output: None

Purpose: To set a phage’s burst timer.

double GetLysisChance()

Input: None

Output: The double representing a phage’s change of lysis.

Purpose: To determine a phage’s chance of lysis.

void SetLysisChance(double _in)

Input: The double to be set as the phage’s chance of lysis.

Output: None

Purpose: To set a phage’s chance of lysis

double GetIncVal()

Input: None

Output: The double representing a phage’s incorporation value.

Purpose: To determine a phage’s incorporation value.

void SetIncVal(double _in)

Input: The double to be set as the phage’s incorporation value.

Output: None

Purpose: To set a phage’s incorporation value.

double GetInductionChance()

Input: None

Output: The double representing a prophage’s chance of induction.

Purpose: To determine a lysogenic phage’s chance of inducing

void SetInductionChance(double _in)

Input: The double to be set as the phage’s chance of induction

Output:None

Purpose: To set a phage’s chance of inducing

bool GetLysogeny()

Input: None

Output: The bool representing if a phage will do lysogeny.

Purpose: To determine if a phage is capable of lysogeny

bool IsPhage()

Input: None

Output: The bool representing if an organism is a phage, always true.

Purpose: To determine if an organism is a phage.

void uponInjection()

Input: None

Output: None

Purpose: To determine if a phage will choose lysis or lysogeny. If a phage chooses to be lytic, their interaction value will be -1 to represent them being antagonistic. If a phage chooses to be lysogenic, their interaction value will be 0 to represent them being neutral.

void mutate()

Input: Optional string that indicates mode of reproduction and therefore which mutation rate and size should be used. Options are vertical (for prophage) or horizontal (for lytic phage)

Output: None

Purpose: To mutate a phage’s chance of lysis. The mutation will be based on a value chosen from a normal distribution centered at 0, with a standard deviation that is equal to the mutation size. Phage mutation can be on or off.

emp::Ptr<Organism> makeNew()

Input: None

Output: The pointer to the newly created organism

Purpose: To produce a new symbiont, identical to the original

void LysisBurst(emp::WorldPosition location)

Input: location of the phage attempting to horizontally transmit

Output: None

Purpose: To burst host and release offspring

void LysisStep()

Input: None

Output: None

Purpose: To allow lytic phage to produce offspring and increment the burst timer

void VerticalTransmission(emp::Ptr<Organism> host_baby)

Input: A pointer to the baby host to have symbionts added.

Output: None

Purpose: To allow for vertical transmission to occur. lysogenic phage have 100% chance of vertical transmission, lytic phage have 0% chance

double ProcessResources(double hostDonation)

Input: The double representing the resources that will be given to a phage.

Output: The double representing the resources that are left over from what was distributed to the phage.

Purpose: To allow a phage to steal or use donated resources from their host.

void Process(emp::WorldPosition location)

Input: The worldposition representing the location of the phage being processed.

Output: None

Purpose: To process a phage, meaning check for reproduction, check for lysis, and move the phage.

Protected Attributes

double burst_timer = 0

Purpose: Represents the time until lysis will be triggered.

bool lysogeny = false

Purpose: Represents if lysogeny is on.

double incorporation_val = 0.0

Purpose: Represents the compatibility of the prophage to it’s placement within the host’s genome.

double chance_of_lysis = 1

Purpose: Represents the chance of lysis

double induction_chance = 1

Purpose: Represents the chance of a prophage inducing to the lytic process

emp::Ptr<LysisWorld> my_world = NULL

Purpose: Represents the world that the phage are living in.

Class SymAnimate
Inheritance Relationships
Base Type

  • public Animate

Class Documentation
class SymAnimate : public Animate

Public Functions

SymAnimate()

The contructor for SymAnimate

void initializeWorld()

Input: None

Output: None

Purpose: To initialize the world based upon the config setting given

void setButtonStyle(std::string but_id)

Input: The string representing the button identification.

Output: None

Purpose: To add style to the buttons displayed.

void drawPetriDish(UI::Canvas &can)

Input: The canvas being used.

Output: None

Purpose: To draw the petri dish of basteria and phage.

std::string matchColor(double intVal)

Input: The double representing symbiont or host’s interaction value

Output: The string representing the hex value for the color of the organism.

Purpose: To determine the color that an organism should be, given its interaction value.

void DoFrame()

Input: None

Output: None

Purpose: To update the frame displayed of the current world state.

Class Symbiont
Inheritance Relationships
Base Type
Derived Types
Class Documentation
class Symbiont : public Organism

Subclassed by EfficientSymbiont, PGGSymbiont, Phage

Public Functions

Symbiont(emp::Ptr<emp::Random> _random, emp::Ptr<SymWorld> _world, emp::Ptr<SymConfigBase> _config, double _intval = 0.0, double _points = 0.0)

The constructor for symbiont

Symbiont(const Symbiont&) = default

Input: None

Output: None

Purpose: To force a copy constructor to be generated by the compiler.

Symbiont(Symbiont&&) = default

Input: None

Output: None

Purpose: To force a move constructor to be generated by the compiler

Symbiont() = default

Input: None

Output: None

Purpose: To tell the compiler to use its default generated variants of the constructor

Symbiont &operator=(const Symbiont&) = default

Input: None

Output: None

Purpose: To force a copy assignment operator to be generated by the compiler.

Symbiont &operator=(Symbiont&&) = default

Input: None

Output: None

Purpose: To force a move assignment operator to be generated by the compiler.

~Symbiont()

Input: None

Output: None

Purpose: To destruct the symbiont and remove the symbiont from the systematic.

double GetIntVal() const

Input: None

Output: The double representing the symbiont’s interaction value

Purpose: To get a symbiont’s interaction value.

double GetPoints()

Input: None

Output: The double representing the symbiont’s points

Purpose: To get a symbiont’s points.

bool IsPhage()

Input: None

Output: The bool representing if a symbiont is a phage

Purpose: To determine if a symbiont is a phage

bool IsHost()

Input: None

Output: The bool representing if a symbiont is a host

Purpose: To determine if a symbiont is a host

double GetInfectionChance()

Input: None

Output: The chance of a symbiont infecting a parallel host during process

Purpose: To determine a symbiont’s infection chance

emp::Ptr<Organism> GetHost()

Input: None

Output: The pointer to a symbiont’s host

Purpose: To retrieve a symbiont’s host

emp::Ptr<emp::Taxon<int>> GetTaxon()

Input: None

Output: The pointer to the symbiont’s taxon

Purpose: To retrieve the symbiont’s taxon

void SetTaxon(emp::Ptr<emp::Taxon<int>> _in)

Input: A pointer to the taxon that this organism should belong to.

Output: None

Purpose: To set the symbiont’s taxon

void SetDead()

Input: None

Output: None

Purpose: To set a symbiont to dead

bool GetDead()

Input: None

Output: The bool representing if a symbiont is dead

Purpose: To determine if a symbiont is dead

void SetIntVal(double _in)

Input: The double representing the new interaction value of a symbiont

Output: None

Purpose: To set a symbiont’s interaction value

void SetPoints(double _in)

Input: The double representing the points to be set as a symbinot’s points

Output: None

Purpose: To set a symbiont’s points

void AddPoints(double _in)

Input: The double representing the points to be added to a symbinot’s points

Output: None

Purpose: To increment a symbiont’s points

int GetAge()

Input: None

Output: an int representing the current age of the Symbiont

Purpose: To get the Symbiont’s age.

void SetAge(int _in)

Input: An int of what age the Symbiont should be set to

Output: None

Purpose: To set the Symbiont’s age for testing purposes.

void SetHost(emp::Ptr<Organism> _in)

Input: The pointer to an organism that will be set as the symbinot’s host

Output: None

Purpose: To set a symbiont’s host

void SetInfectionChance(double _in)
void uponInjection()

Input: None

Output: None

Purpose: Does nothing for now, added for backwards compatibility from phage to symbiont

void GrowOlder()

Input: None

Output: None

Purpose: Increments age by one and kills it if too old.

void mutate()

Input: None

Output: None

Purpose: To mutate a symbiont’s interaction value. The mutation value is chosen from a normal distribution centered on 0 with the mutation size as the standard deviation.

double ProcessResources(double hostDonation)

Input: The double representing the resources to be distributed to the symbionts

Output: The double representing the host’s resources

Purpose: To process and distribute resources.

double ProcessResources(double hostDonation, emp::Ptr<Organism> host)

Input: The double representing the resources to be distributed to the symbionts and the host from whom it comes

Output: The double representing the host’s resources

Purpose: To process and distribute resources.

bool WantsToInfect()

Input: None

Output: The boolean representing if a symbiont will seek out to infect a host.

Purpose: To determine if a symbiont wants to infect a host based upon its infection chance

bool InfectionFails()

Input: None

Output: The boolean representing if a symbiont will survive crossing over into the host world.

Purpose: To determine if a symbiont will survive crossing over into the host world based on infection risk.

void LoseResources(double resources)

Input: The double representing the resources given by the world.

Output: None

Purpose: Free living symbionts specialized to interact with hosts (extreme interaction value in either direction) lose some of the resources that they get from the world.

void Process(emp::WorldPosition location)

Input: The size_t representing the location of the symbiont, and the size_t representation of the symbiont’s position in the host (default -1 if it doesn’t have a host)

Output: None

Purpose: To process a symbiont, meaning to check for reproduction, distribute resources, and to allow for movement

emp::Ptr<Organism> makeNew()

Input: None

Output: The pointer to the newly created organism

Purpose: To produce a new symbiont, identical to the original

emp::Ptr<Organism> reproduce()

Input: None

Output: The pointer to the newly created organism

Purpose: To produce a new symbiont; does not remove resources from the parent, assumes that is handled by calling function

void VerticalTransmission(emp::Ptr<Organism> host_baby)

Input: The pointer to the organism that is the new host baby

Output: None

Purpose: To allow for vertical transmission to occur

void HorizontalTransmission(emp::WorldPosition location)

Input: The location of the organism (and it’s Host) as a size_t

Output: None

Purpose: To check and allow for horizontal transmission to occur

Protected Attributes

double interaction_val = 0

Purpose: Represents the interaction value between the host and symbiont. A negative interaction value represent antagonism, while a positive one represents mutualism. Zero is a neutral value.

double points = 0

Purpose: Represents the resource points possessed by a symbiont. This is what host’s must collect to reproduce.

bool dead = false

Purpose: Represents if a symbiont is alive. This is set to true when a symbiont is killed.

double infection_chance = 0.0

Purpose: Represents the chance (between 0 and 1) that a free-living sym will infect a parallel host on process

int age = 0

Purpose: Represents the number of updates the symbiont has lived through; at birth is set to 0.

emp::Ptr<emp::Random> random = NULL

Purpose: Represents an instance of random.

emp::Ptr<SymWorld> my_world = NULL

Purpose: Represents the world that the hosts are living in.

emp::Ptr<Organism> my_host = NULL

Purpose: Represents the symbiont’s host.

emp::Ptr<SymConfigBase> my_config = NULL

Purpose: Represents the configuration settings for a particular run.

emp::Ptr<emp::Taxon<int>> my_taxon = NULL

Purpose: Tracks the taxon of this organism.

Class SymWorld
Inheritance Relationships
Base Type

  • public emp::World< Organism >

Derived Types
Class Documentation
class SymWorld : public emp::World<Organism>

Subclassed by EfficientWorld, LysisWorld, PggWorld

Public Functions

SymWorld(emp::Random &_random)

Input: The world’s random seed

Output: None

Purpose: To construct an instance of SymWorld

~SymWorld()

Input: None

Output: None

Purpose: To destruct the data nodes belonging to SymWorld to conserve memory.

void SetVertTrans(double vt)

Input: The double representing the vertical transmission rate

Output: None

Purpose: To set the vertical transmission rate

void SetResPerUpdate(double val)

Input: The double representing the number of resources each host gets in each update.

