Merge branch 'main' into docs_navs

Makefile

@@ -6,14 +6,11 @@ build: typecheck test
 	python -m build
 
 lint:
-	ruff check $(LIB)/
+	ruff check .
 
 format:
 	ruff format $(LIB)/
 
-pylint:
-	pylint --disable=all --enable=attribute-defined-outside-init mikeio/
-
 test:
 	pytest --disable-warnings
 

README.md

@@ -11,7 +11,7 @@
 
 Read, write and manipulate dfs0, dfs1, dfs2, dfs3, dfsu and mesh files.
 
-MIKE IO facilitates common data processing workflows for [MIKE files in Python](https://www.mikepoweredbydhi.com/products/mike-for-developers#io).
+MIKE IO facilitates common data processing workflows for [MIKE files](https://www.dhigroup.com/technologies/mikepoweredbydhi) using Python.
 
 [![MIKEIO. Read, write and analyze MIKE dfs files with Python on Vimeo](https://raw.githubusercontent.com/DHI/mikeio/main/images/youtube1.png)](https://player.vimeo.com/video/708275619)
 

mikeio/dataset/_data_plot.py

@@ -847,6 +847,8 @@ def __init__(self, da: DataArray) -> None:
 
 
 class _DatasetPlotter:
+    """Class for plotting scatter plots from datasets."""
+
     def __init__(self, ds: Dataset) -> None:
         self.ds = ds
 

mikeio/dfs/_dfs0.py

@@ -82,6 +82,8 @@ def _write_dfs0(
 
 
 class Dfs0:
+    """Class for reading/writing dfs0 files."""
+
     def __init__(self, filename: str | Path):
         """Create a Dfs0 object for reading, writing.
 

mikeio/dfs/_dfs1.py

@@ -66,6 +66,8 @@ def _write_dfs1_header(filename: str | Path, ds: Dataset, title: str) -> DfsFile
 
 
 class Dfs1(_Dfs123):
+    """Class for reading/writing dfs1 files."""
+
     _ndim = 1
 
     def __init__(self, filename: str | Path) -> None:

mikeio/dfs/_dfs2.py

@@ -108,6 +108,8 @@ def _write_dfs2_spatial_axis(
 
 
 class Dfs2(_Dfs123):
+    """Class for reading/writing dfs2 files."""
+
     _ndim = 2
 
     def __init__(

mikeio/dfs/_dfs3.py

@@ -99,6 +99,8 @@ def _write_dfs3_header(filename: str | Path, ds: Dataset, title: str) -> DfsFile
 
 
 class Dfs3(_Dfs123):
+    """Class for reading/writing dfs3 files."""
+
     _ndim = 3
 
     def __init__(self, filename: str | Path):

mikeio/dfsu/_dfsu.py

@@ -278,6 +278,8 @@ def _get_dfsu_info(filename: str | Path) -> _DfsuInfo:
 
 
 class Dfsu2DH:
+    """Class for reading/writing dfsu 2d horizontal files."""
+
     show_progress = False
 
     def __init__(self, filename: str | Path) -> None:

mikeio/dfsu/_factory.py

@@ -37,5 +37,7 @@ def dfsu(filename: str | Path) -> Any:
 
 
 class Dfsu:
+    """Factory class for dfsu files."""
+
     def __new__(self, filename: str | Path) -> Any:
         return dfsu(filename)

mikeio/dfsu/_layered.py

@@ -411,6 +411,8 @@ def append(self, ds: Dataset, validate: bool = True) -> None:
 
 
 class Dfsu2DV(DfsuLayered):
+    """Class for reading/writing dfsu 2d vertical files."""
+
     def plot_vertical_profile(
         self,
         values: np.ndarray | DataArray,
@@ -465,6 +467,8 @@ def plot_vertical_profile(
 
 
 class Dfsu3D(DfsuLayered):
+    """Class for reading/writing dfsu 3d files."""
+
     @property
     def geometry2d(self) -> GeometryFM2D:
         """The 2d geometry for a 3d object."""

mikeio/dfsu/_spectral.py

@@ -26,6 +26,8 @@
 
 
 class DfsuSpectral:
+    """Dfsu for Spectral data."""
+
     show_progress = False
 
     def __init__(self, filename: str | Path) -> None:

mikeio/eum/_eum.py

@@ -1399,7 +1399,7 @@ def __repr__(self) -> str:
 
 
 class ItemInfo:
-    """ItemInfo.
+    """Info for dynamicc items (variables).
 
