$Merge branch 'main' into grouper-objects

* main: (34 commits) Update whats-new.rst Fix binning by unsorted array (pydata#7762) Bump codecov/codecov-action from 3.1.1 to 3.1.2 (pydata#7760) Fix typing errors using mypy 1.2 (pydata#7752) [skip-ci] dev whats-new Add whats-new for v2023.04.0 (pydata#7757) remove the `black` hook (pydata#7756) reword the what's new entry for the `pandas` 2.0 dtype changes (pydata#7755) restructure the contributing guide (pydata#7681) Continue to use nanosecond-precision Timestamps in precision-sensitive areas (pydata#7731) minor doc updates to clarify extensions using accessors (pydata#7751) align: Avoid reindexing when join="exact" (pydata#7736) `pandas=2.0` support (pydata#7724) Clarify vectorized indexing documentation (pydata#7747) Avoid recasting a CFTimeIndex (pydata#7735) fix typo (pydata#7746) [pre-commit.ci] pre-commit autoupdate (pydata#7745) Bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 (pydata#7743) preserve boolean dtype in encoding (pydata#7720) [skip-ci] Add alignment benchmarks (pydata#7738) ...
dcherian · Apr 18, 2023 · 5a0ba46 · 5a0ba46
2 parents 2188a17 + 4f5675c
commit 5a0ba46
Show file tree

Hide file tree

Showing 75 changed files with 1,865 additions and 577 deletions.
diff --git a/.github/config.yml b/.github/config.yml
@@ -0,0 +1,23 @@
+# Comment to be posted to on first time issues
+newIssueWelcomeComment: >
+  Thanks for opening your first issue here at xarray! Be sure to follow the issue template!
+
+  If you have an idea for a solution, we would really welcome a Pull Request with proposed changes.
+
+  See the [Contributing Guide](https://docs.xarray.dev/en/latest/contributing.html) for more.
+
+  It may take us a while to respond here, but we really value your contribution. Contributors like you help make xarray better.
+
+  Thank you!
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  Thank you for opening this pull request! It may take us a few days to respond here, so thank you for being patient.
+
+  If you have questions, some answers may be found in our [contributing guidelines](http://docs.xarray.dev/en/stable/contributing.html).
+
+# Comment to be posted to on pull requests merged by a first time user
+firstPRMergeComment: >
+  Congratulations on completing your first pull request! Welcome to Xarray!
+  We are proud of you, and hope to see you again!
+  ![celebration gif](https://media.giphy.com/media/umYMU8G2ixG5mJBDo5/giphy.gif)
diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -119,14 +119,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install 'mypy<0.990'
+          python -m pip install mypy --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.1
+        uses: codecov/codecov-action@v3.1.2
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -173,14 +173,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install 'mypy<0.990'
+          python -m pip install mypy --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.1
+        uses: codecov/codecov-action@v3.1.2
         with:
           file: mypy_report/cobertura.xml
           flags: mypy39

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -139,7 +139,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.1
+        uses: codecov/codecov-action@v3.1.2
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/pypi-release.yaml b/.github/workflows/pypi-release.yaml
@@ -72,7 +72,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.8.3
+        uses: pypa/gh-action-pypi-publish@v1.8.5
         with:
           user: __token__
           password: ${{ secrets.TESTPYPI_TOKEN }}
@@ -90,7 +90,7 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.8.3
+        uses: pypa/gh-action-pypi-publish@v1.8.5
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

diff --git a/.github/workflows/testpypi-release.yaml b/.github/workflows/testpypi-release.yaml
@@ -78,7 +78,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.8.3
+        uses: pypa/gh-action-pypi-publish@v1.8.5
         with:
           user: __token__
           password: ${{ secrets.TESTPYPI_TOKEN }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -16,25 +16,24 @@ repos:
         files: ^xarray/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.259'
+    rev: 'v0.0.261'
     hooks:
       - id: ruff
         args: ["--fix"]
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
-      - id: black
       - id: black-jupyter
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.8
     hooks:
       - id: blackdoc
         exclude: "generate_aggregations.py"
-        additional_dependencies: ["black==23.1.0"]
+        additional_dependencies: ["black==23.3.0"]
       - id: blackdoc-autoupdate-black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
+    rev: v1.2.0
     hooks:
       - id: mypy
         # Copied from setup.cfg

diff --git a/asv_bench/asv.conf.json b/asv_bench/asv.conf.json
@@ -68,7 +68,8 @@
         "distributed": [""],
         "flox": [""],
         "numpy_groupies": [""],
-        "sparse": [""]
+        "sparse": [""],
+        "cftime": [""]
     },
 