Output: None

Purpose: To set the resources that each host gets per update.

void SetLimitedRes(bool val)

Input: To boolean representing if resources are limited or not.

Output: None

Purpose: To allow for resources to be limited or unlimited.

void SetFreeLivingSyms(bool flp)

Input: The boolean representing if symbionts are allowed to be free living.

Output: None

Purpose: To allow for free-living symbionts

void SetMoveFreeSyms(bool mfs)

Input: The bool representing if free living symbionts are permitted to move around in the world.

Output: None

Purpose: To set the value representing if FLS are permitted to move around.

void SetNumPhyloBins(size_t _in)

Input: The size_t number of bins that organisms should be placed into when phylogeny tracking is on.

Output: None

Purpose: To set the number of bins used by phylogenies.

void SetTrackPhylogeny(bool _in)

Input: The bool representing whether phylogenies should be tracked.

Output: None

Purpose: To set the value representing whether phylogenies should be tracked.

void SetTotalRes(int val)

Input: The int representing the total number of resources for the world.

Output: None

Purpose: To set the total number of resources in the world. If limited resources is off, then the total resource value is of no consequence.

emp::World<Organism>::pop_t GetPop()

Input: None

Output: The pop_t value that represents the world’s population.

Purpose: To get the world’s population of organisms.

emp::World<Organism>::pop_t GetSymPop()

Input: None

Output: The pop_t value that represent the world’s symbiont population.

Purpose: To get the world’s symbiont population.

bool WillTransmit()

Input: None

Output: The boolean representing if vertical transmission will occur

Purpose: To determine if vertical transmission will occur

emp::Ptr<emp::Systematics<Organism, int>> GetHostSys()

Input: None

Output: The systematic object tracking hosts

Purpose: To retrieve the host systematic

emp::Ptr<emp::Systematics<Organism, int>> GetSymSys()

Input: None

Output: The systematic object tracking hosts

Purpose: To retrieve the symbiont systematic

fun_calc_info_t GetCalcInfoFun()

Input: None

Output: The standard function object that determines which bin organisms should belong to depending on their interaction value

Purpose: To classify organsims based on their interaction value.

emp::Ptr<emp::Taxon<int>> AddSymToSystematic(emp::Ptr<Organism> sym, emp::Ptr<emp::Taxon<int>> parent_taxon = nullptr)

Input: The symbiont to be added to the systematic

Output: the taxon the symbiont is added to.

Purpose: To add a symbiont to the systematic and to set it to track its taxon

int PullResources(int desired_resources)

Input: The amount of resourcces an organism wants from the world.

Output: If there are unlimited resources or the total resources are greater than those requested, returns the amount of desired resources. If total_res is less than the desired resources, but greater than 0, then total_res will be returned. If none of these are true, then 0 will be returned.

Purpose: To determine how many resources to distribute to each organism.

void Resize(size_t new_width, size_t new_height)

Input: The size_t representing the world’s new width; the size_t representing the world’s new height.

Output: None

Purpose: To overwrite the Empirical resize so that sym_pop is also resized

void Resize(size_t new_size)

Input: The size_t representing the new size of the world

Output: None

Purpose: To override the Empirical Resize function with a single-arg method that can be used for AddOrgAt vector expansions

void AddOrgAt(emp::Ptr<Organism> new_org, emp::WorldPosition pos, emp::WorldPosition p_pos = emp::WorldPosition())

Input: The pointer to the new organism; the world position of the location to add the new organism.

Output: None

Purpose: To overwrite the empirical AddOrgAt function to permit syms to be added into sym_pop

emp::WorldPosition DoBirth(emp::Ptr<Organism> new_org, emp::WorldPosition p_pos)

Input: (1) The pointer to the organism that is being birthed; (2) The size_t location of the parent organism.

Output: The WorldPosition of the position of the new organism.

Purpose: To introduce new organisms to the world.

int GetNeighborHost(size_t i)

Input: The size_t value representing the location whose neighbors are being searched.

Output: If there are no occupied neighboring positions, -1 will be returned. If there are occupied neighboring positions, then the location of one occupied position will be returned.

Purpose: To determine the location of a valid occupied neighboring position.

void InjectSymbiont(emp::Ptr<Organism> new_sym)

Input: The pointer to an organism that will be injected into a host.

Output: None

Purpose: To add a symbiont to a host’s symbionts.

void WritePhylogenyFile(const std::string &filename)

Definitions of data node functions, expanded in DataNodes.h

Input: The address of the string representing the suffixes for the files to be created.

Output: None.

Purpose: To setup and write to the files that track the symbiont systematic information and the host systematic information

void WriteDominantPhylogenyFiles(const std::string &filename)
emp::Ptr<emp::Taxon<int>> GetDominantSymTaxon()
emp::Ptr<emp::Taxon<int>> GetDominantHostTaxon()
emp::vector<emp::Ptr<emp::Taxon<int>>> GetDominantFreeHostedSymTaxon()
emp::DataFile &SetupSymIntValFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track the average symbiont interaction value, the total number of symbionts, the total number of symbionts in a host, the total number of free syms and set up a histogram of the symbiont’s interaction values.

emp::DataFile &SetupHostIntValFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track host’s interaction values, the total number of hosts, the total number of colony forming units, and the histogram of the host’s interaction values

emp::DataFile &SetUpFreeLivingSymFile(const std::string &filename)

Input: The address of the string representing the file to be created’s name

Output: The address of the DataFile that has been created.

Purpose: To set up the file that will be used to track mean information about the free living symbionts in the world. This includes: (1) their total count, (2) the counts of the free and hosted symbionts, (3) the interaction values for the free and hosted symbionts, and (4) the infection chances from the total population, free symbionts, and hosted symbionts.

emp::DataMonitor<int> &GetHostCountDataNode()

Input: None

Output: The DataMonitor<int>& that has the information representing the host count.

Purpose: To collect data on the host count to be saved to the data file that is tracking host count

emp::DataMonitor<int> &GetSymCountDataNode()

Input: None

Output: The DataMonitor<int>& that has the information representing the symbiont count.

Purpose: To collect data on the symbiont count to be saved to the data file that is tracking symbiont count

emp::DataMonitor<int> &GetCountHostedSymsDataNode()

Input: None

Output: The DataMonitor<double>& that has the information representing the count of the hosted symbionts.

Purpose: To collect data on the count of the hosted symbionts to be saved to the data file that is tracking the count of the hosted symbionts.

emp::DataMonitor<int> &GetCountFreeSymsDataNode()

Input: None

Output: The DataMonitor<double>& that has the information representing the count of the free symbionts.

Purpose: To collect data on the count of the free symbionts to be saved to the data file that is tracking the count of the free symbionts.

emp::DataMonitor<int> &GetUninfectedHostsDataNode()

Input: None

Output: The DataMonitor<int>& that has the information representing the count of the uninfected hosts

Purpose: To collect data on the count of the uninfected hosts to be saved to the data file that is tracking the count of the uninfected hosts.

emp::DataMonitor<int> &GetCFUDataNode()

Input: None

Output: The DataMonitor<int>& that has the information representing the number of colony forming units.

Purpose: To collect data on the CFU count to be saved to the data file that is tracking CFU

emp::DataMonitor<double, emp::data::Histogram> &GetHostIntValDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the host interaction value.

Purpose: To collect data on the host interaction value to be saved to the data file that is tracking host interaction value.

emp::DataMonitor<double, emp::data::Histogram> &GetSymIntValDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the symbiont interaction value.

Purpose: To collect data on the symbiont interaction value to be saved to the data file that is tracking symbionts interaction value.

emp::DataMonitor<double, emp::data::Histogram> &GetFreeSymIntValDataNode()

Input: None

Output: The DataMonitor<double>& that has the information representing the free symbiont’s interaction value.

Purpose: To collect data on the interaction value of the free symbionts to be saved to the data file that is tracking the interaction value of the free symbionts.

emp::DataMonitor<double, emp::data::Histogram> &GetHostedSymIntValDataNode()

Input:None

Output:

Purpose: To access the data node that is tracking the hosted symbiont interaction value

emp::DataMonitor<double, emp::data::Histogram> &GetSymInfectChanceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the infection chance for each symbionts.

Purpose: To access the data node that is tracking the symbiont infection chance

emp::DataMonitor<double, emp::data::Histogram> &GetFreeSymInfectChanceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the free symbionts’ chance of infection

Purpose: To access the data node that is tracking the infection chance within the free symbionts.

emp::DataMonitor<double, emp::data::Histogram> &GetHostedSymInfectChanceDataNode()

Input: None

Output: The DataMonitor<double, emp::data::Histogram>& that has the information representing the infection chance for the hosted symbionts

Purpose: To retrieve the data nodes that is tracking the infection chance within the hosted symbionts.

void MoveIntoNewFreeWorldPos(emp::Ptr<Organism> sym, emp::WorldPosition parent_pos)

Input: The pointer to the symbiont that is moving, the WorldPosition of its current location.

Output: None

Purpose: To move a symbiont into a new world position.

void SymDoBirth(emp::Ptr<Organism> sym_baby, emp::WorldPosition parent_pos)

Input: The pointer to the organism that is being birthed, and the WorldPosition location of the parent symbiont.

Output: None

Purpose: To birth a new symbiont. If free living symbionts is on, the new symbiont can be put into an unoccupied place in the world. If not, then it will be placed in a host near its parent’s location, or deleted if the parent’s location has no eligible near-by hosts.

void MoveFreeSym(emp::WorldPosition pos)

Input: The WorldPosition location of the symbiont to be moved.

Output: None

Purpose: To move a symbiont, either into a host, or into a free world position

emp::Ptr<Organism> GetSymAt(size_t location)
emp::Ptr<Organism> ExtractSym(size_t i)

Input: The size_t representing the location of the symbiont to be extracted from the world.

Output: The pointer to the organism that was removed from the world

Purpose: To remove a symbiont from the world

void DoSymDeath(size_t i)

Input: The size_t representing the location of the symbiont to be deleted from the world.

Output: None

Purpose: To delete a symbiont from the world.

void Update()

Input: None

Output: None

Purpose: To call the process functions for hosts and symbionts.

Protected Types

using fun_calc_info_t = std::function<int(Organism&)>

Protected Attributes

double vertTrans = 0

Purpose: Represents the vertical transmission rate. This can be set with SetVertTrans()

int total_res = -1

Purpose: Represents the total resources in the world. This can be set with SetTotalRes()

bool limited_res = false

Purpose: Represents if resources are limited or not. This can be set with SetLimitedRes()

bool do_free_living_syms = false

Purpose: Represents if free living symbionts are allowed. This can be set with SetFreeLivingSyms()

double resources_per_host_per_update = 0

Purpose: Represents how many resources each host gets per update. This can be set with SetResPerUpdate()

bool move_free_syms = false

Purpose: Represents if free living symbionts are permitted to move around the world.

bool track_phylogeny = false

Purpose: Represents if phylogeneis should be tracked. This can be set with SetTrackPhylogeny()

size_t num_phylo_bins

Purpose: Represents how many bins to place organisms into when tracking phylogenies.

pop_t sym_pop

Purpose: Represents the free living sym environment, parallel to “pop” for hosts

fun_calc_info_t calc_info_fun

Purpose: Represents a standard function object which determines which taxon an organism belongs to.

emp::Ptr<emp::Systematics<Organism, int>> host_sys

Purpose: Represents the systematics object tracking hosts.

emp::Ptr<emp::Systematics<Organism, int>> sym_sys

Purpose: Represents the systematics object tracking symbionts.

emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_hostintval
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_symintval
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_freesymintval
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_hostedsymintval
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_syminfectchance
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_freesyminfectchance
emp::Ptr<emp::DataMonitor<double, emp::data::Histogram>> data_node_hostedsyminfectchance
emp::Ptr<emp::DataMonitor<int>> data_node_hostcount
emp::Ptr<emp::DataMonitor<int>> data_node_symcount
emp::Ptr<emp::DataMonitor<int>> data_node_freesymcount
emp::Ptr<emp::DataMonitor<int>> data_node_hostedsymcount
emp::Ptr<emp::DataMonitor<int>> data_node_cfu
emp::Ptr<emp::DataMonitor<int>> data_node_uninf_hosts
Enums
Enum Verbosity
Enum Documentation
enum Catch::Verbosity

Values:

