Use numpy & dask sliding_window_view for rolling #4977

dcherian · 2021-03-01T15:54:22Z

Should merge after dask/dask#7234 is merged

Closes xarray, chunking and rolling operation adds chunking along new dimension (previously worked) #3277, closes DataArray.rolling() does not preserve chunksizes in some cases #2531, closes [WIP] Fix problem with wrong chunksizes when using rolling_window on dask.array #2532, closes interpolate_na with limit argument changes size of chunks #2514
Tests added
Passes pre-commit run --all-files
User visible changes (including notable bug fixes) are documented in whats-new.rst

xarray/tests/test_duck_array_ops.py

xarray/core/rolling.py

xarray/tests/test_variable.py

dcherian · 2021-03-01T17:49:52Z

xarray/tests/test_nputils.py

    vindex[[0, 1], :, [0, 1]] = vindex[[0, 1], :, [0, 1]]
    vindex[:, [0, 1], [0, 1]] = vindex[:, [0, 1], [0, 1]]
-
-


moved to test_variable

dcherian · 2021-03-01T20:54:36Z

sliding_window_view dispatches with array_function so we could support other duck array libraries if they implemented it. cc @keewis

keewis

I didn't do a thorough review, but I have a few comments.

sliding_window_view dispatches with array_function

yes, this is really great.

doc/duckarrays.rst

xarray/core/npcompat.py

xarray/core/variable.py

…indow * upstream/master: add polyval to polyfit see also (pydata#5020) mention map_blocks in the docstring of apply_ufunc (pydata#5011) Switch backend API to v2 (pydata#4989) WIP: add new backend api documentation (pydata#4810) pin netCDF4=1.5.3 in min-all-deps (pydata#4982) fix matplotlib errors for single level discrete colormaps (pydata#4256) Adapt exception handling in CFTimeIndex.__sub__ and __rsub__ (pydata#5006) Update options.py (pydata#5000) Adjust tests to use updated pandas syntax for offsets (pydata#4537) add a combine_attrs parameter to Dataset.merge (pydata#4895) Support for dask.graph_manipulation (pydata#4965) raise on passing axis to Dataset.reduce methods (pydata#4940)

mathause

Looks good. I am still interested to eventually fix #2007. This PR may also make that easier as it now uses Variable.pad.

xarray/core/npcompat.py

xarray/core/dask_array_compat.py

Co-authored-by: Mathias Hauser <[email protected]>

dcherian · 2021-03-13T20:43:43Z

I am still interested to eventually fix #2007. This PR may also make that easier as it now uses Variable.pad.

That's the goal i.e. make it easier to fix #2007 and minimize number of code paths for rolling. This PR reduces the number of places we call pad from 4 to 3 :P. The two bottleneck code paths still do their own padding.

xarray/core/npcompat.py

Co-authored-by: Mathias Hauser <[email protected]>

…indow * upstream/master: Fix regression in decoding large standard calendar times (pydata#5050) Fix sticky sidebar responsiveness on small screens (pydata#5039) Flexible indexes refactoring notes (pydata#4979) add a install xarray step to the upstream-dev CI (pydata#5044) Adds Dataset.query() method, analogous to pandas DataFrame.query() (pydata#4984) run tests on python 3.9 (pydata#5040) Add date attribute to datetime accessor (pydata#4994) 📚 New theme & rearrangement of the docs (pydata#4835) upgrade ci-trigger to the most recent version (pydata#5037) GH5005 fix documentation on open_rasterio (pydata#5021) GHA for automatically canceling previous CI runs (pydata#5025) Implement GroupBy.__getitem__ (pydata#3691) conventions: decode unsigned integers to signed if _Unsigned=false (pydata#4966) Added support for numpy.bool_ (pydata#4986) Add additional str accessor methods for DataArray (pydata#4622)

…nto rolling-sliding-window * 'rolling-sliding-window' of github.com:dcherian/xarray: Update xarray/core/npcompat.py Apply suggestions from code review

dcherian · 2021-03-18T16:31:13Z

The dask PR was merged so this should be ready to go.

mathause · 2021-03-18T16:47:52Z

It looked pretty good when I reviewed it, so 👍

Just quickly skimming the code it did not become entirely clear to me why this had to be after dask/dask#7234? You don't import sliding_window_view from dask. Also you re-define sliding_window_view in dask_array_compat.py - why don't you need this in dask proper? (Not complaining just wondering. Also feel free to not answer the question if you don't have time.)

dcherian · 2021-03-18T17:01:34Z

You don't import sliding_window_view from dask.

haha. fixed!

I was waiting on that PR to see if the reviews would catch any bugs.

andersy005 · 2021-03-18T17:06:46Z

@dcherian, should we test this in upstream-dev CI workflow (via the [test-upstream] keyword)?

dcherian · 2021-03-18T17:10:28Z

thanks @andersy005 !

dcherian added 5 commits March 1, 2021 08:48

Add sliding_window_view functions

76d2c5c

Variable.rolling_window uses Variable.pad & sliding_window_view

979d366

Delete old code

d654942

Update tests

a292c2a

update duckarrays doc

b60617b

dcherian marked this pull request as draft March 1, 2021 15:54

dcherian commented Mar 1, 2021

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dcherian added 3 commits March 1, 2021 10:06

convert more nputils tests to Variable tests

5a9f9ef

Undo deletion of bottleneck + dask path

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lint

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dcherian commented Mar 1, 2021

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dcherian added 2 commits March 1, 2021 11:06

vendor ensure minimum chunksize

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support older map_overlap signature

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more backcompat

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keewis reviewed Mar 1, 2021

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dcherian mentioned this pull request Mar 4, 2021

Bottleneck and dask objects ignore min_periods on rolling #4922

Open

dcherian added 3 commits March 5, 2021 07:07

review feedback

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Add some extra tests

61c5e43

mathause reviewed Mar 13, 2021

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Co-authored-by: Mathias Hauser <[email protected]>

mathause reviewed Mar 13, 2021

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Update xarray/core/npcompat.py

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Co-authored-by: Mathias Hauser <[email protected]>

dcherian marked this pull request as ready for review March 18, 2021 16:29

dcherian added 3 commits March 18, 2021 10:29

sync with dask PR

cdefb15

Merge branch 'rolling-sliding-window' of github.com:dcherian/xarray i…

f458b7b

…nto rolling-sliding-window * 'rolling-sliding-window' of github.com:dcherian/xarray: Update xarray/core/npcompat.py Apply suggestions from code review

[test-upstream] Actually use dask_array_compat.

39f9e28

dcherian force-pushed the rolling-sliding-window branch from d7c37a7 to 39f9e28 Compare March 18, 2021 17:10

dcherian merged commit fdf024c into pydata:master Mar 26, 2021

dcherian deleted the rolling-sliding-window branch March 26, 2021 19:50

keewis mentioned this pull request Mar 31, 2021

Feature Request: Efficient rolling with strides #3608

Open

		vindex[[0, 1], :, [0, 1]] = vindex[[0, 1], :, [0, 1]]
		vindex[:, [0, 1], [0, 1]] = vindex[:, [0, 1], [0, 1]]

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Use numpy & dask sliding_window_view for rolling #4977

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