From d58142b9ad975d7a1939cd94e71c2202b03858e1 Mon Sep 17 00:00:00 2001 From: Rob Fatland Date: Wed, 19 Jun 2024 14:10:18 -0700 Subject: [PATCH] mo bettah --- book/chapters/rob/documentation.ipynb | 2 +- book/chapters/rob/ocean_science.ipynb | 266 +++++++------------------- 2 files changed, 69 insertions(+), 199 deletions(-) diff --git a/book/chapters/rob/documentation.ipynb b/book/chapters/rob/documentation.ipynb index 9d880cf..1330c46 100644 --- a/book/chapters/rob/documentation.ipynb +++ b/book/chapters/rob/documentation.ipynb @@ -3950,7 +3950,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.3" + "version": "3.11.4" } }, "nbformat": 4, diff --git a/book/chapters/rob/ocean_science.ipynb b/book/chapters/rob/ocean_science.ipynb index 93a8693..e5a58ca 100644 --- a/book/chapters/rob/ocean_science.ipynb +++ b/book/chapters/rob/ocean_science.ipynb @@ -10,16 +10,35 @@ "[Jupyter Book](https://geo-smart.github.io/oceanography/intro.html) and [GitHub repo](https://github.com/geo-smart/oceanography).\n", "\n", "\n", - "`img` html Try 1 \n", + "This image-includer works locally for jpg, png and svg.\n", "\n", "\n", "
\n", - "\"drawing\"\n", + "\"drawing\"\n", "
\n", "
\n", + "\n", + " \n", + "



\n", + " \n", " \n", + "
\n", + "\"drawing\"\n", + "
\n", + "
\n", "\n", - "figure construct Try 1\n", + "



\n", + " \n", + "\n", + "
\n", + "\"drawing\"\n", + "
\n", + "
\n", + " \n", + "

\n", + "\n", + "\n", + "The *figure* and *image* directives work in the Jupyter Book but not locally (yet):\n", "\n", " \n", "

\n", @@ -30,18 +49,10 @@ "height: 300px\n", "name: directive-fig\n", "---\n", - "Here is my figure caption!\n", + "Research Vessel Revelle (Scripps)\n", "```\n", " \n", "

\n", - " \n", - "Markdown B: Use a more complicated back-tick construct to show the Revelle:\n", - "\n", - "\n", - " \n", - "image construct Try 1\n", - " \n", - "\n", "

\n", "\n", "\n", @@ -75,42 +86,58 @@ "```\n", " \n", "

\n", + "

\n", + "

\n", "\n", - " \n", - "Bang Try 1\n", "\n", + "Here is the `![alt](link)` construct which works locally and in the Book.\n", + "Down side: Renders are actual size.\n", + "\n", + "

\n", + "

\n", " \n", "![Revelle](../../img/revelle.jpg)\n", "\n", + "

\n", + "

\n", "\n", "![Badge](../../img/use_case_badge.svg)\n", "\n", + "

\n", + "

\n", "\n", "![Dubious](../../img/dubious.png)\n", "\n", + "

\n", + "

