Update to 0.5.2

.github/workflows/ci.yml

@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - main
+      - dev
   pull_request:
     branches:
       - main

.gitignore

@@ -139,10 +139,12 @@ cython_debug/
 
 # vscode
 .vscode
-.code-workspace
+*.code-workspace
 
 # nlmod specific
 nlmod/bin/
 flowchartnlmod.pptx
 tests/data/
-docs/examples/*/
+docs/examples/*/
+!docs/examples/data/
+!docs/examples/data/chloride_hbossche.nc

docs/examples/00_model_from_scratch.ipynb

@@ -31,7 +31,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nlmod.util.get_color_logger('INFO');"
+    "nlmod.util.get_color_logger(\"INFO\");"
    ]
   },
   {
@@ -94,7 +94,6 @@
     "    extent,\n",
     "    delr=dx,\n",
     "    delc=dy,\n",
-    "    layer=len(kh),\n",
     "    top=top,\n",
     "    botm=botm,\n",
     "    kh=kh,\n",
@@ -118,9 +117,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = nlmod.time.set_ds_time(\n",
-    "    ds, time=[pd.Timestamp.today()], steady_state=True\n",
-    ")\n"
+    "ds = nlmod.time.set_ds_time(ds, time=pd.Timestamp.today())"
    ]
   },
   {
@@ -143,7 +140,7 @@
     "dis = nlmod.gwf.dis(ds, gwf)\n",
     "npf = nlmod.gwf.npf(ds, gwf)\n",
     "ic = nlmod.gwf.ic(ds, gwf, starting_head=1.0)\n",
-    "oc = nlmod.gwf.oc(ds, gwf, save_head=True)\n"
+    "oc = nlmod.gwf.oc(ds, gwf, save_head=True)"
    ]
   },
   {
@@ -163,7 +160,7 @@
     "wells.index.name = \"well no.\"\n",
     "wells.loc[0] = 100, -50, -5, -10, -100.0\n",
     "wells.loc[1] = 200, 150, -20, -30, -300.0\n",
-    "wells\n"
+    "wells"
    ]
   },
   {
@@ -210,7 +207,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "riv_data = nlmod.gwf.surface_water.rivdata_from_xylist( \n",
+    "riv_data = nlmod.gwf.surface_water.rivdata_from_xylist(\n",
     "    gwf, xyriv, riv_layer, riv_stage, riv_cond, riv_botm\n",
     ")\n",
     "\n",

docs/examples/01_basic_model.ipynb

@@ -24,7 +24,7 @@
     "import flopy\n",
     "import geopandas as gpd\n",
     "import matplotlib.pyplot as plt\n",
-    "import nlmod\n"
+    "import nlmod"
    ]
   },
   {
@@ -35,7 +35,7 @@
    "source": [
     "print(f\"nlmod version: {nlmod.__version__}\")\n",
     "\n",
-    "nlmod.util.get_color_logger('INFO');"
+    "nlmod.util.get_color_logger(\"INFO\");"
    ]
   },
   {
@@ -94,9 +94,7 @@
     ")\n",
     "\n",
     "# create a model ds by changing grid of layer_model\n",
-    "ds = nlmod.to_model_ds(\n",
-    "    layer_model, model_name, model_ws, delr=delr, delc=delc\n",
-    ")\n",
+    "ds = nlmod.to_model_ds(layer_model, model_name, model_ws, delr=delr, delc=delc)\n",
     "\n",
     "# add time discretisation\n",
     "ds = nlmod.time.set_ds_time(\n",
@@ -135,7 +133,7 @@
     "ic = nlmod.gwf.ic(ds, gwf, starting_head=starting_head)\n",
     "\n",
     "# Create the output control package\n",
-    "oc = nlmod.gwf.oc(ds, gwf)\n"
+    "oc = nlmod.gwf.oc(ds, gwf)"
    ]
   },
   {
@@ -153,7 +151,7 @@
     "ds.update(rws_ds)\n",
     "\n",
     "# build ghb package\n",
-    "ghb = nlmod.gwf.ghb(ds, gwf, da_name)\n"
+    "ghb = nlmod.gwf.ghb(ds, gwf, da_name)"
    ]
   },
   {
@@ -179,7 +177,7 @@
    "source": [
     "# add constant head cells at model boundaries\n",
     "ds.update(nlmod.grid.mask_model_edge(ds, ds[\"idomain\"]))\n",
-    "chd = nlmod.gwf.chd(ds, gwf, chd=\"edge_mask\", head=\"starting_head\")\n"
+    "chd = nlmod.gwf.chd(ds, gwf, chd=\"edge_mask\", head=\"starting_head\")"
    ]
   },
   {
@@ -189,14 +187,12 @@
    "outputs": [],
    "source": [
     "# download knmi recharge data\n",
-    "knmi_ds = nlmod.read.knmi.get_recharge(\n",
-    "    ds, cachedir=ds.cachedir, cachename=\"recharge\"\n",
-    ")\n",
+    "knmi_ds = nlmod.read.knmi.get_recharge(ds, cachedir=ds.cachedir, cachename=\"recharge\")\n",
     "# update model dataset\n",
     "ds.update(knmi_ds)\n",
     "\n",
     "# create recharge package\n",
-    "rch = nlmod.gwf.rch(ds, gwf)\n"
+    "rch = nlmod.gwf.rch(ds, gwf)"
    ]
   },
   {
@@ -231,9 +227,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nlmod.sim.write_and_run(\n",
-    "    sim, ds, write_ds=True, nb_path=\"01_basic_model.ipynb\"\n",
-    ")"
+    "nlmod.sim.write_and_run(sim, ds, write_ds=True, nb_path=\"01_basic_model.ipynb\")"
    ]
   },
   {

