Merge branch 'main' into groupby-shuffle

* main: (29 commits)
  Release notes for v2024.09.0 (pydata#9480)
  Fix `DataTree.coords.__setitem__` by adding `DataTreeCoordinates` class (pydata#9451)
  Rename DataTree's "ds" and "data" to "dataset" (pydata#9476)
  Update DataTree repr to indicate inheritance (pydata#9470)
  Bump pypa/gh-action-pypi-publish in the actions group (pydata#9460)
  Repo checker (pydata#9450)
  Add days_in_year and decimal_year to dt accessor (pydata#9105)
  remove parent argument from DataTree.__init__ (pydata#9465)
  Fix inheritance in DataTree.copy() (pydata#9457)
  Implement `DataTree.__delitem__` (pydata#9453)
  Add ASV for datatree.from_dict (pydata#9459)
  Make the first argument in DataTree.from_dict positional only (pydata#9446)
  Fix typos across the code, doc and comments (pydata#9443)
  DataTree should not be "Generic" (pydata#9445)
  Disallow passing a DataArray as data into the DataTree constructor (pydata#9444)
  Support additional dtypes in `resample` (pydata#9413)
  Shallow copy parent and children in DataTree constructor (pydata#9297)
  Bump minimum versions for dependencies (pydata#9434)
  Always include at least one category in random test data (pydata#9436)
  Avoid deep-copy when constructing groupby codes (pydata#9429)
  ...

Author: dcherian

.github/workflows/ci-additional.yaml

@@ -123,11 +123,11 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.9" --force-reinstall
+          python -m pip install "mypy" --force-reinstall
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/[email protected]
@@ -138,7 +138,7 @@ jobs:
           name: codecov-umbrella
           fail_ci_if_error: false
 
-  mypy39:
+  mypy-min:
     name: Mypy 3.10
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
@@ -177,32 +177,30 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.9" --force-reinstall
+          python -m pip install "mypy" --force-reinstall
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/[email protected]
         with:
           file: mypy_report/cobertura.xml
-          flags: mypy39
+          flags: mypy-min
           env_vars: PYTHON_VERSION
           name: codecov-umbrella
           fail_ci_if_error: false
 
-
-
   pyright:
     name: Pyright
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: |
-        always()
-        && (
-            contains( github.event.pull_request.labels.*.name, 'run-pyright')
-        )
+      always()
+      && (
+          contains( github.event.pull_request.labels.*.name, 'run-pyright')
+      )
     defaults:
       run:
         shell: bash -l {0}
@@ -258,10 +256,10 @@ jobs:
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: |
-        always()
-        && (
-            contains( github.event.pull_request.labels.*.name, 'run-pyright')
-        )
+      always()
+      && (
+          contains( github.event.pull_request.labels.*.name, 'run-pyright')
+      )
     defaults:
       run:
         shell: bash -l {0}
@@ -312,8 +310,6 @@ jobs:
           name: codecov-umbrella
           fail_ci_if_error: false
 
-
-
   min-version-policy:
     name: Minimum Version Policy
     runs-on: "ubuntu-latest"

.github/workflows/pypi-release.yaml

@@ -88,7 +88,7 @@ jobs:
           path: dist
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.1
         with:
           repository_url: https://test.pypi.org/legacy/
           verbose: true
@@ -111,6 +111,6 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.1
         with:
           verbose: true

.pre-commit-config.yaml

@@ -1,6 +1,7 @@
 # https://pre-commit.com/
 ci:
     autoupdate_schedule: monthly
+    autoupdate_commit_msg: 'Update pre-commit hooks'
 exclude: 'xarray/datatree_.*'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -13,7 +14,7 @@ repos:
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.6.2'
+    rev: 'v0.6.3'
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]

asv_bench/benchmarks/dataset_io.py

@@ -724,7 +724,7 @@ class PerformanceBackend(xr.backends.BackendEntrypoint):
             def open_dataset(
                 self,
                 filename_or_obj: str | os.PathLike | None,
-                drop_variables: tuple[str] = None,
+                drop_variables: tuple[str, ...] = None,
                 *,
                 mask_and_scale=True,
                 decode_times=True,

asv_bench/benchmarks/datatree.py

@@ -0,0 +1,15 @@
+import xarray as xr
+from xarray.core.datatree import DataTree
+
+
+class Datatree:
+    def setup(self):
+        run1 = DataTree.from_dict({"run1": xr.Dataset({"a": 1})})
+        self.d_few = {"run1": run1}
+        self.d_many = {f"run{i}": xr.Dataset({"a": 1}) for i in range(100)}
+
+    def time_from_dict_few(self):
+        DataTree.from_dict(self.d_few)
+
+    def time_from_dict_many(self):
+        DataTree.from_dict(self.d_many)

asv_bench/benchmarks/groupby.py

@@ -1,4 +1,5 @@
 # import flox to avoid the cost of first import
+import cftime
 import flox.xarray  # noqa
 import numpy as np
 import pandas as pd
@@ -96,7 +97,7 @@ def setup(self, *args, **kwargs):
 
         requires_dask()
         super().setup(**kwargs)
-        self.ds1d = self.ds1d.chunk({"dim_0": 50}).to_dataframe()
+        self.ds1d = self.ds1d.chunk({"dim_0": 50}).to_dask_dataframe()
         self.ds1d_mean = self.ds1d.groupby("b").mean().compute()
 
