Merge pull request #160 from mcflugen/mcflugen/minor-edits-to-landlab-notebooks

Minor edits of the landlab notebooks

Author: mcflugen

lessons/landlab/landlab/00_welcome.ipynb

@@ -16,11 +16,11 @@
     "Landlab is an open-source Python-language package for numerical modeling of Earth surface dynamics.\n",
     "It contains:\n",
     "\n",
-    "*  A gridding engine which represents the model domain. Regular and irregular grids are supported.\n",
-    "*  A library of process components, each of which represents a physical process (e.g., generation\n",
+    "*  A **gridding engine** that represents the model domain. Regular and irregular grids are supported.\n",
+    "*  A **library of process components**, each of which represents a physical process (e.g., generation\n",
     "   of rain, erosion by flowing water). These components have a common interface and can be combined\n",
     "   based on a user's needs.\n",
-    "*  Utilities that support general numerical methods, file input/output, and visualization.\n"
+    "*  Utilities that support general **numerical methods**, file **input/output**, and **visualization**.\n"
    ]
   },
   {
@@ -42,7 +42,7 @@
     "  * Grid elements: *cells*\n",
     "  \n",
     "* [Numerics](04-numerics.ipynb)\n",
-    "  * Calculations on a grid elements\n",
+    "  * Calculations on grid elements\n",
     "  * Example: Fault scarp\n",
     "\n",
     "* [Components](05-components.ipynb)\n",
@@ -54,10 +54,10 @@
     "*  [HyLands demo](bedrock_landslides_on_dems.ipynb)\n",
     "*  [Overland flow](overland_flow.ipynb)\n",
     "   * This notebook illustrates running the deAlmeida overland flow component in an extremely\n",
-    "     simple-minded way on a real topography, then shows it creating a flood sequence along\n",
+    "     simple-minded way on real topography, it then shows how to create a flood sequence along\n",
     "     an inclined surface with an oscillating water surface at one end.\n",
     "\n",
-    "**For more Landlab tutorials, click here:** <a href=\"https://landlab.readthedocs.io/en/latest/user_guide/tutorials.html\">https://landlab.readthedocs.io/en/latest/user_guide/tutorials.html</a></small>\n"
+    "For more Landlab tutorials, see the [Tutorial Gallery](https://landlab.csdms.io/generated/tutorials)\n"
    ]
   },
   {
@@ -67,12 +67,20 @@
     "## Links\n",
     "\n",
     "* Reference\n",
-    "  * [Documentation](https://landlab.readthedocs.io)\n",
+    "  * [Documentation](https://landlab.csdms.io)\n",
+    "  * [Tutorial Gallery](https://landlab.csdms.io/generated/tutorials)\n",
     "  * [Source code](https://github.com/landlab/landlab)\n",
     "* Ask for help\n",
     "  * [Issues on GitHub](https://github.com/csdms/landlab/issues)\n",
     "  * [CSDMS Help Desk](https://csdms.github.io/help-desk)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "👉 [Introduction to grids](01-intro.ipynb)"
+   ]
   }
  ],
  "metadata": {

