make coarsen reductions consistent with reductions on other classes by dcherian · Pull Request #3500 · pydata/xarray

dcherian · 2019-11-08T21:56:03Z

Tests added
Passes black . && mypy . && flake8
Fully documented, including whats-new.rst for all changes and api.rst for new API

This PR uses inject_reduce_methods to inject reduction methods into the Coarsen classes. So now we can do coarsen.count() and pass skipna down to the reduction methods.

This brings in support for coarsen.count as well as passing skipna down to the other reduction functions.

max-sixty · 2019-11-09T04:25:57Z

Great idea, there's lots of room to centralize some of these!

dcherian · 2019-11-16T15:38:47Z

@fujisoup this could use a review if you have time.

fujiisoup

Thanks, @dcherian.

It looks very nice!
I don't remember why I added a separate injection function...

Can you add some tests for coarsen.count() and skipna in the reduction methods?

xarray/core/variable.py

* upstream/master: (22 commits) Added fill_value for unstack (pydata#3541) Add DatasetGroupBy.quantile (pydata#3527) ensure rename does not change index type (pydata#3532) Leave empty slot when not using accessors interpolate_na: Add max_gap support. (pydata#3302) units & deprecation merge (pydata#3530) Fix set_index when an existing dimension becomes a level (pydata#3520) add Variable._replace (pydata#3528) Tests for module-level functions with units (pydata#3493) Harmonize `FillValue` and `missing_value` during encoding and decoding steps (pydata#3502) FUNDING.yml (pydata#3523) Allow appending datetime & boolean variables to zarr stores (pydata#3504) warn if dim is passed to rolling operations. (pydata#3513) Deprecate allow_lazy (pydata#3435) Recursive tokenization (pydata#3515) format indexing.rst code with black (pydata#3511) add missing pint integration tests (pydata#3508) DOC: update bottleneck repo url (pydata#3507) add drop_sel, drop_vars, map to api.rst (pydata#3506) remove syntax warning (pydata#3505) ...

…sen-reduce * 'coarsen-reduce' of github.com:dcherian/xarray:

dcherian · 2019-11-17T15:00:18Z

I don't remember why I added a separate injection function...

👍

Can you add some tests for coarsen.count() and skipna in the reduction methods?

There is a count test in test_variable. I've added sum(skipna=...) tests there too now.

fujiisoup

Thanks for adding the tests. It looks nice!

Probably I wondered if bottleneck works with multiple reduction axes.

doc/whats-new.rst

Co-Authored-By: keewis <keewis@users.noreply.github.com>

dcherian · 2019-11-19T17:11:19Z

Probably I wondered if bottleneck works with multiple reduction axes.

I'll check this before merging.

dcherian · 2019-12-04T15:48:22Z

In the case of multiple reduction axes i.e. isinstance(axis, tuple) is True we don't use the bottleneck method so things should be fine.

xarray/xarray/core/nputils.py

Lines 210 to 218 in ed05f98

    
           if ( 
        
               _USE_BOTTLENECK 
        
               and isinstance(values, np.ndarray) 
        
               and bn_func is not None 
        
               and not isinstance(axis, tuple) 
        
               and values.dtype.kind in "uifc" 
        
               and values.dtype.isnative 
        
               and (dtype is None or np.dtype(dtype) == values.dtype) 
        
           ):

* upstream/master: (22 commits) Resolve the version issues on RTD (pydata#3589) Add bottleneck & rasterio git tip to upstream-dev CI (pydata#3585) update whats-new.rst (pydata#3581) Examples for quantile (pydata#3576) add cftime intersphinx entries (pydata#3577) Add pyXpcm to Related Projects doc page (pydata#3578) Reimplement quantile with apply_ufunc (pydata#3559) add environment file for binderized examples (pydata#3568) Add drop to api.rst under pending deprecations (pydata#3561) replace duplicate method _from_vars_and_coord_names (pydata#3565) propagate indexes in to_dataset, from_dataset (pydata#3519) Switch examples to notebooks + scipy19 docs improvements (pydata#3557) fix whats-new.rst (pydata#3554) Tweaks to release instructions (pydata#3555) Clarify conda environments for new contributors (pydata#3551) Revert to dev version 0.14.1 whatsnew (pydata#3547) sparse option to reindex and unstack (pydata#3542) Silence sphinx warnings (pydata#3516) Numpy 1.18 support (pydata#3537) ...

…sen-reduce * 'coarsen-reduce' of github.com:dcherian/xarray: Update doc/whats-new.rst

* upstream/master: (35 commits) fix plotting with transposed nondim coords. (pydata#3441) make coarsen reductions consistent with reductions on other classes (pydata#3500) Resolve the version issues on RTD (pydata#3589) Add bottleneck & rasterio git tip to upstream-dev CI (pydata#3585) update whats-new.rst (pydata#3581) Examples for quantile (pydata#3576) add cftime intersphinx entries (pydata#3577) Add pyXpcm to Related Projects doc page (pydata#3578) Reimplement quantile with apply_ufunc (pydata#3559) add environment file for binderized examples (pydata#3568) Add drop to api.rst under pending deprecations (pydata#3561) replace duplicate method _from_vars_and_coord_names (pydata#3565) propagate indexes in to_dataset, from_dataset (pydata#3519) Switch examples to notebooks + scipy19 docs improvements (pydata#3557) fix whats-new.rst (pydata#3554) Tweaks to release instructions (pydata#3555) Clarify conda environments for new contributors (pydata#3551) Revert to dev version 0.14.1 whatsnew (pydata#3547) sparse option to reindex and unstack (pydata#3542) ...

* upstream/master: Fix map_blocks HLG layering (pydata#3598) Silence sphinx warnings: Round 2 (pydata#3592) 2x~5x speed up for isel() in most cases (pydata#3533) remove xarray again (pydata#3591) fix plotting with transposed nondim coords. (pydata#3441) make coarsen reductions consistent with reductions on other classes (pydata#3500) Resolve the version issues on RTD (pydata#3589) Add bottleneck & rasterio git tip to upstream-dev CI (pydata#3585)

…equiv * 'master' of github.com:pydata/xarray: (28 commits) Add nanmedian for dask arrays (pydata#3604) added pyinterp to related projects (pydata#3655) Allow incomplete hypercubes in combine_by_coords (pydata#3649) concat keeps attrs from first variable. (pydata#3637) Extend DatetimeAccessor properties and support `.dt` accessor for Timedelta (pydata#3612) update readthedocs.yml (pydata#3639) silence sphinx warnings round 3 (pydata#3602) Fix/quantile wrong errmsg (pydata#3635) Provide shape info in shape mismatch error. (pydata#3619) Minor doc fixes (pydata#3615) Respect user-specified coordinates attribute. (pydata#3487) Add Facetgrid.row_labels & Facetgrid.col_labels (pydata#3597) Fix pint integration tests (pydata#3600) Minor fix to combine_by_coords to allow for the combination of CFTimeIndexes separated by large time intervals (pydata#3543) Fix map_blocks HLG layering (pydata#3598) Silence sphinx warnings: Round 2 (pydata#3592) 2x~5x speed up for isel() in most cases (pydata#3533) remove xarray again (pydata#3591) fix plotting with transposed nondim coords. (pydata#3441) make coarsen reductions consistent with reductions on other classes (pydata#3500) ...

dcherian added 4 commits November 8, 2019 14:32

Coarsen now has the same reduction methods as groupby & rolling.

dbf5d00

This brings in support for coarsen.count as well as passing skipna down to the other reduction functions.

test for count

c1977c8

Test that dims passed to coarsen are present in dataset.

01729eb

Add whats-new

b93a19f

dcherian and others added 2 commits November 9, 2019 11:45

fix tests.

d7f677c

Merge branch 'master' into coarsen-reduce

305c193

fujiisoup reviewed Nov 17, 2019

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xarray/core/variable.py Outdated Show resolved Hide resolved

dcherian and others added 4 commits November 17, 2019 07:50

review comments.

7336a0b

Merge branch 'coarsen-reduce' of github.com:dcherian/xarray into coar…

efbfa88

…sen-reduce * 'coarsen-reduce' of github.com:dcherian/xarray:

Merge branch 'master' into coarsen-reduce

eaf8aca

fujiisoup approved these changes Nov 18, 2019

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keewis reviewed Nov 19, 2019

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doc/whats-new.rst Outdated Show resolved Hide resolved

Update doc/whats-new.rst

fd2352d

Co-Authored-By: keewis <keewis@users.noreply.github.com>

dcherian added 3 commits December 4, 2019 08:49

fix whats-new

9c26f43

Merge branch 'coarsen-reduce' of github.com:dcherian/xarray into coar…

6f05c6e

…sen-reduce * 'coarsen-reduce' of github.com:dcherian/xarray: Update doc/whats-new.rst

dcherian merged commit 308bb37 into pydata:master Dec 4, 2019

dcherian deleted the coarsen-reduce branch December 4, 2019 16:11

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make coarsen reductions consistent with reductions on other classes#3500

make coarsen reductions consistent with reductions on other classes#3500
dcherian merged 14 commits intopydata:masterfrom
dcherian:coarsen-reduce

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