Add Scipy stubs (pydata#11225)

* update mypy to 1.19.1

* add scipy-stubs to typing deps

* add typing to scipy backend

* dirty workaround to keep scipy import lazy

* restore scipy lazy import test

* add test reports to gitignore

* pin scipy-stubs for a required fix

* fix deprecated variable for codecov

* fix more deprecated variable for codecov

* fix mypy tests for pytest-mypy-plugins>=4.0.0

Author: headtr1ck

.github/workflows/ci-additional.yaml

@@ -134,7 +134,7 @@ jobs:
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
         with:
-          file: mypy_report/cobertura.xml
+          files: mypy_report/cobertura.xml
           flags: mypy
           env_vars: PYTHON_VERSION
           name: codecov-umbrella
@@ -179,7 +179,7 @@ jobs:
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
         with:
-          file: mypy_report/cobertura.xml
+          files: mypy_report/cobertura.xml
           flags: mypy-min
           env_vars: PYTHON_VERSION
           name: codecov-umbrella
@@ -278,7 +278,7 @@ jobs:
       - name: Upload pyright coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
         with:
-          file: pyright_report/cobertura.xml
+          files: pyright_report/cobertura.xml
           flags: pyright
           env_vars: PYTHON_VERSION
           name: codecov-umbrella

.github/workflows/ci.yaml

@@ -170,7 +170,7 @@ jobs:
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
-          file: ./coverage.xml
+          files: ./coverage.xml
           flags: unittests
           env_vars: RUNNER_OS,PYTHON_VERSION
           name: codecov-umbrella

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

@@ -160,7 +160,7 @@ jobs:
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.2
         with:
-          file: mypy_report/cobertura.xml
+          files: mypy_report/cobertura.xml
           flags: mypy
           env_vars: PYTHON_VERSION
           name: codecov-umbrella

.gitignore

@@ -36,6 +36,7 @@ pip-log.txt
 # Unit test / coverage reports
 .coverage
 .coverage.*
+coverage.xml
 .tox
 nosetests.xml
 .cache
@@ -47,6 +48,7 @@ nosetests.xml
 .testmon*
 .tmontmp/
 .pytest_cache
+pytest.xml
 dask-worker-space/
 
 # asv environments

pixi.toml

@@ -205,7 +205,7 @@ pytest = "*"
 pytest-asyncio = "*"
 pytest-cov = "*"
 pytest-env = "*"
-pytest-mypy-plugins = "*"
+pytest-mypy-plugins = ">=4.0.0"
 pytest-reportlog = "*"
 pytest-timeout = "*"
 pytest-xdist = "*"
@@ -250,21 +250,24 @@ linkcheck = { cmd = "make linkcheck", cwd = "doc", description = "Check URLs in
 
 
 [feature.typing.dependencies]
-mypy = "==1.18.1"
+mypy = "==1.19.1"
 pyright = "*"
 hypothesis = "*"
 lxml = "*"
 pandas-stubs = "<=2.3.3.251219"
+scipy-stubs = ">=1.17.1.2"
 types-colorama = "*"
 types-docutils = "*"
+types-decorator = "*"
+types-networkx = "*"
+types-openpyxl = "*"
 types-psutil = "*"
 types-Pygments = "*"
 types-python-dateutil = "*"
 types-pytz = "*"
 types-PyYAML = "*"
 types-requests = "*"
 types-setuptools = "*"
-types-openpyxl = "*"
 typing_extensions = "*"
 pip = "*"
 

pyproject.toml

@@ -51,38 +51,39 @@ viz = ["cartopy>=0.24", "matplotlib>=3.10", "nc-time-axis", "seaborn"]
 types = [
   "pandas-stubs",
   "scipy-stubs",
-  "types-PyYAML",
-  "types-Pygments",
   "types-colorama",
   "types-decorator",
   "types-defusedxml",
   "types-docutils",
   "types-networkx",
+  "types-openpyxl",
   "types-pexpect",
   "types-psutil",
   "types-pycurl",
-  "types-openpyxl",
+  "types-Pygments",
   "types-python-dateutil",
   "types-pytz",
+  "types-PyYAML",
   "types-requests",
   "types-setuptools",
+  "types-xlrd",
 ]
 
 [dependency-groups]
 dev = [
   "hypothesis",
   "jinja2",
-  "mypy==1.18.1",
+  "mypy==1.19.1",
   "pre-commit",
   "pytest",
   "pytest-cov",
   "pytest-env",
-  "pytest-mypy-plugins",
+  "pytest-mypy-plugins>=4.0.0",
   "pytest-timeout",
   "pytest-xdist",
   "pytest-asyncio",
   "pytz",
-  "ruff>=0.8.0",
+  "ruff>=0.15.0",
   "sphinx",
   "sphinx_autosummary_accessors",
   "xarray[complete,types]",
@@ -158,7 +159,6 @@ module = [
   "pooch.*",
   "pyarrow.*",
   "pydap.*",
-  "scipy.*",
   "seaborn.*",
   "setuptools",
   "sparse.*",
@@ -176,6 +176,7 @@ module = [
 [[tool.mypy.overrides]]
 check_untyped_defs = true
 module = [
+  "xarray.backends.scipy_",
   "xarray.core.accessor_dt",
   "xarray.core.accessor_str",
   "xarray.structure.alignment",

xarray/backends/common.py

@@ -12,6 +12,7 @@
     Any,
     ClassVar,
     Self,
+    TypeAlias,
     TypeVar,
     Union,
     overload,
@@ -381,7 +382,7 @@ def __exit__(self, exception_type, exception_value, traceback):
         self.close()
 
 
-T_PathFileOrDataStore = (
+T_PathFileOrDataStore: TypeAlias = (
     str | os.PathLike[Any] | ReadBuffer | bytes | memoryview | AbstractDataStore
 )
 
@@ -776,12 +777,7 @@ def __repr__(self) -> str:
 
     def open_dataset(
         self,
-        filename_or_obj: str
-        | os.PathLike[Any]
-        | ReadBuffer
-        | bytes
-        | memoryview
-        | AbstractDataStore,
+        filename_or_obj: T_PathFileOrDataStore,
         *,
         drop_variables: str | Iterable[str] | None = None,
     ) -> Dataset:
@@ -793,12 +789,7 @@ def open_dataset(
 
     def guess_can_open(
         self,
-        filename_or_obj: str
-        | os.PathLike[Any]
-        | ReadBuffer
-        | bytes
-        | memoryview
-        | AbstractDataStore,
+        filename_or_obj: T_PathFileOrDataStore,
     ) -> bool:
         """
         Backend open_dataset method used by Xarray in :py:func:`~xarray.open_dataset`.
@@ -808,12 +799,7 @@ def guess_can_open(
 
     def open_datatree(
         self,
-        filename_or_obj: str
-        | os.PathLike[Any]
-        | ReadBuffer
-        | bytes
-        | memoryview
-        | AbstractDataStore,
+        filename_or_obj: T_PathFileOrDataStore,
         *,
         drop_variables: str | Iterable[str] | None = None,
     ) -> DataTree:
@@ -827,12 +813,7 @@ def open_datatree(
 
     def open_groups_as_dict(
         self,
-        filename_or_obj: str
-        | os.PathLike[Any]
-        | ReadBuffer
-        | bytes
-        | memoryview
-        | AbstractDataStore,
+        filename_or_obj: T_PathFileOrDataStore,
         *,
         drop_variables: str | Iterable[str] | None = None,
     ) -> dict[str, Dataset]: