Check type hints in tests

Author: ecomodeller

Makefile

@@ -1,3 +1,5 @@
+SHELL := /bin/bash
+
 LIB = mikeio
 
 check: lint typecheck test
@@ -15,7 +17,7 @@ test:
 	pytest
 
 typecheck:
-	mypy $(LIB)/
+	mypy $(LIB)/ tests/test_{dataarray,dataset,generic,dfs0,dfs1,dfs2,dfs3,dfsu2dh}.py
 
 coverage: 
 	pytest --cov-report html --cov=$(LIB) tests/

mikeio/__init__.py

@@ -34,7 +34,7 @@ def read(
     filename: str | Path,
     *,
     items: str | int | Sequence[str | int] | None = None,
-    time: int | str | slice | None = None,
+    time: int | str | slice | Sequence[int] | None = None,
     keepdims: bool = False,
     **kwargs: Any,
 ) -> Dataset:
@@ -126,6 +126,7 @@ def read(
     return dfs.read(items=items, time=time, keepdims=keepdims, **kwargs)
 
 
+# TODO Mesh doesn't comply with the interface of dfs files
 def open(
     filename: str | Path, **kwargs: Any
 ) -> Dfs0 | Dfs1 | Dfs2 | Dfs3 | Dfsu2DH | Dfsu2DV | Dfsu3D | DfsuSpectral | Mesh:

mikeio/dataset/_dataarray.py

@@ -31,6 +31,7 @@
 if TYPE_CHECKING:
     from ._dataset import Dataset
     import xarray
+    from numpy.typing import ArrayLike
 
 
 from ..spatial import (
@@ -174,7 +175,7 @@ class DataArray:
 
     def __init__(
         self,
-        data: np.ndarray,
+        data: ArrayLike,
         *,
         time: pd.DatetimeIndex | str | None = None,
         name: str | None = None,
@@ -186,8 +187,7 @@ def __init__(
         dims: Sequence[str] | None = None,
         dt: float = 1.0,
     ) -> None:
-        # TODO: add optional validation validate=True
-        self._values = self._parse_data(data)
+        self._values = np.asarray(data)
         self.time: pd.DatetimeIndex = self._parse_time(time)
         self._dt = dt
 
@@ -202,15 +202,6 @@ def __init__(
         self._set_spectral_attributes(geometry)
         self.plot = self._get_plotter_by_geometry()
 
-    @staticmethod
-    def _parse_data(data: Any) -> Any:  # np.ndarray | float:
-        if not hasattr(data, "shape"):
-            try:
-                data = np.array(data, dtype=float)
-            except ValueError:
-                raise ValueError("Data must be convertible to a numpy array")
-        return data
-
     def _parse_dims(
         self, dims: Sequence[str] | None, geometry: GeometryType
     ) -> tuple[str, ...]:
@@ -1581,7 +1572,7 @@ def nanmin(self, axis: int | str = 0, **kwargs: Any) -> "DataArray":
         """
         return self.aggregate(axis=axis, func=np.nanmin, **kwargs)
 
-    def nanmean(self, axis: int | str = 0, **kwargs: Any) -> "DataArray":
+    def nanmean(self, axis: int | str | None = 0, **kwargs: Any) -> "DataArray":
         """Mean value along an axis (NaN removed).
 
         Parameters
@@ -1626,7 +1617,10 @@ def nanstd(self, axis: int | str = 0, **kwargs: Any) -> "DataArray":
         return self.aggregate(axis=axis, func=np.nanstd, **kwargs)
 
     def aggregate(
-        self, axis: int | str = 0, func: Callable[..., Any] = np.nanmean, **kwargs: Any
+        self,
+        axis: int | str | None = 0,
+        func: Callable[..., Any] = np.nanmean,
+        **kwargs: Any,
     ) -> "DataArray":
         """Aggregate along an axis.
 
@@ -2088,7 +2082,6 @@ def _time_by_agg_axis(
 
         return time
 
-
     @staticmethod
     def _is_boolean_mask(x: Any) -> bool:
         if hasattr(x, "dtype"):  # isinstance(x, (np.ndarray, DataArray)):

mikeio/dataset/_dataset.py

@@ -49,6 +49,7 @@
 
 from ._dataarray import IndexType
 
+
 def _to_safe_name(name: str) -> str:
     tmp = re.sub("[^0-9a-zA-Z]", "_", name)
     return re.sub("_+", "_", tmp)  # Collapse multiple underscores
@@ -545,7 +546,10 @@ def squeeze(self) -> "Dataset":
         return Dataset(data=res, validate=False)
 
     def create_data_array(
-        self, data: NDArray[np.floating], item: ItemInfo | None = None
+        self,
+        data: NDArray[np.floating],
+        item: ItemInfo | None = None,
+        name: str | None = None,
     ) -> DataArray:
         """Create a new  DataArray with the same time and geometry as the dataset.
 
@@ -560,7 +564,12 @@ def create_data_array(
 
         """
         return DataArray(
-            data=data, time=self.time, geometry=self.geometry, zn=self._zn, item=item
+            data=data,
+            time=self.time,
+            geometry=self.geometry,
+            zn=self._zn,
+            item=item,
+            name=name,
         )
 
     # TODO: delete this?
@@ -715,6 +724,9 @@ def _del_name_attr(self, name: str) -> None:
     @overload
     def __getitem__(self, key: Hashable | int) -> DataArray: ...
 
