use ruff.flake8-tidy-imports to enforce absolute imports

• https://github.com/MarcoGorelli/absolufy-imports has been archived (no reason given)
• removes a pre-commit hook which should make it faster locally

I think we should use extend-exclude instead of exclude for ruff. We can then also remove ".eggs" as this is in the default.

From https://docs.astral.sh/ruff/settings/#exclude:

Note that you'll typically want to use extend-exclude to modify the excluded paths.

Default value: [".bzr", ".direnv", ".eggs", ".git", ".git-rewrite", ".hg", ".mypy_cache", ".nox", ".pants.d", ".pytype", ".ruff_cache", ".svn", ".tox", ".venv", "__pypackages__", "_build", "buck-out", "build", "dist", "node_modules", "venv"]

(I really dislike how github formats toml files... What would be the correct syntax, then?)

• [x] Closes #7298
• [x] Tests added
• [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
• [ ] New functions/methods are listed in api.rst

Otherwise da.indexes and the html repr raise a ValueError. I first had "<undefined>" but I think None is better. cc @spencerkclark @keewis

What happened?

The html repr of a cftime array wants to display the "calendar", which it cannot if it is empty.

What did you expect to happen?

No error.

Minimal Complete Verifiable Example

```Python import numpy as np import xarray as xr

data_obs = np.random.randn(3) time_obs = xr.date_range("2000-01-01", periods=3, freq="YS", calendar="noleap")

obs = xr.DataArray(data_obs, coords={"time": time_obs})

o = obs[:0]

xr.core.formatting_html.array_repr(o) ```

MVCE confirmation

• [ ] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
• [ ] Complete example — the example is self-contained, including all data and the text of any traceback.
• [ ] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
• [ ] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

```Python ValueError Traceback (most recent call last) Input In [1], in <cell line: 12>() 8 obs = xr.DataArray(data_obs, coords={"time": time_obs}) 10 o = obs[:0] ---> 12 xr.core.formatting_html.array_repr(o)

File ~/code/xarray/xarray/core/formatting_html.py:318, in array_repr(arr) 316 if hasattr(arr, "xindexes"): 317 indexes = _get_indexes_dict(arr.xindexes) --> 318 sections.append(index_section(indexes)) 320 sections.append(attr_section(arr.attrs)) 322 return _obj_repr(arr, header_components, sections)

File ~/code/xarray/xarray/core/formatting_html.py:195, in _mapping_section(mapping, name, details_func, max_items_collapse, expand_option_name, enabled) 188 expanded = _get_boolean_with_default( 189 expand_option_name, n_items < max_items_collapse 190 ) 191 collapsed = not expanded 193 return collapsible_section( 194 name, --> 195 details=details_func(mapping), 196 n_items=n_items, 197 enabled=enabled, 198 collapsed=collapsed, 199 )

File ~/code/xarray/xarray/core/formatting_html.py:155, in summarize_indexes(indexes) 154 def summarize_indexes(indexes): --> 155 indexes_li = "".join( 156 f"

{indexes_li}

File ~/code/xarray/xarray/core/formatting_html.py:156, in <genexpr>(.0) 154 def summarize_indexes(indexes): 155 indexes_li = "".join( --> 156 f"

{indexes_li}

File ~/code/xarray/xarray/core/formatting_html.py:140, in summarize_index(coord_names, index) 138 index_id = f"index-{uuid.uuid4()}" 139 preview = escape(inline_index_repr(index)) --> 140 details = short_index_repr_html(index) 142 data_icon = _icon("icon-database") 144 return ( 145 f"

File ~/code/xarray/xarray/core/formatting_html.py:132, in short_index_repr_html(index) 129 if hasattr(index, "repr_html"): 130 return index.repr_html() --> 132 return f"

{escape(repr(index))}

File ~/code/xarray/xarray/core/indexes.py:547, in PandasIndex.repr(self) 546 def repr(self): --> 547 return f"PandasIndex({repr(self.index)})"

File ~/code/xarray/xarray/coding/cftimeindex.py:353, in CFTimeIndex.repr(self) 345 end_str = format_times( 346 self.values[-REPR_ELLIPSIS_SHOW_ITEMS_FRONT_END:], 347 display_width, 348 offset=offset, 349 first_row_offset=offset, 350 ) 351 datastr = "\n".join([front_str, f"{' '*offset}...", end_str]) --> 353 attrs_str = format_attrs(self) 354 # oneliner only if smaller than display_width 355 full_repr_str = f"{klass_name}([{datastr}], {attrs_str})"

File ~/code/xarray/xarray/coding/cftimeindex.py:272, in format_attrs(index, separator) 267 def format_attrs(index, separator=", "): 268 """Format attributes of CFTimeIndex for repr.""" 269 attrs = { 270 "dtype": f"'{index.dtype}'", 271 "length": f"{len(index)}", --> 272 "calendar": f"'{index.calendar}'", 273 "freq": f"'{index.freq}'" if len(index) >= 3 else None, 274 } 276 attrs_str = [f"{k}={v}" for k, v in attrs.items()] 277 attrs_str = f"{separator}".join(attrs_str)

File ~/code/xarray/xarray/coding/cftimeindex.py:698, in CFTimeIndex.calendar(self) 695 """The calendar used by the datetimes in the index.""" 696 from .times import infer_calendar_name --> 698 return infer_calendar_name(self)

File ~/code/xarray/xarray/coding/times.py:374, in infer_calendar_name(dates) 371 return sample.calendar 373 # Error raise if dtype is neither datetime or "O", if cftime is not importable, and if element of 'O' dtype is not cftime. --> 374 raise ValueError("Array does not contain datetime objects.")

ValueError: Array does not contain datetime objects. ```

Anything else we need to know?

Bisected to 7379923de756a2bcc59044d548f8ab7a68b91d4e use _repr_inline_ for indexes that define it.

Environment

What happened?

da.xindexes or da.indexes raises an error when trying to generate the repr if there are no coords (indexes)

What did you expect to happen?

Displaying an empty Mappable?

Minimal Complete Verifiable Example

Python xr.DataArray([3, 5]).indexes xr.DataArray([3, 5]).xindexes

MVCE confirmation

• [x] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
• [x] Complete example — the example is self-contained, including all data and the text of any traceback.
• [x] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
• [x] New issue — a search of GitHub Issues suggests this is not a duplicate.
• [x] Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

```Python Out[9]: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) File ~/.conda/envs/xarray_dev/lib/python3.10/site-packages/IPython/core/formatters.py:708, in PlainTextFormatter.call(self, obj) 701 stream = StringIO() 702 printer = pretty.RepresentationPrinter(stream, self.verbose, 703 self.max_width, self.newline, 704 max_seq_length=self.max_seq_length, 705 singleton_pprinters=self.singleton_printers, 706 type_pprinters=self.type_printers, 707 deferred_pprinters=self.deferred_printers) --> 708 printer.pretty(obj) 709 printer.flush() 710 return stream.getvalue()

File ~/.conda/envs/xarray_dev/lib/python3.10/site-packages/IPython/lib/pretty.py:410, in RepresentationPrinter.pretty(self, obj) 407 return meth(obj, self, cycle) 408 if cls is not object \ 409 and callable(cls.dict.get('repr')): --> 410 return _repr_pprint(obj, self, cycle) 412 return _default_pprint(obj, self, cycle) 413 finally:

File ~/.conda/envs/xarray_dev/lib/python3.10/site-packages/IPython/lib/pretty.py:778, in repr_pprint(obj, p, cycle) 776 """A pprint that just redirects to the normal repr function.""" 777 # Find newlines and replace them with p.break() --> 778 output = repr(obj) 779 lines = output.splitlines() 780 with p.group():

File ~/code/xarray/xarray/core/indexes.py:1659, in Indexes.repr(self) 1657 def repr(self): 1658 indexes = formatting._get_indexes_dict(self) -> 1659 return formatting.indexes_repr(indexes)

File ~/code/xarray/xarray/core/formatting.py:474, in indexes_repr(indexes, max_rows) 473 def indexes_repr(indexes, max_rows: int | None = None) -> str: --> 474 col_width = _calculate_col_width(chain.from_iterable(indexes)) 476 return _mapping_repr( 477 indexes, 478 "Indexes", (...) 482 max_rows=max_rows, 483 )

File ~/code/xarray/xarray/core/formatting.py:341, in _calculate_col_width(col_items) 340 def _calculate_col_width(col_items): --> 341 max_name_length = max(len(str(s)) for s in col_items) if col_items else 0 342 col_width = max(max_name_length, 7) + 6 343 return col_width

ValueError: max() arg is an empty sequence ```

Anything else we need to know?

No response

Environment

• [ ] Towards #8239
• [ ] Tests added
• [ ] User visible changes (including notable bug fixes) are documented in whats-new.rst
• [ ] New functions/methods are listed in api.rst

This partly updates the pytest config as suggested in #8239 and un-xfails some tests (or xfails the tests more precisely).

See https://github.com/pydata/xarray/issues/8239#issuecomment-1739363809 for why we cannot exactly follow the suggestions given in #8239

• [x] Closes #7322

In #4864 I added a a decorator for the xarray.testing.assert_* functions to ensure warnings that were to errors (pytest.mark.filterwarnings("error")) do not error in assert_* (see https://github.com/pydata/xarray/pull/4760#issuecomment-774101639). As a solution I added

https://github.com/pydata/xarray/blob/5470d933452d88deb17cc9294a164c4a03f55dec/xarray/testing.py#L32

However, this is sub-optimal because this now removes all ignore filters! As dask stuff only gets evaluated in assert_* filters like warnings.filterwarnings("ignore", "Mean of empty slice") don't work for dask arrays!

I thought of setting

python warnings.simplefilter("ignore")

but this could suppress warnings we want to keep.

So now I remove all "error" warning filters and keep the rest. Note that the original filters get restored after with warnings.catch_warnings():. ().

I am not sure I expressed myself very clearly... let me know and I can try again. @keewis you had a look at #4864 maybe you can review this PR as well?

5844 excluded pydap from our tests - but the new version has been released in the meantime (on conda not on pypi, though, pydap/pydap#268) - so let's see if this still works.

• [x] Closes #6186

pydata/bottleneck#378 was merged - so this should work again.

Fixes or suppresses a number of warnings that turn up in our upstream CI.

pd.Index.is_monotonic is an alias for pd.Index.is_monotonic_increasing and does not stand for pd.Index.is_monotonic_increasing or pd.Index.is_monotonic_decreasing.

In #6096 I realized that DuckArrayModule("dask") is called a lot in our tests - 145'835 times. Most of those are from is_dask_collection (is_duck_dask_array) This change avoids that the instance needs to be built every time.

