Merge pull request #385 from gwmod/dev

Release v0.9.0

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2020 O.N. Ebbens, D.A. Brakenhoff, R. Calje
+Copyright (c) 2024 O.N. Ebbens, D.A. Brakenhoff, R. Calje
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -57,9 +57,10 @@ Install the module with pip:
 * `bottleneck`
 
 There are some optional dependecies, only needed (and imported) in a single method.
-Examples of this are `geocube` (used in
-add_min_ahn_to_gdf), `h5netcdf` (used for hdf5 files backend in xarray), `scikit-image`
-(used in calculate_sea_coverage). To install `nlmod` with the optional dependencies use:
+Examples of this are `geocube`, `rasterstats` (both used in nlmod.util.zonal_statistics),
+`h5netcdf` (used for hdf5 files backend in xarray), `scikit-image`
+(used in nlmod.read.rws.calculate_sea_coverage).
+To install `nlmod` with the optional dependencies use:
 
 `pip install nlmod[full]`
 

docs/conf.py

@@ -21,7 +21,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "nlmod"
-copyright = "2021, O.N. Ebbens, D.A. Brakenhoff, R. Caljé"
+copyright = "2024, O.N. Ebbens, D.A. Brakenhoff, R. Caljé"
 author = "O.N. Ebbens, D.A. Brakenhoff, R. Caljé"
 
 # The short X.Y version

docs/examples/02_surface_water.ipynb

@@ -89,7 +89,7 @@
    "source": [
     "fname_ahn = os.path.join(cachedir, \"ahn.tif\")\n",
     "if not os.path.isfile(fname_ahn):\n",
-    "    ahn = nlmod.read.ahn.get_ahn4(extent, identifier=\"AHN4_DTM_5m\")\n",
+    "    ahn = nlmod.read.ahn.get_ahn4(extent)\n",
     "    ahn.rio.to_raster(fname_ahn)\n",
     "ahn = rioxarray.open_rasterio(fname_ahn, mask_and_scale=True)[0]"
    ]

docs/examples/04_modifying_layermodels.ipynb

@@ -263,24 +263,6 @@
     "split_reindexer"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "The new layers are named according to the REGIS codes, with an added number if the layer was split into multiple sub-layers. For plotting a cross-section we want to use the original color from the REGIS cross-section plot for the new sub-layers."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "for j, i in split_reindexer.items():\n",
-    "    if j not in colors:\n",
-    "        colors[j] = colors[i]"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