 

diff --git a/asv_bench/benchmarks/alignment.py b/asv_bench/benchmarks/alignment.py
@@ -0,0 +1,54 @@
+import numpy as np
+
+import xarray as xr
+
+from . import parameterized, requires_dask
+
+ntime = 365 * 30
+nx = 50
+ny = 50
+
+rng = np.random.default_rng(0)
+
+
+class Align:
+    def setup(self, *args, **kwargs):
+        data = rng.standard_normal((ntime, nx, ny))
+        self.ds = xr.Dataset(
+            {"temperature": (("time", "x", "y"), data)},
+            coords={
+                "time": xr.date_range("2000", periods=ntime),
+                "x": np.arange(nx),
+                "y": np.arange(ny),
+            },
+        )
+        self.year = self.ds.time.dt.year
+        self.idx = np.unique(rng.integers(low=0, high=ntime, size=ntime // 2))
+        self.year_subset = self.year.isel(time=self.idx)
+
+    @parameterized(["join"], [("outer", "inner", "left", "right", "exact", "override")])
+    def time_already_aligned(self, join):
+        xr.align(self.ds, self.year, join=join)
+
+    @parameterized(["join"], [("outer", "inner", "left", "right")])
+    def time_not_aligned(self, join):
+        xr.align(self.ds, self.year[-100:], join=join)
+
+    @parameterized(["join"], [("outer", "inner", "left", "right")])
+    def time_not_aligned_random_integers(self, join):
+        xr.align(self.ds, self.year_subset, join=join)
+
+
+class AlignCFTime(Align):
+    def setup(self, *args, **kwargs):
+        super().setup()
+        self.ds["time"] = xr.date_range("2000", periods=ntime, calendar="noleap")
+        self.year = self.ds.time.dt.year
+        self.year_subset = self.year.isel(time=self.idx)
+
+
+class AlignDask(Align):
+    def setup(self, *args, **kwargs):
+        requires_dask()
+        super().setup()
+        self.ds = self.ds.chunk({"time": 100})
diff --git a/ci/requirements/all-but-dask.yml b/ci/requirements/all-but-dask.yml
@@ -25,7 +25,7 @@ dependencies:
   - numbagg
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pseudonetcdf

diff --git a/ci/requirements/doc.yml b/ci/requirements/doc.yml
@@ -19,7 +19,7 @@ dependencies:
   - numba
   - numpy>=1.21,<1.24
   - packaging>=21.3
-  - pandas>=1.4,<2
+  - pandas>=1.4
   - pooch
   - pip
   - pre-commit

diff --git a/ci/requirements/environment-py311.yml b/ci/requirements/environment-py311.yml
@@ -27,7 +27,7 @@ dependencies:
   - numexpr
   - numpy
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pooch

diff --git a/ci/requirements/environment-windows-py311.yml b/ci/requirements/environment-windows-py311.yml
@@ -24,7 +24,7 @@ dependencies:
   # - numbagg
   - numpy
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pre-commit

diff --git a/ci/requirements/environment-windows.yml b/ci/requirements/environment-windows.yml
@@ -24,7 +24,7 @@ dependencies:
   - numbagg
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pre-commit

diff --git a/ci/requirements/environment.yml b/ci/requirements/environment.yml
@@ -27,7 +27,7 @@ dependencies:
   - numexpr
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pooch