```python import xarray as xr

%timeit xr.core.pycompat.DuckArrayModule("dask").available %timeit xr.core.pycompat.dsk.available ```

18.9 µs ± 97.7 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each) 77.1 ns ± 1.22 ns per loop (mean ± std. dev. of 7 runs, 10000000 loops each)

Which leads to an incredible speed up of our tests of about 2.7 s :grin: ((18.9 - 0.0771) * 145835 / 1e6).

• dask 2022.01 is out, so we can remove the pin

• [x] Part of #4513
• [x] Tests added
• [x] Passes pre-commit run --all-files
• [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

This PR warns when passing keep_attrs to resample(..., keep_attrs=True) and rolling_exp(..., keep_attrs=True) as they have no effect (rightfully). Also removes keep_attrs from the docstring of resample.

iris moved its documentation to https://scitools-iris.readthedocs.io/en/stable/

and put the comment on the same line

Silences a number of warnings that accumulated in our test suite (c.f. #3266). The changes are mostly unrelated but small.

• [x] Closes #4970

The clean thing here would be to update min_deps_check.py so it works properly for this case. I am not sure it's really worth it.

We currently pin netCDF4 to version 1.5. However, I think netCDF4 does not really follow semantic versioning, e.g. python 2 support was dropped in version 1.5.6. So they may actually be doing something like 1.major.minor[.patch] - I asked about their versioning scheme in Unidata/netcdf4-python#1090.

So I wonder if we would need to pin netCDF to version to version 1.5.4.

The last 5 days our Upstream CI failed silently with a timeout after 6h:

https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml?query=branch%3Amaster+event%3Aschedule

This was probably caused by #4934. As mentioned in dask/dask#4934 this is probably dask/dask#6738 which was merged 5 days ago.

Small doc fix, see http://xarray.pydata.org/en/stable/io.html#formats-supported-by-pynio (the ..note:: did not get picked up)

mypy v0.800 was ignoring our config (https://github.com/pydata/xarray/pull/4874#issuecomment-774771523)... Adding an (empty) [mypy] section to setup.cfg seems to do the trick, this is in contrast to the documentation and may get changed again (c.f. python/mypy#9940), but it does not hurt either.

