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Be able to define whether file(s) on disk are opened read-only or read-write #2345

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AndyGabey opened this issue Aug 6, 2018 · 1 comment · Fixed by #2746
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Be able to define whether file(s) on disk are opened read-only or read-write #2345

AndyGabey opened this issue Aug 6, 2018 · 1 comment · Fixed by #2746

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@AndyGabey
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AndyGabey commented Aug 6, 2018

From a testing point of view, it would be helpful to explicitly specify whether to open the source file(s) on disk as read-only or read-write in open_dataset() and open_mfdataset(). It'd also be a nice backstop for anybody concerned about data corruption from unexpected behaviour.

@AndyGabey AndyGabey reopened this Aug 6, 2018
@shoyer
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shoyer commented Aug 6, 2018

open_dataset and open_mfdataset never open files for read-write. To write data to files with xarray, you have to use to_netcdf().

Arguably, these functions would be better named read_dataset. I think we stuck with open_dataset because the reading is done in a lazy fashion.

@dcherian dcherian mentioned this issue Mar 7, 2019
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dcherian pushed a commit to dcherian/xarray that referenced this issue Mar 7, 2019
dcherian added a commit that referenced this issue Mar 12, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes #2289

* Add metpy accessor. Closes #461

* fix transpose docstring. Closes #2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes #2345).

* Update metpy 1

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

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
pletchm pushed a commit to pletchm/xarray that referenced this issue Mar 21, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes pydata#2289

* Add metpy accessor. Closes pydata#461

* fix transpose docstring. Closes pydata#2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes pydata#2345).

* Update metpy 1

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

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
pletchm pushed a commit to pletchm/xarray that referenced this issue Mar 21, 2019
* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes pydata#2289

* Add metpy accessor. Closes pydata#461

* fix transpose docstring. Closes pydata#2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes pydata#2345).

* Update metpy 1

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

* Update doc/weather-climate.rst

Co-Authored-By: dcherian <dcherian@users.noreply.github.com>
shoyer pushed a commit that referenced this issue Mar 26, 2019
…ns with size>1 (#2757)

* Quarter offset implemented (base is now latest pydata-master). (#2721)

* Quarter offset implemented (base is now latest pydata-master).

* Fixed issues raised in review (#2721 (review))

* Updated whats-new.rst with info on quarter offset support.

* Updated whats-new.rst with info on quarter offset support.

* Update doc/whats-new.rst

Co-Authored-By: jwenfai <jwenfai@gmail.com>

* Added support for quarter frequencies when resampling CFTimeIndex. Less redundancy in CFTimeIndex resampling tests.

* Removed normalization code (unnecessary for cftime_range) in cftime_offsets.py. Removed redundant lines in whats-new.rst.

* Removed invalid option from _get_day_of_month docstring. Added tests back in that raises ValueError when resampling (base=24 when resampling to daily freq, e.g., '8D').

* Minor edits to docstrings/comments

* lint

* Add `Dataset.drop_dims` (#2767)

* ENH: Add Dataset.drop_dims()

* Drops full dimensions and any corresponding variables in a
  Dataset
* Fixes GH1949

* DOC: Add Dataset.drop_dims() documentation

* Improve name concat (#2792)

* Added tests of desired name inferring behaviour

* Infers names

* updated what's new

* Don't use deprecated np.asscalar() (#2800)

It got deprecated in numpy 1.16 and throws a ton of warnings due to
that.
All the function does is returning .item() anyway, which is why it got
deprecated.

* Add support for cftime.datetime coordinates with coarsen (#2778)

* some docs updates (#2746)

* Friendlier io title.

* Fix lists.

* Fix *args, **kwargs

"inline emphasis..."

* misc

* Reference xarray_extras for csv writing. Closes #2289

* Add metpy accessor. Closes #461

* fix transpose docstring. Closes #2576

* Revert "Fix lists."

This reverts commit 39983a5.

* Revert "Fix *args, **kwargs"

This reverts commit 1b9da35.

* Add MetPy to related projects.

* Add Weather and Climate specific page.

* Add hvplot.

* Note open_dataset, mfdataset open files as read-only (closes #2345).

* Update metpy 1

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

* Update doc/weather-climate.rst

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

* Drop failing tests writing multi-dimensional arrays as attributes (#2810)

These aren't valid for netCDF files.

Fixes GH2803

* Push back finalizing deprecations for 0.12 (#2809)

0.12 will already have a big change in dropping Python 2.7 support. I'd rather
wait a bit longer to finalize these deprecations to minimize the impact on
users.

* enable loading remote hdf5 files (#2782)

* attempt at loading remote hdf5

* added a couple tests

* rewind bytes after reading header

* addressed comments for tests and error message

* fixed pep8 formatting

* created _get_engine_from_magic_number function, new tests

* added description in whats-new

* fixed test failure on windows

* same error on windows and nix

* Release 0.12.0

* Add whats-new for 0.12.1

* Rework whats-new for 0.12

* DOC: Update donation links

* DOC: remove outdated warning (#2818)

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * use .size attribute to determine the size of a dimension, rather than converting to a list, which can be slow for large iterables

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5

* Allow expand_dims() method to support inserting/broadcasting dimensions with size>1 (#2757)

 * Move enhancement description up to 0.12.1

 * use .size attribute to determine the size of a dimension, rather than converting to a list, which can be slow for large iterables

 * Make using dim_kwargs for python 3.5 illegal -- a ValueError is thrown

 * dataset.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * dataarray.expand_dims() method take dict like object where values represent length of dimensions or coordinates of dimesnsions

 * Add alternative option to passing a dict to the dim argument, which is now an optional kwarg, passing in each new dimension as its own kwarg

 * Add expand_dims enhancement from issue 2710 to whats-new.rst

 * Fix test_dataarray.TestDataArray.test_expand_dims_with_greater_dim_size tests to pass in python 3.5 using ordered dicts instead of regular dicts. This was needed because python 3.5 and earlier did not maintain insertion order for dicts

 * Restrict core logic to use 'dim' as a dict--it will be converted into a dict on entry if it is a str or a sequence of str

 * Don't cast dim values (coords) as a list since IndexVariable/Variable will internally convert it into a numpy.ndarray. So just use IndexVariable((k,), v)

 * TypeErrors should be raised for invalid input types, rather than ValueErrors.

 * Force 'dim' to be OrderedDict for python 3.5
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