docs/examples/09_schoonhoven.ipynb

@@ -119,7 +119,7 @@
     "norm = matplotlib.colors.Normalize(vmin=-3, vmax=1)\n",
     "cmap = \"viridis\"\n",
     "bgt.plot(\"summer_stage\", ax=ax, norm=norm, cmap=cmap)\n",
-    "nlmod.plot.colorbar_inside(norm=norm, cmap=cmap)"
+    "nlmod.plot.colorbar_inside(norm=norm, cmap=cmap);"
    ]
   },
   {
@@ -139,7 +139,7 @@
    "source": [
     "f, ax = nlmod.plot.get_map(extent)\n",
     "bgt.plot(\"ahn_min\", ax=ax, norm=norm, cmap=cmap)\n",
-    "nlmod.plot.colorbar_inside(norm=norm, cmap=cmap)"
+    "nlmod.plot.colorbar_inside(norm=norm, cmap=cmap);"
    ]
   },
   {
@@ -308,9 +308,7 @@
    "source": [
     "bed_resistance = 1.0\n",
     "\n",
-    "mg = nlmod.grid.modelgrid_from_ds(ds)\n",
-    "gi = flopy.utils.GridIntersect(mg, method=\"vertex\")\n",
-    "bgt_grid = nlmod.grid.gdf_to_grid(bgt, ix=gi).set_index(\"cellid\")\n",
+    "bgt_grid = nlmod.grid.gdf_to_grid(bgt, ds).set_index(\"cellid\")\n",
     "\n",
     "bgt_grid[\"cond\"] = bgt_grid.area / bed_resistance\n",
     "\n",
@@ -332,14 +330,17 @@
     "    \"W0656.cb3c3a25de4141d18c573b561f02e84a\",\n",
     "]\n",
     "\n",
-    "mask = bgt_grid[\"identificatie\"].isin(ids_grote_gracht) | bgt_grid[\n",
-    "    \"identificatie\"\n",
-    "].isin(ids_oude_haven)\n",
+    "mask = bgt_grid[\"identificatie\"].isin(ids_grote_gracht + ids_oude_haven)\n",
     "lakes = bgt_grid[mask].copy()\n",
     "lakes[\"name\"] = \"\"\n",
     "lakes.loc[lakes[\"identificatie\"].isin(ids_grote_gracht), \"name\"] = \"grotegracht\"\n",
     "lakes.loc[lakes[\"identificatie\"].isin(ids_oude_haven), \"name\"] = \"oudehaven\"\n",
-    "bgt_grid = bgt_grid[~mask]"
+    "bgt_grid = bgt_grid[~mask]\n",
+    "\n",
+    "# cut rainfall and evaporation from model dataset\n",
+    "lak_rainfall, lak_evaporation = nlmod.gwf.lake.clip_meteorological_data_from_ds(\n",
+    "    lakes, ds, boundname_column=\"name\"\n",
+    ")"
    ]
   },
   {
@@ -400,12 +401,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# add specific properties to the lake gdf\n",
-    "lakes.loc[lakes[\"identificatie\"].isin(ids_grote_gracht), \"lakeno\"] = 0\n",
-    "lakes.loc[lakes[\"identificatie\"].isin(ids_oude_haven), \"lakeno\"] = 1\n",
-    "\n",
     "# add general properties to the lake gdf\n",
-    "lakes[\"elev\"] = lakes[\"ahn_min\"] - 0.5\n",
     "summer_months = (4, 5, 6, 7, 8, 9)\n",
     "if pd.to_datetime(ds.time.start).month in summer_months:\n",
     "    lakes[\"strt\"] = lakes[\"summer_stage\"]\n",
@@ -418,13 +414,18 @@
     "# lakes.loc[lakes['identificatie'].isin(ids_oude_haven), 'INFLOW'] = 'inflow_lake'\n",
     "\n",
     "# add outlet to Oude Haven, water flows from Oude Haven to Grote Gracht.\n",
-    "lakes.loc[lakes[\"identificatie\"].isin(ids_oude_haven), \"lakeout\"] = 0\n",
-    "lakes.loc[lakes[\"identificatie\"].isin(ids_oude_haven), \"outlet_invert\"] = (\n",
-    "    1.0  # overstort hoogte\n",
-    ")\n",
+    "lakes.loc[lakes[\"name\"] == \"oudehaven\", \"lakeout\"] = \"grotegracht\"\n",
+    "lakes.loc[lakes[\"name\"] == \"oudehaven\", \"outlet_invert\"] = 1.0  # overstort hoogte\n",
     "\n",
     "# add lake to groundwaterflow model\n",
-    "lak = nlmod.gwf.lake_from_gdf(gwf, lakes, ds, boundname_column=\"name\")"
+    "lak = nlmod.gwf.lake_from_gdf(\n",
+    "    gwf,\n",
+    "    lakes,\n",
+    "    ds,\n",
+    "    boundname_column=\"name\",\n",
+    "    rainfall=lak_rainfall,\n",
+    "    evaporation=lak_evaporation,\n",
+    ")"
    ]
   },
   {
@@ -501,7 +502,7 @@
     "    colorbar_label=\"head [m NAP]\",\n",
     "    title=\"mean head\",\n",
     ")\n",
-    "bgt.dissolve().plot(ax=pc.axes, edgecolor=\"k\", facecolor=\"none\")"
+    "bgt.dissolve().plot(ax=pc.axes, edgecolor=\"k\", facecolor=\"none\");"
    ]
   },
   {
@@ -784,7 +785,7 @@
     "line = ax.add_collection(lc)\n",
     "nlmod.plot.colorbar_inside(line, label=\"Travel time (years)\")\n",
     "\n",
-    "bgt.dissolve().plot(ax=ax, edgecolor=\"k\", facecolor=\"none\")"
+    "bgt.dissolve().plot(ax=ax, edgecolor=\"k\", facecolor=\"none\");"
    ]
   },
   {

docs/getting_started.rst

@@ -120,9 +120,10 @@ potential solutions.
 
 On top of that there are some optional dependecies:
 
-- geocube (used in add_min_ahn_to_gdf)
+- geocube (used in nlmod.util.zonal_statistics)
+- rasterstats  (used in nlmod.util.zonal_statistics)
 - h5netcdf (used for the hdf5 backend of xarray)
-- scikit-image (used in calculate_sea_coverage)
+- scikit-image (used in nlmod.read.rws.calculate_sea_coverage)
 
 These dependencies are only needed (and imported) in a single method or function.
 They can be installed using ``pip install nlmod[full]`` or ``pip install -e .[full]``.