Merge branch 'main' into init-zarr

.github/workflows/benchmarks-last-release.yml

@@ -72,7 +72,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

.github/workflows/benchmarks.yml

@@ -67,7 +67,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

.github/workflows/ci-additional.yaml

@@ -320,11 +320,6 @@ jobs:
       run:
         shell: bash -l {0}
 
-    strategy:
-      matrix:
-        environment-file: ["bare-minimum", "min-all-deps"]
-      fail-fast: false
-
     steps:
       - uses: actions/checkout@v4
         with:
@@ -340,6 +335,10 @@ jobs:
             conda
             python-dateutil
 
-      - name: minimum versions policy
+      - name: All-deps minimum versions policy
+        run: |
+          python ci/min_deps_check.py ci/requirements/min-all-deps.yml
+
+      - name: Bare minimum versions policy
         run: |
-          python ci/min_deps_check.py ci/requirements/${{ matrix.environment-file }}.yml
+          python ci/min_deps_check.py ci/requirements/bare-minimum.yml

.github/workflows/ci.yaml

@@ -34,6 +34,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    env:
+      ZARR_V3_EXPERIMENTAL_API: 1
     defaults:
       run:
         shell: bash -l {0}
@@ -127,9 +129,9 @@ jobs:
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
+          name: Test results for ${{ runner.os }}-${{ matrix.python-version }} ${{ matrix.env }}
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
@@ -147,7 +149,7 @@ jobs:
     if: github.repository == 'pydata/xarray'
     steps:
       - name: Upload
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Event File
           path: ${{ github.event_path }}

.github/workflows/pypi-release.yaml

@@ -41,7 +41,7 @@ jobs:
           else
             echo "✅ Looks good"
           fi
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist

.github/workflows/upstream-dev-ci.yaml

@@ -37,6 +37,8 @@ jobs:
     name: upstream-dev
     runs-on: ubuntu-latest
     needs: detect-ci-trigger
+    env:
+      ZARR_V3_EXPERIMENTAL_API: 1
     if: |
         always()
         && (
@@ -82,7 +84,6 @@ jobs:
         if: success()
         id: status
         run: |
-          export ZARR_V3_EXPERIMENTAL_API=1
           python -m pytest --timeout=60 -rf \
             --report-log output-${{ matrix.python-version }}-log.jsonl
       - name: Generate and publish the report

ci/requirements/bare-minimum.yml

@@ -11,6 +11,6 @@ dependencies:
   - pytest-env
   - pytest-xdist
   - pytest-timeout
-  - numpy=1.22
-  - packaging=21.3
-  - pandas=1.4
+  - numpy=1.23
+  - packaging=22.0
+  - pandas=1.5

ci/requirements/min-all-deps.yml

@@ -10,30 +10,35 @@ dependencies:
   - python=3.9
   - boto3=1.24
   - bottleneck=1.3
-  - cartopy=0.20
+  - cartopy=0.21
   - cftime=1.6
   - coveralls
-  - dask-core=2022.7
-  - distributed=2022.7
-  - flox=0.5
+  - dask-core=2022.12
+  - distributed=2022.12
+  # 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
   # h5py and hdf5 tend to cause conflicts
   # for e.g. hdf5 1.12 conflicts with h5py=3.1
   # prioritize bumping other packages instead
   - h5py=3.7
   - hdf5=1.12
   - hypothesis
-  - iris=3.2
+  - iris=3.4
   - lxml=4.9  # Optional dep of pydap
-  - matplotlib-base=3.5
+  - matplotlib-base=3.6
   - 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=0.55
-  - numpy=1.22
-  - packaging=21.3
-  - pandas=1.4
+  - numba=0.56
+  - numbagg=0.2.1
+  - numpy=1.23
+  - packaging=22.0
+  - pandas=1.5
   - pint=0.22
   - pip
   - pydap=3.3
@@ -43,11 +48,9 @@ dependencies:
   - pytest-xdist
   - pytest-timeout
   - rasterio=1.3
-  - scipy=1.8
-  - seaborn=0.11
+  - scipy=1.10
+  - seaborn=0.12
   - sparse=0.13
   - toolz=0.12
-  - typing_extensions=4.3
-  - zarr=2.12
-  - pip:
-    - numbagg==0.2.1
+  - typing_extensions=4.4
+  - zarr=2.13