enumerator Quiet
enumerator Normal
enumerator High
Functions
Function Catch::cerr
Function Documentation
std::ostream &Catch::cerr()
Function Catch::cleanUp
Function Documentation
void Catch::cleanUp()
Function Catch::cleanUpContext
Function Documentation
void Catch::cleanUpContext()
Function Catch::clog
Function Documentation
std::ostream &Catch::clog()
Template Function Catch::compareEqual(LhsT const&, RhsT const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareEqual” with arguments (LhsT const&, RhsT const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareEqual(T *const&, int)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareEqual” with arguments (T *const&, int) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareEqual(T *const&, long)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareEqual” with arguments (T *const&, long) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareEqual(int, T *const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareEqual” with arguments (int, T *const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareEqual(long, T *const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareEqual” with arguments (long, T *const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareEqual(LhsT const &lhs, RhsT const &rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareNotEqual(LhsT const&, RhsT&&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareNotEqual” with arguments (LhsT const&, RhsT&&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareNotEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareNotEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareNotEqual(T *const&, int)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareNotEqual” with arguments (T *const&, int) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareNotEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareNotEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareNotEqual(T *const&, long)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareNotEqual” with arguments (T *const&, long) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareNotEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareNotEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareNotEqual(int, T *const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareNotEqual” with arguments (int, T *const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareNotEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareNotEqual(long lhs, T *const &rhs) -> bool
Template Function Catch::compareNotEqual(long, T *const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::compareNotEqual” with arguments (long, T *const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename LhsT, typename RhsT> auto compareNotEqual(LhsT const &lhs, RhsT &&rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, int rhs) -> bool
- template<typename T> auto compareNotEqual(T *const &lhs, long rhs) -> bool
- template<typename T> auto compareNotEqual(int lhs, T *const &rhs) -> bool
- template<typename T> auto compareNotEqual(long lhs, T *const &rhs) -> bool
Function Catch::contains
Function Documentation
bool Catch::contains(std::string const &s, std::string const &infix)
Function Catch::cout
Function Documentation
std::ostream &Catch::cout()
Template Function Catch::Detail::convertUnknownEnumToString
Function Documentation
template<typename E>
std::string Catch::Detail::convertUnknownEnumToString(E e)
Template Function Catch::Detail::convertUnstreamable(T const&)
Function Documentation
template<typename T>
std::enable_if<!std::is_enum<T>::value && !std::is_base_of<std::exception, T>::value, std::string>::type Catch::Detail::convertUnstreamable(T const&)
Template Function Catch::Detail::convertUnstreamable(T const&)
Function Documentation
template<typename T>
std::enable_if<!std::is_enum<T>::value && !std::is_base_of<std::exception, T>::value, std::string>::type Catch::Detail::convertUnstreamable(T const&)
Template Function Catch::Detail::convertUnstreamable(T const&)
Function Documentation
template<typename T>
std::enable_if<!std::is_enum<T>::value && !std::is_base_of<std::exception, T>::value, std::string>::type Catch::Detail::convertUnstreamable(T const&)
Template Function Catch::Detail::rangeToString
Function Documentation
template<typename InputIterator>
std::string Catch::Detail::rangeToString(InputIterator first, InputIterator last)
Function Catch::Detail::rawMemoryToString(const void *, std::size_t)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Detail::rawMemoryToString” with arguments (const void *, std::size_t) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- std::string rawMemoryToString(const void *object, std::size_t size)
- template<typename T> std::string rawMemoryToString(const T &object)
Template Function Catch::Detail::rawMemoryToString(const T&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Detail::rawMemoryToString” with arguments (const T&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- std::string rawMemoryToString(const void *object, std::size_t size)
- template<typename T> std::string rawMemoryToString(const T &object)
Template Function Catch::Detail::stringify
Function Documentation
template<typename T>
std::string Catch::Detail::stringify(const T &e)
Function Catch::endsWith(std::string const&, std::string const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::endsWith” with arguments (std::string const&, std::string const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- bool endsWith(std::string const &s, char suffix)
- bool endsWith(std::string const &s, std::string const &suffix)
Function Catch::endsWith(std::string const&, char)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::endsWith” with arguments (std::string const&, char) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- bool endsWith(std::string const &s, char suffix)
- bool endsWith(std::string const &s, std::string const &suffix)
Function Catch::filterTests
Function Documentation
std::vector<TestCase> Catch::filterTests(std::vector<TestCase> const &testCases, TestSpec const &testSpec, IConfig const &config)
Function Catch::formatReconstructedExpression
Function Documentation
void Catch::formatReconstructedExpression(std::ostream &os, std::string const &lhs, StringRef op, std::string const &rhs)
Function Catch::Generators::acquireGeneratorTracker
Function Documentation
auto Catch::Generators::acquireGeneratorTracker(SourceLineInfo const &lineInfo) -> IGeneratorTracker&
Template Function Catch::Generators::chunk
Function Documentation
template<typename T>
GeneratorWrapper<std::vector<T>> Catch::Generators::chunk(size_t size, GeneratorWrapper<T> &&generator)
Template Function Catch::Generators::filter
Function Documentation
template<typename T, typename Predicate>
GeneratorWrapper<T> Catch::Generators::filter(Predicate &&pred, GeneratorWrapper<T> &&generator)
Template Function Catch::Generators::from_range(InputIterator, InputSentinel)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::from_range” with arguments (InputIterator, InputSentinel) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename Container, typename ResultType = typename Container::value_type> GeneratorWrapper<ResultType> from_range(Container const &cnt)
- template<typename InputIterator, typename InputSentinel, typename ResultType = typename std::iterator_traits<InputIterator>::value_type> GeneratorWrapper<ResultType> from_range(InputIterator from, InputSentinel to)
Template Function Catch::Generators::from_range(Container const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::from_range” with arguments (Container const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename Container, typename ResultType = typename Container::value_type> GeneratorWrapper<ResultType> from_range(Container const &cnt)
- template<typename InputIterator, typename InputSentinel, typename ResultType = typename std::iterator_traits<InputIterator>::value_type> GeneratorWrapper<ResultType> from_range(InputIterator from, InputSentinel to)
Template Function Catch::Generators::generate
Function Documentation
template<typename L>
auto Catch::Generators::generate(SourceLineInfo const &lineInfo, L const &generatorExpression) -> decltype(std::declval<decltype(generatorExpression())>().get())
Template Function Catch::Generators::makeGenerators(GeneratorWrapper<T>&&, Gs&&…)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::makeGenerators” with arguments (GeneratorWrapper<T>&&, Gs&&…) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T, typename ...Gs> auto makeGenerators(GeneratorWrapper<T> &&generator, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename ...Gs> auto makeGenerators(T &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename U, typename ...Gs> auto makeGenerators(as<T>, U &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T> auto makeGenerators(GeneratorWrapper<T> &&generator) -> Generators<T>
Template Function Catch::Generators::makeGenerators(GeneratorWrapper<T>&&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::makeGenerators” with arguments (GeneratorWrapper<T>&&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T, typename ...Gs> auto makeGenerators(GeneratorWrapper<T> &&generator, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename ...Gs> auto makeGenerators(T &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename U, typename ...Gs> auto makeGenerators(as<T>, U &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T> auto makeGenerators(GeneratorWrapper<T> &&generator) -> Generators<T>
Template Function Catch::Generators::makeGenerators(T&&, Gs&&…)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::makeGenerators” with arguments (T&&, Gs&&…) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T, typename ...Gs> auto makeGenerators(GeneratorWrapper<T> &&generator, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename ...Gs> auto makeGenerators(T &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename U, typename ...Gs> auto makeGenerators(as<T>, U &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T> auto makeGenerators(GeneratorWrapper<T> &&generator) -> Generators<T>
Template Function Catch::Generators::makeGenerators(as<T>, U&&, Gs&&…)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::makeGenerators” with arguments (as<T>, U&&, Gs&&…) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T, typename ...Gs> auto makeGenerators(GeneratorWrapper<T> &&generator, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename ...Gs> auto makeGenerators(T &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T, typename U, typename ...Gs> auto makeGenerators(as<T>, U &&val, Gs&&... moreGenerators) -> Generators<T>
- template<typename T> auto makeGenerators(GeneratorWrapper<T> &&generator) -> Generators<T>
Template Function Catch::Generators::map
Function Documentation
template<typename Func, typename U, typename T = FunctionReturnType<Func, U>>
GeneratorWrapper<T> Catch::Generators::map(Func &&function, GeneratorWrapper<U> &&generator)
Template Function Catch::Generators::pf::make_unique
Function Documentation
template<typename T, typename ...Args>
std::unique_ptr<T> Catch::Generators::pf::make_unique(Args&&... args)
Template Function Catch::Generators::random(T, T)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::random” with arguments (T, T) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> std::enable_if<std::is_floating_point<T>::value, GeneratorWrapper<T>>::type random(T a, T b)
- template<typename T> std::enable_if<std::is_integral<T>::value && !std::is_same<T, bool>::value, GeneratorWrapper<T>>::type random(T a, T b)
Template Function Catch::Generators::random(T, T)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::random” with arguments (T, T) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> std::enable_if<std::is_floating_point<T>::value, GeneratorWrapper<T>>::type random(T a, T b)
- template<typename T> std::enable_if<std::is_integral<T>::value && !std::is_same<T, bool>::value, GeneratorWrapper<T>>::type random(T a, T b)
Template Function Catch::Generators::range(T const&, T const&, T const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::range” with arguments (T const&, T const&, T const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> GeneratorWrapper<T> range(T const &start, T const &end)
- template<typename T> GeneratorWrapper<T> range(T const &start, T const &end, T const &step)
Template Function Catch::Generators::range(T const&, T const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Generators::range” with arguments (T const&, T const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> GeneratorWrapper<T> range(T const &start, T const &end)
- template<typename T> GeneratorWrapper<T> range(T const &start, T const &end, T const &step)
Template Function Catch::Generators::repeat
Function Documentation
template<typename T>
GeneratorWrapper<T> Catch::Generators::repeat(size_t repeats, GeneratorWrapper<T> &&generator)
Template Function Catch::Generators::table
Function Documentation
template<typename ...Ts>
GeneratorWrapper<std::tuple<Ts...>> Catch::Generators::table(std::initializer_list<std::tuple<typename std::decay<Ts>::type...>> tuples)
Template Function Catch::Generators::take
Function Documentation
template<typename T>
GeneratorWrapper<T> Catch::Generators::take(size_t target, GeneratorWrapper<T> &&generator)
Template Function Catch::Generators::value
Function Documentation
template<typename T>
GeneratorWrapper<T> Catch::Generators::value(T &&value)
Template Function Catch::Generators::values
Function Documentation
template<typename T>
GeneratorWrapper<T> Catch::Generators::values(std::initializer_list<T> values)
Function Catch::getAllTestCasesSorted
Function Documentation
std::vector<TestCase> const &Catch::getAllTestCasesSorted(IConfig const &config)
Function Catch::getCurrentContext
Function Documentation
IContext &Catch::getCurrentContext()
Function Catch::getCurrentMutableContext
Function Documentation
IMutableContext &Catch::getCurrentMutableContext()
Function Catch::getCurrentNanosecondsSinceEpoch
Function Documentation
auto Catch::getCurrentNanosecondsSinceEpoch() -> uint64_t
Function Catch::getEstimatedClockResolution
Function Documentation
auto Catch::getEstimatedClockResolution() -> uint64_t
Function Catch::getMutableRegistryHub
Function Documentation
IMutableRegistryHub &Catch::getMutableRegistryHub()
Function Catch::getRegistryHub
Function Documentation
IRegistryHub const &Catch::getRegistryHub()
Function Catch::getResultCapture
Function Documentation
IResultCapture &Catch::getResultCapture()
Function Catch::handleExceptionMatchExpr(AssertionHandler&, std::string const&, StringRef const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::handleExceptionMatchExpr” with arguments (AssertionHandler&, std::string const&, StringRef const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- void handleExceptionMatchExpr(AssertionHandler &handler, StringMatcher const &matcher, StringRef const &matcherString)
- void handleExceptionMatchExpr(AssertionHandler &handler, std::string const &str, StringRef const &matcherString)
Function Catch::handleExceptionMatchExpr(AssertionHandler&, StringMatcher const&, StringRef const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::handleExceptionMatchExpr” with arguments (AssertionHandler&, StringMatcher const&, StringRef const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- void handleExceptionMatchExpr(AssertionHandler &handler, StringMatcher const &matcher, StringRef const &matcherString)
- void handleExceptionMatchExpr(AssertionHandler &handler, std::string const &str, StringRef const &matcherString)
Function Catch::handleExpression(ITransientExpression const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::handleExpression” with arguments (ITransientExpression const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> void handleExpression(ExprLhs<T> const &expr)
- void handleExpression(ITransientExpression const &expr)
Template Function Catch::handleExpression(ExprLhs<T> const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::handleExpression” with arguments (ExprLhs<T> const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename T> void handleExpression(ExprLhs<T> const &expr)
- void handleExpression(ITransientExpression const &expr)
Function Catch::isFalseTest
Function Documentation
bool Catch::isFalseTest(int flags)
Function Catch::isJustInfo
Function Documentation
bool Catch::isJustInfo(int flags)
Function Catch::isOk
Function Documentation
bool Catch::isOk(ResultWas::OfType resultType)
Function Catch::isThrowSafe
Function Documentation
bool Catch::isThrowSafe(TestCase const &testCase, IConfig const &config)
Function Catch::literals::operator”” _a(long double)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::literals::operator”” _a” with arguments (long double) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Detail::Approx operator""_a(long double val)
- Detail::Approx operator""_a(unsigned long long val)
Function Catch::literals::operator”” _a(unsigned long long)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::literals::operator”” _a” with arguments (unsigned long long) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Detail::Approx operator""_a(long double val)
- Detail::Approx operator""_a(unsigned long long val)
Template Function Catch::makeMatchExpr
Function Documentation
template<typename ArgT, typename MatcherT>
auto Catch::makeMatchExpr(ArgT const &arg, MatcherT const &matcher, StringRef const &matcherString) -> MatchExpr<ArgT, MatcherT>
Function Catch::makeStream
Function Documentation
auto Catch::makeStream(StringRef const &filename) -> IStream const*
Function Catch::makeTestCase
Function Documentation
TestCase Catch::makeTestCase(ITestInvoker *testCase, std::string const &className, NameAndTags const &nameAndTags, SourceLineInfo const &lineInfo)
Function Catch::makeTestInvoker(void(*)())
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::makeTestInvoker” with arguments (void(*)()) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- auto makeTestInvoker(void (*testAsFunction)()) noexcept -> ITestInvoker*
- template<typename C> auto makeTestInvoker(void (C::* testAsMethod)()) noexcept -> ITestInvoker*
Template Function Catch::makeTestInvoker(void(C::*)())
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::makeTestInvoker” with arguments (void(C::*)()) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- auto makeTestInvoker(void (*testAsFunction)()) noexcept -> ITestInvoker*
- template<typename C> auto makeTestInvoker(void (C::* testAsMethod)()) noexcept -> ITestInvoker*
Template Function Catch::Matchers::Approx
Function Documentation
template<typename T>
Vector::ApproxMatcher<T> Catch::Matchers::Approx(std::vector<T> const &comparator)
Function Catch::Matchers::Contains(std::string const&, CaseSensitive::Choice)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::Contains” with arguments (std::string const&, CaseSensitive::Choice) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StdString::ContainsMatcher Contains(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
- template<typename T> Vector::ContainsMatcher<T> Contains(std::vector<T> const &comparator)
Template Function Catch::Matchers::Contains(std::vector<T> const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::Contains” with arguments (std::vector<T> const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StdString::ContainsMatcher Contains(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
- template<typename T> Vector::ContainsMatcher<T> Contains(std::vector<T> const &comparator)
Function Catch::Matchers::EndsWith
Function Documentation
StdString::EndsWithMatcher Catch::Matchers::EndsWith(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
Function Catch::Matchers::Equals(std::string const&, CaseSensitive::Choice)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::Equals” with arguments (std::string const&, CaseSensitive::Choice) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StdString::EqualsMatcher Equals(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
- template<typename T> Vector::EqualsMatcher<T> Equals(std::vector<T> const &comparator)
Template Function Catch::Matchers::Equals(std::vector<T> const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::Equals” with arguments (std::vector<T> const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StdString::EqualsMatcher Equals(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
- template<typename T> Vector::EqualsMatcher<T> Equals(std::vector<T> const &comparator)
Function Catch::Matchers::Generic::Detail::finalizeDescription
Function Documentation
std::string Catch::Matchers::Generic::Detail::finalizeDescription(const std::string &desc)
Function Catch::Matchers::Matches
Function Documentation
StdString::RegexMatcher Catch::Matchers::Matches(std::string const &regex, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
Function Catch::Matchers::Message
Function Documentation
Exception::ExceptionMessageMatcher Catch::Matchers::Message(std::string const &message)
Template Function Catch::Matchers::Predicate
Function Documentation
template<typename T>
Generic::PredicateMatcher<T> Catch::Matchers::Predicate(std::function<bool(T const&)> const &predicate, std::string const &description = "", )
Function Catch::Matchers::StartsWith
Function Documentation
StdString::StartsWithMatcher Catch::Matchers::StartsWith(std::string const &str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes)
Template Function Catch::Matchers::UnorderedEquals
Function Documentation
template<typename T>
Vector::UnorderedEqualsMatcher<T> Catch::Matchers::UnorderedEquals(std::vector<T> const &target)
Template Function Catch::Matchers::VectorContains
Function Documentation
template<typename T>
Vector::ContainsElementMatcher<T> Catch::Matchers::VectorContains(T const &comparator)
Function Catch::Matchers::WithinAbs
Function Documentation
Floating::WithinAbsMatcher Catch::Matchers::WithinAbs(double target, double margin)
Function Catch::Matchers::WithinRel(double, double)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinRel” with arguments (double, double) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinRelMatcher WithinRel(double target)
- Floating::WithinRelMatcher WithinRel(double target, double eps)
- Floating::WithinRelMatcher WithinRel(float target)
- Floating::WithinRelMatcher WithinRel(float target, float eps)
Function Catch::Matchers::WithinRel(double)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinRel” with arguments (double) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinRelMatcher WithinRel(double target)
- Floating::WithinRelMatcher WithinRel(double target, double eps)
- Floating::WithinRelMatcher WithinRel(float target)
- Floating::WithinRelMatcher WithinRel(float target, float eps)
Function Catch::Matchers::WithinRel(float, float)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinRel” with arguments (float, float) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinRelMatcher WithinRel(double target)
- Floating::WithinRelMatcher WithinRel(double target, double eps)
- Floating::WithinRelMatcher WithinRel(float target)
- Floating::WithinRelMatcher WithinRel(float target, float eps)
Function Catch::Matchers::WithinRel(float)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinRel” with arguments (float) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinRelMatcher WithinRel(double target)
- Floating::WithinRelMatcher WithinRel(double target, double eps)
- Floating::WithinRelMatcher WithinRel(float target)
- Floating::WithinRelMatcher WithinRel(float target, float eps)
Function Catch::Matchers::WithinULP(double, uint64_t)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinULP” with arguments (double, uint64_t) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinUlpsMatcher WithinULP(double target, uint64_t maxUlpDiff)
- Floating::WithinUlpsMatcher WithinULP(float target, uint64_t maxUlpDiff)
Function Catch::Matchers::WithinULP(float, uint64_t)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::Matchers::WithinULP” with arguments (float, uint64_t) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- Floating::WithinUlpsMatcher WithinULP(double target, uint64_t maxUlpDiff)
- Floating::WithinUlpsMatcher WithinULP(float target, uint64_t maxUlpDiff)
Function Catch::matchTest
Function Documentation
bool Catch::matchTest(TestCase const &testCase, TestSpec const &testSpec, IConfig const &config)
Function Catch::operator”” _sr
Function Documentation
constexpr auto Catch::operator""_sr(char const *rawChars, std::size_t size) noexcept -> StringRef
Template Function Catch::operator+
Function Documentation
template<typename T>
T const &Catch::operator+(T const &value, StreamEndStop)
Function Catch::operator+=
Function Documentation
auto Catch::operator+=(std::string &lhs, StringRef const &sr) -> std::string&
Function Catch::operator<<(std::ostream&, SourceLineInfo const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::operator<<” with arguments (std::ostream&, SourceLineInfo const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- auto operator<<(std::ostream &os, StringRef const &sr) -> std::ostream&
- std::ostream &operator<<(std::ostream &os, SourceLineInfo const &info)
Function Catch::operator<<(std::ostream&, StringRef const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::operator<<” with arguments (std::ostream&, StringRef const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- auto operator<<(std::ostream &os, StringRef const &sr) -> std::ostream&
- std::ostream &operator<<(std::ostream &os, SourceLineInfo const &info)
Function Catch::operator|
Function Documentation
ResultDisposition::Flags Catch::operator|(ResultDisposition::Flags lhs, ResultDisposition::Flags rhs)
Template Function Catch::rangeToString(Range const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::rangeToString” with arguments (Range const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename Allocator> std::string rangeToString(std::vector<bool, Allocator> const &v)
- template<typename Range> std::string rangeToString(Range const &range)
Template Function Catch::rangeToString(std::vector<bool, Allocator> const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::rangeToString” with arguments (std::vector<bool, Allocator> const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- template<typename Allocator> std::string rangeToString(std::vector<bool, Allocator> const &v)
- template<typename Range> std::string rangeToString(Range const &range)
Function Catch::replaceInPlace
Function Documentation
bool Catch::replaceInPlace(std::string &str, std::string const &replaceThis, std::string const &withThis)
Function Catch::rng
Function Documentation
SimplePcg32 &Catch::rng()
Function Catch::rngSeed
Function Documentation
unsigned int Catch::rngSeed()
Function Catch::shouldContinueOnFailure
Function Documentation
bool Catch::shouldContinueOnFailure(int flags)
Function Catch::shouldSuppressFailure
Function Documentation
bool Catch::shouldSuppressFailure(int flags)
Function Catch::splitStringRef
Function Documentation
std::vector<StringRef> Catch::splitStringRef(StringRef str, char delimiter)
Function Catch::startsWith(std::string const&, std::string const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::startsWith” with arguments (std::string const&, std::string const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- bool startsWith(std::string const &s, char prefix)
- bool startsWith(std::string const &s, std::string const &prefix)
Function Catch::startsWith(std::string const&, char)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::startsWith” with arguments (std::string const&, char) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- bool startsWith(std::string const &s, char prefix)
- bool startsWith(std::string const &s, std::string const &prefix)
Function Catch::throw_domain_error
Function Documentation
void Catch::throw_domain_error(std::string const &msg)
Function Catch::throw_exception
Function Documentation
void Catch::throw_exception(std::exception const &e)
Function Catch::throw_logic_error
Function Documentation
void Catch::throw_logic_error(std::string const &msg)
Function Catch::throw_runtime_error
Function Documentation
void Catch::throw_runtime_error(std::string const &msg)
Function Catch::toLower
Function Documentation
std::string Catch::toLower(std::string const &s)
Function Catch::toLowerInPlace
Function Documentation
void Catch::toLowerInPlace(std::string &s)
Function Catch::translateActiveException
Function Documentation
std::string Catch::translateActiveException()
Function Catch::trim(std::string const&)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::trim” with arguments (std::string const&) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StringRef trim(StringRef ref)
- std::string trim(std::string const &str)
Function Catch::trim(StringRef)
Function Documentation

