Add image to all notebooks and add a notebook template (#18)

.scripts/fix_format.py

@@ -0,0 +1,9 @@
+import subprocess
+
+cmd = ("ruff", "format", "../")
+proc = subprocess.run(cmd)
+assert proc.returncode == 0, f"Error running command: {' '.join(cmd)}"
+
+cmd = ("ruff", "check", "../", "--fix")
+proc = subprocess.run(cmd)
+assert proc.returncode == 0, f"Error running command: {' '.join(cmd)}"

base/watershed/build_base_watershed.ipynb

@@ -4,7 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Build the watershed model"
+    "# U.S. Geological Survey Class GW3099\n",
+    "Advanced Modeling of Groundwater Flow (GW3099)\\\n",
+    "Boise, Idaho\\\n",
+    "September 16 - 20, 2024\n",
+    "\n",
+    "![title](../../images/ClassLocation.jpg)\n",
+    "\n",
+    "## Build the watershed model"
    ]
   },
   {
@@ -66,7 +73,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Load the topology"
+    "### Develop the data for the watershed model\n",
+    "\n",
+    "#### Load the topology"
    ]
   },
   {
@@ -94,7 +103,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Structured grid parameters"
+    "#### Structured grid parameters"
    ]
   },
   {
@@ -119,7 +128,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Read in boundary data\n",
+    "#### Read in boundary data\n",
     "\n",
     "Load the boundary data from `defaults.py` and plot"
    ]
@@ -158,7 +167,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create a structured grid"
+    "#### Create a structured grid"
    ]
   },
   {
@@ -185,7 +194,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Sample the raw topographic data"
+    "#### Sample the raw topographic data"
    ]
   },
   {
@@ -206,7 +215,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Intersect river segments with grid"
+    "#### Intersect river segments with grid"
    ]
   },
   {
@@ -222,7 +231,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Plot the river intersection"
+    "#### Plot the river intersection"
    ]
   },
   {
@@ -267,7 +276,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Set the idomain value to 2 where the river intersects the grid"
+    "#### Set the idomain value to 2 where the river intersects the grid"
    ]
   },
   {
@@ -288,7 +297,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Define the number of layers and the thickness of layer 1"
+    "#### Define the number of layers and the thickness of layer 1"
    ]
   },
   {
@@ -305,7 +314,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create the drain data for the river segments"
+    "#### Create the drain data for the river segments"
    ]
   },
   {
@@ -329,7 +338,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create the groundwater discharge drain data"
+    "#### Create the groundwater discharge drain data"
    ]
   },
   {
@@ -350,7 +359,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create the top and bottom arrays.\n",
+    "#### Create the top and bottom arrays.\n",
     "\n",
     "Top array is not used by the model."
    ]
@@ -393,7 +402,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Create idomain and starting head data"
+    "#### Create idomain and starting head data"
    ]
   },
   {
@@ -410,7 +419,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Build the model files using FloPy\n",
+    "### Build the model files using FloPy\n",
     "Note that the CSV solver output is enabled. We will use that in one of the other notebooks."
    ]
   },
@@ -502,7 +511,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Count the number of active cells"
+    "#### Count the number of active cells"
    ]
   },
   {
@@ -519,7 +528,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Write the model files"
+    "#### Write the model files"
    ]
   },
   {

exercises-completed/flopy/flopy_getting_started.ipynb

@@ -1,5 +1,19 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# U.S. Geological Survey Class GW3099\n",
+    "Advanced Modeling of Groundwater Flow (GW3099)\\\n",
+    "Boise, Idaho\\\n",
+    "September 16 - 20, 2024\n",
+    "\n",
+    "![title](../../images/ClassLocation.jpg)\n",
+    "\n",
+    "## Building and post-processing a MODFLOW 6 model"
+   ]
+  },
   {
    "attachments": {
     "ex01a.png": {
@@ -16,8 +30,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Building and post-processing a MODFLOW 6 model\n",
-    "\n",
     "A MODFLOW 6 model will be developed of the domain shown above. This model simulation is based on example 1 in [Pollock, D.W., 2016, User guide for MODPATH Version 7—A particle-tracking model for MODFLOW: U.S. Geological Survey Open-File Report 2016–1086, 35 p., http://dx.doi.org/10.3133/ofr20161086](https://doi.org/10.3133/ofr20161086).\n",
     "\n",
     "The model domain will be discretized into 3 layers, 21 rows, and 20 columns. A constant value of 500 ft will be specified for `delr` and `delc`. The top (`TOP`) of the model should be set to 400 ft and the bottom of the three layers (`BOTM`) should be set to 220 ft, 200 ft, and 0 ft, respectively. The model has one steady-state stress period. \n",
@@ -112,6 +124,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "### Build the model\n",
+    "\n",
     "Create a simulation object, a temporal discretization object, and a iterative model solution object using `flopy.mf6.MFSimulation()`, `flopy.mf6.ModflowTdis()`, and `flopy.mf6.ModflowIms()`, respectively. Set the `sim_name` to `name` and `sim_ws` to `ws` in the simulation object. Use default values for all temporal discretization and iterative model solution variables. Make sure to include the simulation object (`sim`) as the first variable in the temporal discretization and iterative model solution objects."
    ]
   },
@@ -440,7 +454,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Post-process the results\n",
+    "### Post-process the results\n",
     "\n",
     "Load the heads and face flows from the hds and cbc files. The head file can be loaded with the `gwf.output.head()` method. The cell-by-cell file can be loaded with the `gwf.output.budget()` method. \n",
     "\n",

