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  • xarray · 39 ✖
id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
2239835092 PR_kwDOAMm_X85seXWW 8932 FIX: use str dtype without size information kmuehlbauer 5821660 closed 0     11 2024-04-12T10:59:45Z 2024-04-15T19:43:22Z 2024-04-13T12:25:48Z MEMBER   0 pydata/xarray/pulls/8932

Aims to resolve parts of #8844.

python xarray/tests/test_accessor_str.py::test_case_str: AssertionError: assert dtype('<U26') == dtype('<U30') I'm not sure this is the right location for the fix, at least it fixes those errors. AFAICT this is some issue somewhere inside apply_ufunc where the string dtype size is kept. So this fix removes the size information from the dtype (actually recreating it).

  • [ ] Closes #xxxx
  • [ ] Tests added
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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2205598061 PR_kwDOAMm_X85qplfG 8874 warn and return bytes undecoded in case of UnicodeDecodeError in h5netcdf-backend kmuehlbauer 5821660 closed 0     0 2024-03-25T12:06:07Z 2024-03-26T15:08:40Z 2024-03-26T15:08:40Z MEMBER   0 pydata/xarray/pulls/8874
  • [x] Closes #5563
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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2202068638 PR_kwDOAMm_X85qdzHk 8865 numpy 2.0 copy-keyword and trapz vs trapezoid kmuehlbauer 5821660 closed 0     2 2024-03-22T09:29:27Z 2024-03-22T15:30:11Z 2024-03-22T15:30:11Z MEMBER   0 pydata/xarray/pulls/8865

This fixes two issues with numpy 2.0 (see #8844)

  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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2194276625 PR_kwDOAMm_X85qDXOy 8851 FIX: adapt handling of copy keyword argument in scipy backend for numpy >= 2.0dev kmuehlbauer 5821660 closed 0     0 2024-03-19T07:56:12Z 2024-03-20T14:54:47Z 2024-03-20T14:47:45Z MEMBER   0 pydata/xarray/pulls/8851
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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2194414193 PR_kwDOAMm_X85qD0hP 8852 FIX: do not cast _FillValue/missing_value in CFMaskCoder if _Unsigned is provided kmuehlbauer 5821660 closed 0     0 2024-03-19T09:10:11Z 2024-03-19T14:35:26Z 2024-03-19T14:25:37Z MEMBER   0 pydata/xarray/pulls/8852
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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2120261196 PR_kwDOAMm_X85mHZDI 8713 correctly encode/decode _FillValues/missing_values/dtypes for packed data kmuehlbauer 5821660 closed 0     10 2024-02-06T08:51:47Z 2024-03-15T16:31:05Z 2024-03-15T16:31:04Z MEMBER   0 pydata/xarray/pulls/8713
  • [x] Closes #7691
  • [x] Closes #5597
  • [x] Closes #2304
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

This resurrects some of #7654. It takes special care of correctly handling dtypes when encoding/decoding packed data

 
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2066854721 PR_kwDOAMm_X85jSUBD 8591 Remove xfails related to SerializeableLock kmuehlbauer 5821660 closed 0     1 2024-01-05T07:18:47Z 2024-01-05T16:12:52Z 2024-01-05T16:12:52Z MEMBER   0 pydata/xarray/pulls/8591

That's a follow-up to #8571.

 
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2053560589 PR_kwDOAMm_X85iodqD 8571 ENH: vendor SerializableLock from dask and use as default backend lock, adapt tests kmuehlbauer 5821660 closed 0     4 2023-12-22T08:22:40Z 2024-01-04T06:41:39Z 2024-01-04T06:41:36Z MEMBER   0 pydata/xarray/pulls/8571
  • [x] Closes #8442
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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2043626960 PR_kwDOAMm_X85iGwKH 8552 FIX: reverse index output of bottleneck move_argmax/move_argmin functions kmuehlbauer 5821660 closed 0     0 2023-12-15T12:16:28Z 2023-12-21T06:15:08Z 2023-12-21T02:08:00Z MEMBER   0 pydata/xarray/pulls/8552
  • reverse index output of bottleneck move_argmax/move_argmin functions
  • add move_argmax/move_argmin to bottleneck tests
  • [x] Closes #8541
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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1676309093 PR_kwDOAMm_X85Ovv30 7771 implement scale_factor/add_offset CF conformance test, add and align tests kmuehlbauer 5821660 closed 0     3 2023-04-20T09:03:06Z 2023-11-17T20:59:38Z 2023-11-17T20:59:38Z MEMBER   1 pydata/xarray/pulls/7771
  • [ ] Closes #xxxx
  • [x] Tests added
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst

This is adding conformance tests for scale_factor/add_offset/dtype when encoding/decoding cf packed data with https://github.com/pydata/xarray/blob/c75ac8b7ab33be95f74d9e6f10b8173c68828751/xarray/coding/variables.py#L217. This doesn't include tests for _FillValue/missing_value/valid_range etc. which need a separate test.

