Merge branch 'main' into Illviljan-dont_transpose_1d_arrays_during_interp

Author: Illviljan

.github/workflows/ci-pre-commit-autoupdate.yaml

@@ -35,7 +35,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           EXECUTE_COMMANDS: |
             python -m pre_commit autoupdate
-            python .github/workflows/sync_linter_versions.py .pre-commit-config.yaml ci/requirements/mypy_only
             python -m pre_commit run --all-files
           COMMIT_MESSAGE: 'pre-commit: autoupdate hook versions'
           COMMIT_NAME: 'github-actions[bot]'

.github/workflows/sync_linter_versions.py

@@ -8,16 +8,16 @@ repos:
       - id: check-yaml
   # isort should run before black as black sometimes tweaks the isort output
   - repo: https://github.com/PyCQA/isort
-    rev: 5.9.1
+    rev: 5.9.2
     hooks:
       - id: isort
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 21.6b0
+    rev: 21.7b0
     hooks:
       - id: black
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.3
+    rev: v0.3.4
     hooks:
       - id: blackdoc
   - repo: https://gitlab.com/pycqa/flake8
@@ -30,7 +30,6 @@ repos:
   #     - id: velin
   #       args: ["--write", "--compact"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    # version must correspond to the one in .github/workflows/ci-additional.yaml
     rev: v0.910
     hooks:
       - id: mypy

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ conda uninstall -y --force \
     matplotlib \
     dask \
     distributed \
+    fsspec \
     zarr \
     cftime \
     rasterio \
@@ -40,4 +41,5 @@ python -m pip install \
     git+https://github.com/mapbox/rasterio \
     git+https://github.com/hgrecco/pint \
     git+https://github.com/pydata/bottleneck \
-    git+https://github.com/pydata/sparse
+    git+https://github.com/pydata/sparse \
+    git+https://github.com/intake/filesystem_spec

ci/install-upstream-wheels.sh

@@ -96,7 +96,7 @@ dependencies:
 - **setuptools:** 42 months (but no older than 40.4)
 - **numpy:** 18 months
   (`NEP-29 <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_)
-- **dask and dask.distributed:** 12 months (but no older than 2.9)
+- **dask and dask.distributed:** 12 months
 - **sparse, pint** and other libraries that rely on
   `NEP-18 <https://numpy.org/neps/nep-0018-array-function-protocol.html>`_
   for integration: very latest available versions only, until the technology will have

doc/getting-started-guide/installing.rst

@@ -21,6 +21,9 @@ v0.18.3 (unreleased)
 
 New Features
 ~~~~~~~~~~~~
+- Allow passing argument ``missing_dims`` to :py:meth:`Variable.transpose` and :py:meth:`Dataset.transpose`
+  (:issue:`5550`, :pull:`5586`)
+  By `Giacomo Caria <https://github.com/gcaria>`_.
 - Allow passing a dictionary as coords to a :py:class:`DataArray` (:issue:`5527`,
   reverts :pull:`1539`, which had deprecated this due to python's inconsistent ordering in earlier versions).
   By `Sander van Rijn <https://github.com/sjvrijn>`_.
@@ -62,6 +65,10 @@ Breaking changes
   pre-existing array values. This is a safer default than the prior ``mode="a"``,
   and allows for higher performance writes (:pull:`5252`).
   By `Stephan Hoyer <https://github.com/shoyer>`_.
+- The main parameter to :py:func:`combine_by_coords` is renamed to `data_objects` instead
+  of `datasets` so anyone calling this method using a named parameter will need to update
+  the name accordingly (:issue:`3248`, :pull:`4696`).
+  By `Augustus Ijams <https://github.com/aijams>`_.
 
 Deprecations
 ~~~~~~~~~~~~
@@ -85,6 +92,9 @@ Bug fixes
 - Plotting a pcolormesh with ``xscale="log"`` and/or ``yscale="log"`` works as
   expected after improving the way the interval breaks are generated (:issue:`5333`).
   By `Santiago Soler <https://github.com/santisoler>`_
+- :py:func:`combine_by_coords` can now handle combining a list of unnamed
+  ``DataArray`` as input (:issue:`3248`, :pull:`4696`).
+  By `Augustus Ijams <https://github.com/aijams>`_.
 
