(chore) min versions bump (#8022)

* chore: bump minimum versions in min-all-deps.yml

* docs

* bump bare minimum

* chore: cleanup deprecations following minimum version bump

* more cleanup

---------

Co-authored-by: Anderson Banihirwe <[email protected]>

Author: jhamman

ci/min_deps_check.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 """Fetch from conda database all available versions of the xarray dependencies and their
-publication date. Compare it against requirements/py37-min-all-deps.yml to verify the
+publication date. Compare it against requirements/min-all-deps.yml to verify the
 policy on obsolete dependencies is being followed. Print a pretty report :)
 """
 import itertools
@@ -46,7 +46,7 @@ def warning(msg: str) -> None:
 
 
 def parse_requirements(fname) -> Iterator[tuple[str, int, int, int | None]]:
-    """Load requirements/py37-min-all-deps.yml
+    """Load requirements/min-all-deps.yml
 
     Yield (package name, major version, minor version, [patch version])
     """

ci/requirements/bare-minimum.yml

@@ -11,6 +11,6 @@ dependencies:
   - pytest-env
   - pytest-xdist
   - pytest-timeout
-  - numpy=1.21
+  - numpy=1.22
   - packaging=21.3
   - pandas=1.4

ci/requirements/min-all-deps.yml

@@ -8,48 +8,48 @@ dependencies:
   # When upgrading python, numpy, or pandas, must also change
   # doc/user-guide/installing.rst, doc/user-guide/plotting.rst and setup.py.
   - python=3.9
-  - boto3=1.20
+  - boto3=1.24
   - bottleneck=1.3
   - cartopy=0.20
   - cdms2=3.1
-  - cftime=1.5
+  - cftime=1.6
   - coveralls
-  - dask-core=2022.1
-  - distributed=2022.1
+  - dask-core=2022.7
+  - distributed=2022.7
   - flox=0.5
-  - h5netcdf=0.13
+  - h5netcdf=1.0
   # h5py and hdf5 tend to cause conflicts
   # for e.g. hdf5 1.12 conflicts with h5py=3.1
   # prioritize bumping other packages instead
   - h5py=3.6
   - hdf5=1.12
   - hypothesis
-  - iris=3.1
-  - lxml=4.7  # Optional dep of pydap
+  - iris=3.2
+  - lxml=4.9  # Optional dep of pydap
   - matplotlib-base=3.5
   - nc-time-axis=1.4
   # netcdf follows a 1.major.minor[.patch] convention
   # (see https://github.com/Unidata/netcdf4-python/issues/1090)
-  - netcdf4=1.5.7
+  - netcdf4=1.6.0
   - numba=0.55
-  - numpy=1.21
+  - numpy=1.22
   - packaging=21.3
   - pandas=1.4
-  - pint=0.18
+  - pint=0.19
   - pip
   - pseudonetcdf=3.2
-  - pydap=3.2
+  - pydap=3.3
   - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist
   - pytest-timeout
-  - rasterio=1.2
-  - scipy=1.7
+  - rasterio=1.3
+  - scipy=1.8
   - seaborn=0.11
   - sparse=0.13
-  - toolz=0.11
-  - typing_extensions=4.0
-  - zarr=2.10
+  - toolz=0.12
+  - typing_extensions=4.3
+  - zarr=2.12
   - pip:
-    - numbagg==0.1
+    - numbagg==0.2.1

doc/getting-started-guide/installing.rst

@@ -7,7 +7,7 @@ Required dependencies
 ---------------------
 
 - Python (3.9 or later)
-- `numpy <https://www.numpy.org/>`__ (1.21 or later)
+- `numpy <https://www.numpy.org/>`__ (1.22 or later)
 - `packaging <https://packaging.pypa.io/en/latest/#>`__ (21.3 or later)
 - `pandas <https://pandas.pydata.org/>`__ (1.4 or later)
 

doc/whats-new.rst

@@ -47,6 +47,29 @@ New Features
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
+- The minimum versions of some dependencies were changed (:pull:`8022`):
+
+  ===================== =========  ========
+   Package                    Old      New
+  ===================== =========  ========
+   boto3                     1.20     1.24
+   cftime                     1.5      1.6
+   dask-core               2022.1   2022.7
+   distributed             2022.1   2022.7
+   hfnetcdf                  0.13      1.0
+   iris                       3.1      3.2
+   lxml                       4.7      4.9
+   netcdf4                  1.5.7    1.6.0
+   numpy                     1.21     1.22
+   pint                      0.18     0.19
+   pydap                      3.2      3.3
+   rasterio                   1.2      1.3
+   scipy                      1.7      1.8
+   toolz                     0.11     0.12
+   typing_extensions          4.0      4.3
+   zarr                      2.10     2.12
+   numbagg                    0.1    0.2.1
+  ===================== =========  ========
 
