pydata / pydata/xarray

`DataTree.to_dict()` method does not behave as expected

Open
#9,611 4 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug topic-DataTree
Dominant language
Python
Stars
4.2k
Forks
1.4k
Avg merge
2d 15h
Merged PRs (30d)
14

Description

What happened?

I am working with DataTree and find it very useful! However, I think I found a bug in the .to_dict() method.
When I build a DataTree from a dict with DataTree.from_dict() and then want to get the dict again with DataTree.to_dict() the resulting dict differs from the original one.

What did you expect to happen?

I expected the two dicts to be the same. Instead, the root node receives a dict entry with an empty Dataset. I argue that empty nodes should not appear in the dict.

Minimal Complete Verifiable Example
import xarray as xr
from xarray.core.datatree import DataTree

example_dict = {"set1": xr.Dataset({"var1": xr.DataArray([1, 2, 3], dims = "time")}),
                "set2": xr.Dataset({"var1": xr.DataArray([7, 8, 9], dims = "time")})}
dt = DataTree.from_dict(example_dict)
dt.to_dict() == example_dict # False
# should be True imo

# or even just
DataTree.from_dict({}).to_dict == {} # False
MVCE confirmation
  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output

No response

Anything else we need to know?

No response

Environment

:488: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

INSTALLED VERSIONS

commit: None
python: 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:54:21) [Clang 16.0.6 ]
python-bits: 64
OS: Darwin
OS-release: 23.6.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: None
LOCALE: (None, 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2

xarray: 2024.9.0
pandas: 2.2.0
numpy: 1.26.4
scipy: 1.12.0
netCDF4: 1.7.1
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: 1.6.3
nc_time_axis: 1.4.1
iris: None
bottleneck: None
dask: 2024.2.0
distributed: 2024.2.0
matplotlib: 3.8.3
cartopy: 0.22.0
seaborn: None
numbagg: None
fsspec: 2024.2.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 69.1.0
pip: 24.0
conda: None
pytest: 8.0.1
mypy: None
IPython: 8.21.0
sphinx: 7.2.6

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the DataTree.from_dict() and DataTree.to_dict() entry points using the minimal Python example in the issue. Check how the root node and empty Dataset are represented during the round trip. Done means converting the provided dictionaries to a DataTree and back produces the original dictionaries, including an empty input producing {}.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.