     Parameters
     ----------

mikeio/pfs/_pfssection.py

@@ -33,6 +33,8 @@ class PfsNonUniqueList(list):
 
 
 class PfsSection(SimpleNamespace, MutableMapping[str, Any]):
+    """Class for reading/writing sections in a pfs file."""
+
     @staticmethod
     def from_dataframe(df: pd.DataFrame, prefix: str) -> "PfsSection":
         """Create a PfsSection from a DataFrame.

mikeio/spatial/_FM_geometry.py

@@ -399,6 +399,8 @@ def __eq__(self, value: Any) -> bool:
 
 
 class GeometryFM2D(_GeometryFM):
+    """Flexible 2d mesh geometry."""
+
     def __init__(
         self,
         node_coordinates: np.ndarray,

mikeio/spatial/_FM_geometry_layered.py

@@ -226,23 +226,27 @@ def to_2d_geometry(self) -> GeometryFM2D:
 
         Returns
         -------
-        UnstructuredGeometry
-            2d geometry (bottom nodes)
+        GeometryFM2D
+            2d geometry
 
         """
         # extract information for selected elements
-        elem_ids = self.bottom_elements
-        if self._type == DfsuFileType.Dfsu3DSigmaZ:
-            # for z-layers nodes will not match on neighboring elements!
-            elem_ids = self.top_elements
+        match self._type:
+            case DfsuFileType.Dfsu3DSigmaZ:
+                elem_ids = self.top_elements
+            case DfsuFileType.Dfsu3DSigma:
+                elem_ids = self.bottom_elements
+            case _:
+                raise NotImplementedError(
+                    f"Conversion to 2D not implemented for {self._type}"
+                )
 
         node_ids, elem_tbl = self._get_nodes_and_table_for_elements(
             elem_ids, node_layers="bottom"
         )
         node_coords = self.node_coordinates[node_ids]
         codes = self._codes[node_ids]
 
-        # create new geometry
         geom = GeometryFM2D(
             node_coordinates=node_coords,
             codes=codes,
@@ -255,6 +259,9 @@ def to_2d_geometry(self) -> GeometryFM2D:
             reindex=True,
         )
 
+        # TODO do this before creating the geometry
+
+        # TODO extract method
         # Fix z-coordinate for sigma-z:
         if self._type == DfsuFileType.Dfsu3DSigmaZ:
             zn = geom.node_coordinates[:, 2].copy()
@@ -613,6 +620,8 @@ def _calc_dz(self) -> np.ndarray:
 
 
 class GeometryFM3D(_GeometryFMLayered):
+    """Flexible 3d mesh geometry."""
+
     def __init__(
         self,
         *,
@@ -701,6 +710,8 @@ def find_index(
 
 
 class GeometryFMVerticalProfile(_GeometryFMLayered):
+    """Flexible mesh 2d vertical profile geometry."""
+
     def __init__(
         self,
         node_coordinates: np.ndarray,

mikeio/spatial/_FM_geometry_spectral.py

@@ -12,6 +12,8 @@
 
 
 class GeometryFMPointSpectrum(_Geometry):
+    """Flexible mesh point spectrum."""
+
     def __init__(
         self,
         frequencies: np.ndarray | None = None,
@@ -126,6 +128,8 @@ def directions(self) -> np.ndarray | None:
 
 # TODO reconsider inheritance to avoid overriding method signature
 class GeometryFMAreaSpectrum(_GeometryFMSpectrum):
+    """Flexible mesh area spectrum geometry."""
+
     def isel(  # type: ignore
         self, idx: Sequence[int], **kwargs: Any
     ) -> "GeometryFMPointSpectrum" | "GeometryFMAreaSpectrum":
@@ -178,6 +182,8 @@ def elements_to_geometry(  # type: ignore
 
 # TODO this inherits indirectly from GeometryFM2D, which is not ideal
 class GeometryFMLineSpectrum(_GeometryFMSpectrum):
+    """Flexible mesh line spectrum geometry."""
+
     def isel(  # type: ignore
         self, idx: Sequence[int], axis: str = "node"
     ) -> GeometryFMPointSpectrum | GeometryFMLineSpectrum:

mikeio/spatial/_grid_geometry.py

@@ -69,6 +69,8 @@ def _print_axis_txt(name: str, x: np.ndarray, dx: float) -> str:
 
 @dataclass
 class Grid1D(_Geometry):
+    """1D grid (node-based)."""
+
     _dx: float
     _nx: int
     _x0: float
@@ -89,9 +91,9 @@ def __init__(
         node_coordinates: np.ndarray | None = None,
         axis_name: str = "x",
     ):
-        """1D grid (node-based).
+        """Create a Grid1D.
 
-        axis is increasing and equidistant
+        The axis is increasing and equidistant
 
         Parameters
         ----------

notebooks/DataArray - Dfs123 plotting.ipynb

@@ -308,7 +308,7 @@
     }
    ],
    "source": [
-    "da.plot.contourf(figsize=(10,6), levels=4, label=\"Højde (m)\");\n",
+    "da.plot.contourf(figsize=(10,6), levels=4, label=\"Højde (m)\")\n",
     "plt.xlabel(\"Længdekreds (°)\")\n",
     "plt.ylabel(\"Breddekreds (°)\")"
    ]
@@ -331,7 +331,7 @@
    ],
    "source": [
     "ax = da.plot.contour(figsize=(8,8), cmap=\"plasma\")\n",
-    "ax.set_xlim([12.5, 12.9]);\n",
+    "ax.set_xlim([12.5, 12.9])\n",
     "ax.set_ylim([55.8, 56]);"
    ]
   },
@@ -477,7 +477,7 @@
     }
    ],
    "source": [
-    "ax = ds.Temperature[:,0,:,:].plot.contourf();\n",
+    "ax = ds.Temperature[:,0,:,:].plot.contourf()\n",
     "ax.grid()"
    ]
   },

