From c41022eaae3576ed8c6b5704ad3255413581dceb Mon Sep 17 00:00:00 2001
From: "Von P. Walden" <v.walden@wsu.edu>
Date: Wed, 10 Jan 2024 22:39:55 -0800
Subject: [PATCH] Added Chapter 0 with lessons from Software Carpentry

---
 .../html/_sources/chapter4/Insolation.ipynb   | 41 ++++++---
 _toc.yml                                      |  4 +
 chapter0.md                                   |  5 ++
 chapter0/inflammation-01.csv                  | 60 +++++++++++++
 ...ftwareCarpentry-AnalyzingPatientData.ipynb | 88 +++++++++++++++++++
 ...softwareCarpentry-PythonFundamentals.ipynb | 50 +++++++++++
 chapter4/Insolation.ipynb                     |  2 +-
 7 files changed, 236 insertions(+), 14 deletions(-)
 create mode 100644 chapter0.md
 create mode 100644 chapter0/inflammation-01.csv
 create mode 100644 chapter0/softwareCarpentry-AnalyzingPatientData.ipynb
 create mode 100644 chapter0/softwareCarpentry-PythonFundamentals.ipynb

diff --git a/_build/html/_sources/chapter4/Insolation.ipynb b/_build/html/_sources/chapter4/Insolation.ipynb
index 2d67ee7..afc2114 100644
--- a/_build/html/_sources/chapter4/Insolation.ipynb
+++ b/_build/html/_sources/chapter4/Insolation.ipynb
@@ -130,6 +130,25 @@
     "    return sza\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def Q_instantaneous(latitude, day, hour):\n",
+    "    lat = latitude\n",
+    "    So  = 1370.\n",
+    "    d   = earth_sun_distance(day)\n",
+    "    dm  = 149.6e6\n",
+    "    da  = declination(day)\n",
+    "    sza = solar_zenith_angle(lat, da, hour)\n",
+    "    Q   = So * (dm/d)**2 * np.cos(sza)\n",
+    "    if Q < 0:\n",
+    "        Q = 0.\n",
+    "    return Q\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -156,7 +175,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [
     {
@@ -165,12 +184,15 @@
      "text": [
       "Declination =  -0.12600714770976626\n",
       "Earth distance =  148981817.36070523\n",
-      "Q = 300.456485702979\n"
+      "Q = 354.38665779405136\n"
      ]
     }
    ],
    "source": [
-    "lat = 46.7\n",
+    "# Pullman, WA\n",
+    "#lat = 46.7\n",
+    "# Greensboro, NC\n",
+    "lat = 36.1\n",
     "day = 31+28+22\n",
     "print('Declination = ', declination(day))\n",
     "print('Earth distance = ', earth_sun_distance(day))\n",
@@ -187,7 +209,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -256,7 +278,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -265,7 +287,7 @@
        "Text(0.5, 1.0, 'TOA Insolation over Pullman, WA')"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -298,13 +320,6 @@
     "plt.ylabel('Daily-Average Insolation (W m-2)')\n",
     "plt.title('TOA Insolation over Pullman, WA')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/_toc.yml b/_toc.yml
index eb65d31..a10209a 100644
--- a/_toc.yml
+++ b/_toc.yml
@@ -4,6 +4,10 @@
 format: jb-book
 root: intro
 chapters:
+- file: chapter0.md
+  sections:
+    - file: chapter0/softwareCarpentry_PythonFundamentals.ipynb
+    - file: chapter0/softwareCarpentry_AnalyzingPatientData.ipynb
 - file: chapter1.md
   sections:
     - file: chapter1/FairbanksTemperatures.ipynb
diff --git a/chapter0.md b/chapter0.md
new file mode 100644
index 0000000..443e624
--- /dev/null
+++ b/chapter0.md
@@ -0,0 +1,5 @@
+# Background - Blank Notebooks for Programming in Python (by Software Carpentry)
+
+Chapter 0 includes the following computational notebooks:
+- [Software Carpentry's Python Fundamentals](https://swcarpentry.github.io/python-novice-inflammation/01-intro.html)
+- [Software Carpentry's Analyzing Patient Data](https://swcarpentry.github.io/python-novice-inflammation/01-intro.html)
diff --git a/chapter0/inflammation-01.csv b/chapter0/inflammation-01.csv
new file mode 100644
index 0000000..07a2e60
--- /dev/null
+++ b/chapter0/inflammation-01.csv
@@ -0,0 +1,60 @@
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diff --git a/chapter0/softwareCarpentry-AnalyzingPatientData.ipynb b/chapter0/softwareCarpentry-AnalyzingPatientData.ipynb
new file mode 100644
index 0000000..3b1a57e
--- /dev/null
+++ b/chapter0/softwareCarpentry-AnalyzingPatientData.ipynb
@@ -0,0 +1,88 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Software Carpentry - Analyzing Patient Data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Read [Software Carpentry's Analyzing Patient Data](https://swcarpentry.github.io/python-novice-inflammation/02-numpy.html)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using notebook cells below, type in the commands in the instructions to check your knowledge of Python variables. (The two cells below will get you started.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([[0., 0., 1., ..., 3., 0., 0.],\n",
+       "       [0., 1., 2., ..., 1., 0., 1.],\n",
+       "       [0., 1., 1., ..., 2., 1., 1.],\n",
+       "       ...,\n",
+       "       [0., 1., 1., ..., 1., 1., 1.],\n",
+       "       [0., 0., 0., ..., 0., 2., 0.],\n",
+       "       [0., 0., 1., ..., 1., 1., 0.]])"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "numpy.loadtxt(fname='inflammation-01.csv', delimiter=',')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "work",
+   "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": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/chapter0/softwareCarpentry-PythonFundamentals.ipynb b/chapter0/softwareCarpentry-PythonFundamentals.ipynb
new file mode 100644
index 0000000..68c4340
--- /dev/null
+++ b/chapter0/softwareCarpentry-PythonFundamentals.ipynb
@@ -0,0 +1,50 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Software Carpentry - Python Fundamentals"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Read [Software Carpentry's Python Fundamentals](https://swcarpentry.github.io/python-novice-inflammation/01-intro.html). Start by scrolling down to the section on Variables."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using notebook cells below, type in the commands in the instructions to check your knowledge of Python variables. (The cell below is the first example.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "3 + 5 * 4"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!wget https://github.com/swcarpentry/python-novice-inflammation/tree/main/episodes/data/inflammation-01.csv"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/chapter4/Insolation.ipynb b/chapter4/Insolation.ipynb
index 2d67ee7..dcf98c2 100644
--- a/chapter4/Insolation.ipynb
+++ b/chapter4/Insolation.ipynb
@@ -323,7 +323,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.5"
+   "version": "3.11.4"
   },
   "vscode": {
    "interpreter": {