docs/examples/02_surface_water.ipynb

@@ -42,7 +42,7 @@
    "source": [
     "print(f\"nlmod version: {nlmod.__version__}\")\n",
     "\n",
-    "nlmod.util.get_color_logger('INFO');"
+    "nlmod.util.get_color_logger(\"INFO\");"
    ]
   },
   {
@@ -92,7 +92,7 @@
    "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, identifier=\"AHN4_DTM_5m\")\n",
     "    ahn.rio.to_raster(fname_ahn)\n",
     "ahn = rioxarray.open_rasterio(fname_ahn, mask_and_scale=True)"
    ]
@@ -122,7 +122,7 @@
    "metadata": {},
    "source": [
     "#### Add minimum surface height around surface water bodies\n",
-    "Get the minimum surface level in 1 meter around surface water levels and add these data to the column 'ahn_min'."
+    "Get the minimum surface level in 5 meter around surface water levels and add these data to the column 'ahn_min'."
    ]
   },
   {
@@ -132,18 +132,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# use geocube\n",
-    "gc = make_geocube(\n",
-    "    vector_data=bgt.buffer(5.0).reset_index().rename_geometry('geometry'),\n",
-    "    measurements=[\"index\"],\n",
-    "    like=ahn, # ensure the data are on the same grid\n",
-    "    rasterize_function=partial(rasterize_image, all_touched=True),\n",
-    ")\n",
-    "gc['ahn'] = ahn\n",
-    "\n",
-    "ahn_min = gc.groupby('index').min()['ahn'].to_pandas()\n",
-    "ahn_min.index = ahn_min.index.astype(int)\n",
-    "bgt['ahn_min'] = ahn_min"
+    "bgt = nlmod.gwf.add_min_ahn_to_gdf(bgt, ahn, buffer=5.0, column='ahn_min')"
    ]
   },
   {
@@ -182,7 +171,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pg = nlmod.gwf.surface_water.download_level_areas(bgt, extent=extent)"
+    "la = nlmod.gwf.surface_water.download_level_areas(bgt, extent=extent, raise_exceptions=False)"
    ]
   },
   {
@@ -203,8 +192,8 @@
    "source": [
     "f, ax = nlmod.plot.get_map(extent)\n",
     "bgt.plot(color=\"k\", ax=ax)\n",
-    "for wb in pg:\n",
-    "    pg[wb].plot(\"summer_stage\", ax=ax, vmin=-3, vmax=1, zorder=0)"
+    "for wb in la:\n",
+    "    la[wb].plot(\"summer_stage\", ax=ax, vmin=-3, vmax=1, zorder=0)"
    ]
   },
   {
@@ -223,7 +212,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bgt = nlmod.gwf.surface_water.add_stages_from_waterboards(bgt, pg=pg)"
+    "bgt = nlmod.gwf.surface_water.add_stages_from_waterboards(bgt, la=la)"
    ]
   },
   {
@@ -349,7 +338,9 @@
    "outputs": [],
    "source": [
     "# layer model\n",
-    "layer_model = nlmod.read.get_regis(extent, cachedir=cachedir, cachename=\"layer_model.nc\")\n",
+    "layer_model = nlmod.read.get_regis(\n",
+    "    extent, cachedir=cachedir, cachename=\"layer_model.nc\"\n",
+    ")\n",
     "layer_model"
    ]
   },
@@ -361,9 +352,7 @@
    "outputs": [],
    "source": [
     "# create a model ds by changing grid of layer_model\n",
-    "ds = nlmod.to_model_ds(\n",
-    "    layer_model, model_name, model_ws, delr=delr, delc=delc\n",
-    ")\n",
+    "ds = nlmod.to_model_ds(layer_model, model_name, model_ws, delr=delr, delc=delc)\n",
     "\n",
     "# create model time dataset\n",
     "ds = nlmod.time.set_ds_time(ds, start_time=start_time, steady_state=True)\n",
@@ -502,12 +491,13 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(1, 1, figsize=(10, 8))\n",
-    "sfw_grid.loc[mask].plot(column=\"identificatie\", legend=True, ax=ax,\n",
-    "                        legend_kwds={\"loc\": \"upper left\"})\n",
+    "sfw_grid.loc[mask].plot(\n",
+    "    column=\"identificatie\", legend=True, ax=ax, legend_kwds={\"loc\": \"upper left\"}\n",
+    ")\n",
     "xlim = ax.get_xlim()\n",
     "ylim = ax.get_ylim()\n",
     "gwf.modelgrid.plot(ax=ax)\n",
-    "ax.set_xlim(xlim[0], xlim[0]+ds.delr*1.1)\n",
+    "ax.set_xlim(xlim[0], xlim[0] + ds.delr * 1.1)\n",
     "ax.set_ylim(ylim)\n",
     "ax.set_title(f\"Surface water shapes in cell: {cid}\");"
    ]
@@ -581,9 +571,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "celldata = nlmod.gwf.surface_water.aggregate(\n",
-    "    sfw_grid, \"area_weighted\"\n",
-    ")"
+    "celldata = nlmod.gwf.surface_water.aggregate(sfw_grid, \"area_weighted\")"
    ]
   },
   {
@@ -723,9 +711,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nlmod.sim.write_and_run(\n",
-    "    sim, ds, write_ds=True, nb_path=\"02_surface_water.ipynb\"\n",
-    ")"
+    "nlmod.sim.write_and_run(sim, ds, write_ds=True, nb_path=\"02_surface_water.ipynb\")"
    ]
   },
   {