lessons/landlab/landlab/01-intro.a.ipynb

@@ -63,7 +63,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "\n",
     "## What you need to know about Landlab grids\n",
     "\n",
     "Landlab model grids are 2D data structures that represent the model domain. A few things to know about grid management:\n",
@@ -80,9 +79,14 @@
     "\n",
     "<img src=\"./media/Grids1.png\"/>\n",
     "\n",
-    "**Figure** Geometry and topology of grid elements on various Landlab grids ([Hobley et al. 2017](https://esurf.copernicus.org/articles/5/21/2017/))\n",
-    "\n",
-    "-- [Interactive sketchbook](https://landlab.github.io/grid-sketchbook/)"
+    "**Figure** Geometry and topology of grid elements on various Landlab grids ([Hobley et al. 2017](https://esurf.copernicus.org/articles/5/21/2017/))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 👉 [Interactive sketchbook](https://landlab.github.io/grid-sketchbook/)"
    ]
   },
   {
@@ -113,7 +117,7 @@
     "\n",
     "---\n",
     "\n",
-    "**More complete descriptions of these grid types can be found in [Landlab's documentation](https://landlab.readthedocs.io/en/master/user_guide/grid.html).**\n",
+    "**More complete descriptions of these grid types can be found in [Landlab's documentation](https://landlab.csdms.io/user_guide/reference/grid.html)**\n",
     "\n",
     "---"
    ]
@@ -132,7 +136,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "These are all Python <i>classes</i>, and the instances we create of those classes will be our grid <i>objects</i>. For starters, we'll get some basic information on `RasterModelGrid`. Then we'll create an instance of the class `RasterModelGrid` with 3 rows, 4 columns, and 10-unit grid spacing."
+    "These are all Python <i>classes</i>, and the instances we create of those classes will be our grid <i>objects</i>. For starters, we'll get some basic information on `RasterModelGrid`. Then we'll create an instance of the class `RasterModelGrid` with 4 rows, 5 columns, and 10.0-unit grid spacing in the *x* (column) direction and 5.0 in the *y* (row) direction."
    ]
   },
   {
@@ -150,7 +154,7 @@
    "source": [
     "#### Nodes\n",
     "\n",
-    "*nodes* are simply points that have *x* and *y* coordinates. Different grid types simply lay out\n",
+    "*nodes* are simply points that have *x* and *y* coordinates. Different grid types lay out\n",
     "*nodes* in different ways.\n",
     "\n",
     "Below we create a `RasterModelGrid` that has four rows and 5 columns of nodes."

lessons/landlab/landlab/01-intro.ipynb

@@ -63,7 +63,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "\n",
     "## What you need to know about Landlab grids\n",
     "\n",
     "Landlab model grids are 2D data structures that represent the model domain. A few things to know about grid management:\n",
@@ -80,9 +79,14 @@
     "\n",
     "<img src=\"./media/Grids1.png\"/>\n",
     "\n",
-    "**Figure** Geometry and topology of grid elements on various Landlab grids ([Hobley et al. 2017](https://esurf.copernicus.org/articles/5/21/2017/))\n",
-    "\n",
-    "-- [Interactive sketchbook](https://landlab.github.io/grid-sketchbook/)"
+    "**Figure** Geometry and topology of grid elements on various Landlab grids ([Hobley et al. 2017](https://esurf.copernicus.org/articles/5/21/2017/))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 👉 [Interactive sketchbook](https://landlab.github.io/grid-sketchbook/)"
    ]
   },
   {
@@ -113,7 +117,7 @@
     "\n",
     "---\n",
     "\n",
-    "**More complete descriptions of these grid types can be found in [Landlab's documentation](https://landlab.readthedocs.io/en/master/user_guide/grid.html).**\n",
+    "**More complete descriptions of these grid types can be found in [Landlab's documentation](https://landlab.csdms.io/user_guide/reference/grid.html)**\n",
     "\n",
     "---"
    ]
@@ -132,7 +136,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "These are all Python <i>classes</i>, and the instances we create of those classes will be our grid <i>objects</i>. For starters, we'll get some basic information on `RasterModelGrid`. Then we'll create an instance of the class `RasterModelGrid` with 3 rows, 4 columns, and 10-unit grid spacing."
+    "These are all Python <i>classes</i>, and the instances we create of those classes will be our grid <i>objects</i>. For starters, we'll get some basic information on `RasterModelGrid`. Then we'll create an instance of the class `RasterModelGrid` with 4 rows, 5 columns, and 10.0-unit grid spacing in the *x* (column) direction and 5.0 in the *y* (row) direction."
    ]
   },
   {
@@ -150,7 +154,7 @@
    "source": [
     "#### Nodes\n",
     "\n",
-    "*nodes* are simply points that have *x* and *y* coordinates. Different grid types simply lay out\n",
+    "*nodes* are simply points that have *x* and *y* coordinates. Different grid types lay out\n",
     "*nodes* in different ways.\n",
     "\n",
     "Below we create a `RasterModelGrid` that has four rows and 5 columns of nodes."