The idea behind is two-fold:

  • be strict when encoding to only write CF conforming data, raise Errors if non-conforming
  • be liberal when decoding, but issue warnings

This is another step to move forward to finally fix issues like #2304 and a bunch more.

 
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1633623916 PR_kwDOAMm_X85Mh9TO 7654 cf-coding kmuehlbauer 5821660 closed 0     22 2023-03-21T10:34:44Z 2023-11-17T20:57:44Z 2023-11-17T20:57:44Z MEMBER   1 pydata/xarray/pulls/7654
  • [x] xref #7652
  • [x] Tests added
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
  • includes
    • implement coders
    • preserve boolean-dtype within encoding, adapt test
    • determine cf packed data type
    • ~transform numpy object-dtype strings (vlen) to numpy unicode strings~

This should also fix:

 
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1722614601 PR_kwDOAMm_X85RLNla 7869 preserve vlen string dtypes, allow vlen string fill_values kmuehlbauer 5821660 closed 0     7 2023-05-23T18:53:58Z 2023-11-17T15:26:00Z 2023-11-17T15:26:00Z MEMBER   0 pydata/xarray/pulls/7869
  • [x] Closes (partly) #1647
  • [x] Closes #7652
  • [x] Closes #7868
  • [x] Tests adapted
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1929620947 PR_kwDOAMm_X85cFMJJ 8277 fix regression in time-like check when decoding masked data kmuehlbauer 5821660 closed 0     10 2023-10-06T07:46:03Z 2023-10-18T16:50:19Z 2023-10-18T16:50:19Z MEMBER   0 pydata/xarray/pulls/8277
  • [x] Closes #8269
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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1913089793 PR_kwDOAMm_X85bNXAT 8232 [skip-ci] dev whats-new kmuehlbauer 5821660 closed 0     3 2023-09-26T09:27:58Z 2023-09-26T15:34:12Z 2023-09-26T15:24:50Z MEMBER   0 pydata/xarray/pulls/8232   
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1910369528 PR_kwDOAMm_X85bEI-s 8229 Release 2023.09.0 kmuehlbauer 5821660 closed 0     3 2023-09-24T20:30:43Z 2023-09-26T08:13:02Z 2023-09-26T08:12:45Z MEMBER   0 pydata/xarray/pulls/8229

As requested in #8223 I'm preparing for Xarray release 2023.09.0.

ToDo:

  • [x] Add final date
  • [x] Approve headline and other changes in whats-new.rst
  • [x] add plan-to-merge PR
  • [x] Closes #8223
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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1899505570 PR_kwDOAMm_X85afxBh 8195 decode variable with mismatched coordinate attribute kmuehlbauer 5821660 closed 0     8 2023-09-16T17:11:14Z 2023-09-25T11:30:37Z 2023-09-25T11:30:34Z MEMBER   0 pydata/xarray/pulls/8195
  • decode variable with mismatched coordinate attribute
  • propagate coordinates to encoding in any case
  • [x] Closes #1809
  • [x] Closes #5170
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1898420996 PR_kwDOAMm_X85acMrs 8189 test_interpolate_pd_compat with range of fill_value's kmuehlbauer 5821660 closed 0     1 2023-09-15T13:18:11Z 2023-09-24T15:28:34Z 2023-09-24T15:28:31Z MEMBER   0 pydata/xarray/pulls/8189

Update: The enhanced test works well in Upstream-dev tests, Pandas 2.1.1 is available for safe merge.

