Assorted C++ headers

Overview

assorthead vendors an assortment of header-only C++ libraries for compilation of downstream packages. This centralizes the acquisition and versioning of these libraries for a smoother development experience. It is primarily intended for the various BiocPy packages with C++ extensions, e.g., scranpy, singler.

Quick start

Developers can install assorthead via the usual pip commands:

pip install assorthead

We can then add all headers to the compiler's search path, using the include_dirs argument in the setup() command in our setup.py:

setup(
    use_scm_version={"version_scheme": "no-guess-dev"},
    ext_modules=[
        Extension(
            "foo.core",
            [
                "src/lib/foo.cpp",
                "src/lib/bar.cpp",
            ],
            include_dirs=[
                assorthead.includes(),
            ],
            language="c++",
            extra_compile_args=[
                "-std=c++17",
            ],
        )
    ],
)

Of course, this is only relevant for developers; all going well, end users should never be aware of these details.

Available libraries

Name	Description
byteme	Lightweight file readers/writers
aarand	Random distribution functions
powerit	Power iterations
kmeans	Hartigan-Wong or Lloyd k-means
Annoy	Approximate nearest neighbor search
hnswlib	Approximate nearest neighbor search
knncolle	Common interface to neighbor search algorithms
tatami	Interface for matrix representations
qdtsne	Visualiation with t-SNE
umappp	Visualization with UMAP
Eigen	Matrix operations and linear algebra
irlba	Approximate SVD via IRLBA
WeightedLowess	Trend fitting via weighted LOWESS
mnncorrect	Batch correction with MNNs

The exact versions of each library can be found in extern/fetch.sh.

Note

This project has been set up using PyScaffold 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.