Merge pull request #6 from UXARRAY/orhan_init

Revise dir structure a bit
ProjectPythia · Nov 9, 2023 · e1503eb · e1503eb
2 parents c073128 + 4bc8d78
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diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
 This Cookbook showcases how to visualize Unstructured Grids using UXarray paired with community tool sets such as HoloViz and Matplotlib. It was put together as part of
 Project Raijin's NCAR Summer Internships in Parallel Computational Science (SIParCS) project, which is titled "Python Data Analysis and Visualization for Unstructured Grid Data." This cookbook is currently being adapted from
-our 2023 intern Ian's notebook which can be found [here](https://github.com/NCAR/geocat-scratch/blob/ifranda/viz-notebook/SIParCS2023/Visualization_Notebook.ipynb).
+our 2023 intern Ian's notebook which can be found [here](https://github.com/NCAR/geocat-scratch/blob/main/uxarray/SIParCS2023/Visualization_Notebook.ipynb).
 
 ## Authors
 
@@ -34,15 +34,11 @@ This cookbook is split up into six chapters which provide a comprehensive overvi
 
 #### 1. Introduction to UXarray & Unstructured Grids
 
-#### 2. Methods for Unstructured Grid Visualization
+#### 2. Methods & Libraries for Unstructured Grid Visualization
 
-#### 3. Visualization Libraries & Rendering Techniques
+#### 3. UXarray Visualization
 
-#### 4. Grid Topology Visualization
-
-#### 5. Data Variable Visualization
-
-#### 6. Performance & Data Fidelity Considerations
+#### 4. Performance & Data Fidelity Considerations
 
 
 ## Running the Notebooks

diff --git a/_toc.yml b/_toc.yml
@@ -6,29 +6,24 @@ parts:
       - file: notebooks/how-to-cite
   - caption: Introduction to UXarray & Unstructured Grids
     chapters:
-      - file: notebooks/01-intro/unstructured-grid-overview
-      - file: notebooks/01-intro/data-structures
-      - file: notebooks/01-intro/plot-api
+      - file: notebooks/01-intro/01-unstructured-grid-overview
+      - file: notebooks/01-intro/02-data-structures
+      - file: notebooks/01-intro/03-plot-api
 
-  - caption: Methods for Unstructured Grid Visualization
+  - caption: Methods & Libraries for Unstructured Grid Visualization
     chapters:
-      - file: notebooks/02-methods/template
+      - file: notebooks/02-methods/01-data-mapping
+      - file: notebooks/02-methods/02-plotting-libraries
+      - file: notebooks/02-methods/03-rendering-techniques
 
-  - caption: Visualization Libraries & Rendering Techniques
+  - caption: UXarray Visualization
     chapters:
-      - file: notebooks/03-libraries/template
-
-  - caption: Grid Topology Visualization
-    chapters:
-      - file: notebooks/04-topology/nodes
-      - file: notebooks/04-topology/edges
-
-  - caption: Data Variable Visualization
-    chapters:
-      - file: notebooks/05-data-vars/polygons
-      - file: notebooks/05-data-vars/triangles
-      - file: notebooks/05-data-vars/point-raster
+      - file: notebooks/03-uxarray-vis/01-grid-topology
+      - file: notebooks/03-uxarray-vis/02-data-variable
+      - file: notebooks/03-uxarray-vis/03-polygons
+      - file: notebooks/03-uxarray-vis/04-triangles
+      - file: notebooks/03-uxarray-vis/05-point-raster
 
   - caption: Performance & Data Fidelity Considerations
     chapters:
-      - file: notebooks/06-considerations/template
+      - file: notebooks/04-considerations/template
diff --git a/environment.yml b/environment.yml
@@ -1,7 +1,6 @@
 name: unstructured-grid-viz-cookbook-dev
 channels:
   - conda-forge
-  - pyviz
 dependencies:
   - jupyter-book
   - jupyterlab

diff --git a/...01-intro/unstructured-grid-overview.ipynb → ...intro/01-unstructured-grid-overview.ipynb b/...01-intro/unstructured-grid-overview.ipynb → ...intro/01-unstructured-grid-overview.ipynb
diff --git a/notebooks/01-intro/data-structures.ipynb → notebooks/01-intro/02-data-structures.ipynb b/notebooks/01-intro/data-structures.ipynb → notebooks/01-intro/02-data-structures.ipynb
diff --git a/notebooks/01-intro/plot-api.ipynb → notebooks/01-intro/03-plot-api.ipynb b/notebooks/01-intro/plot-api.ipynb → notebooks/01-intro/03-plot-api.ipynb
diff --git a/notebooks/05-data-vars/polygons.ipynb → notebooks/02-methods/01-data-mapping.ipynb b/notebooks/05-data-vars/polygons.ipynb → notebooks/02-methods/01-data-mapping.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Polygons"
+    "# Data Mapping"
    ]
   },
   {

