Scanpy Benchmarks

This directory contains code for benchmarking Scanpy using asv.

The functionality is checked using the benchmark.yml workflow. Benchmarks are run using the benchmark bot.

Data processing in benchmarks

Each dataset is processed so it has

• .layers['counts'] (containing data in C/row-major format) and .layers['counts-off-axis'] (containing data in FORTRAN/column-major format)
• .X and .layers['off-axis'] with log-transformed data (formats like above)
• a .var['mt'] boolean column indicating mitochondrial genes

The benchmarks are set up so the layer parameter indicates the layer that will be moved into .X before the benchmark. That way, we don’t need to add layer=layer everywhere.