  • [x] Closes #8146
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1900923297 PR_kwDOAMm_X85akZg0 8201 override `units` for datetime64/timedelta64 variables to preserve integer dtype kmuehlbauer 5821660 closed 0     17 2023-09-18T13:17:19Z 2023-09-24T15:27:13Z 2023-09-24T15:05:26Z MEMBER   0 pydata/xarray/pulls/8201
  • [x] Closes #1064
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1899413232 PR_kwDOAMm_X85affPA 8194 remove invalid statement from doc/user-guide/io.rst kmuehlbauer 5821660 closed 0     0 2023-09-16T12:01:42Z 2023-09-19T01:02:23Z 2023-09-19T01:02:23Z MEMBER   0 pydata/xarray/pulls/8194
  • [x] Closes #6570 
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1700227455 PR_kwDOAMm_X85P_7oN 7827 Preserve nanosecond resolution when encoding/decoding times kmuehlbauer 5821660 closed 0     17 2023-05-08T13:08:34Z 2023-09-17T16:35:29Z 2023-09-17T08:15:26Z MEMBER   0 pydata/xarray/pulls/7827
  • [x] Closes #7817,
  • [x] closes #7942,
  • [x] closes #7790,
  • [x] closes #6191
  • [x] closes #7096
  • [x] closes #1064
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst

Closes #7098 as not needed, but worked around to preserve the fast int-based timedelta calculation.

 
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1897760813 PR_kwDOAMm_X85aZ9iD 8187 FIX: use "krogh" as interpolator method-string instead of "krog" kmuehlbauer 5821660 closed 0     0 2023-09-15T06:00:37Z 2023-09-16T15:55:37Z 2023-09-16T15:55:37Z MEMBER   0 pydata/xarray/pulls/8187

While working on #8146 this came up. Aligning with upstream naming convention.

  • [ ] Closes #xxxx
  • [ ] Tests added
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1856627163 PR_kwDOAMm_X85YPpRy 8084 FIX: handle NaT values in dt-accessor kmuehlbauer 5821660 closed 0     10 2023-08-18T12:17:58Z 2023-09-14T13:57:40Z 2023-09-14T13:57:37Z MEMBER   0 pydata/xarray/pulls/8084
  • [x] Closes #7928
  • [ ] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
 
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1782037699 PR_kwDOAMm_X85UTjwg 7953 ensure no forward slashes in names for HDF5-based backends kmuehlbauer 5821660 closed 0     0 2023-06-30T07:26:17Z 2023-07-06T15:11:50Z 2023-07-06T15:11:50Z MEMBER   0 pydata/xarray/pulls/7953
  • [x] Closes #7943
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1039274574 PR_kwDOAMm_X84t1e28 5915 Add wradlib to ecosystem in docs kmuehlbauer 5821660 closed 0     3 2021-10-29T07:54:21Z 2023-05-25T07:24:07Z 2021-10-29T11:29:18Z MEMBER   0 pydata/xarray/pulls/5915
  • [ ] Closes #xxxx
  • [ ] Tests added
  • [ ] Passes pre-commit run --all-files
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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741341141 MDExOlB1bGxSZXF1ZXN0NTE5NjcyMTI5 4576 Fix: make copy of dask_gufunc_kwargs before changing content kmuehlbauer 5821660 closed 0     1 2020-11-12T07:07:06Z 2023-05-25T07:22:42Z 2020-11-12T18:30:43Z MEMBER   0 pydata/xarray/pulls/4576
  • [x] Fixes downstream https://github.com/pangeo-data/xESMF/issues/36
  • [x] Tests added
  • [x] Passes isort . && black . && mypy . && flake8
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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591101988 MDExOlB1bGxSZXF1ZXN0Mzk2MzI5Mzkx 3922 FIX: correct dask array handling in _calc_idxminmax kmuehlbauer 5821660 closed 0     35 2020-03-31T13:18:35Z 2023-05-25T07:22:40Z 2020-05-13T15:51:44Z MEMBER   0 pydata/xarray/pulls/3922

Fixes dask handling for implementation in #3871.

  • [ ] Closes #xxxx
  • [x] Tests added
  • [x] Passes isort -rc . && black . && mypy . && flake8
  • [x] Fully documented, including whats-new.rst for all changes and api.rst for new API
 
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1508009922 PR_kwDOAMm_X85GDGpY 7400 Fill missing data_vars during concat by reindexing kmuehlbauer 5821660 closed 0     22 2022-12-22T14:41:56Z 2023-05-25T07:21:20Z 2023-01-20T16:04:26Z MEMBER   0 pydata/xarray/pulls/7400
  • [x] Closes #508,
  • [x] Closes #3545
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst

This is another attempt to solve #508. Took inspiration from #3545 by @scottcha.