     def time_binary_op_2d(self):
@@ -169,7 +170,21 @@ class GroupByLongTime:
     def setup(self, use_cftime, use_flox):
         arr = np.random.randn(10, 10, 365 * 30)
         time = xr.date_range("2000", periods=30 * 365, use_cftime=use_cftime)
-        self.da = xr.DataArray(arr, dims=("y", "x", "time"), coords={"time": time})
+
+        # GH9426 - deep-copying CFTime object arrays is weirdly slow
+        asda = xr.DataArray(time)
+        labeled_time = []
+        for year, month in zip(asda.dt.year, asda.dt.month, strict=True):
+            labeled_time.append(cftime.datetime(year, month, 1))
+
+        self.da = xr.DataArray(
+            arr,
+            dims=("y", "x", "time"),
+            coords={"time": time, "time2": ("time", labeled_time)},
+        )
+
+    def time_setup(self, use_cftime, use_flox):
+        self.da.groupby("time.month")
 
     def time_mean(self, use_cftime, use_flox):
         with xr.set_options(use_flox=use_flox):

asv_bench/benchmarks/rolling.py

@@ -64,7 +64,7 @@ def time_rolling_long(self, func, pandas, use_bottleneck):
     def time_rolling_np(self, window_, min_periods, use_bottleneck):
         with xr.set_options(use_bottleneck=use_bottleneck):
             self.ds.rolling(x=window_, center=False, min_periods=min_periods).reduce(
-                getattr(np, "nansum")
+                np.nansum
             ).load()
 
     @parameterized(

ci/requirements/bare-minimum.yml

@@ -11,6 +11,6 @@ dependencies:
   - pytest-env
   - pytest-xdist
   - pytest-timeout
-  - numpy=1.23
+  - numpy=1.24
   - packaging=23.1
-  - pandas=2.0
+  - pandas=2.1

ci/requirements/min-all-deps.yml

@@ -9,37 +9,37 @@ dependencies:
   # doc/user-guide/installing.rst, doc/user-guide/plotting.rst and setup.py.
   - python=3.10
   - array-api-strict=1.0  # dependency for testing the array api compat
-  - boto3=1.26
+  - boto3=1.28
   - bottleneck=1.3
-  - cartopy=0.21
+  - cartopy=0.22
   - cftime=1.6
   - coveralls
-  - dask-core=2023.4
-  - distributed=2023.4
+  - dask-core=2023.9
+  - distributed=2023.9
   # Flox > 0.8 has a bug with numbagg versions
   # It will require numbagg > 0.6
   # so we should just skip that series eventually
   # or keep flox pinned for longer than necessary
   - flox=0.7
-  - h5netcdf=1.1
+  - h5netcdf=1.2
   # h5py and hdf5 tend to cause conflicts
   # for e.g. hdf5 1.12 conflicts with h5py=3.1
   # prioritize bumping other packages instead
   - h5py=3.8
   - hdf5=1.12
   - hypothesis
-  - iris=3.4
+  - iris=3.7
   - lxml=4.9  # Optional dep of pydap
   - matplotlib-base=3.7
   - nc-time-axis=1.4
   # netcdf follows a 1.major.minor[.patch] convention
   # (see https://github.com/Unidata/netcdf4-python/issues/1090)
   - netcdf4=1.6.0
-  - numba=0.56
+  - numba=0.57
   - numbagg=0.2.1
-  - numpy=1.23
+  - numpy=1.24
   - packaging=23.1
-  - pandas=2.0
+  - pandas=2.1
   - pint=0.22
   - pip
   - pydap=3.4
@@ -49,9 +49,9 @@ dependencies:
   - pytest-xdist
   - pytest-timeout
   - rasterio=1.3
-  - scipy=1.10
+  - scipy=1.11
   - seaborn=0.12
   - sparse=0.14
   - toolz=0.12
-  - typing_extensions=4.5
-  - zarr=2.14
+  - typing_extensions=4.7
+  - zarr=2.16

design_notes/flexible_indexes_notes.md

@@ -71,7 +71,7 @@ An `XarrayIndex` subclass must/should/may implement the following properties/met
 - a `data` property to access index's data and map it to coordinate data (see [Section 4](#4-indexvariable))
 - a `__getitem__()` implementation to propagate the index through DataArray/Dataset indexing operations
 - `equals()`, `union()` and `intersection()` methods for data alignment (see [Section 2.6](#26-using-indexes-for-data-alignment))
-- Xarray coordinate getters (see [Section 2.2.4](#224-implicit-coodinates))
+- Xarray coordinate getters (see [Section 2.2.4](#224-implicit-coordinates))
 - a method that may return a new index and that will be called when one of the corresponding coordinates is dropped from the Dataset/DataArray (multi-coordinate indexes)
 - `encode()`/`decode()` methods that would allow storage-agnostic serialization and fast-path reconstruction of the underlying index object(s) (see [Section 2.8](#28-index-encoding))
 - one or more "non-standard" methods or properties that could be leveraged in Xarray 3rd-party extensions like Dataset/DataArray accessors (see [Section 2.7](#27-using-indexes-for-other-purposes))