Update cmethods.adjust's type annotations (#155)

Author: btschwertfeger

.github/workflows/_codecov.yaml

@@ -48,7 +48,7 @@ jobs:
         run: python -m pip install ".[dev,test]"
 
       - name: Generate coverage report
-        run: pytest --cov --cov-report=xml
+        run: pytest --retries 1 --cov --cov-report=xml
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303 #v5.1.2

.github/workflows/_test.yaml

@@ -33,11 +33,10 @@ jobs:
           python-version: ${{ inputs.python-version }}
 
       - name: Install dependencies
-        run: |
-          python -m pip install --user --upgrade pip
+        run: python -m pip install --user --upgrade pip
 
       - name: Install package
         run: python -m pip install --user ".[dev,test]"
 
       - name: Run unit tests
-        run: pytest -vv tests
+        run: pytest -vv --retries 1 tests

.github/workflows/cicd.yaml

@@ -41,7 +41,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
@@ -65,7 +65,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -5,7 +5,7 @@
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.3
     hooks:
       - id: ruff
         args:
@@ -23,12 +23,12 @@ repos:
   #         - --install-types
   #         - --non-interactive
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: codespell
         additional_dependencies: [tomli]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       # all available hooks can be found here: https://github.com/pre-commit/pre-commit-hooks/blob/main/.pre-commit-hooks.yaml
       - id: check-yaml
@@ -72,7 +72,7 @@ repos:
       - id: isort
         args: [--profile=black]
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.10
+    rev: 1.8.2
     hooks:
       - id: bandit
         exclude: "^tests/.*|examples/.*"

Makefile

@@ -39,9 +39,16 @@ install:
 test:
 	$(PYTHON) -m pytest $(PYTEST_OPTS) $(TESTS)
 
-.PHONY: tests
+.PHONY: test
 tests: test
 
+## retest 	Rerun tests that failed before
+##
+.PHONY: retest
+retest:
+	$(PYTHON) -m pytest $(PYTEST_OPTS) --lf $(TESTS)
+
+
 ## wip  	Run tests marked as wip
 ##
 .PHONY: wip

cmethods/__init__.py

@@ -173,8 +173,8 @@ def cli(**kwargs) -> None:
         datefmt="%Y/%m/%d %H:%M:%S",
         level=logging.INFO,
     )
-
-    logging.info("Loading data sets ...")
+    log = logging.getLogger(__name__)
+    log.info("Loading data sets ...")
     try:
         for key, message in zip(
             ("obs", "simh", "simp"),
@@ -194,15 +194,15 @@ def cli(**kwargs) -> None:
                 )
             kwargs[key] = kwargs[key][kwargs["variable"]]
     except (TypeError, KeyError) as exc:
-        logging.error(exc)
+        log.error(exc)
         sys.exit(1)
 
-    logging.info("Data sets loaded ...")
+    log.info("Data sets loaded ...")
     kwargs["n_quantiles"] = kwargs["quantiles"]
     del kwargs["quantiles"]
 
-    logging.info("Applying %s ..." % kwargs["method"])
+    log.info("Applying %s ...", kwargs["method"])
     result = adjust(**kwargs)
 
-    logging.info("Saving result to %s ..." % kwargs["output"])
+    log.info("Saving result to %s ...", kwargs["output"])
     result.to_netcdf(kwargs["output"])

cmethods/core.py

@@ -21,7 +21,7 @@
 from cmethods.scaling import linear_scaling as __linear_scaling
 from cmethods.scaling import variance_scaling as __variance_scaling
 from cmethods.static import SCALING_METHODS
-from cmethods.utils import UnknownMethodError, check_xr_types
+from cmethods.utils import UnknownMethodError, ensure_xr_dataarray
 
 if TYPE_CHECKING:
     from cmethods.types import XRData
@@ -37,16 +37,16 @@
 
 def apply_ufunc(
     method: str,
-    obs: XRData,
-    simh: XRData,
-    simp: XRData,
+    obs: xr.xarray.core.dataarray.DataArray,
+    simh: xr.xarray.core.dataarray.DataArray,
+    simp: xr.xarray.core.dataarray.DataArray,
     **kwargs: dict,
-) -> XRData:
+) -> xr.xarray.core.dataarray.DataArray:
     """
     Internal function used to apply the bias correction technique to the
     passed input data.
     """
-    check_xr_types(obs=obs, simh=simh, simp=simp)
+    ensure_xr_dataarray(obs=obs, simh=simh, simp=simp)
     if method not in __METHODS_FUNC__:
         raise UnknownMethodError(method, __METHODS_FUNC__.keys())
 
