Merge branch 'main' into timedelta-coding

.github/workflows/ci.yaml

@@ -67,6 +67,16 @@ jobs:
           - env: "flaky"
             python-version: "3.13"
             os: ubuntu-latest
+          # The mypy tests must be executed using only 1 process in order to guarantee
+          # predictable mypy output messages for comparison to expectations.
+          - env: "mypy"
+            python-version: "3.10"
+            numprocesses: 1
+            os: ubuntu-latest
+          - env: "mypy"
+            python-version: "3.13"
+            numprocesses: 1
+            os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
         with:
@@ -88,6 +98,10 @@ jobs:
             then
               echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
               echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
+            elif [[ "${{ matrix.env }}" == "mypy" ]] ;
+            then
+              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
+              echo "PYTEST_ADDOPTS=-n 1 -m 'mypy' --run-mypy -W default" >> $GITHUB_ENV
             else
               echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
             fi
@@ -144,7 +158,7 @@ jobs:
           save-always: true
 
       - name: Run tests
-        run: python -m pytest -n 4
+        run: python -m pytest -n ${{ matrix.numprocesses || 4 }}
           --timeout 180
           --cov=xarray
           --cov-report=xml

ci/minimum_versions.py

@@ -26,8 +26,9 @@
     "pytest",
     "pytest-cov",
     "pytest-env",
-    "pytest-xdist",
+    "pytest-mypy-plugins",
     "pytest-timeout",
+    "pytest-xdist",
     "hypothesis",
 ]
 

ci/requirements/all-but-dask.yml

@@ -30,8 +30,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn

ci/requirements/all-but-numba.yml

@@ -43,8 +43,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn

ci/requirements/bare-minimum.yml

@@ -9,8 +9,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - numpy=1.24
   - packaging=23.1
   - pandas=2.1

ci/requirements/environment-3.14.yml

@@ -29,6 +29,7 @@ dependencies:
   - opt_einsum
   - packaging
   - pandas
+  - pandas-stubs
   # - pint>=0.22
   - pip
   - pooch
@@ -38,14 +39,25 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   # - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
   - pip:
       - jax # no way to get cpu-only jaxlib from conda if gpu is present
+      - types-defusedxml
+      - types-pexpect

ci/requirements/environment-windows-3.14.yml

@@ -25,6 +25,7 @@ dependencies:
   - numpy
   - packaging
   - pandas
+  - pandas-stubs
   # - pint>=0.22
   - pip
   - pre-commit
@@ -33,12 +34,24 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   # - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
+  - pip:
+      - types-defusedxml
+      - types-pexpect

ci/requirements/environment-windows.yml

@@ -25,6 +25,7 @@ dependencies:
   - numpy
   - packaging
   - pandas
+  - pandas-stubs
   # - pint>=0.22
   - pip
   - pre-commit
@@ -33,12 +34,24 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
+  - pip:
+      - types-defusedxml
+      - types-pexpect

ci/requirements/environment.yml

@@ -29,6 +29,7 @@ dependencies:
   - opt_einsum
   - packaging
   - pandas
+  - pandas-stubs
   # - pint>=0.22
   - pip
   - pooch
@@ -39,14 +40,25 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
   - pip:
       - jax # no way to get cpu-only jaxlib from conda if gpu is present
+      - types-defusedxml
+      - types-pexpect

ci/requirements/min-all-deps.yml

@@ -46,8 +46,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio=1.3
   - scipy=1.11
   - seaborn=0.13

conftest.py

@@ -3,14 +3,15 @@
 import pytest
 
 
-def pytest_addoption(parser):
+def pytest_addoption(parser: pytest.Parser):
     """Add command-line flags for pytest."""
     parser.addoption("--run-flaky", action="store_true", help="runs flaky tests")
     parser.addoption(
         "--run-network-tests",
         action="store_true",
         help="runs tests requiring a network connection",
     )
+    parser.addoption("--run-mypy", action="store_true", help="runs mypy tests")
 
 
 def pytest_runtest_setup(item):
@@ -21,6 +22,21 @@ def pytest_runtest_setup(item):
         pytest.skip(
             "set --run-network-tests to run test requiring an internet connection"
         )
+    if "mypy" in item.keywords and not item.config.getoption("--run-mypy"):
+        pytest.skip("set --run-mypy option to run mypy tests")
+
+
+# See https://docs.pytest.org/en/stable/example/markers.html#automatically-adding-markers-based-on-test-names
+def pytest_collection_modifyitems(items):
+    for item in items:
+        if "mypy" in item.nodeid:
+            # IMPORTANT: mypy type annotation tests leverage the pytest-mypy-plugins
+            # plugin, and are thus written in test_*.yml files.  As such, there are
+            # no explicit test functions on which we can apply a pytest.mark.mypy
+            # decorator.  Therefore, we mark them via this name-based, automatic
+            # marking approach, meaning that each test case must contain "mypy" in the
+            # name.
+            item.add_marker(pytest.mark.mypy)
 
 
 @pytest.fixture(autouse=True)

doc/whats-new.rst

@@ -28,14 +28,18 @@ New Features
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 - support python 3.13 (no free-threading) (:issue:`9664`, :pull:`9681`)
   By `Justus Magin <https://github.com/keewis>`_.
+- Added experimental support for coordinate transforms (not ready for public use yet!) (:pull:`9543`)
+  By `Benoit Bovy <https://github.com/benbovy>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
-
+- Warn instead of raise if phony_dims are detected when using h5netcdf-backend and ``phony_dims=None`` (:issue:`10049`, :pull:`10058`)
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
 Deprecations
 ~~~~~~~~~~~~
-
+- Move from phony_dims=None to phony_dims="access" for h5netcdf-backend(:issue:`10049`, :pull:`10058`)
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
 Bug fixes
 ~~~~~~~~~
@@ -51,6 +55,8 @@ Bug fixes
 - Fix DataArray().drop_attrs(deep=False) and add support for attrs to
   DataArray()._replace(). (:issue:`10027`, :pull:`10030`). By `Jan
   Haacker <https://github.com/j-haacker>`_.
+- Fix ``isel`` for multi-coordinate Xarray indexes (:issue:`10063`, :pull:`10066`).
+  By `Benoit Bovy <https://github.com/benbovy>`_.
 
 
 Documentation

pyproject.toml

@@ -44,8 +44,9 @@ dev = [
   "pytest",
   "pytest-cov",
   "pytest-env",
-  "pytest-xdist",
+  "pytest-mypy-plugins",
   "pytest-timeout",
+  "pytest-xdist",
   "ruff>=0.8.0",
   "sphinx",
   "sphinx_autosummary_accessors",
@@ -304,7 +305,12 @@ known-first-party = ["xarray"]
 ban-relative-imports = "all"
 
 [tool.pytest.ini_options]
-addopts = ["--strict-config", "--strict-markers"]
+addopts = [
+  "--strict-config",
+  "--strict-markers",
+  "--mypy-only-local-stub",
+  "--mypy-pyproject-toml-file=pyproject.toml",
+]
 
 # We want to forbid warnings from within xarray in our tests — instead we should
 # fix our own code, or mark the test itself as expecting a warning. So this:
@@ -361,6 +367,7 @@ filterwarnings = [
 log_cli_level = "INFO"
 markers = [
   "flaky: flaky tests",
+  "mypy: type annotation tests",
   "network: tests requiring a network connection",
   "slow: slow tests",
   "slow_hypothesis: slow hypothesis tests",