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Migration guide for users of xarray-contrib/datatree

15th October 2024

This guide is for previous users of the prototype datatree.DataTree class in the xarray-contrib/datatree repository. That repository has now been archived, and will not be maintained. This guide is intended to help smooth your transition to using the new, updated xarray.DataTree class.

Important

There are breaking changes! You should not expect that code written with xarray-contrib/datatree will work without any modifications. At the absolute minimum you will need to change the top-level import statement, but there are other changes too.

We have made various changes compared to the prototype version. These can be split into three categories: data model changes, which affect the hierarchal structure itself; integration with xarray's IO backends; and minor API changes, which mostly consist of renaming methods to be more self-consistent.

Data model changes

The most important changes made are to the data model of DataTree. Whilst previously data in different nodes was unrelated and therefore unconstrained, now trees have "internal alignment" - meaning that dimensions and indexes in child nodes must exactly align with those in their parents.

These alignment checks happen at tree construction time, meaning there are some netCDF4 files and zarr stores that could previously be opened as datatree.DataTree objects using datatree.open_datatree, but now cannot be opened as xr.DataTree objects using xr.open_datatree. For these cases we added a new opener function xr.open_groups, which returns a dict[str, Dataset]. This is intended as a fallback for tricky cases, where the idea is that you can still open the entire contents of the file using open_groups, edit the Dataset objects, then construct a valid tree from the edited dictionary using DataTree.from_dict.

The alignment checks allowed us to add "Coordinate Inheritance", a much-requested feature where indexed coordinate variables are now "inherited" down to child nodes. This allows you to define common coordinates in a parent group that are then automatically available on every child node. The distinction between a locally-defined coordinate variables and an inherited coordinate that was defined on a parent node is reflected in the DataTree.__repr__. Generally if you prefer not to have these variables be inherited you can get more similar behaviour to the old datatree package by removing indexes from coordinates, as this prevents inheritance.

Tree structure checks between multiple trees (i.e., DataTree.isomorophic) and pairing of nodes in arithmetic has also changed. Nodes are now matched (with xarray.group_subtrees) based on their relative paths, without regard to the order in which child nodes are defined.

For further documentation see the page in the user guide on Hierarchical Data.

Integrated backends

Previously datatree.open_datatree used a different codepath from xarray.open_dataset, and was hard-coded to only support opening netCDF files and Zarr stores. Now xarray's backend entrypoint system has been generalized to include open_datatree and the new open_groups. This means we can now extend other xarray backends to support open_datatree! If you are the maintainer of an xarray backend we encourage you to add support for open_datatree and open_groups!

Additionally:

  • A group kwarg has been added to open_datatree for choosing which group in the file should become the root group of the created tree.
  • Various performance improvements have been made, which should help when opening netCDF files and Zarr stores with large numbers of groups.
  • We anticipate further performance improvements being possible for datatree IO.

API changes

A number of other API changes have been made, which should only require minor modifications to your code:

  • The top-level import has changed, from from datatree import DataTree, open_datatree to from xarray import DataTree, open_datatree. Alternatively you can now just use the import xarray as xr namespace convention for everything datatree-related.
  • The DataTree.ds property has been changed to DataTree.dataset, though DataTree.ds remains as an alias for DataTree.dataset.
  • Similarly the ds kwarg in the DataTree.__init__ constructor has been replaced by dataset, i.e. use DataTree(dataset=) instead of DataTree(ds=...).
  • The method DataTree.to_dataset() still exists but now has different options for controlling which variables are present on the resulting Dataset, e.g. inherit=True/False.
  • DataTree.copy() also has a new inherit keyword argument for controlling whether or not coordinates defined on parents are copied (only relevant when copying a non-root node).
  • The DataTree.parent property is now read-only. To assign a ancestral relationships directly you must instead use the .children property on the parent node, which remains settable.
  • Similarly the parent kwarg has been removed from the DataTree.__init__ constructor.
  • DataTree objects passed to the children kwarg in DataTree.__init__ are now shallow-copied.
  • DataTree.as_array has been replaced by DataTree.to_dataarray.
  • A number of methods which were not well tested have been (temporarily) disabled. In general we have tried to only keep things that are known to work, with the plan to increase API surface incrementally after release.

Thank you!

Thank you for trying out xarray-contrib/datatree!

We welcome contributions of any kind, including good ideas that never quite made it into the original datatree repository. Please also let us know if we have forgotten to mention a change that should have been listed in this guide.

Sincerely, the datatree team:

Tom Nicholas, Owen Littlejohns, Matt Savoie, Eni Awowale, Alfonso Ladino, Justus Magin, Stephan Hoyer