This follows along @dcherian's comment in the same above PR (https://github.com/pydata/xarray/pull/3545#issuecomment-586346637).

Update:

After review the variable order is estimated by order of appearance in the list of datasets. That keeps full backwards compatibility and is deterministic. Thanks @dcherian and @keewis for the suggestions.

 
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1655000231 PR_kwDOAMm_X85NpOIk 7720 preserve boolean dtype in encoding kmuehlbauer 5821660 closed 0     2 2023-04-05T06:11:40Z 2023-05-25T07:20:57Z 2023-04-10T09:26:26Z MEMBER   0 pydata/xarray/pulls/7720
  • [x] Closes #4826
  • [x] Tests added
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

Split out of #7654. Follow up to #7719. Needs rebase after #7719 is merged.

 
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812655506 MDExOlB1bGxSZXF1ZXN0NTc2OTY5NTU1 4933 FIX: decode/encode `time_reference` kmuehlbauer 5821660 closed 0     3 2021-02-20T16:28:38Z 2023-05-25T07:19:49Z 2021-02-21T08:31:22Z MEMBER   0 pydata/xarray/pulls/4933

This is a fix for #4927.

  • time_reference is overwritten with the actual time string inside time_reference before decoding, but only if a variable with the name exists.
  • time_reference name is kept in encoding (the name might change, eg. reference_time).
  • time_reference is added back to units attribute when encoding, to make roundtrips possible.
  • [x] Closes #4927
  • [x] Tests added
  • [ ] Passes pre-commit run --all-files
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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806334969 MDExOlB1bGxSZXF1ZXN0NTcxNzc0MTk3 4893 FIX: h5py>=3 string decoding kmuehlbauer 5821660 closed 0     8 2021-02-11T12:13:46Z 2023-05-25T07:12:39Z 2021-02-17T08:41:20Z MEMBER   0 pydata/xarray/pulls/4893
  • set decode_vlen_strings=True for h5netcdf backend
  • unpin h5py

This is an attempt to align with h5py=>3.0.0 string decoding changes. Now all strings are read as bytes objects for variable-length strings, or numpy bytes arrays ('S' dtypes) for fixed-length strings [1]. From h5netcdf=0.10.0 kwarg decode_vlen_strings is available. This PR makes use of this to keep backwards compatibility with h5py=2 and conformance with netcdf4-python.

[1] https://docs.h5py.org/en/stable/strings.html

  • [x] Closes #4570
  • [ ] Tests added
  • [ ] Passes pre-commit run --all-files
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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618081836 MDExOlB1bGxSZXF1ZXN0NDE3ODc1NDEx 4060 ENH: use `dask.array.apply_gufunc` in `xr.apply_ufunc` kmuehlbauer 5821660 closed 0     63 2020-05-14T09:38:15Z 2023-05-25T07:12:03Z 2020-08-19T06:57:56Z MEMBER   0 pydata/xarray/pulls/4060

use dask.array.apply_gufunc in xr.apply_ufunc for multiple outputs when dask='parallelized', add/fix tests

  • [x] Closes #1815, closes #4015
  • [x] Tests added
  • [x] Passes isort -rc . && black . && mypy . && flake8
  • [x] Fully documented, including whats-new.rst for all changes and api.rst for new API

Remaining Issues:

  • [ ] fitting name for current dask_gufunc_kwargs
  • [ ] rephrase dask docs to fit new behaviour
  • [ ] combine output_core_dims and output_sizes, eg. xr.apply_ufunc(..., output_core_dims=[{"abc": 2]])
 
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688684690 MDExOlB1bGxSZXF1ZXN0NDc1ODg2MTQ0 4391 move kwarg's `output_sizes` and `meta` to `dask_gufunc_kwargs` for in… kmuehlbauer 5821660 closed 0     2 2020-08-30T09:20:05Z 2023-05-25T07:08:13Z 2020-08-30T16:37:52Z MEMBER   0 pydata/xarray/pulls/4391

…ternal use of apply_ufunc (follow-up to #4060, fixes #4385)