 Deprecations
 ~~~~~~~~~~~~

xarray/backends/h5netcdf_.py

@@ -6,8 +6,6 @@
 from collections.abc import Iterable
 from typing import TYPE_CHECKING, Any
 
-from packaging.version import Version
-
 from xarray.backends.common import (
     BACKEND_ENTRYPOINTS,
     BackendEntrypoint,
@@ -233,28 +231,14 @@ def get_attrs(self):
         return FrozenDict(_read_attributes(self.ds))
 
     def get_dimensions(self):
-        import h5netcdf
-
-        if Version(h5netcdf.__version__) >= Version("0.14.0.dev0"):
-            return FrozenDict((k, len(v)) for k, v in self.ds.dimensions.items())
-        else:
-            return self.ds.dimensions
+        return FrozenDict((k, len(v)) for k, v in self.ds.dimensions.items())
 
     def get_encoding(self):
-        import h5netcdf
-
-        if Version(h5netcdf.__version__) >= Version("0.14.0.dev0"):
-            return {
-                "unlimited_dims": {
-                    k for k, v in self.ds.dimensions.items() if v.isunlimited()
-                }
-            }
-        else:
-            return {
-                "unlimited_dims": {
-                    k for k, v in self.ds.dimensions.items() if v is None
-                }
+        return {
+            "unlimited_dims": {
+                k for k, v in self.ds.dimensions.items() if v.isunlimited()
             }
+        }
 
     def set_dimension(self, name, length, is_unlimited=False):
         _ensure_no_forward_slash_in_name(name)

xarray/backends/pydap_.py

@@ -4,7 +4,6 @@
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
-from packaging.version import Version
 
 from xarray.backends.common import (
     BACKEND_ENTRYPOINTS,
@@ -123,11 +122,10 @@ def open(
             "output_grid": output_grid or True,
             "timeout": timeout,
         }
-        if Version(pydap.lib.__version__) >= Version("3.3.0"):
-            if verify is not None:
-                kwargs.update({"verify": verify})
-            if user_charset is not None:
-                kwargs.update({"user_charset": user_charset})
+        if verify is not None:
+            kwargs.update({"verify": verify})
+        if user_charset is not None:
+            kwargs.update({"user_charset": user_charset})
         ds = pydap.client.open_url(**kwargs)
         return cls(ds)
 

xarray/coding/cftimeindex.py

@@ -470,13 +470,9 @@ def get_loc(self, key):
         else:
             return super().get_loc(key)
 
-    def _maybe_cast_slice_bound(self, label, side, kind=None):
+    def _maybe_cast_slice_bound(self, label, side):
         """Adapted from
         pandas.tseries.index.DatetimeIndex._maybe_cast_slice_bound
-
-        Note that we have never used the kind argument in CFTimeIndex and it is
-        deprecated as of pandas version 1.3.0.  It exists only for compatibility
-        reasons.  We can remove it when our minimum version of pandas is 1.3.0.
         """
         if not isinstance(label, str):
             return label

xarray/core/combine.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import itertools
-import warnings
 from collections import Counter
 from collections.abc import Iterable, Sequence
 from typing import TYPE_CHECKING, Literal, Union
@@ -653,7 +652,6 @@ def _combine_single_variable_hypercube(
     return concatenated
 
 
-# TODO remove empty list default param after version 0.21, see PR4696
 def combine_by_coords(
     data_objects: Iterable[Dataset | DataArray] = [],
     compat: CompatOptions = "no_conflicts",
@@ -662,7 +660,6 @@ def combine_by_coords(
     fill_value: object = dtypes.NA,
     join: JoinOptions = "outer",
     combine_attrs: CombineAttrsOptions = "no_conflicts",
-    datasets: Iterable[Dataset] | None = None,
 ) -> Dataset | DataArray:
     """
 
@@ -760,8 +757,6 @@ def combine_by_coords(
         If a callable, it must expect a sequence of ``attrs`` dicts and a context object
         as its only parameters.
 
-    datasets : Iterable of Datasets
-
     Returns
     -------
     combined : xarray.Dataset or xarray.DataArray
@@ -918,14 +913,6 @@ def combine_by_coords(
     DataArrays or Datasets, a ValueError will be raised (as this is an ambiguous operation).
     """
 
-    # TODO remove after version 0.21, see PR4696
-    if datasets is not None:
-        warnings.warn(
-            "The datasets argument has been renamed to `data_objects`."
-            " From 0.21 on passing a value for datasets will raise an error."
-        )
-        data_objects = datasets
-
     if not data_objects:
         return Dataset()
 

xarray/core/dataarray.py

@@ -5036,15 +5036,15 @@ def quantile(
             desired quantile lies between two data points. The options sorted by their R
             type as summarized in the H&F paper [1]_ are:
 
-                1. "inverted_cdf" (*)
-                2. "averaged_inverted_cdf" (*)
-                3. "closest_observation" (*)
-                4. "interpolated_inverted_cdf" (*)
-                5. "hazen" (*)
-                6. "weibull" (*)
+                1. "inverted_cdf"
+                2. "averaged_inverted_cdf"
+                3. "closest_observation"
+                4. "interpolated_inverted_cdf"
+                5. "hazen"
+                6. "weibull"
                 7. "linear"  (default)
-                8. "median_unbiased" (*)
-                9. "normal_unbiased" (*)
+                8. "median_unbiased"
+                9. "normal_unbiased"
 
             The first three methods are discontiuous. The following discontinuous
             variations of the default "linear" (7.) option are also available:
@@ -5058,8 +5058,6 @@ def quantile(
             was previously called "interpolation", renamed in accordance with numpy
             version 1.22.0.
 
-            (*) These methods require numpy version 1.22 or newer.
-
         keep_attrs : bool or None, optional
             If True, the dataset's attributes (`attrs`) will be copied from
             the original object to the new one.  If False (default), the new