Speed up docs (#144)

* Disable some cells to speed up docs

* Update ahn.py

* Remove metadata of notebooks and add run_all_notebooks.py

* Some small improvements to notebooks

Specify raw_mimetype as "python"

* replace geodata.nationaalgeoregister.nl by geodata.nationaalgeoregister.nl

wcs-services from https://geodata.nationaalgeoregister.nl are not available anymore

* point nijmuiden notebooks to the same directory

* Update description in schoonhoven notebooks

* fix bug where modpath

reverts part of commit 6413c6f

* Add get_ahn_at_point

* change "full_ds.nc" to f"{ds.model_name}.nc"

* Update python-publish.yml

because of warning at version 4.0:
https://github.com/ArtesiaWater/nlmod/actions/runs/3377917857

And the fact that version 5.0 was not sent to pypi

.github/workflows/python-publish.yml

@@ -26,7 +26,7 @@ jobs:
       run: |
         python -m build --sdist --wheel --outdir dist/
     - name: Publish a Python distribution to PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

docs/examples/00_model_from_scratch.ipynb

@@ -305,27 +305,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "dace5e1b41a98a8e52d2a8eebc3b981caf2c12e7a76736ebfb89a489e3b62e79"
-   }
+   "name": "python"
   }
  },
  "nbformat": 4,

docs/examples/01_basic_model.ipynb

@@ -12,16 +12,6 @@
     "This example notebook shows a basic example of a model created using online data with the `nlmod` package. `nlmod` contains functions to create modflow models anywhere in the Netherlands."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Contents<a name=\"TOC\"></a>\n",
-    "1. [Create model](#create)\n",
-    "2. [Run model](#run)\n",
-    "3. [Visualise](#visualise)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -52,7 +42,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### [1. Create model](#TOC)<a name=\"create\"></a>\n",
+    "## Create model\n",
     "\n",
     "With the code below we create a modflow model with the name 'IJmuiden'. This model has the following properties :\n",
     "- an extent that covers part of the Northsea, Noordzeekanaal and the small port city IJmuiden.\n",
@@ -76,19 +66,16 @@
    "outputs": [],
    "source": [
     "# model settings\n",
-    "model_ws = \"model1\"\n",
+    "model_ws = \"ijmuiden\"\n",
     "model_name = \"IJmuiden\"\n",
     "figdir, cachedir = nlmod.util.get_model_dirs(model_ws)\n",
     "extent = [95000.0, 105000.0, 494000.0, 500000.0]\n",
     "delr = 100.0\n",
     "delc = 100.0\n",
     "steady_state = True\n",
     "start_time = \"2015-1-1\"\n",
-    "use_regis = True\n",
-    "regis_botm_layer = \"MSz1\"\n",
-    "use_geotop = True\n",
     "add_northsea = True\n",
-    "starting_head = 1.0\n"
+    "starting_head = 1.0"
    ]
   },
   {
@@ -99,9 +86,9 @@
    "source": [
     "layer_model = nlmod.read.regis.get_combined_layer_models(\n",
     "    extent,\n",
-    "    use_regis=use_regis,\n",
-    "    regis_botm_layer=regis_botm_layer,\n",
-    "    use_geotop=use_geotop,\n",
+    "    use_regis=True,\n",
+    "    regis_botm_layer=\"MSz1\",\n",
+    "    use_geotop=True,\n",
     "    cachedir=cachedir,\n",
     "    cachename=\"combined_layer_ds.nc\",\n",
     ")\n",
@@ -232,7 +219,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### [2. Write and Run](#TOC)<a name=\"run\"></a>\n",
+    "## Write and Run\n",
     "Now that we've created all the modflow packages we need to write them to modflow files. You always have to write the modflow data to the model workspace before you can run the model. You can write the model files and run the model using the function `nlmod.sim.write_and_run)` as shown below. This function has two additional options:\n",
     "1. Write the model dataset to the disk if `write_ds` is `True`. This makes it easier and faster to load model data if you ever need it. \n",
     "2. Write a copy of this Jupyter Notebook to the same directory as the modflow files if `nb_path` is the name of this Jupyter Notebook. It can be useful to have a copy of the script that created the modflow files, together with the files. "
@@ -253,8 +240,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### [3. Visualise](#TOC)<a name=\"visualise\"></a>\n",
-    "\n",
+    "## Visualise\n",
     "Using the `ds` and `gwf` variables it is quite easy to visualise model data. Below the modelgrid together with the surface water is shown."
    ]
   },
@@ -264,7 +250,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ax = nlmod.plot.modelgrid(ds)"
+    "ax = nlmod.plot.modelgrid(ds)\n",
+    "nlmod.plot.surface_water(ds, ax=ax)"
    ]
   },
   {
@@ -302,42 +289,8 @@
   }
  ],
  "metadata": {
-  "CodeCell": {
-   "cm_config": {
-    "lineWrapping": true
-   }
-  },
-  "MarkdownCell": {
-   "cm_config": {
-    "lineWrapping": true
-   }
-  },
-  "anaconda-cloud": {},
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "dace5e1b41a98a8e52d2a8eebc3b981caf2c12e7a76736ebfb89a489e3b62e79"
-   }
-  },
-  "widgets": {
-   "state": {},
-   "version": "1.1.2"
+   "name": "python"
   }
  },
  "nbformat": 4,