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- stanwest · 10 ✖
id | html_url | issue_url | node_id | user | created_at | updated_at ▲ | author_association | body | reactions | performed_via_github_app | issue |
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1094118500 | https://github.com/pydata/xarray/pull/6402#issuecomment-1094118500 | https://api.github.com/repos/pydata/xarray/issues/6402 | IC_kwDOAMm_X85BNuxk | stanwest 38358698 | 2022-04-09T20:19:02Z | 2022-04-09T20:19:02Z | CONTRIBUTOR |
That looks great to me. |
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No chunk warning if empty 1177669703 | |
1093300764 | https://github.com/pydata/xarray/pull/6402#issuecomment-1093300764 | https://api.github.com/repos/pydata/xarray/issues/6402 | IC_kwDOAMm_X85BKnIc | stanwest 38358698 | 2022-04-08T19:51:24Z | 2022-04-08T19:51:24Z | CONTRIBUTOR |
Sure. I recommend the following before the ```python Warn where requested chunks break preferred chunks, provided that the variablecontains data.if var.size: for dim, size, chunk_sizes in zip(dims, shape, chunk_shape): try: preferred_chunk_sizes = preferred_chunks[dim] except KeyError: continue # Determine the stop indices of the preferred chunks, but omit the last stop # (equal to the dim size). In particular, assume that when a sequence # expresses the preferred chunks, the sequence sums to the size. preferred_stops = ( range(preferred_chunk_sizes, size, preferred_chunk_sizes) if isinstance(preferred_chunk_sizes, Number) else itertools.accumulate(preferred_chunk_sizes[:-1]) ) # Gather any stop indices of the specified chunks that are not a stop index # of a preferred chunk. Again, omit the last stop, assuming that it equals # the dim size. breaks = set(itertools.accumulate(chunk_sizes[:-1])).difference( preferred_stops ) if breaks: warnings.warn( "The specified Dask chunks separate the stored chunks along " f'dimension "{dim}" starting at index {min(breaks)}. This could ' "degrade performance. Instead, consider rechunking after loading." ) ``` |
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No chunk warning if empty 1177669703 | |
1093061133 | https://github.com/pydata/xarray/pull/6334#issuecomment-1093061133 | https://api.github.com/repos/pydata/xarray/issues/6334 | IC_kwDOAMm_X85BJsoN | stanwest 38358698 | 2022-04-08T16:23:01Z | 2022-04-08T16:23:01Z | CONTRIBUTOR | For my understanding and curiosity, what are the perceived benefits of a separate function to warn about splitting the preferred chunks? It seemed better to me to avoid the overhead of the function call and the unnecessary internal interface, particularly considering that the function was private, had only one caller, and was so closely related to its caller. |
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In backends, support expressing a dimension's preferred chunk sizes as a tuple of integers 1160073438 | |
1091797026 | https://github.com/pydata/xarray/pull/6334#issuecomment-1091797026 | https://api.github.com/repos/pydata/xarray/issues/6334 | IC_kwDOAMm_X85BE4Ai | stanwest 38358698 | 2022-04-07T14:15:13Z | 2022-04-07T14:15:13Z | CONTRIBUTOR |
Thanks for the review and approval. Is this PR ready to trade the "needs review" label for the "plan to merge" label? |
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In backends, support expressing a dimension's preferred chunk sizes as a tuple of integers 1160073438 | |
1054400787 | https://github.com/pydata/xarray/pull/6305#issuecomment-1054400787 | https://api.github.com/repos/pydata/xarray/issues/6305 | IC_kwDOAMm_X84-2OET | stanwest 38358698 | 2022-02-28T15:56:34Z | 2022-02-28T15:56:34Z | CONTRIBUTOR | Thanks for accepting the fix! |
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On Windows, enable successful test of opening a dataset containing a cftime index 1150484906 | |
