dotemacs

org-roam.info (97661B)

---

 This is org-roam.info, produced by makeinfo version 6.7 from
 org-roam.texi.
 
      Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 
      You can redistribute this document and/or modify it under the terms
      of the GNU General Public License as published by the Free Software
      Foundation, either version 3 of the License, or (at your option)
      any later version.
 
      This document is distributed in the hope that it will be useful,
      but WITHOUT ANY WARRANTY; without even the implied warranty of
      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
      General Public License for more details.
 
 INFO-DIR-SECTION Emacs
 START-INFO-DIR-ENTRY
 * Org-roam: (org-roam). Roam Research for Emacs.
 END-INFO-DIR-ENTRY
 
 
 File: org-roam.info,  Node: Top,  Next: Introduction,  Up: (dir)
 
 Org-roam User Manual
 ********************
 
 
    This manual is for Org-roam version 2.2.2.
 
      Copyright (C) 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 
      You can redistribute this document and/or modify it under the terms
      of the GNU General Public License as published by the Free Software
      Foundation, either version 3 of the License, or (at your option)
      any later version.
 
      This document is distributed in the hope that it will be useful,
      but WITHOUT ANY WARRANTY; without even the implied warranty of
      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
      General Public License for more details.
 
 * Menu:
 
 * Introduction::
 * Target Audience::
 * A Brief Introduction to the Zettelkasten Method::
 * Installation::
 * Getting Started::
 * Customizing Node Caching::
 * The Org-roam Buffer::
 * Node Properties::
 * Citations::
 * Completion::
 * Encryption::
 * The Templating System::
 * Extensions::
 * Performance Optimization::
 * The Org-mode Ecosystem::
 * FAQ::
 * Developer's Guide to Org-roam::
 * Appendix::
 * Keystroke Index::
 * Command Index::
 * Function Index::
 * Variable Index::
 
 — The Detailed Node Listing —
 
 Installation
 
 * Installing from MELPA::
 * Installing from Source::
 * Installation Troubleshooting::
 
 Installation Troubleshooting
 
 * C Compiler::
 
 C Compiler
 
 * C Compiler for Windows::
 
 Getting Started
 
 * The Org-roam Node::
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
 * Customizing Node Completions::
 
 Customizing Node Caching
 
 * How to cache::
 * What to cache::
 * When to cache::
 
 The Org-roam Buffer
 
 * Navigating the Org-roam Buffer::
 * Configuring what is displayed in the buffer::
 * Configuring the Org-roam buffer display::
 * Styling the Org-roam buffer::
 
 Node Properties
 
 * Standard Org properties::
 * Titles and Aliases::
 * Tags::
 * Refs::
 
 Citations
 
 * Using the Cached Information::
 
 Completion
 
 * Completing within Link Brackets::
 * Completing anywhere::
 
 The Templating System
 
 * Template Walkthrough::
 * Org-roam Template Expansion::
 
 Extensions
 
 * org-roam-protocol::
 * org-roam-graph::
 * org-roam-dailies::
 * org-roam-export::
 
 org-roam-protocol
 
 * Installation: Installation (1).
 * The roam-node protocol::
 * The roam-ref protocol::
 
 Installation
 
 * Linux::
 * Mac OS::
 * Windows::
 
 org-roam-graph
 
 * Graph Options::
 
 org-roam-dailies
 
 * Configuration::
 * Usage::
 
 Performance Optimization
 
 * Garbage Collection::
 
 The Org-mode Ecosystem
 
 * Browsing History with winner-mode::
 * Versioning Notes::
 * Full-text search with Deft::
 * Org-journal::
 * Org-download::
 * mathpix.el: mathpixel.
 * Org-noter / Interleave::
 * Bibliography::
 * Spaced Repetition::
 
 FAQ
 
 * How do I have more than one Org-roam directory?::
 * How do I create a note whose title already matches one of the candidates?::
 * How can I stop Org-roam from creating IDs everywhere?::
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
 * I’m seeing this “Selecting deleted buffer” error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?.
 
 How do I publish my notes with an Internet-friendly graph?
 
 * Configure org-mode for publishing::
 * Overriding the default link creation function::
 * Copying the generated file to the export directory::
 
 Developer’s Guide to Org-roam
 
 * Org-roam's Design Principle::
 * Building Extensions and Advanced Customization of Org-roam::
 
 Building Extensions and Advanced Customization of Org-roam
 
 * Accessing the Database::
 * Accessing and Modifying Nodes::
 * Extending the Capture System::
 
 Appendix
 
 * Note-taking Workflows::
 * Ecosystem::
 
 
 
 File: org-roam.info,  Node: Introduction,  Next: Target Audience,  Prev: Top,  Up: Top
 
 1 Introduction
 **************
 
 Org-roam is a tool for networked thought.  It reproduces some of Roam
 Research’s (https://roamresearch.com/) (1) key features within Org-mode
 (https://orgmode.org/).
 
    Org-roam allows for effortless non-hierarchical note-taking: with
 Org-roam, notes flow naturally, making note-taking fun and easy.
 Org-roam augments the Org-mode syntax, and will work for anyone already
 using Org-mode for their personal wiki.
 
    Org-roam leverages the mature ecosystem around Org-mode.  For
 example, it has first-class support for org-ref
 (https://github.com/jkitchin/org-ref) for citation management, and is
 able to piggyback off Org’s excellent LaTeX and source-block evaluation
 capabilities.
 
    Org-roam provides these benefits over other tooling:
 
    • *Privacy and Security:* Your personal wiki belongs only to you,
      entirely offline and in your control.  Encrypt your notes with GPG.
 