Warning

doxygenfunction: Unable to resolve multiple matches for function “Catch::trim” with arguments (StringRef) in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml. Potential matches: 

- StringRef trim(StringRef ref)
- std::string trim(std::string const &str)
Function Cube
Function Documentation

Warning

doxygenfunction: Cannot find function “Cube” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function operator”” _catch_sr
Function Documentation
constexpr auto operator""_catch_sr(char const *rawChars, std::size_t size) noexcept -> Catch::StringRef
Function operator<<
Function Documentation
std::ostream &operator<<(std::ostream&, Catch_global_namespace_dummy)
Function symbulation_main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “symbulation_main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function symbulation_main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “symbulation_main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function symbulation_main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “symbulation_main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function symbulation_main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “symbulation_main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function symbulation_main(int, char *)
Function Documentation

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doxygenfunction: Cannot find function “symbulation_main” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function Test
Function Documentation

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doxygenfunction: Cannot find function “Test” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE()
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Cubes are computed”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetHostCountDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetSymCountDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetCountHostedSymsDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetCountFreeSymsDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetUninfectedHostsDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetSymIntValDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetFreeSymIntValDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetHostedSymIntValDataNode”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetCFUDataNode”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host Constructor”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host, GetIntVal”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, AddPoints, GetPoints”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, GetResTypes”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“HasSym”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host Mutate”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“DistributeResources”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, GetResInProcess”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Steal resources unit test”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetDoEctosymbiosis”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host GrowOlder”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host makeNew”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host reproduce”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host-Symbiont interactions”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont, GetHost”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host SetSymbionts”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host SymLimit”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host AddSymbiont”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host, ClearReproSym, GetReproSymbionts”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host DistribResources”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Vertical Transmission of Symbiont”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“HandleEctosymbiosis”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont Constructor”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, GetIntVal”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, GetInfectionChance”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, GetPoints”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont, GetDead”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“WantsToInfect”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“InfectionFails”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“mutate”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“reproduce”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Process”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont ProcessResources”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont GrowOlder”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont makeNew”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PullResources”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Vertical Transmission”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“World Capacity”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Interaction Patterns”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Hosts injected correctly”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“InjectSymbiont”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“DoBirth”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“SymDoBirth”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Update”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“MoveFreeSym”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“ExtractSym”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“MoveIntoNewFreeWorldPos”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Resize”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“AddOrgAt”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“GetSymAt”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“DoSymDeath”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host Phylogeny”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Symbiont Phylogeny”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientHost Constructor”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientHost makeNew”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientHost SetEfficiency and GetEfficiency”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont Constructor”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont mutate”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont AddPoints”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“INT_VAL_MUT_RATE”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont reproduce”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont HorizMutate”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont mutate with horizontal transmission”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont mutate with vertical transmission”, “”)
Function Documentation

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doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont’s Process called from Host when mutation rate and size are zero”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont makeNew”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“EfficientSymbiont SetEfficiency and GetEfficiency”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“End To End”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium, host_incorporation_val”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium, GetIncVal”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium mutate”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“ProcessLysogenResources”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium Process”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage Exclude”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium makeNew”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Bacterium reproduce”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage Process”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage Vertical Transmission”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Host phage death and removal from syms list”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage LysisBurst”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage LysisStep”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage, GetIntVal”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage reproduce”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“, IncBurstTimer”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage, GetLysisChance”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage, GetInductionChance”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage, GetIncVal”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage uponInjection”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“phage_mutate”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage process”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage ProcessResources”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Phage makeNew”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PggHost constructor”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PggHost get pool”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Pgghost DistributeResources”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PggHost makeNew”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PggSymbiont, GetHost”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGHost DistribResources”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGVertical Transmission of Symbiont”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGSymbiont PGGHost Pool Interaction”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGSYM Dead and Removal”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGSymbiont Constructor”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“Pggmutate”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGSymbiont ProcessPool”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGProcess”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PGGSymbiont ProcessResources”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function TEST_CASE(“PggSymbiont makeNew”, “”)
Function Documentation

Warning

doxygenfunction: Cannot find function “TEST_CASE” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function worldSetup(emp::Ptr<SymWorld>, emp::Ptr<SymConfigBase>)
Function Documentation

Warning

doxygenfunction: Cannot find function “worldSetup” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function worldSetup(emp::Ptr<EfficientWorld>, emp::Ptr<SymConfigBase>)
Function Documentation

Warning

doxygenfunction: Cannot find function “worldSetup” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function worldSetup(emp::Ptr<LysisWorld>, emp::Ptr<SymConfigBase>)
Function Documentation

Warning

doxygenfunction: Cannot find function “worldSetup” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Function worldSetup(emp::Ptr<PggWorld>, emp::Ptr<SymConfigBase>)
Function Documentation

Warning

doxygenfunction: Cannot find function “worldSetup” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Variables
Variable anim
Variable Documentation

Warning

doxygenvariable: Cannot find variable “anim” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Variable Catch::begin
Variable Documentation
not_this_one Catch::begin(...)
Variable Catch::Detail::unprintableString
Variable Documentation
const std::string Catch::Detail::unprintableString
Variable Catch::end
Variable Documentation
not_this_one Catch::end(...)
Variable config
Variable Documentation
SymConfigBase config
Defines
Define AND_GIVEN
Define Documentation
AND_GIVEN(desc)
Define AND_THEN
Define Documentation
AND_THEN(desc)
Define AND_WHEN
Define Documentation
AND_WHEN(desc)
Define ANON_TEST_CASE
Define Documentation
ANON_TEST_CASE()
Define CAPTURE
Define Documentation
CAPTURE(...)
Define CATCH_CATCH_ALL
Define Documentation
CATCH_CATCH_ALL
Define CATCH_CATCH_ANON
Define Documentation
CATCH_CATCH_ANON(type)
Define CATCH_CONFIG_COUNTER
Define Documentation
CATCH_CONFIG_COUNTER
Define CATCH_CONFIG_CPP11_TO_STRING
Define Documentation
CATCH_CONFIG_CPP11_TO_STRING
Define CATCH_CONFIG_DISABLE_EXCEPTIONS
Define Documentation
CATCH_CONFIG_DISABLE_EXCEPTIONS
Define CATCH_CONFIG_GLOBAL_NEXTAFTER
Define Documentation
CATCH_CONFIG_GLOBAL_NEXTAFTER
Define CATCH_CONFIG_MAIN
Define Documentation

Warning

doxygendefine: Cannot find define “CATCH_CONFIG_MAIN” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Define CATCH_CONFIG_POSIX_SIGNALS
Define Documentation
CATCH_CONFIG_POSIX_SIGNALS
Define CATCH_CONFIG_WCHAR
Define Documentation
CATCH_CONFIG_WCHAR
Define CATCH_DEFER
Define Documentation
CATCH_DEFER(id)
Define CATCH_EMPTY
Define Documentation
CATCH_EMPTY()
Define CATCH_ENFORCE
Define Documentation
CATCH_ENFORCE(condition, ...)
Define CATCH_ERROR
Define Documentation
CATCH_ERROR(...)
Define CATCH_INTERNAL_CONFIG_COUNTER
Define Documentation
CATCH_INTERNAL_CONFIG_COUNTER
Define CATCH_INTERNAL_CONFIG_GLOBAL_NEXTAFTER
Define Documentation
CATCH_INTERNAL_CONFIG_GLOBAL_NEXTAFTER
Define CATCH_INTERNAL_CONFIG_POSIX_SIGNALS
Define Documentation
CATCH_INTERNAL_CONFIG_POSIX_SIGNALS
Define CATCH_INTERNAL_ERROR
Define Documentation
CATCH_INTERNAL_ERROR(...)
Define CATCH_INTERNAL_IGNORE_BUT_WARN
Define Documentation
CATCH_INTERNAL_IGNORE_BUT_WARN(...)
Define CATCH_INTERNAL_LINEINFO
Define Documentation
CATCH_INTERNAL_LINEINFO
Define CATCH_INTERNAL_START_WARNINGS_SUPPRESSION
Define Documentation
CATCH_INTERNAL_START_WARNINGS_SUPPRESSION
Define CATCH_INTERNAL_STOP_WARNINGS_SUPPRESSION
Define Documentation
CATCH_INTERNAL_STOP_WARNINGS_SUPPRESSION
Define CATCH_INTERNAL_STRINGIFY
Define Documentation
CATCH_INTERNAL_STRINGIFY(...)
Define CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS
Define Documentation
CATCH_INTERNAL_SUPPRESS_GLOBALS_WARNINGS
Define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS
Define Documentation
CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS
Define CATCH_INTERNAL_SUPPRESS_UNUSED_TEMPLATE_WARNINGS
Define Documentation
CATCH_INTERNAL_SUPPRESS_UNUSED_TEMPLATE_WARNINGS
Define CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS
Define Documentation
CATCH_INTERNAL_SUPPRESS_UNUSED_WARNINGS
Define CATCH_INTERNAL_SUPPRESS_ZERO_VARIADIC_WARNINGS
Define Documentation
CATCH_INTERNAL_SUPPRESS_ZERO_VARIADIC_WARNINGS
Define CATCH_MAKE_MSG
Define Documentation
CATCH_MAKE_MSG(...)
Define CATCH_REC_END
Define Documentation
CATCH_REC_END(...)
Define CATCH_REC_GET_END
Define Documentation
CATCH_REC_GET_END(...)
Define CATCH_REC_GET_END1
Define Documentation
CATCH_REC_GET_END1(...)
Define CATCH_REC_GET_END2
Define Documentation
CATCH_REC_GET_END2()
Define CATCH_REC_LIST
Define Documentation
CATCH_REC_LIST(f, ...)
Define CATCH_REC_LIST0
Define Documentation
CATCH_REC_LIST0(f, x, peek, ...)
Define CATCH_REC_LIST0_UD
Define Documentation
CATCH_REC_LIST0_UD(f, userdata, x, peek, ...)
Define CATCH_REC_LIST1
Define Documentation
CATCH_REC_LIST1(f, x, peek, ...)
Define CATCH_REC_LIST1_UD
Define Documentation
CATCH_REC_LIST1_UD(f, userdata, x, peek, ...)
Define CATCH_REC_LIST2
Define Documentation
CATCH_REC_LIST2(f, x, peek, ...)
Define CATCH_REC_LIST2_UD
Define Documentation
CATCH_REC_LIST2_UD(f, userdata, x, peek, ...)
Define CATCH_REC_LIST_UD
Define Documentation
CATCH_REC_LIST_UD(f, userdata, ...)
Define CATCH_REC_NEXT
Define Documentation
CATCH_REC_NEXT(test, next)
Define CATCH_REC_NEXT0
Define Documentation
CATCH_REC_NEXT0(test, next, ...)
Define CATCH_REC_NEXT1
Define Documentation
CATCH_REC_NEXT1(test, next)
Define CATCH_REC_OUT
Define Documentation
CATCH_REC_OUT
Define CATCH_RECURSE
Define Documentation
CATCH_RECURSE(...)
Define CATCH_RECURSION_LEVEL0
Define Documentation
CATCH_RECURSION_LEVEL0(...)
Define CATCH_RECURSION_LEVEL1
Define Documentation
CATCH_RECURSION_LEVEL1(...)
Define CATCH_RECURSION_LEVEL2
Define Documentation
CATCH_RECURSION_LEVEL2(...)
Define CATCH_RECURSION_LEVEL3
Define Documentation
CATCH_RECURSION_LEVEL3(...)
Define CATCH_RECURSION_LEVEL4
Define Documentation
CATCH_RECURSION_LEVEL4(...)
Define CATCH_RECURSION_LEVEL5
Define Documentation
CATCH_RECURSION_LEVEL5(...)
Define CATCH_REGISTER_ENUM
Define Documentation
CATCH_REGISTER_ENUM(enumName, ...)
Define CATCH_REGISTER_TAG_ALIAS
Define Documentation
CATCH_REGISTER_TAG_ALIAS(alias, spec)
Define CATCH_RUNTIME_ERROR
Define Documentation
CATCH_RUNTIME_ERROR(...)
Define CATCH_TRANSLATE_EXCEPTION
Define Documentation
CATCH_TRANSLATE_EXCEPTION(signature)
Define CATCH_TRY
Define Documentation
CATCH_TRY
Define CATCH_VERSION_MAJOR
Define Documentation
CATCH_VERSION_MAJOR
Define CATCH_VERSION_MINOR
Define Documentation
CATCH_VERSION_MINOR
Define CATCH_VERSION_PATCH
Define Documentation
CATCH_VERSION_PATCH
Define CHECK
Define Documentation
CHECK(...)
Define CHECK_FALSE
Define Documentation
CHECK_FALSE(...)
Define CHECK_NOFAIL
Define Documentation
CHECK_NOFAIL(...)
Define CHECK_NOTHROW
Define Documentation
CHECK_NOTHROW(...)
Define CHECK_THAT
Define Documentation
CHECK_THAT(arg, matcher)
Define CHECK_THROWS
Define Documentation
CHECK_THROWS(...)
Define CHECK_THROWS_AS
Define Documentation
CHECK_THROWS_AS(expr, exceptionType)
Define CHECK_THROWS_MATCHES
Define Documentation
CHECK_THROWS_MATCHES(expr, exceptionType, matcher)
Define CHECK_THROWS_WITH
Define Documentation
CHECK_THROWS_WITH(expr, matcher)
Define CHECKED_ELSE
Define Documentation
CHECKED_ELSE(...)
Define CHECKED_IF
Define Documentation
CHECKED_IF(...)
Define DYNAMIC_SECTION
Define Documentation
DYNAMIC_SECTION(...)
Define EFFWORLD_SETUP_C
Define Documentation

