PyGeode is a software library intended to simplify the management, analysis, and visualization of gridded geophysical datasets such as those generated by climate models. The library provides three main advantages. Firstly, it can define a geophysical coordinate system for any given dataset, and allows operations to be carried conceptually in this physical coordinate system, in a way that is independent of the native coordinate system of a particular dataset. This greatly simplifies working with datasets from different sources. Secondly, the library allows mathematical operations to be performed on datasets which fit on disk but not in memory; this is useful for dealing with the extremely large datasets generated by climate models, and permits operations to be performed over networks. Finally, the library provides tools for visualizing these datasets in a scientifically useful way. The library is written in Python, and makes use of a number of existing packages to perform the underlying computations and to create plots.