docs/examples/03_local_grid_refinement.ipynb

@@ -37,9 +37,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f'nlmod version: {nlmod.__version__}')\n",
+    "print(f\"nlmod version: {nlmod.__version__}\")\n",
     "\n",
-    "nlmod.util.get_color_logger('INFO');"
+    "nlmod.util.get_color_logger(\"INFO\");"
    ]
   },
   {
@@ -91,9 +91,7 @@
     ")\n",
     "\n",
     "# create a model ds by changing grid of layer_model\n",
-    "ds = nlmod.to_model_ds(\n",
-    "    layer_model, model_name, model_ws, delr=delr, delc=delc\n",
-    ")\n",
+    "ds = nlmod.to_model_ds(layer_model, model_name, model_ws, delr=delr, delc=delc)\n",
     "\n",
     "# add time discretisation\n",
     "ds = nlmod.time.set_ds_time(\n",
@@ -122,9 +120,7 @@
    "outputs": [],
    "source": [
     "# use gridgen to create vertex grid\n",
-    "ds = nlmod.grid.refine(\n",
-    "    ds, refinement_features=[(refine_shp_fname, \"line\", levels)]\n",
-    ")\n",
+    "ds = nlmod.grid.refine(ds, refinement_features=[(refine_shp_fname, \"line\", levels)])\n",
     "\n",
     "if add_northsea:\n",
     "    ds = nlmod.read.rws.add_northsea(ds, cachedir=cachedir)"
@@ -194,9 +190,7 @@
    "outputs": [],
    "source": [
     "# add knmi recharge to the model datasets\n",
-    "knmi_ds = nlmod.read.knmi.get_recharge(\n",
-    "    ds, cachedir=ds.cachedir, cachename=\"recharge\"\n",
-    ")\n",
+    "knmi_ds = nlmod.read.knmi.get_recharge(ds, cachedir=ds.cachedir, cachename=\"recharge\")\n",
     "ds.update(knmi_ds)\n",
     "\n",
     "# create recharge package\n",
@@ -321,13 +315,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fname = os.path.join(ds.figdir, 'results.nc')\n",
+    "fname = os.path.join(ds.figdir, \"results.nc\")\n",
     "nlmod.gis.ds_to_ugrid_nc_file(ds, fname)"
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
+   "cell_type": "raw",
+   "metadata": {
+    "raw_mimetype": "text/x-python"
+   },
    "source": [
     "## Compare with measurements\n",
     "We can download the BRO groundwater observation data and compare the model results with this data."