@@ -96,11 +96,11 @@ def apply_ufunc(
 
 def adjust(
     method: str,
-    obs: XRData,
-    simh: XRData,
-    simp: XRData,
+    obs: xr.xarray.core.dataarray.DataArray,
+    simh: xr.xarray.core.dataarray.DataArray,
+    simp: xr.xarray.core.dataarray.DataArray,
     **kwargs,
-) -> XRData:
+) -> xr.xarray.core.dataarray.DataArray | xr.xarray.core.dataarray.Dataset:
     """
     Function to apply a bias correction technique on single and multidimensional
     data sets. For more information please refer to the method specific
@@ -119,19 +119,19 @@ def adjust(
     :param method: Technique to apply
     :type method: str
     :param obs: The reference/observational data set
-    :type obs: XRData
+    :type obs: xr.xarray.core.dataarray.DataArray
     :param simh: The modeled data of the control period
-    :type simh: XRData
+    :type simh: xr.xarray.core.dataarray.DataArray
     :param simp: The modeled data of the period to adjust
-    :type simp: XRData
+    :type simp: xr.xarray.core.dataarray.DataArray
     :param kwargs: Any other method-specific parameter (like
         ``n_quantiles`` and ``kind``)
     :type kwargs: dict
     :return: The bias corrected/adjusted data set
-    :rtype: XRData
+    :rtype: xr.xarray.core.dataarray.DataArray | xr.xarray.core.dataarray.Dataset
     """
     kwargs["adjust_called"] = True
-    check_xr_types(obs=obs, simh=simh, simp=simp)
+    ensure_xr_dataarray(obs=obs, simh=simh, simp=simp)
 
     if method == "detrended_quantile_mapping":  # noqa: PLR2004
         raise ValueError(
@@ -169,6 +169,8 @@ def adjust(
         obs_group = group["obs"]
         simh_group = group["simh"]
         simp_group = group["simp"]
+    else:
+        raise ValueError("'group' must be a string or a dict!")
 
     del kwargs["group"]
 

cmethods/utils.py

@@ -51,11 +51,11 @@ def check_adjust_called(
         )
 
 
-def check_xr_types(obs: XRData, simh: XRData, simp: XRData) -> None:
+def ensure_xr_dataarray(obs: XRData, simh: XRData, simp: XRData) -> None:
     """
     Checks if the parameters are in the correct type. **only used internally**
     """
-    phrase: str = "must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray"
+    phrase: str = "must be type 'xarray.core.dataarray.DataArray'."
 
     if not isinstance(obs, XRData_t):
         raise TypeError(f"'obs' {phrase}")
@@ -73,7 +73,7 @@ def check_np_types(
     """
     Checks if the parameters are in the correct type. **only used internally**
     """
-    phrase: str = "must be type list, np.ndarray or np.generic"
+    phrase: str = "must be type list, np.ndarray, or np.generic"
 
     if not isinstance(obs, NPData_t):
         raise TypeError(f"'obs' {phrase}")
@@ -246,8 +246,8 @@ def get_adjusted_scaling_factor(
     "UnknownMethodError",
     "check_adjust_called",
     "check_np_types",
-    "check_xr_types",
     "ensure_dividable",
+    "ensure_xr_dataarray",
     "get_adjusted_scaling_factor",
     "get_cdf",
     "get_inverse_of_cdf",

pyproject.toml

@@ -39,8 +39,11 @@ keywords = [
 classifiers = [
   "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
   "Programming Language :: Python",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Software Development :: Libraries :: Python Modules",
   "Topic :: Utilities",
   "Topic :: Scientific/Engineering",
@@ -99,20 +102,21 @@ dev = [
   # linting
   "pylint",
   "flake8",
-  "ruff==0.3.5",
+  "ruff",
   # typing
   "mypy",
 ]
 test = [
   # testing
   "pytest",
   "pytest-cov",
+  "pytest-retry",
   "zarr",
   "dask[distributed]",
   "scikit-learn",
   "scipy",
 ]
-examples = ["click", "matplotlib"]
+examples = ["matplotlib"]
 