diff --git a/notebooks/03-libraries/template.ipynb → ...ks/02-methods/02-plotting-libraries.ipynb b/notebooks/03-libraries/template.ipynb → ...ks/02-methods/02-plotting-libraries.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Notebook Title"
+    "# Plotting Libraries"
    ]
   },
   {
@@ -17,13 +17,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "# code and content goes here"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   }
  ],
  "metadata": {

diff --git a/notebooks/04-topology/edges.ipynb → .../02-methods/03-rendering-techniques.ipynb b/notebooks/04-topology/edges.ipynb → .../02-methods/03-rendering-techniques.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Edges"
+    "# Rendering Techniques"
    ]
   },
   {
@@ -17,13 +17,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
    "outputs": [],
    "source": [
     "# code and content goes here"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   ]
   }
  ],
  "metadata": {

diff --git a/notebooks/04-topology/template.ipynb → ...oks/03-uxarray-vis/01-grid-topology.ipynb b/notebooks/04-topology/template.ipynb → ...oks/03-uxarray-vis/01-grid-topology.ipynb
@@ -4,26 +4,52 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Notebook Title"
+    "# Grid Topology"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "---"
+    "It can always be useful to visualize the geometric elements of an unstructured grid (nodes, edges) without any data mapped to them for understanding the mesh topology and perform diagnostics (e.g. analyzing the mesh of a dynamical core prior to running a simulation).\n",
+    "\n",
+    "UXarray provides convenient functions to visualize these elements of the `Grid` object."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Plot Nodes"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Placeholder for a brief paragraph"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Plot Edges"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Placeholder for a brief paragraph"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
    "outputs": [],
-   "source": [
-    "# code and content goes here"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   "source": []
   }
  ],
  "metadata": {
@@ -42,7 +68,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.11.6"
   },
   "nbdime-conflicts": {
    "local_diff": [

diff --git a/notebooks/04-topology/nodes.ipynb → ...oks/03-uxarray-vis/02-data-variable.ipynb b/notebooks/04-topology/nodes.ipynb → ...oks/03-uxarray-vis/02-data-variable.ipynb
@@ -4,26 +4,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Nodes"
+    "# Data Variables"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "---"
+    "Placeholder for intriduction and overview of the visualization of data that is associated with an unstructured grid"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
    "outputs": [],
-   "source": [
-    "# code and content goes here"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   "source": []
   }
  ],
  "metadata": {
@@ -42,7 +38,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.11.6"
   },
   "nbdime-conflicts": {
    "local_diff": [

diff --git a/notebooks/03-uxarray-vis/03-polygons.ipynb b/notebooks/03-uxarray-vis/03-polygons.ipynb
@@ -0,0 +1,94 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Polygons"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.11.6"
+  },
+  "nbdime-conflicts": {
+   "local_diff": [
+    {
+     "diff": [
+      {
+       "diff": [
+        {
+         "key": 0,
+         "op": "addrange",
+         "valuelist": [
+          "Python 3"
+         ]
+        },
+        {
+         "key": 0,
+         "length": 1,
+         "op": "removerange"
+        }
+       ],
+       "key": "display_name",
+       "op": "patch"
+      }
+     ],
+     "key": "kernelspec",
+     "op": "patch"
+    }
+   ],
+   "remote_diff": [
+    {
+     "diff": [
+      {
+       "diff": [
+        {
+         "key": 0,
+         "op": "addrange",
+         "valuelist": [
+          "Python3"
+         ]
+        },
+        {
+         "key": 0,
+         "length": 1,
+         "op": "removerange"
+        }
+       ],
+       "key": "display_name",
+       "op": "patch"
+      }
+     ],
+     "key": "kernelspec",
+     "op": "patch"
+    }
+   ]
+  },
+  "toc-autonumbering": false
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/notebooks/05-data-vars/triangles.ipynb → notebooks/03-uxarray-vis/04-triangles.ipynb b/notebooks/05-data-vars/triangles.ipynb → notebooks/03-uxarray-vis/04-triangles.ipynb
@@ -7,23 +7,12 @@
     "# Triangles"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "---"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
    "outputs": [],
-   "source": [
-    "# code and content goes here"
-   ],
-   "metadata": {
-    "collapsed": false
-   }
+   "source": []
   }
  ],
  "metadata": {
@@ -42,7 +31,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.11.6"
   },
   "nbdime-conflicts": {
    "local_diff": [