\n", + "\n", + "\n", + "## Themes\n", + "\n", + "\n", + "Geo-SMART Jupyter Book theme placeholders:\n", "\n", - "### To Do\n", - "\n", - "- Cover the default chapter purposes here; and chart out the TOC properly, align the notebooks\n", - " - These were deleted from the Jupyter Book 'chapters' folder `_toc.yml` file\n", - " - file: chapters/motivation\n", - " - file: chapters/methods\n", - " - file: chapters/data\n", - " - file: chapters/development\n", - " - file: chapters/training\n", - " - file: chapters/evaluation\n", - " - file: chapters/workflow\n", - " - file: chapters/reproducibility\n", - " - file: chapters/conclusion\n", - " - file: chapters/todo\n", - " - file: chapters/questions\n", - " - file: chapters/troubleshooting\n", + "\n", + "- Motivation: Create an access path to multiple views of ocean near-surface processes\n", + "- Method: Document the data acquisition and analysis process\n", + "- Development history: This project has been underway since 2016\n", + "- Training/Evaluation: Typically refers to ML; not present here yet\n", + "- Workflow\n", + "- Reproducibility\n", + "- Questions\n", + "- To Do\n", + "- Conclusion\n", + "- Troubleshooting\n", " \n", "\n", - "### Introduction\n", + "## Introduction\n", "\n", "\n", - "Let's begin with **Chlorophyll** as a convenient fluorescing marker in the larger context of **marine ecology**.\n", + "The ocean is water and salt; as well as being a reservoir of carbon compounds that\n", + "are the basis for and byproducts of ocean life. Our objective is to explore observational\n", + "data from the ocean with the idea of developing insights into the physical, chemical\n", + "and biological processes in the surface waters that are illuminated by sunlight. \n", + "Let's begin with a table of molecules; as a start on ocean chemistry.\n", "\n", " \n", "| Mass (Daltons) | Substance\n", @@ -120,167 +147,8 @@ "|62|carbonic acid H2CO3\n", "|61|bicarbonate anion HCO3-\n", "|60|carbonate CO32-\n", - "|?|sugars here\n", - "|894|chlorophyll C55H72MgN4O5\n", - " \n", - " \n", - "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n", - "are the basis for and byproducts of ocean life." - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "
\n", - "This Python cell uses %%html cell magic to support html. \n", - "
\n", - "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n", - "are the basis for and byproducts of ocean life.\n", - "
\n", - "
\n", - "Through a molecular\n", - "chemistry lens ocean carbon is both basis for and currency of life. The table below \n", - "lists some important chemical constituents of the ocean sorted by mass. \n", - "The heaviest of these, **chlorophyll**, is a convenient fluorescing marker in the \n", - "context of **marine ecology**.\n", - "
\n", - "\n", - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MassChemical
1Hydrogen ion H+
32dissolved oxygen O2
46carbon dioxide CO2
62carbonic acid H2CO3
61bicarbonate anion HCO3-
60carbonate CO32-
180glucose C6H12O6
892chlorophyll C55H72MgN4O5
\n", - "\n", - "\n", - "\n" - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "%%html\n", - "\n", - "
\n", - "This Python cell uses %%html cell magic to support html. \n", - "
\n", - "The ocean is (of course) more than mere water and salt; it is a reservoir of carbon compounds that\n", - "are the basis for and byproducts of ocean life.\n", - "
\n", - "
\n", - "Through a molecular\n", - "chemistry lens ocean carbon is both basis for and currency of life. The table below \n", - "lists some important chemical constituents of the ocean sorted by mass. \n", - "The heaviest of these, **chlorophyll**, is a convenient fluorescing marker in the \n", - "context of **marine ecology**.\n", - "
\n", - "\n", - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
MassChemical
1Hydrogen ion H+
32dissolved oxygen O2
46carbon dioxide CO2
62carbonic acid H2CO3
61bicarbonate anion HCO3-
60carbonate CO32-
180glucose C6H12O6
892chlorophyll C55H72MgN4O5
\n", - "\n", - "\n", - "\n" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "* FASTQ sequence file format\n", - "* Do prisoners hats: Were you paying attention?\n", - "* Magda still interested?\n", - "* CRC and Hamming\n", - "* S3 non-object access\n", - "* What about a question for which there is no computer code... but then that code gets written\n", - "* Hofstadter self-destroying turntable (Luddites using wrenches from loom builders)\n", - "* Talk to Wendi about using a zar API" + "|180|glucose C6H12O6\n", + "|894|chlorophyll C55H72MgN4O5" ] }, { @@ -449,11 +317,13 @@ "### Metabolic energy for an apex predator\n", "\n", "\n", - "
\n", - "\"drawing\"\n", - "
\n", - "
\n", - "\n", + "```{figure} ../../img/Sphyrna_mokarran.png.jpg\n", + "---\n", + "height: 500px\n", + "name: directive-fig\n", + "---\n", + "Apex predator: Great hammerhead shark (Sphyrna mokarran)\n", + "```\n", " \n", "Sunlight is not a direct energy source for \n", "[Sphyrna mokarran](https://en.wikipedia.org/wiki/Great_hammerhead))\n",