template jupyterbook

.github/workflows/deploy.yml

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+name: deploy-book
+
+on:
+  push:
+    branches:
+      - main
+
+env:
+  BASE_URL: /${{ github.event.repository.name }}
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  deploy-book:
+    #if: github.actor == 'jagar2' && github.repository != 'jagar2/Fall_2024_MEM679_Data-Analysis-and-Machine-Learning-for-Science-and-Manufacturing'
+    runs-on: self-hosted
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build the book
+        run: |
+          jupyter-book build ./notebooks
+
+      # Upload artifact and copy to SMB share
+      - name: Upload and Deploy
+        if: contains(github.event.head_commit.message, '#push')
+        run: |
+          id
+          SMBSHARE="/mnt/drexel_web/2024-CCSTAE" &&
+          rm -rf /mnt/drexel_web/2024-CCSTAE/* &&
+          JBPATH="./jupyterbook" &&
+          cp -r $JBPATH/_build/html/* $SMBSHARE

.gitignore

@@ -160,3 +160,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+notebooks/_build

notebooks/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Extremely Noisy 4DSTEM Strain Mapping Using Cycle Consistent Spatial Transforming Autoencoders 
+author: Authors Here
+logo: assets/Drexel_M3_Logo-01.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/m3-learning/Extremely-Noisy-4DSTEM-Strain-Mapping-Using-Cycle-Consistent-Spatial-Transforming-Autoencoders  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+  static_path:
+    - _static
+  css:
+    - custom.css
+  use_issues_button: true
+  use_repository_button: true
+
+# Adds colab button to book
+launch_buttons:
+  colab_url: "https://colab.research.google.com"
+  jupyterhub_url: "https://engr131.nrp-nautilus.io/"
+  thebe: true

notebooks/_static/theme.css

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+/* Light theme */
+html[data-theme="light"] {
+    --pst-color-primary: #002D72;
+    /* Drexel Blue */
+    --pst-color-secondary: #FFD100;
+    /* Drexel Yellow */
+    --pst-color-success: #9DAD33;
+    /* Light Green */
+    --pst-color-info: #006298;
+    /* Dark Blue */
+    --pst-color-warning: #FF8F1C;
+    /* Light Orange */
+    --pst-color-danger: #A50021;
+    /* Red */
+    --pst-color-text-base: #002D72;
+    /* Drexel Blue */
+    --pst-color-text-muted: #A7A8AA;
+    /* Cool Gray 6C */
+    --pst-color-border: #D1D5D8;
+    /* Light Gray */
+    --pst-color-shadow: #A7A8AA;
+    /* Cool Gray 6C */
+    --pst-color-background: #FFFFFF;
+    /* White */
+    --pst-color-on-background: #F5F5F5;
+    /* Light Gray */
+    --pst-color-surface: #F0F0F0;
+    /* Very Light Gray */
+    --pst-color-on-surface: #EDEDED;
+    /* Lighter Gray */
+    --pst-color-panel-background: var(--pst-color-background);
+    --pst-color-link: var(--pst-color-primary);
+    --pst-color-link-hover: var(--pst-color-secondary);
+    --pst-color-inline-code: #D64309;
+    /* Light Red */
+    --pst-color-target: #C4D600;
+    /* Green */
+
+    .only-dark {
+        display: none !important;
+    }
+
+    /* Header styling for light theme */
+    h1,
+    h2,
+    h3,
+    h4,
+    h5,
+    h6 {
+        color: var(--pst-color-primary);
+        /* Drexel Blue */
+        border-bottom: 2px solid var(--pst-color-secondary);
+        /* Drexel Yellow */
+    }
+}
+
+/* Dark theme */
+html[data-theme="dark"] {
+    --pst-color-primary: #FFD100;
+    /* Drexel Yellow */
+    --pst-color-secondary: #002D72;
+    /* Drexel Blue */
+    --pst-color-success: #6CACE4;
+    /* Light Blue */
+    --pst-color-info: #C7E1D2;
+    /* Light Green */
+    --pst-color-warning: #D86018;
+    /* Orange */
+    --pst-color-danger: #A50021;
+    /* Red */
+    --pst-color-text-base: #ffffff;
+    /* White */
+    --pst-color-text-muted: #BCB4A5;
+    /* Warm Gray 3C */
+    --pst-color-border: #A7A8AA;
+    /* Cool Gray 6C */
+    --pst-color-shadow: var(--pst-color-background);
+    --pst-color-background: #001d48;
+    /* Drexel Blue */
+    --pst-color-on-background: #001d48;
+    /* Drexel Blue */
+    --pst-color-surface: #006298;
+    /* Dark Blue */
+    --pst-color-on-surface: #006298;
+    /* Dark Blue */
+    --pst-color-panel-background: var(--pst-color-background);
+    --pst-color-link: var(--pst-color-primary);
+    --pst-color-link-hover: var(--pst-color-secondary);
+    --pst-color-inline-code: #D86018;
+    /* Orange */
+    --pst-color-target: #FF8F1C;
+    /* Light Orange */
+
+    .only-light {
+        display: none !important;
+    }
+
+    img {
+        filter: brightness(0.8) contrast(1.2);
+    }
+
+    /* Header styling for dark theme */
+    h1,
+    h2,
+    h3,
+    h4,
+    h5,
+    h6 {
+        color: var(--pst-color-primary);
+        /* Drexel Yellow */
+        border-bottom: 2px solid var(--pst-color-secondary);
+        /* Drexel Blue */
+    }
+}

notebooks/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+chapters:
+- file: markdown
+- file: notebooks
+- file: markdown-notebooks

notebooks/intro.md

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+# Welcome to your Jupyter Book
+
+This is a small sample book to give you a feel for how book content is
+structured.
+It shows off a few of the major file types, as well as some sample content.
+It does not go in-depth into any particular topic - check out [the Jupyter Book documentation](https://jupyterbook.org) for more information.
+
+Check out the content pages bundled with this sample book to see more.
+
+```{tableofcontents}
+```

notebooks/markdown-notebooks.md

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+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# Notebooks with MyST Markdown
+
+Jupyter Book also lets you write text-based notebooks using MyST Markdown.
+See [the Notebooks with MyST Markdown documentation](https://jupyterbook.org/file-types/myst-notebooks.html) for more detailed instructions.
+This page shows off a notebook written in MyST Markdown.
+
+## An example cell
+
+With MyST Markdown, you can define code cells with a directive like so:
+
+```{code-cell}
+print(2 + 2)
+```
+
+When your book is built, the contents of any `{code-cell}` blocks will be
+executed with your default Jupyter kernel, and their outputs will be displayed
+in-line with the rest of your content.
+
+```{seealso}
+Jupyter Book uses [Jupytext](https://jupytext.readthedocs.io/en/latest/) to convert text-based files to notebooks, and can support [many other text-based notebook files](https://jupyterbook.org/file-types/jupytext.html).
+```
+
+## Create a notebook with MyST Markdown
+
+MyST Markdown notebooks are defined by two things:
+
+1. YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).
+   See the YAML at the top of this page for example.
+2. The presence of `{code-cell}` directives, which will be executed with your book.
+
+That's all that is needed to get started!
+
+## Quickly add YAML metadata for MyST Notebooks
+
+If you have a markdown file and you'd like to quickly add YAML metadata to it, so that Jupyter Book will treat it as a MyST Markdown Notebook, run the following command:
+
+```
+jupyter-book myst init path/to/markdownfile.md
+```

notebooks/markdown.md

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+# Markdown Files
+
+Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or
+in regular markdown files (`.md`), you'll write in the same flavor of markdown
+called **MyST Markdown**.
+This is a simple file to help you get started and show off some syntax.
+
+## What is MyST?
+
+MyST stands for "Markedly Structured Text". It
+is a slight variation on a flavor of markdown called "CommonMark" markdown,
+with small syntax extensions to allow you to write **roles** and **directives**
+in the Sphinx ecosystem.
+
+For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html).
+
+## Sample Roles and Directives
+
+Roles and directives are two of the most powerful tools in Jupyter Book. They
+are like functions, but written in a markup language. They both
+serve a similar purpose, but **roles are written in one line**, whereas
+**directives span many lines**. They both accept different kinds of inputs,
+and what they do with those inputs depends on the specific role or directive
+that is being called.
+
+Here is a "note" directive:
+
+```{note}
+Here is a note
+```
+
+It will be rendered in a special box when you build your book.
+
+Here is an inline directive to refer to a document: {doc}`markdown-notebooks`.
+
+
+## Citations
+
+You can also cite references that are stored in a `bibtex` file. For example,
+the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like
+this: {cite}`holdgraf_evidence_2014`.
+
+Moreover, you can insert a bibliography into your page with this syntax:
+The `{bibliography}` directive must be used for all the `{cite}` roles to
+render properly.
+For example, if the references for your book are stored in `references.bib`,
+then the bibliography is inserted with:
+
+```{bibliography}
+```
+
+## Learn more
+
+This is just a simple starter to get you started.
+You can learn a lot more at [jupyterbook.org](https://jupyterbook.org).