 [tool.codespell]
 check-filenames = true

tests/test_misc.py

@@ -102,7 +102,7 @@ def test_not_implemented_errors(
 def test_adjust_failing_dqm(datasets: dict) -> None:
     with pytest.raises(
         ValueError,
-        match="This function is not available for detrended quantile mapping. "
+        match=r"This function is not available for detrended quantile mapping. "
         "Please use cmethods.CMethods.detrended_quantile_mapping",
     ):
         adjust(
@@ -118,7 +118,7 @@ def test_adjust_failing_dqm(datasets: dict) -> None:
 def test_adjust_failing_no_group_for_distribution(datasets: dict) -> None:
     with pytest.raises(
         ValueError,
-        match="Can't use group for distribution based methods.",
+        match=r"Can't use group for distribution based methods.",
     ):
         adjust(
             method="quantile_mapping",

tests/test_utils.py

@@ -25,8 +25,8 @@
 from cmethods.static import MAX_SCALING_FACTOR
 from cmethods.utils import (
     check_np_types,
-    check_xr_types,
     ensure_dividable,
+    ensure_xr_dataarray,
     get_adjusted_scaling_factor,
     get_pdf,
     nan_or_equal,
@@ -133,7 +133,7 @@ def test_xr_type_check() -> None:
     correct. No error should occur.
     """
     ds: xr.core.dataarray.Dataset = xr.core.dataarray.Dataset()
-    check_xr_types(obs=ds, simh=ds, simp=ds)
+    ensure_xr_dataarray(obs=ds, simh=ds, simp=ds)
 
 
 def test_type_check_failing() -> None:
@@ -142,7 +142,7 @@ def test_type_check_failing() -> None:
     have the correct type.
     """
 
-    phrase: str = "must be type list, np.ndarray or np.generic"
+    phrase: str = "must be type list, np.ndarray, or np.generic"
     with pytest.raises(TypeError, match=f"'obs' {phrase}"):
         check_np_types(obs=1, simh=[], simp=[])
 
@@ -177,7 +177,7 @@ def test_detrended_quantile_mapping_type_check_simp_failing(datasets: dict) -> N
     """n_quantiles must by type int"""
     with pytest.raises(
         TypeError,
-        match="'simp' must be type xarray.core.dataarray.DataArray",
+        match=r"'simp' must be type xarray.core.dataarray.DataArray",
     ):
         detrended_quantile_mapping(  # type: ignore[attr-defined]
             obs=datasets["+"]["obsh"][:, 0, 0],
@@ -222,7 +222,7 @@ def test_adjust_type_checking_failing() -> None:
     )
     with pytest.raises(
         TypeError,
-        match="'obs' must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray",
+        match=r"'obs' must be type 'xarray.core.dataarray.DataArray'.",
     ):
         adjust(
             method="linear_scaling",
@@ -233,7 +233,7 @@ def test_adjust_type_checking_failing() -> None:
         )
     with pytest.raises(
         TypeError,
-        match="'simh' must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray",
+        match=r"'simh' must be type 'xarray.core.dataarray.DataArray'.",
     ):
         adjust(
             method="linear_scaling",
@@ -245,7 +245,7 @@ def test_adjust_type_checking_failing() -> None:
 
     with pytest.raises(
         TypeError,
-        match="'simp' must be type xarray.core.dataarray.Dataset or xarray.core.dataarray.DataArray",
+        match=r"'simp' must be type 'xarray.core.dataarray.DataArray'.",
     ):
         adjust(
             method="linear_scaling",