dafpy 0.1.0

Data in Axes in Files

DataAxesFormats.jl is a Julia package which provides a uniform generic interface for accessing 1D and 2D data arranged along some set of axes. This is a much-needed generalization of the AnnData functionality. This package (dafpy) is a wrapper around the Julia package that allows accessing Daf data from Python, using the JuliaCall package.

Installation

Just pip install dafpy, like installing any other Python package.

Usage

The Python package provides the same API as the Julia package, with the following modifications:

• (Most) functions are exposed as member functions of the DafReader and DafWriter classes (e.g., write reader.get_scalar("version") in Python instead of get_scalar(reader, "version") in Julia).

• There is no ! suffix for functions that modify the data (e.g., write writer.set_scalar("version", "1.0") in Python instead of set_scalar!(writer, "version", "1.0") in Julia.

• DataAxesFormats.jl supports importing and exporting AnnData objects. However, since it is a Julia package, these objects are not Python anndata objects; instead they use the implementation provides by the Muon.jl Julia package. That is, to import/export AnnData between Daf and Python, your best bet is to go through h5ad files.

See the [Python v0.1.0 documentation](https://tanaylab.github.io/Daf.py/v0.1.0) and [Julia v0.1.0 documentation](https://tanaylab.github.io/DataAxesFormats.jl/v0.1.0) for details.

Status

Version 0.1.0 is an alpha release. We hope it is feature complete and have started using it for internal projects. However, everything is subject to change based on user feedback (so don’t be shy). Comments, bug reports and PRs are welcome!

License (MIT)

Copyright © 2024 Weizmann Institute of Science

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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

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