CI: python 3.12 by default. (#8969)

* CI: python 3.12 by default.

Now that numba supports 3.12.

* limit flaky test run

* More flaky marks

* Use PYTEST_ADDOPTS

* More Nio cleanup

* cleanup

* disable pint

* More bumps

* Ignore pint if not installed

* skip mypy bump

Author: dcherian

.github/workflows/ci-additional.yaml

@@ -41,7 +41,7 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.11"
+      PYTHON_VERSION: "3.12"
     steps:
       - uses: actions/checkout@v4
         with:
@@ -205,7 +205,7 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.10"
+      PYTHON_VERSION: "3.12"
 
     steps:
       - uses: actions/checkout@v4
@@ -330,7 +330,7 @@ jobs:
         with:
           environment-name: xarray-tests
           create-args: >-
-            python=3.11
+            python=3.12
             pyyaml
             conda
             python-dateutil

.github/workflows/ci.yaml

@@ -44,7 +44,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.9", "3.11", "3.12"]
+        python-version: ["3.9",  "3.12"]
         env: [""]
         include:
           # Minimum python version:
@@ -56,10 +56,11 @@ jobs:
             os: ubuntu-latest
           # Latest python version:
           - env: "all-but-dask"
-            python-version: "3.10"
+            # Not 3.12 because of pint
+            python-version: "3.11"
             os: ubuntu-latest
           - env: "flaky"
-            python-version: "3.10"
+            python-version: "3.12"
             os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -71,30 +72,30 @@ jobs:
 
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
-            if [[ ${{ matrix.python-version }} != "3.12" ]]; then
+            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
               echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
             else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.12.yml" >> $GITHUB_ENV
+              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.13.yml" >> $GITHUB_ENV
             fi
           elif [[ "${{ matrix.env }}" != "" ]] ;
           then
             if [[ "${{ matrix.env }}" == "flaky" ]] ;
             then
               echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
-              echo "PYTEST_EXTRA_FLAGS=--run-flaky --run-network-tests -W default" >> $GITHUB_ENV
+              echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
             else
               echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
             fi
             if [[ "${{ matrix.env }}" == "min-all-deps" ]] ;
             then
               # Don't raise on warnings
-              echo "PYTEST_EXTRA_FLAGS=-W default" >> $GITHUB_ENV
+              echo "PYTEST_ADDOPTS=-W default" >> $GITHUB_ENV
             fi
           else
-            if [[ ${{ matrix.python-version }} != "3.12" ]]; then
+            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
               echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
             else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-3.12.yml" >> $GITHUB_ENV
+              echo "CONDA_ENV_FILE=ci/requirements/environment-3.13.yml" >> $GITHUB_ENV
             fi
           fi
 
@@ -114,7 +115,7 @@ jobs:
       # We only want to install this on one run, because otherwise we'll have
       # duplicate annotations.
       - name: Install error reporter
-        if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.10'
+        if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.12'
         run: |
           python -m pip install pytest-github-actions-annotate-failures
 
@@ -146,7 +147,6 @@ jobs:
           --cov=xarray
           --cov-report=xml
           --junitxml=pytest.xml
-          $PYTEST_EXTRA_FLAGS
 
       - name: Upload test results
         if: always()

.github/workflows/pypi-release.yaml

@@ -18,7 +18,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -53,7 +53,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - uses: actions/download-artifact@v4
         with:
           name: releases

ci/requirements/environment-3.12.yml renamed to ci/requirements/environment-3.13.yml

@@ -26,7 +26,7 @@ dependencies:
   - numpy
   - packaging
   - pandas
-  - pint>=0.22
+  # - pint>=0.22
   - pip
   - pre-commit
   - pydap

ci/requirements/environment-windows-3.12.yml renamed to ci/requirements/environment-windows-3.13.yml

@@ -30,7 +30,7 @@ dependencies:
   - opt_einsum
   - packaging
   - pandas
-  - pint>=0.22
+  # - pint>=0.22
   - pip
   - pooch
   - pre-commit

ci/requirements/environment-windows.yml

@@ -117,13 +117,13 @@ module = [
   "iris.*",
   "matplotlib.*",
   "mpl_toolkits.*",
-  "Nio.*",
   "nc_time_axis.*",
   "numbagg.*",
   "netCDF4.*",
   "netcdftime.*",
   "opt_einsum.*",
   "pandas.*",
+  "pint.*",
   "pooch.*",
   "pyarrow.*",
   "pydap.*",

ci/requirements/environment.yml

@@ -2988,14 +2988,6 @@ def test_chunked_cftime_datetime(self) -> None:
                 assert original[name].chunks == actual_var.chunks
             assert original.chunks == actual.chunks
 
-    def test_vectorized_indexing_negative_step(self) -> None:
-        if not has_dask:
-            pytest.xfail(
-                reason="zarr without dask handles negative steps in slices incorrectly"
-            )
-
-        super().test_vectorized_indexing_negative_step()
-
 
 @requires_zarr
 class TestZarrDictStore(ZarrBase):
@@ -3821,6 +3813,7 @@ def skip_if_not_engine(engine):
         pytest.importorskip(engine)
 
 
+# Flaky test. Very open to contributions on fixing this
 @requires_dask
 @pytest.mark.filterwarnings("ignore:use make_scale(name) instead")
 @pytest.mark.xfail(reason="Flaky test. Very open to contributions on fixing this")
@@ -4523,7 +4516,8 @@ def test_open_multi_dataset(self) -> None:
             ) as actual:
                 assert_identical(expected, actual)
 
-    @pytest.mark.xfail(reason="Flaky test. Very open to contributions on fixing this")
+    # Flaky test. Very open to contributions on fixing this
+    @pytest.mark.flaky
     def test_dask_roundtrip(self) -> None:
         with create_tmp_file() as tmp:
             data = create_test_data()

pyproject.toml

@@ -228,7 +228,6 @@ def test_lazy_import() -> None:
         "matplotlib",
         "nc_time_axis",
         "netCDF4",
-        "Nio",
         "numbagg",
         "pint",
         "pydap",

xarray/tests/test_backends.py

@@ -104,7 +104,6 @@ def show_versions(file=sys.stdout):
         ("pydap", lambda mod: mod.__version__),
         ("h5netcdf", lambda mod: mod.__version__),
         ("h5py", lambda mod: mod.__version__),
-        ("Nio", lambda mod: mod.__version__),
         ("zarr", lambda mod: mod.__version__),
         ("cftime", lambda mod: mod.__version__),
         ("nc_time_axis", lambda mod: mod.__version__),