lessons/landlab/landlab/02-data.a.ipynb

@@ -140,9 +140,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from landlab.io import read_esri_ascii\n",
+    "from landlab.io import esri_ascii\n",
     "\n",
-    "(grid, z) = read_esri_ascii(\"data/square-test-basin.asc\", name=\"topographic__elevation\")"
+    "with open(\"data/square-test-basin.asc\") as stream:\n",
+    "    grid = esri_ascii.load(stream, name=\"topographic__elevation\")\n",
+    "z = grid.at_node[\"topographic__elevation\"]"
    ]
   },
   {
@@ -321,7 +323,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "?Topography"
+    "help(Topography)"
    ]
   },
   {

lessons/landlab/landlab/02-data.ipynb

@@ -144,9 +144,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from landlab.io import read_esri_ascii\n",
+    "from landlab.io import esri_ascii\n",
     "\n",
-    "(grid, z) = read_esri_ascii(\"data/square-test-basin.asc\", name=\"topographic__elevation\")"
+    "with open(\"data/square-test-basin.asc\") as stream:\n",
+    "    grid = esri_ascii.load(stream, name=\"topographic__elevation\")\n",
+    "z = grid.at_node[\"topographic__elevation\"]"
    ]
   },
   {
@@ -329,7 +331,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "?Topography"
+    "help(Topography)"
    ]
   },
   {

lessons/landlab/landlab/04-numerics.a.ipynb

@@ -331,6 +331,13 @@
     "\n",
     "grid.imshow(z)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "👉 [Components](05-components.ipynb)"
+   ]
   }
  ],
  "metadata": {

lessons/landlab/landlab/04-numerics.ipynb

@@ -335,6 +335,13 @@
     "```\n",
     "</details>"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "👉 [Components](05-components.ipynb)"
+   ]
   }
  ],
  "metadata": {

lessons/landlab/landlab/05-components.a.ipynb

@@ -18,7 +18,8 @@
     "Component modeling is a bit like the potluck tradition: one can construct a complete simulation by assembling components to represent the different parts of the system to be modeled. In Landlab, a **component** is a semi-standardized Python *class* that represents a particular process or calculation. Components are not stand-alone programs, but rather are designed to be used within another Python program that creates an integrated model or workflow.\n",
     "\n",
     "<img src=\"./media/Eat_Alberta_Potluck.jpg\">\n",
-    "*Figure 1: A potluck meal (\"Eat Alberta Potluck\" from Wikimedia Commons).*\n"
+    "\n",
+    "*Figure 1: A potluck meal (\"Eat Alberta Potluck\" from Wikimedia Commons).*"
    ]
   },
   {
@@ -46,6 +47,7 @@
    },
    "source": [
     "<img src=\"./media/bijou_gully_infiltration.png\">\n",
+    "\n",
     "*Figure 3: cumulative infiltration water depth during a simulated five-minute heavy rainfall (from Landlab tutorial \"Green-Ampt infiltration and kinematic wave overland flow\")*\n",
     "\n",
     "The following code snippets illustrate how the components are imported...\n",

lessons/landlab/landlab/05-components.ipynb

@@ -18,7 +18,8 @@
     "Component modeling is a bit like the potluck tradition: one can construct a complete simulation by assembling components to represent the different parts of the system to be modeled. In Landlab, a **component** is a semi-standardized Python *class* that represents a particular process or calculation. Components are not stand-alone programs, but rather are designed to be used within another Python program that creates an integrated model or workflow.\n",
     "\n",
     "<img src=\"./media/Eat_Alberta_Potluck.jpg\">\n",
-    "*Figure 1: A potluck meal (\"Eat Alberta Potluck\" from Wikimedia Commons).*\n"
+    "\n",
+    "*Figure 1: A potluck meal (\"Eat Alberta Potluck\" from Wikimedia Commons).*"
    ]
   },
   {
@@ -46,6 +47,7 @@
    },
    "source": [
     "<img src=\"./media/bijou_gully_infiltration.png\">\n",
+    "\n",
     "*Figure 3: cumulative infiltration water depth during a simulated five-minute heavy rainfall (from Landlab tutorial \"Green-Ampt infiltration and kinematic wave overland flow\")*\n",
     "\n",
     "The following code snippets illustrate how the components are imported...\n",