 
 Documentation
@@ -146,20 +156,14 @@ New Features
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
-- The main parameter to :py:func:`combine_by_coords` is renamed to `data_objects` instead
-  of `datasets` so anyone calling this method using a named parameter will need to update
-  the name accordingly (:issue:`3248`, :pull:`4696`).
-  By `Augustus Ijams <https://github.com/aijams>`_.
+
 
 Deprecations
 ~~~~~~~~~~~~
 
 
 Bug fixes
 ~~~~~~~~~
-- :py:func:`combine_by_coords` can now handle combining a list of unnamed
-  ``DataArray`` as input (:issue:`3248`, :pull:`4696`).
-  By `Augustus Ijams <https://github.com/aijams>`_.
 - Opening netCDF files from a path that doesn't end in ``.nc`` without supplying
   an explicit ``engine`` works again (:issue:`5295`), fixing a bug introduced in
   0.18.0.

doc/whats-new.rst

@@ -737,6 +737,7 @@ def open_zarr(
     See Also
     --------
     open_dataset
+    open_mfdataset
 
     References
     ----------

xarray/backends/zarr.py

@@ -4543,7 +4543,11 @@ def drop_dims(
         drop_vars = {k for k, v in self._variables.items() if set(v.dims) & drop_dims}
         return self.drop_vars(drop_vars)
 
-    def transpose(self, *dims: Hashable) -> "Dataset":
+    def transpose(
+        self,
+        *dims: Hashable,
+        missing_dims: str = "raise",
+    ) -> "Dataset":
         """Return a new Dataset object with all array dimensions transposed.
 
         Although the order of dimensions on each array will change, the dataset
@@ -4554,6 +4558,12 @@ def transpose(self, *dims: Hashable) -> "Dataset":
         *dims : hashable, optional
             By default, reverse the dimensions on each array. Otherwise,
             reorder the dimensions to this order.
+        missing_dims : {"raise", "warn", "ignore"}, default: "raise"
+            What to do if dimensions that should be selected from are not present in the
+            Dataset:
+            - "raise": raise an exception
+            - "warn": raise a warning, and ignore the missing dimensions
+            - "ignore": ignore the missing dimensions
 
         Returns
         -------
@@ -4572,12 +4582,10 @@ def transpose(self, *dims: Hashable) -> "Dataset":
         numpy.transpose
         DataArray.transpose
         """
-        if dims:
-            if set(dims) ^ set(self.dims) and ... not in dims:
-                raise ValueError(
-                    f"arguments to transpose ({dims}) must be "
-                    f"permuted dataset dimensions ({tuple(self.dims)})"
-                )
+        # Use infix_dims to check once for missing dimensions
+        if len(dims) != 0:
+            _ = list(infix_dims(dims, self.dims, missing_dims))
+
         ds = self.copy()
         for name, var in self._variables.items():
             var_dims = tuple(dim for dim in dims if dim in (var.dims + (...,)))

xarray/core/dataset.py

@@ -1378,14 +1378,24 @@ def roll(self, shifts=None, **shifts_kwargs):
             result = result._roll_one_dim(dim, count)
         return result
 
-    def transpose(self, *dims) -> "Variable":
+    def transpose(
+        self,
+        *dims,
+        missing_dims: str = "raise",
+    ) -> "Variable":
         """Return a new Variable object with transposed dimensions.
 
         Parameters
         ----------
         *dims : str, optional
             By default, reverse the dimensions. Otherwise, reorder the
             dimensions to this order.
+        missing_dims : {"raise", "warn", "ignore"}, default: "raise"
+            What to do if dimensions that should be selected from are not present in the
+            Variable:
+            - "raise": raise an exception
+            - "warn": raise a warning, and ignore the missing dimensions
+            - "ignore": ignore the missing dimensions
 
         Returns
         -------
@@ -1404,7 +1414,9 @@ def transpose(self, *dims) -> "Variable":
         """
         if len(dims) == 0:
             dims = self.dims[::-1]
-        dims = tuple(infix_dims(dims, self.dims))
+        else:
+            dims = tuple(infix_dims(dims, self.dims, missing_dims))
+
         if len(dims) < 2 or dims == self.dims:
             # no need to transpose if only one dimension
             # or dims are in same order