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Raise error when assigning to IndexVariable.values & IndexVariable.data #3862

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merged 10 commits into from
Mar 23, 2020
Merged

Raise error when assigning to IndexVariable.values & IndexVariable.data #3862

merged 10 commits into from
Mar 23, 2020

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dcherian
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@dcherian dcherian requested a review from shoyer March 17, 2020 02:26
@max-sixty
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Great, good spot @dcherian

@dcherian dcherian mentioned this pull request Mar 19, 2020
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@max-sixty
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OK to merge @dcherian ? We can almost release 0.15.1 then

@dcherian
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I think @shoyer should confirm that this is what we want to do

dcherian
dcherian commented Mar 21, 2020
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doc/whats-new.rst Outdated Show resolved Hide resolved
@keewis
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keewis commented Mar 22, 2020

this causes the docs to fail:

xarray/doc/plotting.rst

Line 660 in 0722b42

ds.w.values = [1, 2, 3, 5]

shoyer
shoyer approved these changes Mar 22, 2020
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Looks good to me, thanks!

dcherian added 3 commits March 22, 2020 16:15
@dcherian
fix docs
104620a
@dcherian
update whats-new
705c7eb
@dcherian
Merge remote-tracking branch 'upstream/master' into indexvariable-values
8f464c4 
* upstream/master:
  add spacing in the versions section of the issue report (pydata#3876)
  map_blocks: allow user function to add new unindexed dimension. (pydata#3817)
  Delete associated indexes when deleting coordinate variables. (pydata#3840)
  remove macos build while waiting for libwebp fix (pydata#3875)
  Fix html repr on non-str keys (pydata#3870)
  Allow ellipsis to be used in stack (pydata#3826)
  Improve where docstring (pydata#3836)
  Add DataArray.pad, Dataset.pad, Variable.pad (pydata#3596)
  Fix some warnings (pydata#3864)
  Feature/weighted (pydata#2922)
  Fix recombination in groupby when changing size along the grouped dimension (pydata#3807)
  Blacken the doctest code in docstrings (pydata#3857)
  Fix multi-index with categorical values. (pydata#3860)
  Fix interp bug when indexer shares coordinates with array (pydata#3758)
  Fix alignment with join="override" when some dims are unindexed (pydata#3839)
@dcherian
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I think the failed tests are unrelated since they only fail on the upstream-dev

FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[365_day]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[360_day]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[julian]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[all_leap]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[366_day]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[gregorian]
FAILED xarray/tests/test_cftimeindex.py::test_indexing_in_series_getitem[proleptic_gregorian]

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I think now that you merged #3874, if you re-merge master they should pass.

@dcherian
Merge remote-tracking branch 'upstream/master' into indexvariable-values
20269ae 
* upstream/master:
  Re-enable tests xfailed in pydata#3808 and fix new CFTimeIndex failures due to upstream changes (pydata#3874)
@dcherian
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Great. Thanks all.

Now to find out how many downstream projects test against master on CI :)

@dcherian dcherian merged commit 9eec56c into pydata:master Mar 23, 2020
@dcherian dcherian deleted the indexvariable-values branch March 23, 2020 13:42
dcherian added a commit to dcherian/xarray that referenced this pull request Mar 28, 2020
@dcherian
Merge remote-tracking branch 'upstream/master' into map-blocks-schema
4a355e6 
* upstream/master: (54 commits)
  Limit repr of arrays containing long strings (pydata#3900)
  expose a few zarr backend functions as semi-public api (pydata#3897)
  Use drawstyle instead of linestyle in plot.step. (pydata#3274)
  Implementation of polyfit and polyval (pydata#3733)
  misplaced quote in whatsnew (pydata#3889)
  Rename ordered_dict_intersection -> compat_dict_intersection (pydata#3887)
  Control attrs of result in `merge()`, `concat()`, `combine_by_coords()` and `combine_nested()` (pydata#3877)
  xfail test_uamiv_format_write (pydata#3885)
  Use `fixes` in PR template (pydata#3886)
  Tweaks to "how_to_release" (pydata#3882)
  whatsnew section for 0.16.0
  Release v0.15.1
  whatsnew for 0.15.1 (pydata#3879)
  update panel documentation (pydata#3880)
  reword the whats-new entry for unit support (pydata#3878)
  Raise error when assigning to IndexVariable.values & IndexVariable.data (pydata#3862)
  Re-enable tests xfailed in pydata#3808 and fix new CFTimeIndex failures due to upstream changes (pydata#3874)
  add spacing in the versions section of the issue report (pydata#3876)
  map_blocks: allow user function to add new unindexed dimension. (pydata#3817)
  Delete associated indexes when deleting coordinate variables. (pydata#3840)
  ...
@rsokl
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rsokl commented Apr 10, 2020

@dcherian @max-sixty is there a reason why this change wasn't incorporated into values.setter? This change blocks the ability to update coordinate values in-place. This breaks code in a more fundamental way than just requiring users to rely on assign_coords - it can necessitate a substantial change in code design for people who were relying on the ability to mutate coordinates. This also leads me to ask: was it really appropriate to call such a substantial breaking change only a patch?

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shoyer commented Apr 10, 2020

is there a reason why this change wasn't incorporated into values.setter?

I'm not quite sure what you mean here. That's exactly what this change does, making assignment to IndexVariable.values an error.

If you were mutating .values on an indexed variable, then you already had a likely bug, because only part of xarray's data structures were being updated (the Variable, but not indexes). That's why we put this in as a bug fix -- see the linked issue #3470 for examples.

Unfortunately we couldn't figure out another way to make this work -- see #3470 (comment) for discussion. We're definitely open to alternatives if you can come up with them, though!

@rsokl
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rsokl commented Apr 10, 2020

That's exactly what this change does, making assignment to IndexVariable.values an error.

Sorry, I got a bit criss-crossed between this PR and the thread in #3470.

In light of #3470 (comment) it seems like the next best thing would be to given assign_coords the optional ability to update the DataArray/DataSet in-place. Thoughts?

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shoyer commented Apr 10, 2020 •
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In light of #3470 (comment) it seems like the next best thing would be to given assign_coords the optional ability to update the DataArray/DataSet in-place. Thoughts?

There's no need to use assign_coords. You can also just use normal assignment to a DataArray/Dataset or coords, e.g,

ds['time'] = new_values  # good
ds.coords['time'] = new_values  # good
ds.coords['time'].values = new_values  # broken, disabled by this PR
ds.coords['time'].values[:] = new_values  # also buggy (but harder to disable)

This would probably be worth clarifying in the error message.

(Under the hood, assign_coords basically does the exactly same thing as assignment to coords, it just copies the Dataset/DataArray` first)

@rsokl
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rsokl commented Apr 10, 2020

Ah! Nice! Yeah the error message led me to believe that there was no path for in-place updates.

douglatornell added a commit to SalishSeaCast/SalishSeaNowcast that referenced this pull request Jul 9, 2020
@douglatornell
Fix UTC offset calc VFPA 2nd Narrow HADCP dataset
3286cd5 
This addresses a breaking change in xarray=0.15.1
(see pydata/xarray#3862).
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warn when updating coord.values : indexes are not updated
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@dcherian @max-sixty @keewis @spencerkclark @rsokl @shoyer