Merge pull request #642 from DHI/fix-pandas-deprecations

Fix-pandas-deprecations

mikeio/dataset/_dataset.py

@@ -619,13 +619,11 @@ def _del_name_attr(self, name: str) -> None:
             delattr(self, name)
 
     @overload
-    def __getitem__(self, key: Hashable | int) -> DataArray:
-        ...
+    def __getitem__(self, key: Hashable | int) -> DataArray: ...
 
     # Mapping is Iterable
     @overload
-    def __getitem__(self, key: Iterable[Hashable]) -> "Dataset":
-        ...
+    def __getitem__(self, key: Iterable[Hashable]) -> "Dataset": ...
 
     def __getitem__(self, key) -> DataArray | "Dataset":
         # select time steps

mikeio/dfs/_dfs.py

@@ -704,6 +704,8 @@ def time(self) -> pd.DatetimeIndex:
         # this will fail if the TimeAxisType is not calendar and equidistant, but that is ok
         if not self._is_equidistant:
             raise NotImplementedError("Not implemented for non-equidistant files")
+
+        # TODO using 'S' works in Python 3.8, but is deprecated, 's' doesn't work in 3.8
         return pd.date_range(
             start=self.start_time, periods=self.n_timesteps, freq=f"{self.timestep}S"
         )

mikeio/dfs/_dfs0.py

@@ -84,7 +84,7 @@ def _write_dfs0(filename, dataset: Dataset, title="", dtype=DfsSimpleType.Float)
 
 
 class Dfs0:
-    def __init__(self, filename:str | Path):
+    def __init__(self, filename: str | Path):
         """Create a Dfs0 object for reading, writing
 
         Parameters
@@ -148,7 +148,7 @@ def read(self, items=None, time=None, keepdims=False) -> Dataset:
         -------
         Dataset
             A Dataset with data dimensions [t]
-        """        
+        """
         path = Path(self._filename)
         if not path.exists():
             raise FileNotFoundError(f"File {path} not found")
@@ -244,7 +244,15 @@ def _to_dfs_datatype(dtype):
         raise TypeError("Dfs files only support float or double")
 
     @staticmethod
-    def _setup_header(title:str, filename:str, start_time, dt:float, is_equidistant: bool, dtype, items: Sequence[ItemInfo]):
+    def _setup_header(
+        title: str,
+        filename: str,
+        start_time,
+        dt: float,
+        is_equidistant: bool,
+        dtype,
+        items: Sequence[ItemInfo],
+    ):
         factory = DfsFactory()
         builder = DfsBuilder.Create(title, "mikeio", __dfs_version__)
         builder.SetDataType(1)
@@ -375,15 +383,14 @@ def write(
             self._dt = float(self._dt)
             t_seconds = self._dt * np.arange(float(self._n_timesteps))
 
-
         dfs = self._setup_header(
             title=self._title,
-            filename=self._filename, 
-            dt = self._dt,
-            start_time = self._start_time,
-            is_equidistant = self._is_equidistant,
+            filename=self._filename,
+            dt=self._dt,
+            start_time=self._start_time,
+            is_equidistant=self._is_equidistant,
             dtype=self._dtype,
-            items=self._items
+            items=self._items,
         )
 
         delete_value = dfs.FileInfo.DeleteValueFloat
@@ -471,7 +478,7 @@ def start_time(self):
 
     @cached_property
     def end_time(self):
-        
+
         if self._source.FileInfo.TimeAxis.IsEquidistant():
             dt = self._source.FileInfo.TimeAxis.TimeStep
             n_steps = self._source.FileInfo.TimeAxis.NumberOfTimeSteps
@@ -568,7 +575,10 @@ def dataframe_to_dfs0(
             else:
                 items = [ItemInfo(name, itemtype, unit) for name in self.columns]
 
-    das = {item.name: DataArray(data=d, item=item, time=self.index) for d, item in zip(data, items)}
+    das = {
+        item.name: DataArray(data=d, item=item, time=self.index)
+        for d, item in zip(data, items)
+    }
     ds = Dataset(das)
     _write_dfs0(filename=filename, dataset=ds, title=title, dtype=dtype)
 

mikeio/dfs/_dfs3.py

@@ -25,7 +25,7 @@
 from ..spatial import Grid3D
 
 
-def write_dfs3(filename: str| Path, ds: Dataset, title="") -> None:
+def write_dfs3(filename: str | Path, ds: Dataset, title="") -> None:
     dfs = _write_dfs3_header(filename, ds, title)
     _write_dfs_data(dfs=dfs, ds=ds, n_spatial_dims=3)
 
@@ -142,7 +142,6 @@ def __init__(self, filename=None):
     def __repr__(self):
         out = ["<mikeio.Dfs3>"]
 
-
         if self._filename:
             out.append(f"geometry: {self.geometry}")
 

mikeio/dfsu/_dfsu.py

@@ -1012,8 +1012,6 @@ def _write(
                 "argument dt is deprecated, please supply data in the form of a Dataset",
                 FutureWarning,
             )
-        if keep_open and not dt:
-            warnings.warn("argument dt missing, should be provided when keep_open=True")
 
         filename = str(filename)
 

mikeio/dfsu/_spectral.py

@@ -37,7 +37,7 @@ def _get_spectral_data_shape(self, n_steps: int, elements):
         dims = [] if n_steps == 1 else ["time"]
         n_freq = self.n_frequencies
         n_dir = self.n_directions
-        shape: Tuple[int,...] = (n_dir, n_freq)
+        shape: Tuple[int, ...] = (n_dir, n_freq)
         if n_dir == 0:
             shape = (n_freq,)
         elif n_freq == 0:

tests/test_dataarray.py

@@ -23,7 +23,7 @@ def da0():
 def da1():
     nt = 10
     start = 10.0
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     da = mikeio.DataArray(
         data=np.arange(start, start + nt, dtype=float),
         time=time,
@@ -40,7 +40,7 @@ def da2():
 
     da = mikeio.DataArray(
         data=np.zeros([nt, nx]) + 0.1,
-        time=pd.date_range(start="2000-01-01", freq="S", periods=nt),
+        time=pd.date_range(start="2000-01-01", freq="s", periods=nt),
         item=ItemInfo("Foo"),
         geometry=mikeio.Grid1D(x0=1000.0, dx=10.0, nx=nx),
     )
@@ -56,7 +56,7 @@ def da_grid2d():
 
     da = mikeio.DataArray(
         data=np.zeros([nt, ny, nx]) + 0.1,
-        time=pd.date_range(start="2000-01-01", freq="H", periods=nt),
+        time=pd.date_range(start="2000-01-01", freq="h", periods=nt),
         item=ItemInfo("Foo"),
         geometry=mikeio.Grid2D(x0=10.0, dx=0.1, nx=nx, ny=ny, dy=1.0, y0=-10.0),
     )
@@ -72,7 +72,7 @@ def da_grid2d_proj():
 
     da = mikeio.DataArray(
         data=np.zeros([nt, ny, nx]) + 0.1,
-        time=pd.date_range(start="2000-01-01", freq="S", periods=nt),
+        time=pd.date_range(start="2000-01-01", freq="s", periods=nt),
         item=ItemInfo("Foo"),
         geometry=mikeio.Grid2D(
             x0=1000, dx=100, nx=nx, ny=ny, dy=10, y0=2000, projection="UTM-32"
@@ -85,7 +85,7 @@ def da_grid2d_proj():
 @pytest.fixture
 def da_time_space():
     nt = 10
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     da = mikeio.DataArray(
         data=np.zeros(shape=(nt, 2), dtype=float),
         time=time,
@@ -116,7 +116,7 @@ def test_verify_custom_dims():
     with pytest.raises(ValueError) as excinfo:
         mikeio.DataArray(
             data=np.zeros([nt, nx]) + 0.1,
-            time=pd.date_range(start="2000-01-01", freq="S", periods=nt),
+            time=pd.date_range(start="2000-01-01", freq="s", periods=nt),
             item=ItemInfo("Foo"),
             dims=("space", "ensemble"),  # no time!
             geometry=mikeio.Grid1D(x0=1000.0, dx=10.0, nx=nx),
@@ -126,7 +126,7 @@ def test_verify_custom_dims():
     with pytest.raises(ValueError) as excinfo:
         mikeio.DataArray(
             data=np.zeros([nt, nx]) + 0.1,
-            time=pd.date_range(start="2000-01-01", freq="S", periods=nt),
+            time=pd.date_range(start="2000-01-01", freq="s", periods=nt),
             item=ItemInfo("Foo"),
             dims=("time", "x", "ensemble"),  # inconsistent with data
             geometry=mikeio.Grid1D(x0=1000.0, dx=10.0, nx=nx),
@@ -173,7 +173,7 @@ def test_create_data_1d_default_grid():
 
     da = mikeio.DataArray(
         data=np.zeros((10, 5)),
-        time=pd.date_range(start="2000-01-01", freq="H", periods=10),
+        time=pd.date_range(start="2000-01-01", freq="h", periods=10),
         item=ItemInfo("Foo"),
     )
     assert isinstance(da.geometry, mikeio.Grid1D)
@@ -188,7 +188,7 @@ def test_create_data_1d_default_grid():
 #     with pytest.warns(Warning) as w:
 #         mikeio.DataArray(
 #             data=np.zeros([nt, ny, nx]) + 0.1,
-#             time=pd.date_range(start="2000-01-01", freq="S", periods=nt),
+#             time=pd.date_range(start="2000-01-01", freq="s", periods=nt),
 #             item=ItemInfo("Foo"),
 #         )
 