Warning

doxygendefine: Cannot find define “EFFWORLD_SETUP_C” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Define FAIL
Define Documentation
FAIL(...)
Define FAIL_CHECK
Define Documentation
FAIL_CHECK(...)
Define GENERATE
Define Documentation
GENERATE(...)
Define GENERATE_COPY
Define Documentation
GENERATE_COPY(...)
Define GENERATE_REF
Define Documentation
GENERATE_REF(...)
Define GIVEN
Define Documentation
GIVEN(desc)
Define INFO
Define Documentation
INFO(msg)
Define INTERNAL_CATCH_CAPTURE
Define Documentation
INTERNAL_CATCH_CAPTURE(varName, macroName, ...)
Define INTERNAL_CATCH_CATCH
Define Documentation
INTERNAL_CATCH_CATCH(capturer)
Define INTERNAL_CATCH_DECLARE_SIG_TEST
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST(TestName, ...)
Define INTERNAL_CATCH_DECLARE_SIG_TEST0
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST0(TestName)
Define INTERNAL_CATCH_DECLARE_SIG_TEST1
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST1(TestName, signature)
Define INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD(TestName, ClassName, ...)
Define INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD0
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD0(TestName, ClassName)
Define INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD1
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD1(TestName, ClassName, signature)
Define INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD_X
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST_METHOD_X(TestName, ClassName, signature, ...)
Define INTERNAL_CATCH_DECLARE_SIG_TEST_X
Define Documentation
INTERNAL_CATCH_DECLARE_SIG_TEST_X(TestName, signature, ...)
Define INTERNAL_CATCH_DEF
Define Documentation
INTERNAL_CATCH_DEF(...)
Define INTERNAL_CATCH_DEFINE_SIG_TEST
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST(TestName, ...)
Define INTERNAL_CATCH_DEFINE_SIG_TEST0
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST0(TestName)
Define INTERNAL_CATCH_DEFINE_SIG_TEST1
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST1(TestName, signature)
Define INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD(TestName, ...)
Define INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD0
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD0(TestName)
Define INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD1
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD1(TestName, signature)
Define INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD_X
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST_METHOD_X(TestName, signature, ...)
Define INTERNAL_CATCH_DEFINE_SIG_TEST_X
Define Documentation
INTERNAL_CATCH_DEFINE_SIG_TEST_X(TestName, signature, ...)
Define INTERNAL_CATCH_DYNAMIC_SECTION
Define Documentation
INTERNAL_CATCH_DYNAMIC_SECTION(...)
Define INTERNAL_CATCH_ELSE
Define Documentation
INTERNAL_CATCH_ELSE(macroName, resultDisposition, ...)
Define INTERNAL_CATCH_EXPAND1
Define Documentation
INTERNAL_CATCH_EXPAND1(param)
Define INTERNAL_CATCH_EXPAND2
Define Documentation
INTERNAL_CATCH_EXPAND2(...)
Define INTERNAL_CATCH_IF
Define Documentation
INTERNAL_CATCH_IF(macroName, resultDisposition, ...)
Define INTERNAL_CATCH_INFO
Define Documentation
INTERNAL_CATCH_INFO(macroName, log)
Define INTERNAL_CATCH_MAKE_NAMESPACE
Define Documentation
INTERNAL_CATCH_MAKE_NAMESPACE(name)
Define INTERNAL_CATCH_MAKE_NAMESPACE2
Define Documentation
INTERNAL_CATCH_MAKE_NAMESPACE2(...)
Define INTERNAL_CATCH_MAKE_TYPE_LIST
Define Documentation
INTERNAL_CATCH_MAKE_TYPE_LIST(...)
Define INTERNAL_CATCH_MAKE_TYPE_LIST2
Define Documentation
INTERNAL_CATCH_MAKE_TYPE_LIST2(...)
Define INTERNAL_CATCH_MAKE_TYPE_LISTS_FROM_TYPES
Define Documentation
INTERNAL_CATCH_MAKE_TYPE_LISTS_FROM_TYPES(...)
Define INTERNAL_CATCH_METHOD_AS_TEST_CASE
Define Documentation
INTERNAL_CATCH_METHOD_AS_TEST_CASE(QualifiedMethod, ...)
Define INTERNAL_CATCH_MSG
Define Documentation
INTERNAL_CATCH_MSG(macroName, messageType, resultDisposition, ...)
Define INTERNAL_CATCH_NO_THROW
Define Documentation
INTERNAL_CATCH_NO_THROW(macroName, resultDisposition, ...)
Define INTERNAL_CATCH_NOINTERNAL_CATCH_DEF
Define Documentation
INTERNAL_CATCH_NOINTERNAL_CATCH_DEF
Define INTERNAL_CATCH_NTTP_0
Define Documentation
INTERNAL_CATCH_NTTP_0
Define INTERNAL_CATCH_NTTP_1
Define Documentation
INTERNAL_CATCH_NTTP_1(signature, ...)
Define INTERNAL_CATCH_NTTP_GEN
Define Documentation
INTERNAL_CATCH_NTTP_GEN(...)
Define INTERNAL_CATCH_NTTP_REG_GEN
Define Documentation
INTERNAL_CATCH_NTTP_REG_GEN(TestFunc, ...)
Define INTERNAL_CATCH_NTTP_REG_METHOD_GEN
Define Documentation
INTERNAL_CATCH_NTTP_REG_METHOD_GEN(TestName, ...)
Define INTERNAL_CATCH_NTTP_REGISTER
Define Documentation
INTERNAL_CATCH_NTTP_REGISTER(TestFunc, signature, ...)
Define INTERNAL_CATCH_NTTP_REGISTER0
Define Documentation
INTERNAL_CATCH_NTTP_REGISTER0(TestFunc, signature)
Define INTERNAL_CATCH_NTTP_REGISTER_METHOD
Define Documentation
INTERNAL_CATCH_NTTP_REGISTER_METHOD(TestName, signature, ...)
Define INTERNAL_CATCH_NTTP_REGISTER_METHOD0
Define Documentation
INTERNAL_CATCH_NTTP_REGISTER_METHOD0(TestName, signature, ...)
Define INTERNAL_CATCH_REACT
Define Documentation
INTERNAL_CATCH_REACT(handler)
Define INTERNAL_CATCH_REGISTER_ENUM
Define Documentation
INTERNAL_CATCH_REGISTER_ENUM(enumName, ...)
Define INTERNAL_CATCH_REGISTER_TESTCASE
Define Documentation
INTERNAL_CATCH_REGISTER_TESTCASE(Function, ...)
Define INTERNAL_CATCH_REMOVE_PARENS
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS(...)
Define INTERNAL_CATCH_REMOVE_PARENS_10_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_10_ARG(_0, _1, _2, _3, _4, _5, _6, _7, _8, _9)
Define INTERNAL_CATCH_REMOVE_PARENS_11_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_11_ARG(_0, _1, _2, _3, _4, _5, _6, _7, _8, _9, _10)
Define INTERNAL_CATCH_REMOVE_PARENS_1_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_1_ARG(_0)
Define INTERNAL_CATCH_REMOVE_PARENS_2_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_2_ARG(_0, _1)
Define INTERNAL_CATCH_REMOVE_PARENS_3_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_3_ARG(_0, _1, _2)
Define INTERNAL_CATCH_REMOVE_PARENS_4_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_4_ARG(_0, _1, _2, _3)
Define INTERNAL_CATCH_REMOVE_PARENS_5_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_5_ARG(_0, _1, _2, _3, _4)
Define INTERNAL_CATCH_REMOVE_PARENS_6_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_6_ARG(_0, _1, _2, _3, _4, _5)
Define INTERNAL_CATCH_REMOVE_PARENS_7_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_7_ARG(_0, _1, _2, _3, _4, _5, _6)
Define INTERNAL_CATCH_REMOVE_PARENS_8_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_8_ARG(_0, _1, _2, _3, _4, _5, _6, _7)
Define INTERNAL_CATCH_REMOVE_PARENS_9_ARG
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_9_ARG(_0, _1, _2, _3, _4, _5, _6, _7, _8)
Define INTERNAL_CATCH_REMOVE_PARENS_GEN
Define Documentation
INTERNAL_CATCH_REMOVE_PARENS_GEN(...)
Define INTERNAL_CATCH_SECTION
Define Documentation
INTERNAL_CATCH_SECTION(...)
Define INTERNAL_CATCH_STRINGIZE
Define Documentation
INTERNAL_CATCH_STRINGIZE(...)
Define INTERNAL_CATCH_STRINGIZE2
Define Documentation
INTERNAL_CATCH_STRINGIZE2(...)
Define INTERNAL_CATCH_STRINGIZE_WITHOUT_PARENS
Define Documentation
INTERNAL_CATCH_STRINGIZE_WITHOUT_PARENS(param)
Define INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE
Define Documentation
INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE(Name, Tags, TmplList)
Define INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_2
Define Documentation
INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_2(TestName, TestFunc, Name, Tags, TmplList)
Define INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_METHOD
Define Documentation
INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_METHOD(ClassName, Name, Tags, TmplList)
Define INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_METHOD_2
Define Documentation
INTERNAL_CATCH_TEMPLATE_LIST_TEST_CASE_METHOD_2(TestNameClass, TestName, ClassName, Name, Tags, TmplList)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE(Name, Tags, ...)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE2
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE2(TestName, TestFuncName, Name, Tags, Signature, TmplTypes, TypesList)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD(ClassName, Name, Tags, ...)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_2
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_2(TestNameClass, TestName, ClassName, Name, Tags, Signature, TmplTypes, TypesList)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_SIG
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_METHOD_SIG(ClassName, Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_SIG
Define Documentation
INTERNAL_CATCH_TEMPLATE_PRODUCT_TEST_CASE_SIG(Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE(Name, Tags, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE_2
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE_2(TestName, TestFunc, Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD(ClassName, Name, Tags, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_2
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_2(TestNameClass, TestName, ClassName, Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_SIG
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE_METHOD_SIG(ClassName, Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEMPLATE_TEST_CASE_SIG
Define Documentation
INTERNAL_CATCH_TEMPLATE_TEST_CASE_SIG(Name, Tags, Signature, ...)
Define INTERNAL_CATCH_TEST
Define Documentation
INTERNAL_CATCH_TEST(macroName, resultDisposition, ...)
Define INTERNAL_CATCH_TEST_CASE_METHOD
Define Documentation
INTERNAL_CATCH_TEST_CASE_METHOD(ClassName, ...)
Define INTERNAL_CATCH_TEST_CASE_METHOD2
Define Documentation
INTERNAL_CATCH_TEST_CASE_METHOD2(TestName, ClassName, ...)
Define INTERNAL_CATCH_TESTCASE
Define Documentation
INTERNAL_CATCH_TESTCASE(...)
Define INTERNAL_CATCH_TESTCASE2
Define Documentation
INTERNAL_CATCH_TESTCASE2(TestName, ...)
Define INTERNAL_CATCH_THROWS
Define Documentation
INTERNAL_CATCH_THROWS(macroName, resultDisposition, ...)
Define INTERNAL_CATCH_THROWS_AS
Define Documentation
INTERNAL_CATCH_THROWS_AS(macroName, exceptionType, resultDisposition, expr)
Define INTERNAL_CATCH_THROWS_MATCHES
Define Documentation
INTERNAL_CATCH_THROWS_MATCHES(macroName, exceptionType, resultDisposition, matcher, ...)
Define INTERNAL_CATCH_THROWS_STR_MATCHES
Define Documentation
INTERNAL_CATCH_THROWS_STR_MATCHES(macroName, resultDisposition, matcher, ...)
Define INTERNAL_CATCH_TRANSLATE_EXCEPTION
Define Documentation
INTERNAL_CATCH_TRANSLATE_EXCEPTION(signature)
Define INTERNAL_CATCH_TRANSLATE_EXCEPTION2
Define Documentation
INTERNAL_CATCH_TRANSLATE_EXCEPTION2(translatorName, signature)
Define INTERNAL_CATCH_TRY
Define Documentation
INTERNAL_CATCH_TRY
Define INTERNAL_CATCH_TYPE_GEN
Define Documentation
INTERNAL_CATCH_TYPE_GEN
Define INTERNAL_CATCH_UNIQUE_NAME
Define Documentation
INTERNAL_CATCH_UNIQUE_NAME(name)
Define INTERNAL_CATCH_UNIQUE_NAME_LINE
Define Documentation
INTERNAL_CATCH_UNIQUE_NAME_LINE(name, line)
Define INTERNAL_CATCH_UNIQUE_NAME_LINE2
Define Documentation
INTERNAL_CATCH_UNIQUE_NAME_LINE2(name, line)
Define INTERNAL_CATCH_UNSCOPED_INFO
Define Documentation
INTERNAL_CATCH_UNSCOPED_INFO(macroName, log)
Define INTERNAL_CATCH_VA_NARGS_IMPL
Define Documentation
INTERNAL_CATCH_VA_NARGS_IMPL(_0, _1, _2, _3, _4, _5, _6, _7, _8, _9, _10, N, ...)
Define INTERNAL_CHECK_THAT
Define Documentation
INTERNAL_CHECK_THAT(macroName, matcher, resultDisposition, arg)
Define LYSIS_WORLD_SETUP_C
Define Documentation