+    @overload
+    def __getitem__(self, key: slice) -> Dataset: ...
+
     @overload
     def __getitem__(self, key: Iterable[Hashable]) -> "Dataset": ...
 
@@ -1744,7 +1756,7 @@ def func(x, axis, keepdims):  # type: ignore
 
         return self.aggregate(axis=axis, func=func, **kwargs)
 
-    def nanmax(self, axis: int | str = 0, **kwargs: Any) -> "Dataset":
+    def nanmax(self, axis: int | str | None = 0, **kwargs: Any) -> "Dataset":
         """Max value along an axis (NaN removed).
 
         Parameters
@@ -1766,7 +1778,7 @@ def nanmax(self, axis: int | str = 0, **kwargs: Any) -> "Dataset":
         """
         return self.aggregate(axis=axis, func=np.nanmax, **kwargs)
 
-    def nanmin(self, axis: int | str = 0, **kwargs: Any) -> "Dataset":
+    def nanmin(self, axis: int | str | None = 0, **kwargs: Any) -> "Dataset":
         """Min value along an axis (NaN removed).
 
         Parameters

mikeio/dfs/_dfs.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 from pathlib import Path
 import warnings
-from abc import abstractmethod
 from dataclasses import dataclass
 from datetime import datetime
 from typing import Any, Sequence
@@ -444,12 +443,6 @@ def is_geo(self) -> bool:
         """Are coordinates geographical (LONG/LAT)?"""
         return self._projstr == "LONG/LAT"
 
-    @property
-    @abstractmethod
-    def shape(self) -> tuple[int, ...]:
-        """Shape of the data array."""
-        pass
-
     def _validate_no_orientation_in_geo(self) -> None:
         if self.is_geo and abs(self._orientation) > 1e-6:
             raise ValueError("Orientation is not supported for LONG/LAT coordinates")

mikeio/dfs/_dfs0.py

@@ -253,7 +253,7 @@ def _to_dfs_datatype(dtype: Any = None) -> DfsSimpleType:
         raise TypeError("Dfs files only support float or double")
 
     def to_dataframe(
-        self, unit_in_name: bool = False, round_time: str = "ms"
+        self, unit_in_name: bool = False, round_time: str | bool = "ms"
     ) -> pd.DataFrame:
         """Read data from the dfs0 file and return a Pandas DataFrame.
 
@@ -346,7 +346,7 @@ def time(self) -> pd.DatetimeIndex:
     @staticmethod
     def from_dataframe(
         df: pd.DataFrame,
-        filename: str,
+        filename: str | Path,
         itemtype: EUMType | None = None,
         unit: EUMUnit | None = None,
         items: Sequence[ItemInfo] | None = None,
@@ -369,7 +369,7 @@ def series_to_dfs0(
 
 def dataframe_to_dfs0(
     self: pd.DataFrame,
-    filename: str,
+    filename: str | Path,
     itemtype: EUMType | None = None,
     unit: EUMUnit | None = None,
     items: Sequence[ItemInfo] | None = None,

mikeio/dfsu/_dfsu.py

@@ -298,7 +298,9 @@ def read(
         items: str | int | Sequence[str | int] | None = None,
         time: int | str | slice | Sequence[int] | None = None,
         elements: Sequence[int] | np.ndarray | None = None,
-        area: tuple[float, float, float, float] | None = None,
+        area: tuple[float, float, float, float]
+        | Sequence[tuple[float, float]]
+        | None = None,
         x: float | Sequence[float] | None = None,
         y: float | Sequence[float] | None = None,
         keepdims: bool = False,

mikeio/eum/_eum.py

@@ -1440,8 +1440,8 @@ class ItemInfo:
     def __init__(
         self,
         name: str | EUMType | None = None,
-        itemtype: EUMType | EUMUnit | None = None,
-        unit: EUMUnit | None = None,
+        itemtype: EUMType | EUMUnit | int | None = None,
+        unit: EUMUnit | int | None = None,
         data_value_type: Literal[
             "Instantaneous", "Accumulated", "StepAccumulated", "MeanStepBackward"
         ] = "Instantaneous",

mikeio/generic.py

@@ -823,7 +823,7 @@ def quantile(
     outfilename: str | pathlib.Path,
     q: float | Sequence[float],
     *,
-    items: Sequence[int | str] | None = None,
+    items: Sequence[int | str] | int | str | None = None,
     skipna: bool = True,
     buffer_size: float = 1.0e9,
 ) -> None:

mikeio/spatial/_grid_geometry.py

@@ -21,6 +21,7 @@
 if TYPE_CHECKING:
     from matplotlib.axes import Axes
     from ..spatial import GeometryFM2D
+    from numpy.typing import ArrayLike
 
 
 def _check_equidistant(x: np.ndarray) -> None:
@@ -116,7 +117,7 @@ class Grid1D(_Geometry):
 
     def __init__(
         self,
-        x: np.ndarray | None = None,
+        x: ArrayLike | None = None,
         *,
         x0: float = 0.0,
         dx: float | None = None,
@@ -465,11 +466,11 @@ class Grid2D(_Geometry):
     def __init__(
         self,
         *,
-        x: np.ndarray | None = None,
+        x: ArrayLike | None = None,
         x0: float = 0.0,
         dx: float | None = None,
         nx: int | None = None,
-        y: np.ndarray | None = None,
+        y: ArrayLike | None = None,
         y0: float = 0.0,
         dy: float | None = None,
         ny: int | None = None,