@@ -199,7 +199,7 @@ def test_dataarray_init():
     nt = 10
     start = 10.0
     data = np.arange(start, start + nt, dtype=float)
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     item = ItemInfo(name="Foo")
 
     da = mikeio.DataArray(data=data, time=time)
@@ -230,7 +230,7 @@ def test_dataarray_init_no_item():
 
     nt = 10
     data = data = np.zeros([nt, 4]) + 0.1
-    time = time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
 
     da = mikeio.DataArray(data=data, time=time)
     assert da.type == EUMType.Undefined
@@ -239,7 +239,7 @@ def test_dataarray_init_no_item():
 
 def test_dataarray_init_2d():
     nt = 10
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
 
     # 2d with time
     ny, nx = 5, 6
@@ -276,7 +276,7 @@ def test_dataarray_init_2d():
 
 def test_dataarray_init_5d():
     nt = 10
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
 
     # 5d with named dimensions
     dims = ("x", "y", "layer", "member", "season")
@@ -299,7 +299,7 @@ def test_dataarray_init_wrong_dim():
     nt = 10
     start = 10.0
     data = np.arange(start, start + nt, dtype=float)
-    time_long = pd.date_range(start="2000-01-01", freq="S", periods=(nt + 1))
+    time_long = pd.date_range(start="2000-01-01", freq="s", periods=(nt + 1))
     item = ItemInfo(name="Foo")
 
     with pytest.raises(ValueError):
@@ -312,7 +312,7 @@ def test_dataarray_init_wrong_dim():
 
     # time must be first dim
     dims = ("x", "y", "time")
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     with pytest.raises(ValueError):
         mikeio.DataArray(data=data2d, time=time, dims=dims)
 
@@ -325,7 +325,7 @@ def test_dataarray_init_wrong_dim():
 def test_dataarray_init_grid1d():
     nt = 10
     nx = 5
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     data = np.zeros([nt, nx]) + 0.1
     g = mikeio.Grid1D(nx=nx, dx=1.0)
     da = mikeio.DataArray(data=data, time=time, geometry=g)
@@ -348,7 +348,7 @@ def test_dataarray_init_grid1d():
 def test_dataarray_init_grid2d():
     nt = 10
     ny, nx = 7, 5
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     data = np.zeros([nt, ny, nx]) + 0.1
     g = mikeio.Grid2D(dx=0.5, nx=nx, ny=ny)
     da = mikeio.DataArray(data=data, time=time, geometry=g)
@@ -370,7 +370,7 @@ def test_dataarray_init_grid2d():
 
 def test_dataarray_init_dfsu2d():
     nt = 10
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     filename = "tests/testdata/north_sea_2.mesh"
     msh = Mesh(filename)
     g = msh.geometry
@@ -399,7 +399,7 @@ def test_dataarray_init_dfsu2d():
 
 def test_dataarray_init_dfsu3d():
     nt = 10
-    time = pd.date_range(start="2000-01-01", freq="S", periods=nt)
+    time = pd.date_range(start="2000-01-01", freq="s", periods=nt)
     filename = "tests/testdata/basin_3d.dfsu"
     dfs = mikeio.open(filename)
     g = dfs.geometry
@@ -550,7 +550,7 @@ def test_dataarray_grid3d_indexing():
 
 def test_dataarray_getitem_time(da_grid2d):
     da = da_grid2d
-    # time=pd.date_range("2000-01-01", freq="H", periods=10)
+    # time=pd.date_range("2000-01-01", freq="h", periods=10)
     da_sel = da["2000-1-1"]
     assert da_sel.n_timesteps == da.n_timesteps
     assert da_sel.is_equidistant
@@ -1224,7 +1224,7 @@ def test_write_dfs2(tmp_path):
     assert g.origin == (0, 0)
     da = mikeio.DataArray(
         np.random.random(size=(nt, g.ny, g.nx)),
-        time=pd.date_range(start="2000", freq="H", periods=nt),
+        time=pd.date_range(start="2000", freq="h", periods=nt),
         item=ItemInfo("Random"),
         geometry=g,
     )
@@ -1309,7 +1309,7 @@ def test_time_selection():
     data = []
     d = np.random.rand(nt)
     data.append(d)
-    time = pd.date_range("2000-1-2", freq="H", periods=nt)
+    time = pd.date_range("2000-1-2", freq="h", periods=nt)
     items = [ItemInfo("Foo")]
     ds = mikeio.Dataset(data, time, items)