scran_tests Namespace Reference

Test utilites for libscran. More...

Classes
struct	CompareAlmostEqualParameters
	Parameters for compare_almost_equal(). More...
struct	SimulateCompressedSparseMatrixParameters
	Parameters for simulate_compressed_sparse_matrix(). More...
struct	SimulatedCompressedSparseMatrix
	Results of simulate_compressed_sparse_matrix(). More...
struct	SimulateVectorParameters
	Parameters for simulate_vector(). More...

Typedefs
typedef std::mt19937_64	RngEngine

Functions
bool	compare_almost_equal (double left, double right, const CompareAlmostEqualParameters &params)
template<class LeftContainer_ , class RightContainer_ >
void	compare_almost_equal_containers (const LeftContainer_ &left, const RightContainer_ &right, CompareAlmostEqualParameters params)
template<typename Function_ >
void	expect_error (Function_ fun, std::string match)
int	initial_value ()
template<typename Data_ = double, typename Index_ = int, typename Pointer_ = std::size_t>
SimulatedCompressedSparseMatrix< Data_, Index_, Pointer_ >	simulate_compressed_sparse_matrix (Index_ primary, Index_ secondary, const SimulateCompressedSparseMatrixParameters< Data_ > &params)
template<typename Type_ >
constexpr Type_	default_simulation_min ()
template<typename Type_ = double>
std::vector< Type_ >	simulate_vector (const typename std::vector< Type_ >::size_type length, const SimulateVectorParameters< Type_ > &params)
template<typename Type_ >
std::vector< Type_ >	vector_n (const Type_ *ptr, std::size_t n)

Detailed Description

Test utilites for libscran.

Typedef Documentation

RngEngine

typedef std::mt19937_64 scran_tests::RngEngine

Type of the random number generator for simulating data.

Function Documentation

compare_almost_equal()

bool scran_tests::compare_almost_equal ( double left, double right, const CompareAlmostEqualParameters & params )

inline

Check if two floating-point numbers are equal, accounting for some relative difference.

Two numbers are considered equal if their difference is less than the product of CompareAlmostEqualParameters::relative_tolerance and their mean. If both numbers are close to zero, they are considered equal if the difference is below CompareAlmostEqualParameters::absolute_tolerance; this avoids being overly stringent for numbers that should be zero, at the cost of potentially missing large relative differences.

If both numbers are NaN, they are reported to be equal unless CompareAlmostEqualParameters::nan_equal = false. Obviously, NaNs are considered to be non-equal to any non-NaN number.

Parameters

left	One of the numbers.
right	The other number.
params	Further parameters.

Returns

Whether the two numbers are equal.

compare_almost_equal_containers()

template<class LeftContainer_ , class RightContainer_ >

void scran_tests::compare_almost_equal_containers	(	const LeftContainer_ &	left,
		const RightContainer_ &	right,
		CompareAlmostEqualParameters	params )

Check if two vectors contain an equal number of almost-equal floats. This compares the corresponding elements from each vector using compare_almost_equal(). Any test failure is reported via GoogleTest.

Template Parameters

LeftVector_	Some vector-like container of floating-point values.
RightVector_	Another vector-like container of floating-point values.

Parameters

left	One of the vectors.
right	The other vector.
params	Further parameters. Note that CompareAlmostEqualParameters::report is ignored, any mismatching value will always be reported.

default_simulation_min()

template<typename Type_ >

Type_ scran_tests::default_simulation_min ( )

constexpr

Template Parameters

Type_

Numeric type of the simulated value.

Returns

-10 if Type is signed, otherwise 0.

expect_error()

template<typename Function_ >

void scran_tests::expect_error	(	Function_	fun,
		std::string	match )

Expect an error to be raised with the given message. If no error is raised, or if the error message does not match match, an error is reported via GoogleTest.

Template Parameters

Function_

Function to call with no arguments.

Parameters

fun	Function that should raise an error.
match	String to be matched against the error message.

initial_value()

int scran_tests::initial_value ( )

inline

Some functions store their output in a user-supplied pointer to a pre-allocated array. Such functions should not assume that the array has been zeroed. Incorrectly making this assumption can lead to subtle bugs when the functions are called with non-zeroed buffers. To test that this assumption is not present in function X(), we can initialize an output buffer with a non-zero initial value from the initial_value() function below. After calling X() with output, we can compare the contents of output against the expected output to verify that the function ignores the non-zero initial value. If the expected output is not readily available, we could instead initialize a separate vector with another call to initial_value() and call X() on it. Any inconsistency in the results would indicate that the variable initial_value() is affecting the results.

Returns

An integer in [1, 255] that is incremented on every call (or rolls back to 1).

simulate_compressed_sparse_matrix()

template<typename Data_ = double, typename Index_ = int, typename Pointer_ = std::size_t>

SimulatedCompressedSparseMatrix< Data_, Index_, Pointer_ > scran_tests::simulate_compressed_sparse_matrix	(	Index_	primary,
		Index_	secondary,
		const SimulateCompressedSparseMatrixParameters< Data_ > &	params )

Template Parameters

Data_	Numeric type of the data.
Index_	Integer type of the indices.
Pointer_	Integer type of the compressed sparse pointers.

Parameters

primary	Extent of the primary dimension, i.e., along which the structural non-zero elements are compressed. For example, in a compressed sparse row matrix, the rows would be the primary dimension.
secondary	Extent of the secondary dimension, i.e., not the primary dimension.
params	Simulation parameters.

Returns

Contents of a simulated compressed sparse matrix.

simulate_vector()

template<typename Type_ = double>

std::vector< Type_ > scran_tests::simulate_vector	(	const typename std::vector< Type_ >::size_type	length,
		const SimulateVectorParameters< Type_ > &	params )

Simulate a vector of random values. If SimulationParameters::density < 1, this will be a sparse vector with structural zeros.

Template Parameters

Type_

Numeric type of the simulated value.

Parameters

length	Length of the vector.
params	Simulation parameters.

Returns

Vector of simulated values.

vector_n()

template<typename Type_ >

std::vector< Type_ > scran_tests::vector_n	(	const Type_ *	ptr,
		std::size_t	n )

Quickly create a vector from an array, primarily for convenient use in EXPECT_EQ with another vector.

Parameters

[in]	ptr	Pointer to the start of an array.
	n	Length of the array.

Returns

Vector of the array's values.