Merge pull request #2 from tsalo/init-book

Initialize book.

content/_config.yml

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+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# Users are expected to override these values in their own `_config.yml` file.
+# This is also the "master list" of all allowed keys and values.
+
+#######################################################################################
+# Book settings
+title                       : An Introduction to Neuroimaging Meta-Analysis  # The title of the book. Will be placed in the left navbar.
+author                      : The Neurostuff Team  # The author of the book
+copyright                   : "2022"  # Copyright year to be placed in the footer
+logo                        : ""  # A path to the book logo
+# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
+exclude_patterns            : [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"]
+# Auto-exclude files not in the toc
+only_build_toc_files        : false
+
+#######################################################################################
+# Execution settings
+execute:
+  execute_notebooks         : auto  # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
+  cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
+  exclude_patterns          : []    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
+  timeout                   : 30    # The maximum time (in seconds) each notebook cell is allowed to run.
+  run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),
+                                    # otherwise the notebook's parent directory will be the cwd.
+  allow_errors              : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run.
+  stderr_output             : show  # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe'
+
+#######################################################################################
+# Parse and render settings
+parse:
+  myst_enable_extensions:  # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html
+    # - amsmath
+    - colon_fence
+    # - deflist
+    - dollarmath
+    # - html_admonition
+    # - html_image
+    - linkify
+    # - replacements
+    # - smartquotes
+    - substitution
+    - tasklist
+  myst_url_schemes: [mailto, http, https] # URI schemes that will be recognised as external URLs in Markdown links
+  myst_dmath_double_inline: true  # Allow display math ($$) within an inline context
+
+#######################################################################################
+# HTML-specific settings
+html:
+  favicon                   : ""  # A path to a favicon image
+  use_edit_page_button      : false  # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
+  use_repository_button     : false  # Whether to add a link to your repository button
+  use_issues_button         : false  # Whether to add an "open an issue" button
+  use_multitoc_numbering    : true   # Continuous numbering across parts/chapters
+  extra_navbar              : Powered by <a href="https://jupyterbook.org">Jupyter Book</a>  # Will be displayed underneath the left navbar.
+  extra_footer              : ""  # Will be displayed underneath the footer.
+  google_analytics_id       : ""  # A GA id that can be used to track book views.
+  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
+  baseurl                   : ""  # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/
+  comments:
+    hypothesis              : false
+    utterances              : false
+  announcement              : "" # A banner announcement at the top of the site.
+
+#######################################################################################
+# LaTeX-specific settings
+latex:
+  latex_engine              : pdflatex  # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex'
+  use_jupyterbook_latex     : true # use sphinx-jupyterbook-latex for pdf builds as default
+
+#######################################################################################
+# Launch button settings
+launch_buttons:
+  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
+  binderhub_url             : https://mybinder.org  # The URL of the BinderHub (e.g., https://mybinder.org)
+  jupyterhub_url            : ""  # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu)
+  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)
+  colab_url                 : "" # The URL of Google Colab (https://colab.research.google.com)
+
+repository:
+  url                       : https://github.com/neurostuff/nimare-book  # The URL to your book's repository
+  path_to_book              : ""  # A path to your book's folder, relative to the repository root.
+  branch                    : main  # Which branch of the repository should be used when creating links
+
+#######################################################################################
+# Advanced and power-user settings
+sphinx:
+  extra_extensions          :   # A list of extra extensions to load by Sphinx (added to those already used by JB).
+  local_extensions          :   # A list of local extensions to load by sphinx specified by "name: path" items
+  recursive_update          : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update (false)
+  config                    :   # key-value pairs to directly over-ride the Sphinx configuration

content/_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: download_data
+- file: markdown
+- file: notebooks
+- file: markdown-notebooks

content/download_data.md

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+---
+jupytext:
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.10.3
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# Download Data for the Book
+
++++

content/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}
+```

content/markdown-notebooks.md

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+---
+jupytext:
+  cell_metadata_filter: -all
+  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
+```

content/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 kind of 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).

content/notebooks.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Content with notebooks\n",
+    "\n",
+    "You can also create content with Jupyter Notebooks. This means that you can include\n",
+    "code blocks and their outputs in your book.\n",
+    "\n",
+    "## Markdown + notebooks\n",
+    "\n",
+    "As it is markdown, you can embed images, HTML, etc into your posts!\n",
+    "\n",
+    "![](https://myst-parser.readthedocs.io/en/latest/_static/logo-wide.svg)\n",
+    "\n",
+    "You can also $add_{math}$ and\n",
+    "\n",
+    "$$\n",
+    "math^{blocks}\n",
+    "$$\n",
+    "\n",
+    "or\n",
+    "\n",
+    "$$\n",
+    "\\begin{aligned}\n",
+    "\\mbox{mean} la_{tex} \\\\ \\\\\n",
+    "math blocks\n",
+    "\\end{aligned}\n",
+    "$$\n",
+    "\n",
+    "But make sure you \\$Escape \\$your \\$dollar signs \\$you want to keep!\n",
+    "\n",
+    "## MyST markdown\n",
+    "\n",
+    "MyST markdown works in Jupyter Notebooks as well. For more information about MyST markdown, check\n",
+    "out [the MyST guide in Jupyter Book](https://jupyterbook.org/content/myst.html),\n",
+    "or see [the MyST markdown documentation](https://myst-parser.readthedocs.io/en/latest/).\n",
+    "\n",
+    "## Code blocks and outputs\n",
+    "\n",
+    "Jupyter Book will also embed your code blocks and output in your book.\n",
+    "For example, here's some sample Matplotlib code:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from matplotlib import rcParams, cycler\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "plt.ion()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Fixing random state for reproducibility\n",
+    "np.random.seed(19680801)\n",
+    "\n",
+    "N = 10\n",
+    "data = [np.logspace(0, 1, 100) + np.random.randn(100) + ii for ii in range(N)]\n",
+    "data = np.array(data).T\n",
+    "cmap = plt.cm.coolwarm\n",
+    "rcParams['axes.prop_cycle'] = cycler(color=cmap(np.linspace(0, 1, N)))\n",
+    "\n",
+    "\n",
+    "from matplotlib.lines import Line2D\n",
+    "custom_lines = [Line2D([0], [0], color=cmap(0.), lw=4),\n",
+    "                Line2D([0], [0], color=cmap(.5), lw=4),\n",
+    "                Line2D([0], [0], color=cmap(1.), lw=4)]\n",
+    "\n",
+    "fig, ax = plt.subplots(figsize=(10, 5))\n",
+    "lines = ax.plot(data)\n",
+    "ax.legend(custom_lines, ['Cold', 'Medium', 'Hot']);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "There is a lot more that you can do with outputs (such as including interactive outputs)\n",
+    "with your book. For more information about this, see [the Jupyter Book documentation](https://jupyterbook.org)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.8.0"
+  },
+  "widgets": {
+   "application/vnd.jupyter.widget-state+json": {
+    "state": {},
+    "version_major": 2,
+    "version_minor": 0
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}