1050997589 | https://github.com/pydata/xarray/pull/6305#issuecomment-1050997589 | https://api.github.com/repos/pydata/xarray/issues/6305 | IC_kwDOAMm_X84-pPNV | stanwest 38358698 | 2022-02-25T16:22:13Z | 2022-02-25T16:22:13Z | CONTRIBUTOR | For the sake of cross-references, #6249 originated the test modified here. |
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On Windows, enable successful test of opening a dataset containing a cftime index 1150484906 | |
1035162721 | https://github.com/pydata/xarray/pull/6237#issuecomment-1035162721 | https://api.github.com/repos/pydata/xarray/issues/6237 | IC_kwDOAMm_X849s1Rh | stanwest 38358698 | 2022-02-10T16:56:22Z | 2022-02-10T16:56:22Z | CONTRIBUTOR | Okay. I've committed the changes. |
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Enable running sphinx-build on Windows 1124431593 | |
1034136761 | https://github.com/pydata/xarray/pull/6237#issuecomment-1034136761 | https://api.github.com/repos/pydata/xarray/issues/6237 | IC_kwDOAMm_X849o6y5 | stanwest 38358698 | 2022-02-09T19:53:45Z | 2022-02-09T19:53:45Z | CONTRIBUTOR |
👍
It seems that we can, although closing all of the references was non-trivial in "user-guide/io.rst". Please see the diffs below for the two files with the most extensive changes. Within each document, I've tried to delete the files as early as possible to keep that code close to the last use of the file. "user-guide/dask.rst"```diff @@ -55,6 +55,8 @@ argument to :py:func:`~xarray.open_dataset` or using the .. ipython:: python :suppress: + import os + import numpy as np import pandas as pd import xarray as xr @@ -129,6 +131,11 @@ will return a ``dask.delayed`` object that can be computed later. with ProgressBar(): results = delayed_obj.compute() +.. ipython:: python + :suppress: + + os.remove("manipulated-example-data.nc") # Was not opened. + .. note:: When using Dask's distributed scheduler to write NETCDF4 files, @@ -147,14 +154,6 @@ A dataset can also be converted to a Dask DataFrame using :py:meth:`~xarray.Data Dask DataFrames do not support multi-indexes so the coordinate variables from the dataset are included as columns in the Dask DataFrame. -.. ipython:: python - :okexcept: - :suppress: - - import os - - os.remove("example-data.nc") - os.remove("manipulated-example-data.nc") Using Dask with xarray ---------------------- @@ -211,7 +210,7 @@ Dask arrays using the :py:meth:`~xarray.Dataset.persist` method: .. ipython:: python - ds = ds.persist() + persisted = ds.persist() :py:meth:`~xarray.Dataset.persist` is particularly useful when using a distributed cluster because the data will be loaded into distributed memory @@ -233,11 +232,6 @@ chunk size depends both on your data and on the operations you want to perform. With xarray, both converting data to a Dask arrays and converting the chunk sizes of Dask arrays is done with the :py:meth:`~xarray.Dataset.chunk` method: -.. ipython:: python - :suppress: - - ds = ds.chunk({"time": 10}) - .. ipython:: python rechunked = ds.chunk({"latitude": 100, "longitude": 100}) @@ -509,6 +503,11 @@ Notice that the 0-shaped sizes were not printed to screen. Since ``template`` ha expected = ds + 10 + 10 mapped.identical(expected) +.. ipython:: python + :suppress: + + ds.close() # Closes "example-data.nc". + os.remove("example-data.nc") .. tip:: ``` Above, I've removed the line `ds = ds.chunk({"time": 10})`, because the call to open the dataset already specified that chunking."user-guide/io.rst"```diff @@ -11,6 +11,8 @@ format (recommended). .. ipython:: python :suppress: + import os + import numpy as np import pandas as pd import xarray as xr @@ -84,6 +86,13 @@ We can load netCDF files to create a new Dataset using ds_disk = xr.open_dataset("saved_on_disk.nc") ds_disk +.. ipython:: python + :suppress: + + # Close "saved_on_disk.nc", but retain the file until after closing or deleting other + # datasets that will refer to it. + ds_disk.close() + Similarly, a DataArray can be saved to disk using the :py:meth:`DataArray.to_netcdf` method, and loaded from disk using the :py:func:`open_dataarray` function. As netCDF files @@ -204,11 +213,6 @@ You can view this encoding information (among others) in the Note that all operations that manipulate variables other than indexing will remove encoding information. -.. ipython:: python - :suppress: - - ds_disk.close() - .. _combining multiple files: @@ -484,14 +488,13 @@ and currently raises a warning unless ``invalid_netcdf=True`` is set: da.to_netcdf("complex.nc", engine="h5netcdf", invalid_netcdf=True) # Reading it back - xr.open_dataarray("complex.nc", engine="h5netcdf") + reopened = xr.open_dataarray("complex.nc", engine="h5netcdf") + reopened .. ipython:: python - :okexcept: :suppress: - import os - + reopened.close() os.remove("complex.nc") .. warning:: @@ -724,17 +727,19 @@ To export just the dataset schema without the data itself, use the ds.to_dict(data=False) -This can be useful for generating indices of dataset contents to expose to -search indices or other automated data discovery tools. - .. ipython:: python - :okexcept: :suppress: - import os - + # We're now done with the dataset named `ds`. Although the `with` statement closed + # the dataset, displaying the unpickled pickle of `ds` re-opened "saved_on_disk.nc". + # However, `ds` (rather than the unpickled dataset) refers to the open file. Delete + # `ds` to close the file. + del ds os.remove("saved_on_disk.nc") +This can be useful for generating indices of dataset contents to expose to +search indices or other automated data discovery tools. + .. _io.rasterio: Rasterio ```We can also straightforwardly remove the "rasm.zarr" directory: "internals/zarr-encoding-spec.rst"```diff @@ -63,3 +63,9 @@ re-open it directly with Zarr: print(os.listdir("rasm.zarr")) print(zgroup.tree()) dict(zgroup["Tair"].attrs) + +.. ipython:: python + :suppress: + + import shutil + shutil.rmtree("rasm.zarr") ```Is that general approach agreeable? If so, I'll commit the changes for further comment and review. |
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Enable running sphinx-build on Windows 1124431593 | |
1030292653 | https://github.com/pydata/xarray/pull/6237#issuecomment-1030292653 | https://api.github.com/repos/pydata/xarray/issues/6237 | IC_kwDOAMm_X849aQSt | stanwest 38358698 | 2022-02-04T19:38:02Z | 2022-02-04T19:38:02Z | CONTRIBUTOR | Following #3270, on which this PR builds, I added a "whats-new" entry in the "Documentation" section. It seems that readthedocs lacks support for the |
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Enable running sphinx-build on Windows 1124431593 | |
747621248 | https://github.com/pydata/xarray/issues/4702#issuecomment-747621248 | https://api.github.com/repos/pydata/xarray/issues/4702 | MDEyOklzc3VlQ29tbWVudDc0NzYyMTI0OA== | stanwest 38358698 | 2020-12-17T18:35:13Z | 2020-12-17T18:35:13Z | CONTRIBUTOR |
Yes. I didn't readily see that I needed to specify both
I agree that, if xarray is going to guess, handling non-dimension coordinates would be an improvement. It might be specified to work only with 1-D coordinates and to do nothing for multi-dimensional coordinates. Alternatively, is it at all preferable to remove the guessing feature? Although the behavior has been present for years, I found mention of it in the documentation only in "What's New." The motivating use case in #1290 could have been addressed instead simply with |
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Plotting in 2D with one non-dimension coordinate given behaves contrary to documentation and can cause cryptic ValueError 769348008 |
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