Fix missing ruff defaults

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
 

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()

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 - Export to shapefile.ipynb

@@ -318,7 +318,7 @@
     "        y = v[:,1]\n",
     "        poly = LineString([(i[0], i[1]) for i in zip(x,y)])\n",
     "        if(poly.is_empty):\n",
-    "            print(f\"{i} is empty\")\n",
+    "            print(f\"{p} is empty\")\n",
     "        poly_list.append(dict(wind_speed = level, poly = poly))"
    ]
   },
@@ -733,7 +733,8 @@
     "for file in files:\n",
     "    for ext in exts:\n",
     "        filename = f\"{file}.{ext}\"\n",
-    "        if os.path.exists(filename): os.remove(filename)"
+    "        if os.path.exists(filename):\n",
+    "            os.remove(filename)"
    ]
   }
  ],
@@ -753,7 +754,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

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():