pydata / pydata/xarray

weighted polyfit with NaNs appears broken

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bug
Dominant language
Python
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Avg merge
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Merged PRs (30d)
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Description

What happened?

polyfit can't seem to handle weights still (despite https://github.com/pydata/xarray/pull/5933). nans are involved.

What did you expect to happen?

No response

Minimal Complete Verifiable Example
np.random.seed(10)
y = np.random.rand(10)
x = np.arange(len(y))
y[3] = np.nan
y[5] = np.nan
w = y/10

msk = ~np.isnan(y)
x = x[msk]
y = y[msk]
w = w[msk]

da_test = xr.DataArray(y, dims='time', coords={'time': x})
da_test.polyfit('time', 1, w=w)

# np.polyfit(x, y, 1)#, w=w) # <-- should match this
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?

not inserting the nans and/or converting the weights to a data array didn't matter

Environment

INSTALLED VERSIONS

commit: None
python: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
python-bits: 64
OS: Linux
OS-release: 5.14.0-284.30.1.el9_2.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2

xarray: 2024.3.0
pandas: 2.2.2
numpy: 1.26.4
scipy: 1.13.0
netCDF4: 1.6.5
pydap: None
h5netcdf: 1.3.0
h5py: 3.11.0
Nio: None
zarr: None
cftime: 1.6.3
nc_time_axis: None
iris: None
bottleneck: None
dask: 2024.5.0
distributed: 2024.5.0
matplotlib: 3.8.4
cartopy: 0.23.0
seaborn: 0.13.2
numbagg: None
fsspec: 2024.3.1
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 69.5.1
pip: 24.0
conda: None
pytest: None
mypy: None
IPython: 8.22.2
sphinx: None

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 at the DataArray.polyfit entry point and run the provided minimal example with the shown weighted, NaN-filtered arrays. Compare its result with numpy.polyfit using the same x, y, and w inputs, then add or update coverage so weighted fitting produces the expected matching result.

Written by the indexing model from the issue text.

Assessment

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

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