Deep copy not deep?

[whophil]

What happened?

I have a NetCDF file produced by an upstream process. After loading this into an xarray dataset and calling DataSet.copy(deep=True), I find that some coordinates still share memory with the source of the copy.

The NetCDF file in question:
data_clean.nc.zip

What did you expect to happen?

I expected a deep copy to be deep, with no shared memory between.

Minimal Complete Verifiable Example

import xarray as xr
import numpy as np

ds = xr.load_dataset("/Users/philchiu/repos/spheres/tests/data_clean.nc")
ds2 = ds.copy(deep=True)

print(ds.variables["FREQUENCY"].data)
ds2.variables["FREQUENCY"].data[:] = 99.99

# This should be the original array, but instead it's all 99.99
print(ds.variables["FREQUENCY"].data)

# I would expect both of these to print False, but it prints True, False
print(np.shares_memory(ds.variables["FREQUENCY"].data, ds2.variables["FREQUENCY"].data))
print(np.shares_memory(ds.variables["AMPLITUDE"].data, ds2.variables["AMPLITUDE"].data))

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

import xarray as xr
import numpy as np

ds = xr.load_dataset("data_clean.nc")
ds2 = ds.copy(deep=True)

print(ds.variables["FREQUENCY"].data)
ds2.variables["FREQUENCY"].data[:] = 99.99

# This should be the original array, but instead it's all 99.99
print(ds.variables["FREQUENCY"].data)

# I would expect both of these to print False, but it prints True, False
print(np.shares_memory(ds.variables["FREQUENCY"].data, ds2.variables["FREQUENCY"].data))
print(np.shares_memory(ds.variables["AMPLITUDE"].data, ds2.variables["AMPLITUDE"].data))

Anything else we need to know?

No response

Environment

>>> xr.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 3.10.15 | packaged by conda-forge | (main, Sep 20 2024, 16:31:41) [Clang 17.0.6 ]
python-bits: 64
OS: Darwin
OS-release: 21.6.0
machine: x86_64
processor: i386
byteorder: little
LC_ALL: None
LANG: None
LOCALE: (None, 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2

xarray: 2024.9.0
pandas: 2.2.3
numpy: 2.1.1
scipy: 1.14.1
netCDF4: 1.7.1
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: 1.6.4
nc_time_axis: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: 3.9.2
cartopy: None
seaborn: None
numbagg: None
fsspec: 2024.9.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 75.1.0
pip: 24.2
conda: None
pytest: 8.3.3
mypy: None
IPython: None
sphinx: None

[kmuehlbauer]

Dupe of #7463, your FREQUENCY is also a Coordinate.

[kmuehlbauer]

One more detail here:

ds2.variables["FREQUENCY"].data[:] = 99.99

With this you are sidestepping all security measures and you need to know what you are doing.

This would be the canonical invocation:

ds2["FREQUENCY"][:] = 99.99

[  100.   125.   160.   200.   250.   315.   400.   500.   630.   800.
  1000.  1250.  1600.  2000.  2500.  3150.  4000.  5000.  6300.  8000.
 10000.]

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[10], line 8
      5 ds2 = ds.copy(deep=True)
      7 print(ds.variables["FREQUENCY"].data)
----> 8 ds2.variables["FREQUENCY"][:] = 99.99
     10 # This should be the original array, but instead it's all 99.99
     11 print(ds.variables["FREQUENCY"].data)

File [/home/kai/data/mambaforge/envs/xr_312_np2/lib/python3.12/site-packages/xarray/core/variable.py:2710](http://localhost:8888/lab/tree/automount/hubhome/k.muehlbauer/home/kai/data/mambaforge/envs/xr_312_np2/lib/python3.12/site-packages/xarray/core/variable.py#line=2709), in IndexVariable.__setitem__(self, key, value)
   2709 def __setitem__(self, key, value):
-> 2710     raise TypeError(f"{type(self).__name__} values cannot be modified")

TypeError: IndexVariable values cannot be modified