doc/ecosystem.rst

@@ -98,7 +98,6 @@ Visualization
 Non-Python projects
 ~~~~~~~~~~~~~~~~~~~
 - `xframe <https://github.com/xtensor-stack/xframe>`_: C++ data structures inspired by xarray.
-- `AxisArrays <https://github.com/JuliaArrays/AxisArrays.jl>`_ and
-  `NamedArrays <https://github.com/davidavdav/NamedArrays.jl>`_: similar data structures for Julia.
+- `AxisArrays <https://github.com/JuliaArrays/AxisArrays.jl>`_, `NamedArrays <https://github.com/davidavdav/NamedArrays.jl>`_ and `YAXArrays.jl <https://github.com/JuliaDataCubes/YAXArrays.jl>`_: similar data structures for Julia.
 
 More projects can be found at the `"xarray" Github topic <https://github.com/topics/xarray>`_.

doc/whats-new.rst

@@ -34,6 +34,26 @@ New Features
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
+- The minimum versions of some dependencies were changed (:pull:`8586`):
+
+  ===================== =========  ========
+   Package                    Old      New
+  ===================== =========  ========
+   cartopy                   0.20      0.21
+   dask-core               2022.7   2022.12
+   distributed             2022.7   2022.12
+   flox                       0.5      0.7
+   iris                       3.2      3.4
+   matplotlib-base            3.5      3.6
+   numpy                     1.22     1.23
+   numba                     0.55     0.56
+   packaging                 21.3     22.0
+   seaborn                   0.11     0.12
+   scipy                      1.8     1.10
+   typing_extensions          4.3      4.4
+   zarr                      2.12     2.13
+  ===================== =========  ========
+
 
 Deprecations
 ~~~~~~~~~~~~

pyproject.toml

@@ -22,9 +22,9 @@ readme = "README.md"
 requires-python = ">=3.9"
 
 dependencies = [
-  "numpy>=1.22",
-  "packaging>=21.3",
-  "pandas>=1.4",
+  "numpy>=1.23",
+  "packaging>=22",
+  "pandas>=1.5",
 ]
 
 [project.urls]

xarray/coding/variables.py

@@ -414,7 +414,7 @@ def decode(self, variable: Variable, name: T_Name = None) -> Variable:
 class UnsignedIntegerCoder(VariableCoder):
     def encode(self, variable: Variable, name: T_Name = None) -> Variable:
         # from netCDF best practices
-        # https://www.unidata.ucar.edu/software/netcdf/docs/BestPractices.html
+        # https://docs.unidata.ucar.edu/nug/current/best_practices.html#bp_Unsigned-Data
         #     "_Unsigned = "true" to indicate that
         #      integer data should be treated as unsigned"
         if variable.encoding.get("_Unsigned", "false") == "true":

xarray/tests/test_backends.py

@@ -443,8 +443,6 @@ def test_pickle(self) -> None:
 
     @pytest.mark.filterwarnings("ignore:deallocating CachingFileManager")
     def test_pickle_dataarray(self) -> None:
-        if not has_dask:
-            pytest.xfail("pickling requires dask for SerializableLock")
         expected = Dataset({"foo": ("x", [42])})
         with self.roundtrip(expected, allow_cleanup_failure=ON_WINDOWS) as roundtripped:
             with roundtripped:

xarray/tests/test_conventions.py

@@ -52,10 +52,9 @@ def test_decode_cf_with_conflicting_fill_missing_value() -> None:
     var = Variable(
         ["t"], np.arange(3), {"units": "foobar", "missing_value": 0, "_FillValue": 1}
     )
-    with warnings.catch_warnings(record=True) as w:
+    with pytest.warns(SerializationWarning, match="has multiple fill"):
         actual = conventions.decode_cf_variable("t", var)
         assert_identical(actual, expected)
-        assert "has multiple fill" in str(w[0].message)
 
     expected = Variable(["t"], np.arange(10), {"units": "foobar"})
 
@@ -293,10 +292,9 @@ def test_0d_int32_encoding(self) -> None:
     def test_decode_cf_with_multiple_missing_values(self) -> None:
         original = Variable(["t"], [0, 1, 2], {"missing_value": np.array([0, 1])})
         expected = Variable(["t"], [np.nan, np.nan, 2], {})
-        with warnings.catch_warnings(record=True) as w:
+        with pytest.warns(SerializationWarning, match="has multiple fill"):
             actual = conventions.decode_cf_variable("t", original)
             assert_identical(expected, actual)
-            assert "has multiple fill" in str(w[0].message)
 
     def test_decode_cf_with_drop_variables(self) -> None:
         original = Dataset(
@@ -387,7 +385,6 @@ def test_decode_cf_with_dask(self) -> None:
             }
         ).chunk()
         decoded = conventions.decode_cf(original)
-        print(decoded)
         assert all(
             isinstance(var.data, da.Array)
             for name, var in decoded.variables.items()