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issue 8

  • Added convenience method for saving DataArray to netCDF file 9
  • Added validation of attrs before saving to netCDF files 3
  • size and aspect arguments for plotting methods even without faceting 1
  • KeyError on saving to NetCDF - due to objects in attrs? 1
  • dtype changes after .load() 1
  • Hooks for custom attribute handling in xarray operations 1
  • Should the transform attribute be a six-element or nine-element tuple when reading from rasterio? 1
  • Remove redundant code from open_rasterio and ensure all transform tuples are six elements long 1

user 1

  • robintw · 18 ✖

author_association 1

  • CONTRIBUTOR · 18 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
411211864 https://github.com/pydata/xarray/pull/2351#issuecomment-411211864 https://api.github.com/repos/pydata/xarray/issues/2351 MDEyOklzc3VlQ29tbWVudDQxMTIxMTg2NA== robintw 296686 2018-08-07T21:40:34Z 2018-08-07T21:40:34Z CONTRIBUTOR

Strangely, the Travis-CI build seems to have failed with some errors unrelated to this PR. The two errors are on:

  • Python 3.6 with the development version of dask, giving an error of AttributeError: module 'dask.array' has no attribute 'ghost'
  • Python 2.7 with cdat, iris and pynio which gives various errors of arrays not being equal for test_to_and_from_cdms2_sgrid and test_to_and_from_cdms2_ugrid

For what it's worth, all of the tests related to this PR passed.

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  Remove redundant code from open_rasterio and ensure all transform tuples are six elements long 348462356
410864167 https://github.com/pydata/xarray/issues/2348#issuecomment-410864167 https://api.github.com/repos/pydata/xarray/issues/2348 MDEyOklzc3VlQ29tbWVudDQxMDg2NDE2Nw== robintw 296686 2018-08-06T21:50:47Z 2018-08-06T21:50:47Z CONTRIBUTOR

Ok great, I'll make a PR to remove that last chunk - thanks!

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  Should the transform attribute be a six-element or nine-element tuple when reading from rasterio? 348081353
244801125 https://github.com/pydata/xarray/pull/990#issuecomment-244801125 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0NDgwMTEyNQ== robintw 296686 2016-09-05T19:14:38Z 2016-09-05T19:14:38Z CONTRIBUTOR

I realised that the reason that Travis and AppVeyor weren't running properly was because there were conflicts between this PR and master. I think I've managed to rebase and push properly - but let me know if I've done anything wrong.

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  Added convenience method for saving DataArray to netCDF file 173632183
244539361 https://github.com/pydata/xarray/pull/990#issuecomment-244539361 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0NDUzOTM2MQ== robintw 296686 2016-09-03T10:36:03Z 2016-09-03T10:36:03Z CONTRIBUTOR

Ah ok - that works (not entirely sure why, but it works!)

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  Added convenience method for saving DataArray to netCDF file 173632183
244510329 https://github.com/pydata/xarray/pull/990#issuecomment-244510329 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0NDUxMDMyOQ== robintw 296686 2016-09-02T23:35:24Z 2016-09-02T23:35:24Z CONTRIBUTOR

Oops yes, sorry!

I'm having a bit of an issue with changing the strings to constants (which, by the way, I completely agree is how it should be done). I've defined the constants in backends/api.py and am then trying to import them in core/dataarray.py.

I am doing the import as:

from ..backends import DATAARRAY_NAME, DATAARRAY_VARIABLE

But this gives me the following error:

../../anaconda3/lib/python3.5/site-packages/py/_path/local.py:650: in pyimport __import__(modname) xarray/__init__.py:3: in <module> from .core.extensions import (register_dataarray_accessor, xarray/core/extensions.py:3: in <module> from .dataarray import DataArray xarray/core/dataarray.py:9: in <module> from ..backends import DATAARRAY_NAME, DATAARRAY_VARIABLE xarray/backends/__init__.py:8: in <module> from .netCDF4_ import NetCDF4DataStore xarray/backends/netCDF4_.py:6: in <module> from .. import Variable E ImportError: cannot import name 'Variable'

It seems like my relative import is somehow mucking up another relative import inside the netCDF4 stuff. Do you have any ideas how I can solve this? Am I just doing my imports wrong?

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  Added convenience method for saving DataArray to netCDF file 173632183
244395018 https://github.com/pydata/xarray/pull/990#issuecomment-244395018 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0NDM5NTAxOA== robintw 296686 2016-09-02T14:44:24Z 2016-09-02T14:44:24Z CONTRIBUTOR

Great, thanks. I think I've done these changes (frustratingly I can't see a way to use *args/*kwargs after using the full argument list in the function definition, so I've had to write it out. Let me know if there is a better way, but I suspect there isn't).

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  Added convenience method for saving DataArray to netCDF file 173632183
243952679 https://github.com/pydata/xarray/issues/988#issuecomment-243952679 https://api.github.com/repos/pydata/xarray/issues/988 MDEyOklzc3VlQ29tbWVudDI0Mzk1MjY3OQ== robintw 296686 2016-09-01T01:41:51Z 2016-09-01T01:41:51Z CONTRIBUTOR

I also prefer an approach that doesn't use context managers: I agree with @darothen's comments about the issues with their use.

Regardless of the exact implementation, I am strongly in favour of this functionality being added to xarray - I can already think of a number of very useful ways I could use it!

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  Hooks for custom attribute handling in xarray operations 173612265
243951504 https://github.com/pydata/xarray/pull/990#issuecomment-243951504 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0Mzk1MTUwNA== robintw 296686 2016-09-01T01:33:25Z 2016-09-01T01:33:25Z CONTRIBUTOR

Thanks - I've got that working with the close() method, and I did it 'properly' using the BaseDataObject class.

The only failure on here now is the same as #991 - a conda error creating one of the environments.

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  Added convenience method for saving DataArray to netCDF file 173632183
243946499 https://github.com/pydata/xarray/pull/991#issuecomment-243946499 https://api.github.com/repos/pydata/xarray/issues/991 MDEyOklzc3VlQ29tbWVudDI0Mzk0NjQ5OQ== robintw 296686 2016-09-01T00:58:54Z 2016-09-01T00:58:54Z CONTRIBUTOR

The Travis builds seem to have all passed except for py27-cdat+pynio which has failed with a conda error that seems to be unrelated to these changes (Error: HTTPError: 403 Client Error: Forbidden for url)

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  Added validation of attrs before saving to netCDF files 173640823
243946174 https://github.com/pydata/xarray/pull/990#issuecomment-243946174 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0Mzk0NjE3NA== robintw 296686 2016-09-01T00:56:50Z 2016-09-01T00:56:50Z CONTRIBUTOR

Also, it seems like there might be an issue with not closing the Dataset - but only on Windows (see the AppVeyor build failure at https://ci.appveyor.com/project/jhamman/xarray-injyf/build/1.0.268/job/kr8ss684ijxg55be).

Any ideas how this could be sorted without having to implement .close() for DataArray (or, alternatively, how to go about implementing that, given that I don't think a DataArray contains a reference to the Dataset that it may have come from)

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  Added convenience method for saving DataArray to netCDF file 173632183
243933961 https://github.com/pydata/xarray/pull/991#issuecomment-243933961 https://api.github.com/repos/pydata/xarray/issues/991 MDEyOklzc3VlQ29tbWVudDI0MzkzMzk2MQ== robintw 296686 2016-08-31T23:32:56Z 2016-08-31T23:32:56Z CONTRIBUTOR

I think I've dealt with all of these.

Refactoring the tests has made them a bit cleaner and safer due to not using mutation - however I still have quite a few repeated lines of code. I've also combined them all into one test with lots of asserts - as otherwise I couldn't keep the helper functions within the test without repeating them loads of times.

Does anything need adding to the docs for this? I'm assuming not as it's just making the code do more checking, it's not adding a feature as such?

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  Added validation of attrs before saving to netCDF files 173640823
243929210 https://github.com/pydata/xarray/pull/990#issuecomment-243929210 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0MzkyOTIxMA== robintw 296686 2016-08-31T23:05:12Z 2016-08-31T23:05:12Z CONTRIBUTOR

Thanks for the useful comments.

