issues

• [ ] 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

I wanted to know what zarr.convenience.consolidate_metadata does which motivated me to add a link to it in the docstring to make it easier for others (and future me) to discover it.

I sorted intersphinx_mapping to make it easier to docs from other projects. I also added :func:zarr.convenience.consolidate_metadata in the doc string.

Testing if it actually works is WIP

• [ ] 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

Help navigation in the docs of going between the DataArray method and the Dataset method.

• [x] Closes #6754
• [x] Tests added
• [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
• [ ] New functions/methods are listed in api.rst

Some tiny overlap with https://github.com/pydata/xarray/pull/6542.

I feel this minor changes helps it easy to navigate to other parts of the docs.

Some motivation behind the PR here: https://github.com/pydata/xarray/discussions/6697

Note: i've forgotten the syntax for how to create a link to https://xarray.pydata.org/en/stable/generated/xarray.Dataset.chunk.html

• [ ] 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

In the section above (http://xarray.pydata.org/en/stable/contributing.html#how-to-build-the-xarray-documentation) i.e. build the env, it assumes you are in the root directory. This holds that assumptions and makes it easier for a user to copy-paste to build the docs

Related to https://github.com/pydata/xarray/issues/4001#issuecomment-779556647

When I worked on https://github.com/pydata/xarray/pull/5615 I did so with a couple of team mates. I added them in the commit message: https://github.com/pydata/xarray/pull/5615/commits/67ccce2f9b31eebf38fffb5dc86b90810299111c

Want to make sure they get a shout out here :)

• [x] Closes #5838
• [ ] 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

• [x] Closes my brain dump in https://github.com/pydata/xarray/discussions/5795
• [ ] 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

• [ ] Tests added
• [x] Passes pre-commit run --all-files
• [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst

What does this PR do?

Adds a storage_options arg to to_zarr.

What is the storage_options arg?

The storage_options arg is used throughout the pydata ecosystem where you can write a file to cloud storage. Such as:

• pandas: https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.to_parquet.html?highlight=to_parquet
• dask.dataframe: https://docs.dask.org/en/latest/generated/dask.dataframe.to_parquet.html
• dask.array: https://docs.dask.org/en/latest/generated/dask.array.to_zarr.html#dask.array.to_zarr

It allows you to write to a prd account or a dev account for example.

It is can be used currently in xarray when reading data via open_dataset e.g. xr.open_dataset(..., backend_kwargs=dict(storage_options=storage_options)

Why is it needed?

When working in cloud based environments you storage options are often automatically created. I recently found when doing things in parallel dask can hiccup on finding the credentials (see https://dask.slack.com/archives/C02282J3Q6Q/p1626201210115500) passing the storage options as an arg gave it some stability.

I imagine this could help when writing multiple zarr stores to cloud storage in parallel (e.g. delayed).

This PR also brings similar functionality of pandas.DataFrame.to_parquet and dask.array.to_zarr to xarray.

How is this tested?

Not obvious how to test. e.g. no storage_options test in dask.array https://github.com/dask/dask/blob/main/dask/array/tests/test_array_core.py

Pandas has more extensive tests https://github.com/pandas-dev/pandas/blob/master/pandas/tests/io/test_fsspec.py

Background:

The idea for this PR is discussed here: https://github.com/pydata/xarray/discussions/5601 cc. @martindurant

Makes life a little easier when navigating the docs

missing code formatting on this https://xarray.pydata.org/en/latest/generated/xarray.open_dataset.html

It took me a while to realize this so I wanted to make a note in the docs for myself in the future and others uses.

I was playing with pint-xarray and I couldn't work out why I couldn't round trip a file (https://github.com/xarray-contrib/pint-xarray/issues/109). It turns out the DataArray had an enconding attribute which was being used (and overriding my unit conversion). In addition, I was also scratching my head for a while as to where my zarr store was getting chunks from which didn't correspomd to my numpy array (https://github.com/pydata/xarray/discussions/5407).

This PR just makes a note of the importance of encoding attribute of DataArray(s) when writing to a zarr store.

docs page change is here: https://xray--5427.org.readthedocs.build/en/5427/generated/xarray.Dataset.to_zarr.html?highlight=zarr#xarray.Dataset.to_zarr

Keewis mentioned other options to merge are concat and combine_by_coords (https://github.com/pydata/xarray/discussions/5462#discussioncomment-861492). This PR adds combine_by_coords in the see also docstring of merge

Add query examples in the docstrings.

