Update documentation

.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 8bb02137e233f38a2bceadbf36f9c8f1
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/intro.md

@@ -0,0 +1,11 @@
+# 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}
+```

_sources/markdown-notebooks.ipynb

@@ -0,0 +1,85 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "88b5e405",
+   "metadata": {},
+   "source": [
+    "# Notebooks with MyST Markdown\n",
+    "\n",
+    "Jupyter Book also lets you write text-based notebooks using MyST Markdown.\n",
+    "See [the Notebooks with MyST Markdown documentation](https://jupyterbook.org/file-types/myst-notebooks.html) for more detailed instructions.\n",
+    "This page shows off a notebook written in MyST Markdown.\n",
+    "\n",
+    "## An example cell\n",
+    "\n",
+    "With MyST Markdown, you can define code cells with a directive like so:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ae813372",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print(2 + 2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "26ba2a70",
+   "metadata": {},
+   "source": [
+    "When your book is built, the contents of any `{code-cell}` blocks will be\n",
+    "executed with your default Jupyter kernel, and their outputs will be displayed\n",
+    "in-line with the rest of your content.\n",
+    "\n",
+    "```{seealso}\n",
+    "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).\n",
+    "```\n",
+    "\n",
+    "## Create a notebook with MyST Markdown\n",
+    "\n",
+    "MyST Markdown notebooks are defined by two things:\n",
+    "\n",
+    "1. YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).\n",
+    "   See the YAML at the top of this page for example.\n",
+    "2. The presence of `{code-cell}` directives, which will be executed with your book.\n",
+    "\n",
+    "That's all that is needed to get started!\n",
+    "\n",
+    "## Quickly add YAML metadata for MyST Notebooks\n",
+    "\n",
+    "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:\n",
+    "\n",
+    "```\n",
+    "jupyter-book myst init path/to/markdownfile.md\n",
+    "```"
+   ]
+  }
+ ],
+ "metadata": {
+  "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"
+  },
+  "source_map": [
+   13,
+   25,
+   27
+  ]
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

_sources/markdown-notebooks.md

@@ -0,0 +1,53 @@
+---
+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
+```

_sources/markdown.md

@@ -0,0 +1,55 @@
+# 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).

_sources/mechinterp/mechinterp_intro.md

@@ -0,0 +1,3 @@
+# Mechanistic Interpretability
+
+Welcome to the Mechanistic Interpretability workshop!