Warning

doxygendefine: Cannot find define “LYSIS_WORLD_SETUP_C” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Define METHOD_AS_TEST_CASE
Define Documentation
METHOD_AS_TEST_CASE(method, ...)
Define PGG_WORLD_SETUP_C
Define Documentation

Warning

doxygendefine: Cannot find define “PGG_WORLD_SETUP_C” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Define REGISTER_TEST_CASE
Define Documentation
REGISTER_TEST_CASE(Function, ...)
Define REQUIRE
Define Documentation
REQUIRE(...)
Define REQUIRE_FALSE
Define Documentation
REQUIRE_FALSE(...)
Define REQUIRE_NOTHROW
Define Documentation
REQUIRE_NOTHROW(...)
Define REQUIRE_THAT
Define Documentation
REQUIRE_THAT(arg, matcher)
Define REQUIRE_THROWS
Define Documentation
REQUIRE_THROWS(...)
Define REQUIRE_THROWS_AS
Define Documentation
REQUIRE_THROWS_AS(expr, exceptionType)
Define REQUIRE_THROWS_MATCHES
Define Documentation
REQUIRE_THROWS_MATCHES(expr, exceptionType, matcher)
Define REQUIRE_THROWS_WITH
Define Documentation
REQUIRE_THROWS_WITH(expr, matcher)
Define SCENARIO
Define Documentation
SCENARIO(...)
Define SCENARIO_METHOD
Define Documentation
SCENARIO_METHOD(className, ...)
Define SECTION
Define Documentation
SECTION(...)
Define STATIC_REQUIRE
Define Documentation
STATIC_REQUIRE(...)
Define STATIC_REQUIRE_FALSE
Define Documentation
STATIC_REQUIRE_FALSE(...)
Define SUCCEED
Define Documentation
SUCCEED(...)
Define TEMPLATE_LIST_TEST_CASE
Define Documentation
TEMPLATE_LIST_TEST_CASE(...)
Define TEMPLATE_LIST_TEST_CASE_METHOD
Define Documentation
TEMPLATE_LIST_TEST_CASE_METHOD(className, ...)
Define TEMPLATE_PRODUCT_TEST_CASE
Define Documentation
TEMPLATE_PRODUCT_TEST_CASE(...)
Define TEMPLATE_PRODUCT_TEST_CASE_METHOD
Define Documentation
TEMPLATE_PRODUCT_TEST_CASE_METHOD(className, ...)
Define TEMPLATE_PRODUCT_TEST_CASE_METHOD_SIG
Define Documentation
TEMPLATE_PRODUCT_TEST_CASE_METHOD_SIG(className, ...)
Define TEMPLATE_PRODUCT_TEST_CASE_SIG
Define Documentation
TEMPLATE_PRODUCT_TEST_CASE_SIG(...)
Define TEMPLATE_TEST_CASE
Define Documentation
TEMPLATE_TEST_CASE(...)
Define TEMPLATE_TEST_CASE_METHOD
Define Documentation
TEMPLATE_TEST_CASE_METHOD(className, ...)
Define TEMPLATE_TEST_CASE_METHOD_SIG
Define Documentation
TEMPLATE_TEST_CASE_METHOD_SIG(className, ...)
Define TEMPLATE_TEST_CASE_SIG
Define Documentation
TEMPLATE_TEST_CASE_SIG(...)
Define TEST_CASE
Define Documentation
TEST_CASE(...)
Define TEST_CASE_METHOD
Define Documentation
TEST_CASE_METHOD(className, ...)
Define THEN
Define Documentation
THEN(desc)
Define UNSCOPED_INFO
Define Documentation
UNSCOPED_INFO(msg)
Define WARN
Define Documentation
WARN(msg)
Define WHEN
Define Documentation
WHEN(desc)
Define WORLD_SETUP_C
Define Documentation

Warning

doxygendefine: Cannot find define “WORLD_SETUP_C” in doxygen xml output for project “Symbulation” from directory: ./doxyoutput/xml

Typedefs
Typedef Catch::exceptionTranslateFunction
Typedef Documentation
using Catch::exceptionTranslateFunction = std::string (*)()
Typedef Catch::ExceptionTranslators
Typedef Documentation
using Catch::ExceptionTranslators = std::vector<std::unique_ptr<IExceptionTranslator const>>
Typedef Catch::FunctionReturnType
Typedef Documentation
using Catch::FunctionReturnType = typename std::remove_reference<typename std::remove_cv<typename std::result_of<Func(U)>::type>::type>::type
Typedef Catch::Generators::GeneratorBasePtr
Typedef Documentation
using Catch::Generators::GeneratorBasePtr = std::unique_ptr<GeneratorUntypedBase>
Typedef Catch::IConfigPtr
Typedef Documentation
typedef std::shared_ptr<IConfig const> Catch::IConfigPtr
Typedef Catch::IReporterFactoryPtr
Typedef Documentation
using Catch::IReporterFactoryPtr = std::shared_ptr<IReporterFactory>
Typedef Catch::StringMatcher
Typedef Documentation
using Catch::StringMatcher = Matchers::Impl::MatcherBase<std::string>

Getting started with Symbulation development

This document is intended to help those just getting started with Symbulation development. It details the initial one-time dependency installs and any similar routines necessary to get started with development.

Start by making your own copy of Symbulation and setting yourself up for development; then, build Symbulation and run the tests; and finally, claim an issue and start developing!

If you’re unfamiliar with git and branching in particular, check out the git-scm book.

One-time Preparation

  1. Get a GitHub account.

    (We use GitHub to manage Symbulation contributions.)

  2. Fork github.com/anyaevostiar/SymbulationEmp.

    Visit that page, and then click on the ‘fork’ button (upper right).

    This makes a copy of the Symbulation source code in your own GitHub account. If you have contributor permissions to the main Symbulation library, this step is optional (you can instead develop on a branch within the main repo).

  3. Clone your copy of Symbulation and Empirical to your local development environment.

    Your clone URLs should look something like this:

    https://github.com/yourusername/SymbulationEmp.git
https://github.com/devosoft/Empirical.git

    and the UNIX shell command should be:

    git clone https://github.com/yourusername/SymbulationEmp.git
git clone https://github.com/devosoft/Empirical.git

    (This makes a local copy of Symbulation on your development machine.)

  4. Add a git reference to the Symbulation repository:

    cd SymbulationEmp
git remote add upstream https://github.com/anyaevostinar/SymbulationEmp.git
cd ../

    (This makes it easy for you to pull down the latest changes in the main repository.)

Building Symbulation and running the tests

To run the tests:

    make test

Congratulations! You’re ready to develop!

Claiming an issue and starting to develop

  1. Find an open issue and claim it.

    Once you’ve found an issue you like, make sure that no one has been assigned to it (see “assignee”, bottom right near “notifications”). Then, add a comment “I am working on this issue.” You’ve staked your claim!

    (We’re trying to avoid having multiple people working on the same issue.)

  2. In your local copy of the source code, update your main branch from the main Symbulation main branch:

    git checkout main
git pull upstream main

    (This pulls in all of the latest changes from whatever we’ve been doing on Symbulation.)

    It is possible that when you do a [git pull]{.title-ref} you will get a “merge conflict” – This is what happens when something changed in the branch you’re pulling in in the same place you made a change in your local copy.

    Git will complain loudly about merges and tell you specifically in which files they occurred. If you open the file, you’ll see something vaguely like this in the place where the merge occurred:

    <<<<<<< HEAD
Changes made on the branch that is being merged into. In most cases,
this is the branch that you have currently checked out
=======
Changes made on the branch that is being merged in, almost certainly
main.
>>>>>>> abcde1234

    Though there are a variety of tools to assist with resolving merge conflicts they can be quite complicated at first glance and it is usually easy enough to manually resolve the conflict.