  • [x] Closes #4385
  • [ ] Tests added
  • [x] Passes isort . && black . && mypy . && flake8
  • [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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688993462 MDExOlB1bGxSZXF1ZXN0NDc2MTI0OTk4 4392 FIX: handle dask ValueErrors in `apply_ufunc` (set ``allow_rechunk=True``) kmuehlbauer 5821660 closed 0     3 2020-08-31T07:40:51Z 2023-05-25T07:07:13Z 2020-09-09T19:00:17Z MEMBER   0 pydata/xarray/pulls/4392

follow-up on #4060

  • [x] Closes #4372
  • [x] Tests added
  • [x] Passes isort . && black . && mypy . && flake8
 
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560219049 MDExOlB1bGxSZXF1ZXN0MzcxMjQ2ODEz 3753 Add new h5netcdf backend phony_dims kwarg kmuehlbauer 5821660 closed 0     4 2020-02-05T08:40:06Z 2023-05-25T07:05:23Z 2020-02-23T19:41:14Z MEMBER   0 pydata/xarray/pulls/3753

This adds support for the new phony_dims keyword for the h5netcdf backend which is available from h5netcdf version 0.8.0.

  • [ ] Closes #xxxx
  • [ ] Tests added
  • [x] Passes isort -rc . && black . && mypy . && flake8
  • [x] Fully documented, including whats-new.rst for all changes and api.rst for new API
 
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1654988876 PR_kwDOAMm_X85NpL0W 7719 Implement more Variable Coders kmuehlbauer 5821660 closed 0     3 2023-04-05T06:01:09Z 2023-04-07T06:27:34Z 2023-04-07T03:57:50Z MEMBER   0 pydata/xarray/pulls/7719
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

This PR implements remaining functionality in encode_cf_variable/decode_cf_variable as VariableCoders (as left as todo by @shoyer). It adapts the needed tests and adds some typing (thanks @Illviljan). Otherwise there are no changes in function to code.

It splits out of #7654 which turns out to be hard to follow (at least for me).

 
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700839138 MDExOlB1bGxSZXF1ZXN0NDg2Mzk2NjMz 4419 preserve original dimension, coordinate and variable order in ``concat`` kmuehlbauer 5821660 closed 0     3 2020-09-14T07:13:33Z 2022-10-09T13:05:14Z 2020-09-19T03:01:28Z MEMBER   0 pydata/xarray/pulls/4419

The problem is that the result_vars-dict is filled in two separate loops, handling variables and coordinates (AFAICT). This can change the ordering of dimensions and coordinates depending over which dimensions is concatenated.

This fix hooks into the second loop and reinsert the variable in question at the appropriate position by popping it out of the result_vars. There might be a more elegant solution to this.

  • [x] Closes #2811, closes #4072
  • [x] Tests added
  • [x] Passes isort . && black . && mypy . && flake8
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1048309254 PR_kwDOAMm_X84uRTWS 5959 Fix module name retrieval in `backend.plugins.remove_duplicates()`, plugin tests kmuehlbauer 5821660 closed 0     12 2021-11-09T08:14:24Z 2022-02-16T21:31:14Z 2021-11-15T17:33:43Z MEMBER   0 pydata/xarray/pulls/5959
  • fix regression in backend.plugins.remove_duplicates()
  • switch pkg_resources -> importlib in tests/test_plugins.py
  • [x] Closes #5944
  • [x] Tests fixed (switch pkg_resources -> importlib)
  • [ ] Tests added
  • [x] Passes pre-commit run --all-files
  • [x] User visible changes (including notable bug fixes) are documented in whats-new.rst
  • [ ] New functions/methods are listed in api.rst
 
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1116080396 PR_kwDOAMm_X84xqznc 6200 MNT: prepare h5netcdf backend for (coming) change in dimension handling kmuehlbauer 5821660 closed 0     10 2022-01-27T11:11:57Z 2022-01-29T13:20:01Z 2022-01-29T07:55:01Z MEMBER   0 pydata/xarray/pulls/6200
  • [x] Closes #6197
 
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537576675 MDExOlB1bGxSZXF1ZXN0MzUyOTA2NjA4 3618 ENH: enable `H5NetCDFStore` to work with already open h5netcdf.File a… kmuehlbauer 5821660 closed 0     8 2019-12-13T14:23:10Z 2020-01-23T07:40:19Z 2020-01-20T05:46:14Z MEMBER   0 pydata/xarray/pulls/3618

enable H5NetCDFStore to work with open h5netcdf.File and h5netcdf.Group objects, add test

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