@keewis

• [x] Closes #2658, closes #4543
• [x] Tests added
• [x] Passes isort . && black . && mypy . && flake8
• [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

pd.Index("a") has dtype object. Therefore string coords change their dtype on certain operations - e.g. align, __setitem__ (& assign), IndexVariable.concat. This can be avoided by using the coords instead of the index in some cases but in two instances it was unavoidable to cast a pd.Index back to a np.array. I probably did not catch all of these conversions.

What I am not sure: does this somehow contradict the index refactor?

The Linux py36-bare-minimum will likely fail with a TypeError: 'NoneType' object is not callable due to python/importlib_metadata#270

This could be fixed by adding typing_extensions to the CI or maybe they fix that upstream.

Follow up to #4506

Suppress some "Ambiguous reference date string" warnings. See e.g.: https://dev.azure.com/xarray/xarray/_build/results?buildId=4233&view=logs&j=2280efed-fda1-53bd-9213-1fa8ec9b4fa8&t=175181ee-1928-5a6b-f537-168f7a8b7c2d&l=361

I feel I overdid it a bit with the parameterizations of the weighted tests. This brings the number of tests of test_weighted.py from about 1000 down to less than 200 without changing the coverage.

• [x] Closes #4487

Thanks for the pointer @keewis. Let's see if this works.

• [x] Closes #4571

• [x] Closes #4565
• [x] Passes isort . && black . && mypy . && flake8
• [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

Pandas will change pd.Index.__or__ and pd.Index.__and__. Use pd.Index.union and pd.Index.intersection inseated. There should be no change in functionality.

pandas-dev/pandas#20393 was resolved in pandas version 0.23, so this should no longer be necessary. The relevant test is

https://github.com/pydata/xarray/blob/063606b90946d869e90a6273e2e18ed24bffb052/xarray/tests/test_dataarray.py#L955-L957

so let's see if this passes

Fixes the failing doc builds, see #4521

Our upstream tests fail due to a change in dask. The likely culprit is dask/dask#6680 - dask.array.zeros_like does now take the meta keyword and thus it tries to coerce str to a bool which fails (and it didn't do before). The following should trigger the error:

```python import xarray as xr import dask

da = xr.DataArray(dask.array.array("")) xr.zeros_like(da, dtype=bool) `` Note thatzeros_likeis called inisnull` (which triggered the test failures):

https://github.com/pydata/xarray/blob/080caf4246fe2f4d6aa0c5dcb65a99b376fa669b/xarray/core/duck_array_ops.py#L100-L102

What happened:

```python /home/vsts/work/1/s/xarray/tests/test_duck_array_ops.py:499:

/home/vsts/work/1/s/xarray/testing.py:139: in compat_variable return a.dims == b.dims and (a._data is b._data or equiv(a.data, b.data)) /home/vsts/work/1/s/xarray/testing.py:36: in _data_allclose_or_equiv return duck_array_ops.array_equiv(arr1, arr2) /home/vsts/work/1/s/xarray/core/duck_array_ops.py:246: in array_equiv flag_array = (arr1 == arr2) | (isnull(arr1) & isnull(arr2)) /home/vsts/work/1/s/xarray/core/duck_array_ops.py:104: in isnull return zeros_like(data, dtype=bool) /home/vsts/work/1/s/xarray/core/duck_array_ops.py:56: in f return wrapped(args, *kwargs) /usr/share/miniconda/envs/xarray-tests/lib/python3.8/site-packages/dask/array/creation.py:174: in zeros_like return zeros( /usr/share/miniconda/envs/xarray-tests/lib/python3.8/site-packages/dask/array/wrap.py:78: in wrap_func_shape_as_first_arg return Array(dsk, name, chunks, dtype=dtype, meta=kwargs.get("meta", None)) /usr/share/miniconda/envs/xarray-tests/lib/python3.8/site-packages/dask/array/core.py:1083: in new meta = meta_from_array(meta, dtype=dtype)

x = array('', dtype='<U1'), ndim = 0, dtype = dtype('bool')

def meta_from_array(x, ndim=None, dtype=None):
    """Normalize an array to appropriate meta object

    Parameters
    ----------
    x: array-like, callable
        Either an object that looks sufficiently like a Numpy array,
        or a callable that accepts shape and dtype keywords

    if dtype and meta.dtype != dtype:

      meta = meta.astype(dtype)