    To resolve the conflict you simply have to manually ‘meld’ the changes together and remove the merge markers. Make sure that you don’t remove someone else’s changes while resolving the merge conflict!

    After this you’ll have to add and commit the merge just like any other set of changes. You should also run the tests to make sure that everything works as expected.

  3. Create a new branch and link it to your fork on GitHub:

    git checkout -b fix/brief_issue_description
git push -u origin fix/brief_issue_description

    where you replace “brief_issue_description” with 2-3 words, separated by underscores, describing the issue.

    (This is the set of changes you’re going to ask to be merged into Symbulation.)

  4. Make some changes and commit them.

    Though this will largely be issue-dependent the basics of committing are simple. After you’ve made a cohesive set of changes, run the command [git status]{.title-ref}. This will display a list of all the files git has noticed you changed. A file in the ‘untracked’ section are files that haven’t existed previously in the repository but git has noticed.

    To commit changes you have to ‘stage’ them–this is done by issuing the following command:

    git add path/to/file

    If you have a large quantity of changes and you don’t want to add each file manually you can do git add --patch which will display each set of changes to you before staging them for commit.

    Once you have staged your changes, it’s time to make a commit:

    git commit -m "added x change"

    Git will then open your default console text editor to write a commit message – this is a short (typically 1-3 sentence) description of the changes you’ve made. Please make your commit message informative but concise – these messages become part of the ‘official’ history of the project.

    Once your changes have been committed, push them up to the remote branch:

    git push

    If this is your first commit on a new branch git will error out, telling you the remote branch doesn’t exist – This is fine, as it will also provide the command to create the branch. Copy/paste/run and you should be set.

  5. Periodically update your branch from the Symbulation main branch:

    git pull upstream main

    (This pulls in all of the latest changes from whatever we’ve been doing on the upstream branch- important especially during periods of fast change or for long-running pull requests.)

  6. Run the tests before pushing to GitHub:

    make test

    Make sure they all pass!

  7. Push your branch to your own GitHub fork:

    git push origin

    (This pushes all of your changes to your own fork.)

  8. Repeat until you’re ready to merge your changes into “official” Symbulation.

  9. Set up a Pull Request asking to merge things into the central Symbulation repository.

    In a Web browser, go to your GitHub fork of Symbulation, e.g.:

    https://github.com/yourusername/SymbulationEmp

    and you will see a list of “recently pushed branches” just above the source code listing. On the right side of that should be a “Compare & pull request” green button. Click on it!

    Now:

    • add a descriptive title (“updated tests for XXX”)

    • put the issue number in the comment (“fixes issue #532”)

    then click “Create pull request.”

    (This creates a new issue where we can all discuss your proposed changes; the Symbulation team will be automatically notified and you will receive e-mail notifications as we add comments. See GitHub flow for more info.)

  10. As you add new commits to address bugs or formatting issues, you can keep pushing your changes to the pull request by doing:

    git push origin

  11. If we request changes, return to the step “Make some changes and commit them” and go from there. Any additional commits you make and push to your branch will automatically be added to the pull request (which is pretty dang cool.)

After your first issue is successfully merged…

You’re now an experienced GitHub user! Go ahead and take some more tasks; you can broaden out beyond the low hanging fruit if you like.

Your second contribution…

Here are a few pointers on getting started on your second (or third, or fourth, or nth contribution).

So, assuming you’ve found an issue you’d like to work on there are a couple things to do to make sure your local copy of the repository is ready for a new issue–specifically, we need to make sure it’s in sync with the remote repository so you aren’t working on an old copy. So:

git checkout main
git fetch --all
git pull

This puts you on the latest main branch and pulls down updates from GitHub with any changes that may have been made since your last contribution (usually including the merge of your last contribution). Then we merge those changes into your local copy of the main branch.

Now, you can go back to Claiming an issue and starting to develop.

Pull request cleanup (commit squashing)

Submitters are invited to reduce the numbers of commits in their pull requests either via [git rebase -i upstream/main]{.title-ref} or this recipe:

git pull ## make sure the local is up to date
git pull upstream main ## get up to date
## fix any merge conflicts
git status ## sanity check
git diff upstream/main ## does the diff look correct? (no merge markers)
git reset --soft upstream/main ## un-commit the differences from dib/main
git status ## sanity check
git commit --all ## package all differences in one commit
git status ## sanity check
git push ## should fail
git push --force ## override what's in GitHub's copy of the branch/pull request

Coding guidelines and review checklist

This document is for those who want to contribute code or documentation fixes to the Symbulation project and describes our coding standards as well as our code review process.

This document has been adapted from the khmer project

C++ standards

We use C++17 features throughout the project and currently that is the de-facto standard version to use.

All code should be in header files for ease of inclusion into Emscripten projects.

Files that define a single class should be named after that class. Files that define sets of functions or multiple classes should have an all-lowercase name that describes its contents.

All files and all directories must be levelized. This is partly enforced through all files being header files (and thus we cannot have circular dependencies), but for clean coding practices (and easy of unit testing) whole directories should not refer to each other bidirectionally either. See Large-Scale C++ Software Design by John Lakos for a strong pro-levelization argument.

In-code identifier formatting is always hard to settle upon. The guidelines below are for consistency.

  • Variable names should be all_lowercase, with words separated by underscores

  • Function names should be CamelCase() unless they are meant to mimic a function from the C++ standard library, at which point they can be all_lowercase to fit in.

  • User-defined types should be CamelCase

  • Constants should be ALL_UPPERCASE, with words separated by underscores

  • Template parameters should be ALL_UPPERCASE.

  • Typedefs should match the casing of the types they are aliasing. For example, a typedef on a template parameter might be all uppercase, while a typedef on a user-defined type should be CamelCase.

Guidelines based on Emscripten Limitations

  • Try to avoid use of 64-bit integers (that is, the “long long” type). Emscripten has to emulate these and they can cause a notable slowdown.

  • Do not rely on exceptions when possible. Emscripten is slow at dealing with them and they can slow down code even when not triggered.

  • Do not write multithreaded code that uses shared state. Javascript cannot (yet) handle such code and as such Emscripten cannot compile it. Note that Emscripten does have experimental support of pthreads.

  • Obviously, do not use any architecture-specific tricks, such as assuming endianness, doing unaligned reads or writes, directly accessing registers, etc.

Please see the Emscripten doc page for a full list.

General Standards

All plain-text files should have line widths of 100 characters or less unless that is unsupported for the particular file format.

All contributions should have their spelling checked before being committed to the codebase.

Vim users can run:

    :setlocal spell spelllang=en_us

to automagically check the spelling within the file being edited.

It’s expected that before requesting a code review the author of the PR will have checked the code. It’s also expected that whomever reviews the PR will check the code individually as well. Though the CI runs most of these and will pass/fail the PR accordingly it is not infallible and the whole point of having a code review process is to have human eyes go over the changes to the codebase.

Documentation for Symbulation Documentation

This is a quick primer on how to document things within Symbulation.

Symbulation makes use of the Sphinx documentation system based off of XML information gathered from Doxygen via a plugin named Breathe. This means that Doxygen will automatically build documentation for anything written in a C++ source file and Sphinx will be used to organize how that documentation is displayed.

Dependencies

You’ll need to install some additional things to build the documentation locally. If you make additions to the documentation, please build it locally to make sure that it is formatted well before making a pull request.

You need to install

  • Doxygen

  • Sphinx

  • pip/pip3

For Homebrew users, that looks like this:

brew install sphinx
brew install doxygen
brew install pip3

You can then use pip3 to install the rest of the requirements:

cd SymbulationEmp/docs
pip3 install -r requirements.txt

Building Documentation Locally

You are then ready to make your local documentation and run it:

make html
cd _build/html/
python3 -m http.server

How to Comment for Doxygen Autodoc

Doxygen has an entire documentation section on how to comment your code. We’ll provide a trimmed version here so that you can get started quickly.

Doxygen will examine all comments to determine if they are documentation comments or just code comments. To make a documentation comment you must add either an extra * or /, depending on the kind of comment:

/**
 * This is a documentation comment
 * across several lines
 *
 * This comment will be associated with the function immediately following.
*/
void somefunc(sometype param)
{

}

// this is a comment that doxygen will ignore
// note how it only has two leading slashes, like a normal comment
/// This is a comment that will be included in the documentation
/// Note the extra leading slash
/// Huzzah, documentation

Note

Doxygen requires a minimum of three triple slash’d lines before a block is considered documentation:

/// This line will be ignored
int somefunc() { return 5; }

///
/// This line will be included
///
void otherfunc() { ; }

If you wish to make a more visible comment block, e.g. a header for a class, then you may do something like the following:

/********************************************//**
* Here is some text inside a visible block
***********************************************/

Note

Doxygen will view this as any other documentation comment and will not render it any differently than a ‘normal’ documentation comment–it is simply more visible within the source code.

How to include Doxygen’s autodocs within Sphinx files

Through the use of the Breathe extension it is incredibly easy to include Doxygen autodocs within a Sphinx documentation file.

Suppose we have a C++ implementation file name lily.h that has inline comment documentation as detailed above and that lily.h is a component of a module named flowers that was just created.

To document them, you must create a file within the Symbulation Library documentation source to hold the module’s documentation:

    touch doc/library/flowers.md

Within flowers.md you can make an introduction to the module, etc., and then add in the sphinx directives to include auto-documentation. Your flowers.md file should look something like the following:

    # This is the flowers documentation!

    This is a very short introduction.

    ## lily.h

    ```{eval-rst}
    .. doxygenfile:: lily.h
       :project: Symbulation
    ```

When the docs are built Sphinx will automatically pull the available documentation from Doxygen’s XML files to construct the docs.

Additional directives exist to include auto-documentaiton from different levels, the full breakdown of which is available within the Breathe Documentation.

How to add docs to the Sphinx documentation

Sphinx is the system used to generate the developer guide and similar reference documentation. A primer to using ReStructured Text, the markup language used by Sphinx, can be found here. You can also look at any of the [.rst]{.title-ref} files in the [doc/]{.title-ref} directory to get a feel for how thinks work.

New documents must be included in the toctree in the index.md file for the directory the added file lives in. For example, if you add CowFacts.md to the CoolFacts/ directory you must add CowFacts.md to the toctree found in CoolFacts/CowFacts.md:

    # Cool Facts

    A bunch of cool facts!

    ```{toctree}
    AnteaterFacts
    BirdFacts
    CowFacts
    ```

Guide to Testing in Symbulation

This document details how testing works in Symbulation, both for writing and understanding tests.

Running Tests

In the root directory of Symbulation, use the maketarget test, like so:

make test

The tests will compile and execute automatically, and you should see output that looks something like this:

g++ -O3 -DNDEBUG -Wall -Wno-unused-function -std=c++17 -I../Empirical/include/ source/catch/main.cc -o symbulation.test
# Execute tests
./symbulation.test
===============================================================================
All tests passed (592 assertions in 70 test cases)

Writing Tests

It is required that contributions to the Symbulation library have test coverage. Though writing tests can be a complex task in some cases, it can also be easy to do.

In general the best way to understand how to write tests is to look at the existing tests. Each header file in source/ has a file full of tests ending with “class_name.test.cc”. We recommend browsing through those files.

The test cases should have the following layout:

TEST_CASE("Test name goes here", "[test classification here]")
{
        // body of test
}

Within a test case you can use the REQUIRE macro like an assert, to require certain conditions within the test:

REQUIRE(1==1); // will pass, obviously
REQUIRE(1==0); // will fail, and Catch will complain

If a REQUIRE fails, the compiler will give an error when you run “make test”.

Index