Relevent rtd buld links: - https://xray--5249.org.readthedocs.build/en/5249/generated/xarray.Dataset.query.html?highlight=query#xarray.Dataset.query - https://xray--5249.org.readthedocs.build/en/5249/generated/xarray.DataArray.query.html?highlight=query#xarray.DataArray.query

Fixes rendering in https://github.com/pydata/xarray/pull/5163

• [x] Closes #5159
• [ ] 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

Update hyperlink for xskillscore

• [x] Closes #4620

This PR follows a TypeError I got

ds = xr.open_dataset('https://thredds.ucar.edu/thredds/dodsC/grib/NCEP/GFS/Global_0p25deg/Best') ds.rename({'lat': 'latitude', 'lon': 'longitude'}, inplace=True) TypeError: The `inplace` argument has been removed from xarray. You can achieve an identical effect with python's standard assignment.

I saw the option of the inplace in the docs http://xarray.pydata.org/en/stable/generated/xarray.Dataset.rename.html

Removing this argument.

TODO:

• [ ] rm test_rename_inplace

When opening the current url https://github.com/timothycrosley/isort it points to a new url https://github.com/PyCQA/isort.

This PR replaces the old url with the new one

• [x] Closes #4151
• [NA] Tests added
• [NA] Passes isort -rc . && black . && mypy . && flake8
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API

• [X] Closes #3895
• [ ] Tests added
• [ ] Passes isort -rc . && black . && mypy . && flake8
• [ ] Fully documented, including whats-new.rst for all changes and api.rst for new API

Tested the docs build

Think my package should go in the 'extend xarray capabilities' section rather than the 'geoscience' section.

Potentially fixes #1115 as I have a correlation function. http://xarray.pydata.org/en/stable/dask.html?highlight=spearman#automatic-parallelization probably fixes #1115 as well

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

I wanted to add an example as googling 'xarray interp' takes me to http://xarray.pydata.org/en/stable/generated/xarray.Dataset.interp.html.

However, there lots of great examples in http://xarray.pydata.org/en/stable/interpolation.html Perhaps I should edit it to: ``` Examples

See http://xarray.pydata.org/en/stable/interpolation.html ```

I was also thinking about adding a note about interpolating time as it came up in https://github.com/pydata/xarray/issues/2284 but not sure what would be the best way to do so.

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

Added a resample example to reflect the DeprecationWarning: .resample() has been modified to defer calculations. Instead of passing 'dim' and 'how="mean", instead consider using.... There were also some missing parameters in the docs.

Made a minor edit to my rolling example which uses the parameter center. I can't remember if that parameter was there last time but I think it's useful to return the time value for the middle of window.

Added a groupby example. Not sure if this should go here. See text below for my motivation of putting an example in the docstring of the class/object.

I learnt xarray before I learnt pandas so these example will hopefully be useful to other beginners as it took me a minute to get the syntax right.

Whilst there are great examples of these functions in the docs, a google search of a function for example xarray rolling often returns the doc entry that that object. Having a little example there is helpful for me to get the syntax right. The key/value pair in a dictionary for example is very powerful and always takes me a few tries to get the entry right.

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

This seems to be happening to a lot of projects as highlighted on the recent list of people who have cited this issue https://github.com/badges/shields/issues/716.

Here is a project with a recent commit to resolve this which explains the issue better that I can https://github.com/landscapeio/pylint-celery/pull/7

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

These were inspired by a discussion on the mailing list: https://groups.google.com/forum/#!topic/xarray/FyCFkuWbFSk

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

Closes #1757

• [NA] Closes #xxxx (remove if there is no corresponding issue, which should only be the case for minor changes)
• [NA] Tests added (for all bug fixes or enhancements)
• [NA] Tests passed (for all non-documentation changes)
• [NA] Passes git diff upstream/master **/*py | flake8 --diff (remove if you did not edit any Python files)
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API (remove if this change should not be visible to users, e.g., if it is an internal clean-up, or if this is part of a larger project that will be documented later)

• [NA] Closes #xxxx
• [NA] Tests added / passed
• [ ] Passes git diff upstream/master | flake8 --diff
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API

I added an example to apply as I just learnt about it from my Q on stackoverflow (https://stackoverflow.com/questions/46980823/python-xarray-compute-the-absolute-values-of-a-dataset/46981027#46981027).

Also my first time using git and making edits on the command line rather than the web browser.

This idea for this PR was discussed here: https://stackoverflow.com/questions/45992983/python-xarray-rolling-mean-example

I wasn't able to drop the nans using min_periods so I used the dropna method.

If there is a more eloquent method to my example feel free to point me to it.

• [NA] Closes #xxxx
• [NA] Tests added / passed
• [ ] Passes git diff upstream/master | flake8 --diff
• [NA] Fully documented, including whats-new.rst for all changes and api.rst for new API