I've added some bits to the Sphinx docs in the places that I think they should go - but let me know if I need to add any more.

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  Added convenience method for saving DataArray to netCDF file 173632183
243863092 https://github.com/pydata/xarray/pull/990#issuecomment-243863092 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0Mzg2MzA5Mg== robintw 296686 2016-08-31T18:50:41Z 2016-08-31T18:50:41Z CONTRIBUTOR

I think I've dealt with the comments/issues now, but let me know if more needs doing.

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  Added convenience method for saving DataArray to netCDF file 173632183
243001377 https://github.com/pydata/xarray/pull/991#issuecomment-243001377 https://api.github.com/repos/pydata/xarray/issues/991 MDEyOklzc3VlQ29tbWVudDI0MzAwMTM3Nw== robintw 296686 2016-08-28T21:43:49Z 2016-08-28T21:43:49Z CONTRIBUTOR

Thanks, I'll deal with these modifications.

Also, I'm seeing errors from TravisCI saying ValueError: cannot read or write netCDF files without netCDF4-python or scipy installed - what do I need to do to make sure these tests work on Travis? (They pass fine on my local machine)

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  Added validation of attrs before saving to netCDF files 173640823
243000159 https://github.com/pydata/xarray/pull/990#issuecomment-243000159 https://api.github.com/repos/pydata/xarray/issues/990 MDEyOklzc3VlQ29tbWVudDI0MzAwMDE1OQ== robintw 296686 2016-08-28T21:20:44Z 2016-08-28T21:20:44Z CONTRIBUTOR

Thanks @shoyer - I wasn't actually aware that DataArrays can have a name before they're put into a Dataset (that's one of the things I love about contributing to OSS: you always learn things about the software that you never knew before!). I'll deal with the design issues ASAP.

How would you suggest testing this? I wasn't sure where to put the tests, and what exactly to test? Presumably something about the equivalence between this and saving after manually converting to a dataset, but I wasn't really sure how best to go about it.

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  Added convenience method for saving DataArray to netCDF file 173632183
234096888 https://github.com/pydata/xarray/issues/913#issuecomment-234096888 https://api.github.com/repos/pydata/xarray/issues/913 MDEyOklzc3VlQ29tbWVudDIzNDA5Njg4OA== robintw 296686 2016-07-20T21:59:14Z 2016-07-20T21:59:14Z CONTRIBUTOR

I'm not really sure how to work out which one it is a bug in - do you have any advice? Or should I just report it on the dask issue tracker too and see what they think?

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  dtype changes after .load() 166642852
233874116 https://github.com/pydata/xarray/issues/911#issuecomment-233874116 https://api.github.com/repos/pydata/xarray/issues/911 MDEyOklzc3VlQ29tbWVudDIzMzg3NDExNg== robintw 296686 2016-07-20T08:00:08Z 2016-07-20T08:00:08Z CONTRIBUTOR

Thanks. I might raise an issue on the netCDF4-Python project to see if we can improve the error message.

Would you be happy for me to submit a PR updating the xarray docs to note that you can only export attributes with certain values to a netCDF file? (and possibly, longer-term, we could provide an error inside xarray if you try to save out a file with objects as attributes)

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  KeyError on saving to NetCDF - due to objects in attrs? 166511736
232153175 https://github.com/pydata/xarray/pull/637#issuecomment-232153175 https://api.github.com/repos/pydata/xarray/issues/637 MDEyOklzc3VlQ29tbWVudDIzMjE1MzE3NQ== robintw 296686 2016-07-12T19:28:10Z 2016-07-12T19:28:10Z CONTRIBUTOR

Coming here from #897, it seems that we just need to decide to go with matplotlib's version, and therefore switch round the tuple given as figsize at https://github.com/pydata/xarray/pull/637/commits/400b1ef1d142c3c0dec1ff3c9f3cdfffa2229c10#diff-4ee153eb90c5207a5ed2e2b997bf6ce9R212, and then update the docs to go with it.

Does that make sense?

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  size and aspect arguments for plotting methods even without faceting 112928260

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