E ValueError: invalid literal for int() with base 10: ''

```

• [x] Closes #4495
• [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

Let's see if all tests pass or if the numeric_only keyword is new in pandas.

• [x] Closes #4342

mpl 3.3.2 is out so we can try to unpin the version of the docs again. #4313

What happened: da.sum(min_count=1) returns a TypeError if da has an integer dtype. Of course min_count is not necessary for integer data as it cannot contain NaN.

What you expected to happen: min_count should be ignored

Minimal Complete Verifiable Example:

python import xarray as xr da = xr.DataArray([[1, 2, 3], [4, 5, 6]]) da.sum(min_count=1)

Anything else we need to know?:

Full traceback

Environment:

• [x] Closes #4238
• [x] Passes isort . && black . && mypy . && flake8
• [x] User visible changes (including notable bug fixes) are documented in whats-new.rst

The issue mentions xr.Dataset.to_dataframe and xr.concat. xr.Dataset.to_dataframe was annotated in #4333, so only xr.concat is left.

It would be nice to be able to use a level of a MultiIndex for plotting.

MCVE Code Sample

```python import numpy as np import xarray as xr

da = xr.DataArray( np.random.randn(10), dims="x", coords=dict( a=("x", np.arange(10, 20)), b=("x", np.arange(1, 11)) ) )

da = da.set_index(x=["a", "b"]) da This creates the following DataArraypython <xarray.DataArray (x: 10)> array([-1.34516338, 0.97644817, -0.24032189, -0.70112418, -0.8686898 , -0.55607078, 0.56618151, 1.62847463, 0.84947296, -0.5775504 ]) Coordinates: * x (x) MultiIndex - a (x) int64 10 11 12 13 14 15 16 17 18 19 - b (x) int64 1 2 3 4 5 6 7 8 9 10 ```

Is there a way to plot a line using one of the levels of the MultiIindex? python da.plot(x="a") returns python ValueError: x must be either None or one of ('x')

python da.plot() returns

python TypeError: Plotting requires coordinates to be numeric or dates of type np.datetime64, datetime.datetime, cftime.datetime or pd.Interval. (which makes sense). If da is a 2D Variable the error is python ValueError: x and y must be coordinate variables

Expected Output

A line plot

Versions

MCVE Code Sample

```python import xarray as xr da = xr.DataArray([0, 1, 2]) da.quantile(q=50)

ValueError: Percentiles must be in the range [0, 100] ```

Expected Output

python ValueError: Quantiles must be in the range [0, 1]

Problem Description

By wrapping np.nanpercentile (xref: #3559) we also get the numpy error. However, the error message is wrong as xarray needs it to be in 0..1.

BTW: thanks for #3559, makes my life easier!

Output of xr.show_versions()

Edit: uses nanpercentile internally.

MCVE Code Sample

```python import xarray as xr import numpy as np

airtemps = xr.tutorial.load_dataset('air_temperature')

air = airtemps.air.isel(time=0)

levels = np.arange(225, 301, 25)

colors = ['#ffffb2', '#fecc5c', '#fd8d3c', '#e31a1c']

this does not work for me

air.plot.pcolormesh(levels=levels, colors=colors)

```

Expected Output

Should create a plot with the specified colors. According to the the docstring this should work. Or maybe I am doing something wrong here?

Problem Description

Instead I get the following error: ```python /usr/local/Miniconda3-envs/envs/2019/envs/iacpy3_2019/lib/python3.7/site-packages/xarray/plot/utils.py in _process_cmap_cbar_kwargs(func, kwargs, data) 683 # colors is only valid when levels is supplied or the plot is of type 684 # contour or contourf --> 685 if colors and (('contour' not in func.name) and (not levels)): 686 raise ValueError("Can only specify colors with contour or levels") 687

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ```

Instead I use the following, which works:

python air.plot.pcolormesh(levels=levels, cmap=colors)

Output of xr.show_versions()

see #418

Virtual variables such as time.date can not be accessed by dot notation.

``` In [81]: ts.time.date

AttributeError Traceback (most recent call last) <ipython-input-81-4206b510e310> in <module>() ----> 1 ts.time.date

/home/mathause/.local/lib/python2.7/site-packages/xray/core/common.pyc in getattr(self, name) 115 pass 116 raise AttributeError("%r object has no attribute %r" % --> 117 (type(self).name, name)) 118 119 def dir(self):

AttributeError: 'DataArray' object has no attribute 'date' ```

Compare

ts.__getattr__('time.date')

So maybe time.date is not a useful name. time_date? Or don't show these attributes to the user?