diff --git a/doc/api-hidden.rst b/doc/api-hidden.rst
@@ -234,6 +234,7 @@
    Variable.dims
    Variable.dtype
    Variable.encoding
+   Variable.reset_encoding
    Variable.imag
    Variable.nbytes
    Variable.ndim
@@ -374,10 +375,8 @@
    CFTimeIndex.is_floating
    CFTimeIndex.is_integer
    CFTimeIndex.is_interval
-   CFTimeIndex.is_mixed
    CFTimeIndex.is_numeric
    CFTimeIndex.is_object
-   CFTimeIndex.is_type_compatible
    CFTimeIndex.isin
    CFTimeIndex.isna
    CFTimeIndex.isnull
@@ -398,7 +397,6 @@
    CFTimeIndex.round
    CFTimeIndex.searchsorted
    CFTimeIndex.set_names
-   CFTimeIndex.set_value
    CFTimeIndex.shift
    CFTimeIndex.slice_indexer
    CFTimeIndex.slice_locs
@@ -412,7 +410,6 @@
    CFTimeIndex.to_flat_index
    CFTimeIndex.to_frame
    CFTimeIndex.to_list
-   CFTimeIndex.to_native_types
    CFTimeIndex.to_numpy
    CFTimeIndex.to_series
    CFTimeIndex.tolist
@@ -437,8 +434,6 @@
    CFTimeIndex.hasnans
    CFTimeIndex.hour
    CFTimeIndex.inferred_type
-   CFTimeIndex.is_all_dates
-   CFTimeIndex.is_monotonic
    CFTimeIndex.is_monotonic_increasing
    CFTimeIndex.is_monotonic_decreasing
    CFTimeIndex.is_unique
@@ -483,7 +478,6 @@
    backends.NetCDF4DataStore.is_remote
    backends.NetCDF4DataStore.lock
 
-   backends.NetCDF4BackendEntrypoint.available
    backends.NetCDF4BackendEntrypoint.description
    backends.NetCDF4BackendEntrypoint.url
    backends.NetCDF4BackendEntrypoint.guess_can_open
@@ -516,7 +510,6 @@
    backends.H5NetCDFStore.sync
    backends.H5NetCDFStore.ds
 
-   backends.H5netcdfBackendEntrypoint.available
    backends.H5netcdfBackendEntrypoint.description
    backends.H5netcdfBackendEntrypoint.url
    backends.H5netcdfBackendEntrypoint.guess_can_open
@@ -531,7 +524,6 @@
    backends.PseudoNetCDFDataStore.open_store_variable
    backends.PseudoNetCDFDataStore.ds
 
-   backends.PseudoNetCDFBackendEntrypoint.available
    backends.PseudoNetCDFBackendEntrypoint.description
    backends.PseudoNetCDFBackendEntrypoint.url
    backends.PseudoNetCDFBackendEntrypoint.guess_can_open
@@ -546,7 +538,6 @@
    backends.PydapDataStore.open
    backends.PydapDataStore.open_store_variable
 
-   backends.PydapBackendEntrypoint.available
    backends.PydapBackendEntrypoint.description
    backends.PydapBackendEntrypoint.url
    backends.PydapBackendEntrypoint.guess_can_open
@@ -574,7 +565,6 @@
    backends.ScipyDataStore.sync
    backends.ScipyDataStore.ds
 
-   backends.ScipyBackendEntrypoint.available
    backends.ScipyBackendEntrypoint.description
    backends.ScipyBackendEntrypoint.url
    backends.ScipyBackendEntrypoint.guess_can_open
@@ -595,13 +585,11 @@
    backends.ZarrStore.sync
    backends.ZarrStore.ds
 
-   backends.ZarrBackendEntrypoint.available
    backends.ZarrBackendEntrypoint.description
    backends.ZarrBackendEntrypoint.url
    backends.ZarrBackendEntrypoint.guess_can_open
    backends.ZarrBackendEntrypoint.open_dataset
 
-   backends.StoreBackendEntrypoint.available
    backends.StoreBackendEntrypoint.description
    backends.StoreBackendEntrypoint.url
    backends.StoreBackendEntrypoint.guess_can_open

diff --git a/doc/api.rst b/doc/api.rst
@@ -112,6 +112,7 @@ Dataset contents
    Dataset.drop_dims
    Dataset.set_coords
    Dataset.reset_coords
+   Dataset.reset_encoding
    Dataset.convert_calendar
    Dataset.interp_calendar
    Dataset.get_index
@@ -303,6 +304,7 @@ DataArray contents
    DataArray.drop_indexes
    DataArray.drop_duplicates
    DataArray.reset_coords
+   DataArray.reset_encoding
    DataArray.copy
    DataArray.convert_calendar
    DataArray.interp_calendar
@@ -640,6 +642,7 @@ DataArray methods
    DataArray.to_numpy
    DataArray.to_pandas
    DataArray.to_series
+   DataArray.to_zarr
    DataArray.chunk
    DataArray.close
    DataArray.compute
@@ -1094,6 +1097,7 @@ Advanced API
    backends.BackendArray
    backends.BackendEntrypoint
    backends.list_engines
+   backends.refresh_engines
 
 Default, pandas-backed indexes built-in Xarray: