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geo-smart · Aug 11, 2024 · 92cf4c2 · 92cf4c2
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diff --git a/book/_toc.yml b/book/_toc.yml
@@ -14,7 +14,7 @@ parts:
 
 - caption: Ocean Data Science
   chapters:
-    - file: chapters/ocean_science
+    - file: chapters/oceanscience
     - file: chapters/data
     - file: chapters/epipelargosy
     - file: chapters/anomaly
@@ -24,8 +24,8 @@ parts:
     - file: chapters/modis
     - file: chapters/roms
     - file: chapters/spectrophotometer
-    - file: chapters/shallowprofiler_technical
     - file: chapters/dataloader
+    - file: chapters/technicalnotes
     - file: chapters/documentation
     - file: chapters/issues
 

diff --git a/book/chapters/charts.py b/book/chapters/charts.py
@@ -172,7 +172,8 @@ def ChartTwoSensors(p, xrng, pidcs, A, Az, Albl, Acolor, Aleg, \
     ncharts = len(pidcs)
     if ncharts > 100: ncharts = 100
     do_one = True if ncharts == 1 else False
-    print("Attempting", ncharts, "charts\n")
+    chart_case = 'chart' if do_one else 'charts'
+    print("Attempting", ncharts, chart_case, "\n")
 
     # ncharts x 1: charts in a vertical column
     fig, axs = plt.subplots(ncharts, 1, figsize=(wid, hgt*ncharts), tight_layout=True)

diff --git a/book/chapters/documentation.ipynb b/book/chapters/documentation.ipynb
@@ -19,15 +19,16 @@
     "# Documentation\n",
     "\n",
     "\n",
-    "GeoSMART Oceanography Jupyter Book: Some assembly required, and here is how to deal with these technical details. \n",
+    "This chapter describes generic elements of the Oceanography Jupyter Book, for example\n",
+    "on how to embed a YouTube video. It is the companion chapter to the technical notes \n",
+    "chapter. There (in *technical notes*) we have instructions on the pandas DataFrame for\n",
+    "shallow profiler profile metadata. Here (in *documentation*) we have notes on datetime64\n",
+    "and timedelta64 types. \n",
     "\n",
     "\n",
+    "### Potential additional topics\n",
     "\n",
-    "## Sections\n",
-    "- 1 [Technical Elements](#Technical-Elements)\n",
-    "- 2 [Other Data Resources](#Other-Data-Resources)\n",
-    "- 3 [Computing Infrastructure](#Computing-Infrastructure)\n",
-    "\n"
+    "- shell integration"
    ]
   },
   {
@@ -38,19 +39,17 @@
     "## Contents\n",
     "\n",
     "\n",
-    "### 1 Technical Elements\n",
+    "### 1 Formatting\n",
+    "\n",
+    "\n",
+    "### 2 Data science\n",
     "\n",
     "\n",
     "#### Useful References\n",
     "\n",
     "- [Python Data Science Handbook by Jake VanderPlas]((https://jakevdp.github.io/PythonDataScienceHandbook/) (abbreviated herein PDSH).\n",
     "- [GitHub Markdown Cheat Sheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)\n",
-    "\n",
-    "\n",
-    "#### Technical Elements: Topics\n",
-    "\n",
-    "\n",
-    "- [Markdown](#Markdown): General, LaTeX math, tables\n",
+    "- [Markdown](#Markdown) ...including LaTeX and tables\n",
     "- [Embedding content](#Embedding-content): Images, Animations, Audio, YouTube videos\n",
     "- [Shell integration](#Shell-integration)\n",
     "- [Working with NetCDF XArray and Pandas](#Working-with-NetCDF-XArray-and-Pandas)\n",
@@ -60,13 +59,12 @@
     "- [Mapping](#Mapping)\n",
     "- [Visualization](#Visualization) Matplotlib, IPython interaction widgets\n",
     "- [Containerization](#Containerization)\n",
-    "- [Annotation](#Annotation)\n",
-    "\n"
+    "- [Annotation](#Annotation)"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "db56dfb2-c8e0-4a9e-a3b2-e225ec08b3f7",
+   "id": "2134e4e5-3317-43c5-bda9-ab1c60d5c215",
    "metadata": {},
    "source": [
     "### Other Data Resources\n",
@@ -82,17 +80,7 @@
     "- [MODIS](#MODIS)\n",
     "- [ARGO](#ARGO)\n",
     "- [RCA Deep Profilers](#RCA-Deep-Profilers)\n",
-    "- [RCA Sea floor](#RCA-Sea-floor)\n",
-    "\n",
-    "\n",
-    "### Computing Infrastructure\n",
-    "\n",
-    "\n",
-    "[Top](#Documentation)\n",
-    "\n",
-    "\n",
-    "- Toolbox\n",
-    "- Jupyter servers"
+    "- [RCA Sea floor](#RCA-Sea-floor)"
    ]
   },
   {
@@ -137,32 +125,59 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9465d1c4-b25a-44d4-8e40-5ee998c8cd4e",
+   "id": "0a1378e7-efd0-4d94-ab9e-f5f3aba00ce0",
    "metadata": {},
    "source": [
     "#### LaTeX math formulas \n",
     "\n",
     "\n",
-    "A big topic; here are a couple examples to get started.\n",
+    "$LaTeX$ is useful in formatting mathematical expressions. This is not a comprehensive guide; \n",
+    "rather it serves as reminder notes for getting into the LaTeX groove after some time away from it.\n",
+    "The delimiters of LaTeX formatting are as good a starting point as any. \n",
+    "\n",
     "\n",
     "\n",
-    "$LaTeX^{\\pi}$\n",
-    "    \n",
     "Single dollar-sign delimiters put content inline: `$e^x = \\sum_{i=0}^{\\infty}{\\frac{x^i}{i!}}$` looks like this: $e^x = \\sum_{i=0}^{\\infty}{\\frac{x^i}{i!}}$. \n",
     "\n",
     "\n",
-    "Double dollar-sign delimiters create a centered equation:\n",
+    "\n",
+    "The down-side of inline formatting is the scrunching looks not-so-elegant (see summation above). \n",
+    "Next we have *double dollar-sign* delimiters to yield a centered equation:\n",
+    "\n",
     "\n",
     "\n",
     "$$e^x = \\sum_{i=0}^{\\infty}{\\frac{x^i}{i!}}$$\n",
     "\n",
     "\n",
-    "Change size for example with a `\\Large` qualifier:\n",
+    "<br>\n",
     "\n",
     "\n",
-    "$\\Large{e^x = \\sum_{i=0}^{\\infty}{\\frac{x^i}{i!}}}$\n",
+    "Finally we have a construction making use of `\\begin{align}` that left-justifies. Some judicious linebreaks\n",
+    "`<br>` give extra vertical spacing when needed.\n",
+    "\n",
+    "<br>\n",
+    "\n",
+    "$\\begin{align}n = \\frac{ad + bc}{bd} \\implies bdn = ad + bc \\implies \\textrm{ both } b|(ad+bc) \\textrm{ and } d|(ad+bc)\\end{align}$.\n",
+    "\n",
+    "\n",
+    "<br>\n",
     "\n",
     "\n",
+    "We can change font size using qualifiers such as `\\Large`:\n",
+    "\n",
+    "\n",
+    "<br>\n",
+    "\n",
+    "$\\begin{align}\\Large{e^x = \\sum_{i=0}^{\\infty}{\\frac{x^i}{i!}}}\\end{align}$\n",
+    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8f9ca8de-2b9a-46e3-8328-ce41a3480ea0",
+   "metadata": {},
+   "source": [
     "#### Tables\n",
     "\n",
     "\n",
@@ -179,7 +194,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "5fb6c013-b50e-4893-8b2a-563606c0a735",
    "metadata": {
     "tags": []
@@ -190,7 +205,7 @@
       "text/html": [
        "\n",
        "<br>\n",
-       "Here is an HTML tabl running as Python code via %%html cell magic.\n",
+       "Here is an HTML tabl running as Python code via `%%html` cell magic.\n",
        "<br>\n",
        "\n",
        "<html>\n",
@@ -224,7 +239,7 @@
     "%%html\n",
     "\n",
     "<br>\n",
-    "Here is an HTML tabl running as Python code via %%html cell magic.\n",
+    "Here is an HTML tabl running as Python code via `%%html` cell magic.\n",
     "<br>\n",
     "\n",
     "<html>\n",
@@ -253,7 +268,7 @@
    "metadata": {},
    "source": [
     "<br>\n",
-    "Here is the same in a markdown cell\n",
+    "...while in a markdown cell:\n",
     "<br>\n",
     "\n",
     "<!DOCTYPE html>\n",
@@ -451,10 +466,7 @@
    "id": "0d259407-4353-41d6-98c1-6a5b82c30fca",
    "metadata": {},
    "source": [
-    "### Shell integration\n",
-    "\n",
     "\n",
-    "[TOC](#1-Technical-Elements)\n",
     "\n",
     "\n",
     "### Working with NetCDF XArray and Pandas\n",
@@ -2374,21 +2386,6 @@
     "More on the Regional Cabled Array oceanography program [here](https://interactiveoceans.washington.edu).\n",
     "    \n",
     "    \n",
-    "### Study site locations\n",
-    "    \n",
-    "\n",
-    "We begin with three sites in the northeast Pacific: \n",
-    "    \n",
-    "\n",
-    "```\n",
-    "Site name               Latitude          Longitude\n",
-    "------------------      --------          ---------\n",
-    "Oregon Offshore         44.37415          -124.95648\n",
-    "Oregon Slope Base       44.52897          -125.38966 \n",
-    "Axial Base              45.83049          -129.75326\n",
-    "```   \n",
-    "\n",
-    "\n",
     "* The data variable is `spkir_downwelling_vector` x 7 wavelengths per below\n",
     "* 9 months continuous operation at about 4 samples per second gives 91 million samples\n",
     "* DataSet includes `int_ctd_pressure` and `time` Coordinates; Dimensions are `spectra` (0--6) and `time`\n",
@@ -2819,32 +2816,7 @@
     "- Current measurements give three axis results: north, east, up\n",
     "    - ADCP details needed\n",
     "\n",
-    "#### [Contents](#Contents)\n",
-    "\n",
-    "\n",
-    "## Non OOI Data: ROMS, ARGO, MODIS, GLODAP, MSLA\n",
-    "\n",
-    "\n",
-    "### ROMS\n",
-    "\n",
-    "\n",
-    "### ARGO\n",
-    "\n",
-    "\n",
-    "### MODIS\n",
-    "\n",
-    "\n",
-    "### GLODAP\n",
-    "\n",
-    "\n",
-    "### MSLA\n",
-    "\n",
-    "\n",
-    "\n",
-    "#### [Contents](#Contents)\n",
-    "\n",
     "\n",
-    "## Data Product Levels\n",
     "\n",
     "\n",
     "The \n",
@@ -3523,7 +3495,7 @@
    "id": "d5e97bfe-b423-44b4-a464-3f64d9ead3cb",
    "metadata": {},
    "source": [
-    "# This goes where?\n",
+    "## This goes into `technicalnotes.ipynb`\n",
     "\n",
     "\n",
     "### Selecting profile ascent data from the profiler time series\n",