notebooks/DataArray - Dfsu plotting.ipynb

@@ -154,7 +154,7 @@
    ],
    "source": [
     "_, ax = plt.subplots(1,2)\n",
-    "da.plot.mesh(ax=ax[0]);\n",
+    "da.plot.mesh(ax=ax[0])\n",
     "da.plot.outline(ax=ax[1]);"
    ]
   },

notebooks/Dfsu - Export to netcdf.ipynb

@@ -157,7 +157,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
     "os.remove(\"oresund_sigma_z.nc\")"
    ]
   }

notebooks/Dfsu - Spectral data.ipynb

@@ -103,7 +103,7 @@
     }
    ],
    "source": [
-    "ax = da.plot.patch(rmax=8);\n",
+    "ax = da.plot.patch(rmax=8)\n",
     "dird = np.round(da.directions, 2)\n",
     "ax.set_thetagrids(dird, labels=dird);"
    ]
@@ -356,8 +356,8 @@
     "def plot_element(id=(0,da.geometry.n_elements-1), step=(0,da.n_timesteps-1)):\n",
     "    spec = da[step,id]\n",
     "    time = da.start_time + timedelta(seconds=(step*da.timestep))\n",
-    "    spec.plot(vmax=0.04, vmin=0, rmax=8, title=f\"Wave spectrum, {time}, element: {id}\");\n",
-    "    plt.show();"
+    "    spec.plot(vmax=0.04, vmin=0, rmax=8, title=f\"Wave spectrum, {time}, element: {id}\")\n",
+    "    plt.show()"
    ]
   },
   {

notebooks/Dfsu - Vertical Profile.ipynb

@@ -246,7 +246,7 @@
     "ax[0].plot(*ptA, color=\"b\", marker=\"*\", markersize=10)\n",
     "ax[0].plot(*ptB, color=\"b\", marker=\"*\", markersize=10)\n",
     "\n",
-    "g.plot.mesh(ax=ax[1], title=\"Transect mesh\");\n",
+    "g.plot.mesh(ax=ax[1], title=\"Transect mesh\")\n",
     "ax[1].axvline(distA, color=\"0.5\")\n",
     "ax[1].text(distA + 500, -20, 'position A')\n",
     "ax[1].axvline(distB, color=\"0.5\")\n",

notebooks/Dfsu and Mesh - Plotting.ipynb

@@ -272,12 +272,12 @@
    "source": [
     "fig, ax = plt.subplots(3,2)\n",
     "\n",
-    "geom.plot(title='patch', ax=ax[0,0]);\n",
-    "geom.plot.contourf(title='contourf', levels=5, ax=ax[0,1]);\n",
-    "geom.plot(plot_type='shaded', title='shaded', ax=ax[1,0]);\n",
-    "geom.plot.contour(title='contour', show_mesh=True, levels=6, vmin=-30, ax=ax[1,1]);\n",
-    "geom.plot.mesh(title='mesh_only', ax=ax[2,0]);\n",
-    "geom.plot.outline(title='outline_only', ax=ax[2,1]);\n",
+    "geom.plot(title='patch', ax=ax[0,0])\n",
+    "geom.plot.contourf(title='contourf', levels=5, ax=ax[0,1])\n",
+    "geom.plot(plot_type='shaded', title='shaded', ax=ax[1,0])\n",
+    "geom.plot.contour(title='contour', show_mesh=True, levels=6, vmin=-30, ax=ax[1,1])\n",
+    "geom.plot.mesh(title='mesh_only', ax=ax[2,0])\n",
+    "geom.plot.outline(title='outline_only', ax=ax[2,1])\n",
     "\n",
     "plt.tight_layout()"
    ]
@@ -457,7 +457,7 @@
     }
    ],
    "source": [
-    "ax = da.plot(cmap='plasma');\n",
+    "ax = da.plot(cmap='plasma')\n",
     "dfs.geometry.plot.outline(ax=ax, title=None);"
    ]
   },

pyproject.toml

@@ -103,6 +103,12 @@ notebooks = [
 ignore = ["E501", "E741"]
 
 select = [
+    # ruff defaults
+    "E4",
+    "E7",
+    "E9",
+    "F",
+    # ruff defaults
     "D100",
     "D101",
     "D102",
@@ -113,3 +119,8 @@ select = [
     "D415",
     "D417",
 ]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D"]
+"notebooks/*" = ["D", "E402"]
+"conftest.py" = ["D"]

tests/test_dfsu_layered.py

@@ -444,7 +444,7 @@ def test_top_elements_subset() -> None:
 
     assert len(subg.top_elements) == 6
 
-    ds = mikeio.Dfsu3D(filename).read(elements=idx3d)
+    _ = mikeio.Dfsu3D(filename).read(elements=idx3d)
 
 
 def test_bottom_elements():