Data Backend for Expedited Acquisition and Neighbourhood Search

Installation

make install          # data-beans + data-beans-sim, HDF5 if detected
make install HDF5=off # without .h5/.h5ad support
make help             # what was detected on this host, and the overrides

or from crates.io (CPU, no HDF5):

cargo install data-beans
cargo install data-beans --features sim   # data-beans-sim

Here, we implement a wrapper for sparse matrix backends for swift data access by rows and columns without populating everything in memory. Being inspired by anndata-rs, we use hdf5 and zarr as the back-end storage format. The hdf5 file or .zarr.zip archive (or plain zarr directory with --no-zip) is organized as follows:

(root)
    ├── nrow
    ├── ncol
    ├── nnz
    ├── by_column
    │   ├── data
    │   ├── indices (row indices)
    │   └── indptr (column pointers)
    └── by_row
        ├── data
        ├── indices (column indices)
        └── indptr (row pointers)