exercises-completed/gwt/ex1.ipynb

@@ -1,5 +1,17 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# U.S. Geological Survey Class GW3099\n",
+    "Advanced Modeling of Groundwater Flow (GW3099)\\\n",
+    "Boise, Idaho\\\n",
+    "September 16 - 20, 2024\n",
+    "\n",
+    "![title](../../images/ClassLocation.jpg)"
+   ]
+  },
   {
    "attachments": {
     "image.png": {

exercises-completed/netcdf/step0_netcdf_output.ipynb

@@ -1,5 +1,20 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "eb8afb07-3737-4c0d-9c58-528be7dcbade",
+   "metadata": {},
+   "source": [
+    "# U.S. Geological Survey Class GW3099\n",
+    "Advanced Modeling of Groundwater Flow (GW3099)\\\n",
+    "Boise, Idaho\\\n",
+    "September 16 - 20, 2024\n",
+    "\n",
+    "![title](../../images/ClassLocation.jpg)\n",
+    "\n",
+    "# NetCDF Output"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -20,7 +35,7 @@
    "id": "da70620c-e003-40cd-8d78-7c70eb83dc3e",
    "metadata": {},
    "source": [
-    "# Load the base watershed model\n",
+    "## Load the base watershed model\n",
     "\n",
     "We will use the base watershed model to demonstrate MODFLOW NetCDF output functionality.  "
    ]
@@ -38,22 +53,12 @@
     ")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "053b01cc-1e53-435f-9b0a-3fc30abd7874",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!which mf6"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "9fc6cdca-3668-4bd8-a901-91a3651a94c2",
    "metadata": {},
    "source": [
-    "# Modify the model to save NetCDF output\n",
+    "## Modify the model to save structured NetCDF output\n",
     "\n",
     "We need to set the `start_date_time` variable in the TDIS file and define the `export_netcdf` variable in the groundwater flow model `name_file`. We will create `structured` NetCDF output first. "
    ]
@@ -84,7 +89,7 @@
    "id": "69932909-d442-411c-a9ab-c2795038ccb4",
    "metadata": {},
    "source": [
-    "# Change the simulation workspace, write the model files, and run the model"
+    "### Change the simulation workspace, write the model files, and run the model"
    ]
   },
   {
@@ -123,7 +128,7 @@
    "id": "82c2eba0-5d6b-49b4-9f10-51e140529b58",
    "metadata": {},
    "source": [
-    "# Load the structured NetCDF file with `xarray` and plot the results"
+    "### Load the structured NetCDF file with `xarray` and plot the results"
    ]
   },
   {
@@ -173,7 +178,7 @@
    "id": "d74dcd66-4763-43c2-a1ec-700cc1ecd71b",
    "metadata": {},
    "source": [
-    "# Modify the model to save mesh NetCDF output\n",
+    "## Modify the model to save mesh NetCDF output\n",
     "\n",
     "We need modufy the `export_netcdf` variable in the groundwater flow model `name_file` to `ugrid` to create mesh NetCDF output."
    ]
@@ -193,7 +198,7 @@
    "id": "334eb752-77a6-4bf7-b877-772aa19b1f54",
    "metadata": {},
    "source": [
-    "# Change the simulation workspace, write the model files, and run the model"
+    "### Change the simulation workspace, write the model files, and run the model"
    ]
   },
   {
@@ -232,7 +237,7 @@
    "id": "ad61cea1-384a-4245-9cbd-3b66b8c7cae9",
    "metadata": {},
    "source": [
-    "# Load the mesh NetCDF file with `xugrid` and plot the results"
+    "### Load the mesh NetCDF file with `xugrid` and plot the results"
    ]
   },
   {
@@ -272,7 +277,7 @@
    "id": "c01f168d-5019-4c49-b30b-76fc3e4343a3",
    "metadata": {},
    "source": [
-    "# Create cross-sections using `xugrid`\n",
+    "### Create cross-sections using `xugrid`\n",
     "\n",
     "First, we will create a cross-section along a column (y-direction)."
    ]