tatami bindings for irlba

Overview

This library implements a wrapper class to use tatami::Matrix instances in the irlba library. The goal is to support IRLBA on alternative matrix representations (e.g., sparse, file-backed) without requiring realization into a irlba::SimpleMatrix.

Quick start

Not much to say, really. Just pass a irlba_tatami::Normal or irlba_tatami::Transposed anywhere that an irlba::Matrix can be accepted:

#include "irlba_tatami/irlba_tatami.hpp"

// Initialize this with an instance of a concrete tatami subclass.
std::shared_ptr<tatami::Matrix<double, int> > tmat;

// Wrap it for use in IRLBA.
irlba_tatami::Normal<Eigen::VectorXd, Eigen::MatrixXd, double, int> wrapped(std::move(tmat));
auto res = irlba::compute(wrapper, 5, irlba::Options());

// Performing IRLBA on a column-centered matrix.
Eigen::VectorXd centers; // Fill column centers here...
CenteredMatrix<Eigen::VectorXd, Eigen::MatrixXd> centered(&wrapped, &centers);
auto centered_res = irlba::compute(centered, 5, irlba::Options());

See the reference documentation for more details.

Building projects

CMake with FetchContent

If you're using CMake, you just need to add something like this to your CMakeLists.txt:

include(FetchContent)

FetchContent_Declare(
  irlba_tatami
  GIT_REPOSITORY https://github.com/libscran/irlba_tatami
  GIT_TAG master # or any version of interest
)

FetchContent_MakeAvailable(irlba_tatami)

Then you can link to irlba_tatami to make the headers available during compilation:

# For executables:
target_link_libraries(myexe libscran::irlba_tatami)

# For libaries
target_link_libraries(mylib INTERFACE libscran::irlba_tatami)

By default, this will use FetchContent to fetch all external dependencies. Applications are advised to pin the versions of each dependency for stability - see extern/CMakeLists.txt for suggested versions. If you want to install them manually, use -DIRLBA_TATAMI_FETCH_EXTERN=OFF.

CMake with find_package()

To install the library, clone an appropriate version of this repository and run:

mkdir build && cd build
cmake .. -DIRLBA_TATAMI_TESTS=OFF
cmake --build . --target install

Then we can use find_package() as usual:

find_package(libscran_irlba_tatami CONFIG REQUIRED)
target_link_libraries(mylib INTERFACE libscran::irlba_tatami)

Again, this will automatically acquire all its dependencies, see recommendations above.

Manual

If you're not using CMake, the simple approach is to just copy the files in include/ - either directly or with Git submodules - and include their path during compilation with, e.g., GCC's -I. This requires the external dependencies listed in extern/CMakeLists.txt.