updated book for Python

kyleniemeyer · Dec 22, 2022 · bf56ffe · bf56ffe
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diff --git a/.github/workflows/deploy-book.yml b/.github/workflows/deploy-book.yml
@@ -0,0 +1,41 @@
+name: deploy-book
+
+# Only run this when the main branch changes
+on:
+  push:
+    branches:
+    - main
+
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    # Install dependencies
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Setup Miniconda
+      uses: conda-incubator/[email protected]
+      with:
+        environment-file: environment.yml
+        activate-environment: thermo-env
+        python-version: 3.9
+        auto-activate-base: false
+
+    # Build the book
+    - name: Build the book
+      shell: bash -l {0}
+      run: |
+        jupyter-book build book
+
+    # Push the book's HTML to github-pages
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./book/_build/html
diff --git a/apt.txt b/apt.txt
diff --git a/book/_config.yml b/book/_config.yml
@@ -1,19 +1,31 @@
 # Book settings
-title: Mechanical Engineering Methods notes
+title: Mechanical Engineering Methods
 author: Kyle Niemeyer
 #logo: logo.jpg
 
 exclude_patterns: [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints", LICENSE.md]
 
+description: >- # this means to ignore newlines until "baseurl:"
+  This is a collection of notes for mechanical engineering numerical methods. 
+
+execute_notebooks: auto
+
+execute:
+  timeout: 160
+
 latex:
   latex_documents:
     targetname: book.tex
   latex_engine: xelatex
 
+bibtex_bibfiles:
+  - references.bib
+
 sphinx:
   config:
     html_show_copyright: false
-    mathjax_config:
+    bibtex_reference_style: author_year
+    mathjax3_config:
       TeX:
         Macros:
           vector: ["\\vec{#1}", 1]
@@ -42,11 +54,13 @@ parse:
 repository:
   url: https://github.com/kyleniemeyer/ME373-book
   branch: master
+  path_to_book: "book"
 
 html:
   baseurl: https://kyleniemeyer.github.io/ME373-book
   use_edit_page_button: true
   use_repository_button: true
   use_issues_button: true
+  extra_navbar: Powered by <a href="https://jupyterbook.org">Jupyter Book</a>
   extra_footer: |
     <p xmlns:dct="http://purl.org/dc/terms/" xmlns:cc="http://creativecommons.org/ns#" class="license-text"><a rel="cc:attributionURL" property="dct:title" href="https://github.com/kyleniemeyer/ME373-book">Mechanical Engineering Methods notes</a> by <span property="cc:attributionName">Kyle Niemeyer</span> is licensed under <a rel="license" href="https://creativecommons.org/licenses/by-sa/4.0">CC BY-SA 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1" /><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1" /><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/sa.svg?ref=chooser-v1" /></a></p>
diff --git a/book/_toc.yml b/book/_toc.yml
@@ -44,3 +44,4 @@ parts:
   - url: https://github.com/kyleniemeyer/ME373-book
     title: GitHub repository
   - file: content/contributing
+  - file: content/zbibliography
diff --git a/book/content/LICENSE.md b/book/content/LICENSE.md
diff --git a/book/content/bvps/blasius_rhs.m b/book/content/bvps/blasius_rhs.m
diff --git a/book/content/bvps/eigenvalue.ipynb b/book/content/bvps/eigenvalue.ipynb
diff --git a/book/content/bvps/finite-difference.ipynb b/book/content/bvps/finite-difference.ipynb
diff --git a/book/content/bvps/masses.m b/book/content/bvps/masses.m
diff --git a/book/content/bvps/shooting-method.ipynb b/book/content/bvps/shooting-method.ipynb
diff --git a/book/content/bvps/shooting_rhs.m b/book/content/bvps/shooting_rhs.m
diff --git a/book/content/installing-jupyter.ipynb b/book/content/installing-jupyter.ipynb
@@ -87,22 +87,21 @@
  "metadata": {
   "file_extension": ".py",
   "kernelspec": {
-   "display_name": "Matlab",
-   "language": "matlab",
-   "name": "matlab"
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": "octave",
-   "file_extension": ".m",
-   "help_links": [
-    {
-     "text": "MetaKernel Magics",
-     "url": "https://metakernel.readthedocs.io/en/latest/source/README.html"
-    }
-   ],
-   "mimetype": "text/x-octave",
-   "name": "matlab",
-   "version": "0.16.7"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.2"
   },
   "mimetype": "text/x-python",
   "name": "python",
@@ -111,5 +110,5 @@
   "version": 3
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/book/content/intro.md b/book/content/intro.md
@@ -1,3 +1,14 @@
-# Introduction 
+# Mechanical Engineering Methods
 
-This website is an interactive [Jupyter Book](https://jupyterbook.org/intro.html) for ME 373, Mechanical Engineering Methods, taught at Oregon State University.
+**By [Kyle Niemeyer](https://niemeyer-research-group.github.io)**
+
+This ebook contain material and example problems in numerical methods for engineering, in the format of Jupyter notebooks, developed to supplement the course ME 373, Mechanical Engineering Methods, taught in the [School of Mechanical, Industrial, and Manufacturing Engineering](https://mime.oregonstate.edu) at [Oregon State University](https://oregonstate.edu).
+
+All problems here use Python with the [SciPy](https://www.scipy.org) ecosystem of packages {cite:p}`2020SciPy-NMeth`.
+All artwork here is original.
+This interactive website is powered by [Jupyter Book](https://jupyterbook.org/).
+
+
+[![license](../images/cc-by.svg)](https://creativecommons.org/licenses/by/4.0/)
+<br />
+This work is licensed under a <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
diff --git a/book/content/numerical-methods/error.md b/book/content/numerical-methods/error.md
@@ -1,5 +1,7 @@
 # Error
 
+## Types of Error
+
 Applying the trapezoidal rule and Simpson's rule introduces the concept of **error** in numerical solutions.
 
 In our work so far, we have come across two obvious kinds of error, that we'll come back to later:
@@ -19,7 +21,7 @@ In any numerical solution, there are five main sources of error:
 
 5. Human error and machine error: there are many potential sources of error in any code. These can come from typos, human programming errors, errors in input data, or (more rarely) a pure machine error. Even textbooks, tables, and formulas may have errors.
 
-### Absolute and relative error
+## Absolute and relative error
 
 We can also differentiate between **absolute** and **relative** error in a quantity. If $y$ is an exact value and $\tilde{y}$ is an approximation to that value, then we have
 
@@ -29,4 +31,4 @@ We can also differentiate between **absolute** and **relative** error in a quant
 If $y$ is a vector, then we can define error using the maximum of the elements:
 \begin{equation}
 \max_i \frac{ |y_i - \tilde{y}_{i} |}{|y_i|}
-\end{equation}
+\end{equation}
diff --git a/book/content/numerical-methods/initial-value-methods.ipynb b/book/content/numerical-methods/initial-value-methods.ipynb
diff --git a/book/content/numerical-methods/integrals.ipynb b/book/content/numerical-methods/integrals.ipynb
diff --git a/book/content/numerical-methods/stability.ipynb b/book/content/numerical-methods/stability.ipynb