    • *Longevity of Plain Text:* Unlike web solutions like Roam Research,
      the notes are first and foremost plain Org-mode files – Org-roam
      simply builds an auxiliary database to give the personal wiki
      superpowers.  Having your notes in plain-text is crucial for the
      longevity of your wiki.  Never have to worry about proprietary web
      solutions being taken down.  The notes are still functional even if
      Org-roam ceases to exist.
 
    • *Free and Open Source:* Org-roam is free and open-source, which
      means that if you feel unhappy with any part of Org-roam, you may
      choose to extend Org-roam, or open a pull request.
 
    • *Leverage the Org-mode ecosystem:* Over the decades, Emacs and
      Org-mode has developed into a mature system for plain-text
      organization.  Building upon Org-mode already puts Org-roam
      light-years ahead of many other solutions.
 
    • *Built on Emacs:* Emacs is also a fantastic interface for editing
      text, and Org-roam inherits many of the powerful text-navigation
      and editing packages available to Emacs.
 
    ---------- Footnotes ----------
 
    (1) To understand more about Roam, a collection of links are
 available in *note Note-taking Workflows::.
 
 
 File: org-roam.info,  Node: Target Audience,  Next: A Brief Introduction to the Zettelkasten Method,  Prev: Introduction,  Up: Top
 
 2 Target Audience
 *****************
 
 Org-roam is a tool that will appear unfriendly to anyone unfamiliar with
 Emacs and Org-mode, but it is also extremely powerful to those willing
 to put effort in mastering the intricacies.  Org-roam stands on the
 shoulders of giants.  Emacs was first created in 1976, and remains the
 tool of choice for many for editing text and designing textual
 interfaces.  The malleability of Emacs allowed the creation of Org-mode,
 an all-purpose plain-text system for maintaining TODO lists, planning
 projects, and authoring documents.  Both of these tools are incredibly
 vast and require significant time investment to master.
 
    Org-roam assumes only basic familiarity with these tools.  It is not
 difficult to get up and running with basic text-editing functionality,
 but one will only fully appreciate the power of building Roam
 functionality into Emacs and Org-mode when the usage of these tools
 become more advanced.
 
    One key advantage to Org-roam is that building on top of Emacs gives
 it malleability.  This is especially important for note-taking
 workflows.  It is our belief that note-taking workflows are extremely
 personal, and there is no one tool that’s perfect for you.  Org-mode and
 Org-roam allows you to discover what works for you, and build that
 perfect tool for yourself.
 
    If you are new to the software, and choose to take this leap of
 faith, I hope you find yourself equally entranced as Neal Stephenson
 was.
 
      Emacs outshines all other editing software in approximately the
      same way that the noonday sun does the stars.  It is not just
      bigger and brighter; it simply makes everything else vanish.  –
      Neal Stephenson, In the Beginning was the Command Line (1998)
 
 
 File: org-roam.info,  Node: A Brief Introduction to the Zettelkasten Method,  Next: Installation,  Prev: Target Audience,  Up: Top
 
 3 A Brief Introduction to the Zettelkasten Method
 *************************************************
 
 Org-roam provides utilities for maintaining a digital slip-box.  This
 section aims to provide a brief introduction to the “slip-box”, or
 “Zettelkasten” method.  By providing some background on the method, we
 hope that the design decisions of Org-roam will become clear, and that
 will aid in using Org-roam appropriately.  In this section we will
 introduce terms commonly used within the Zettelkasten community and the
 Org-roam forums.
 
    The Zettelkasten is a personal tool for thinking and writing.  It
 places heavy emphasis on connecting ideas, building up a web of thought.
 Hence, it is well suited for knowledge workers and intellectual tasks,
 such as conducting research.  The Zettelkasten can act as a research
 partner, where conversations with it may produce new and surprising
 lines of thought.
 
    This method is attributed to German sociologist Niklas Luhmann, who
 using the method had produced volumes of written works.  Luhmann’s
 slip-box was simply a box of cards.  These cards are small – often only
 large enough to fit a single concept.  The size limitation encourages
 ideas to be broken down into individual concepts.  These ideas are
 explicitly linked together.  The breakdown of ideas encourages
 tangential exploration of ideas, increasing the surface for thought.
 Making linking explicit between notes also encourages one to think about
 the connections between concepts.
 
    At the corner of each note, Luhmann ascribed each note with an
 ordered ID, allowing him to link and jump between notes.  In Org-roam,
 we simply use hyperlinks.
 
    Org-roam is the slip-box, digitalized in Org-mode.  Every zettel
 (card) is a plain-text, Org-mode file.  In the same way one would
 maintain a paper slip-box, Org-roam makes it easy to create new zettels,
 pre-filling boilerplate content using a powerful templating system.
 
    *Fleeting notes*
 
    A slip-box requires a method for quickly capturing ideas.  These are
 called *fleeting notes*: they are simple reminders of information or
 ideas that will need to be processed later on, or trashed.  This is
 typically accomplished using ‘org-capture’ (see *note (org)Capture::),
 or using Org-roam’s daily notes functionality (see *note
 org-roam-dailies::).  This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
    *Permanent notes*
 
    Permanent notes are further split into two categories: *literature
 notes* and *concept notes*.  Literature notes can be brief annotations
 on a particular source (e.g.  book, website or paper), that you’d like
 to access later on.  Concept notes require much more care in authoring:
 they need to be self-explanatory and detailed.  Org-roam’s templating
 system supports the addition of different templates to facilitate the
 creation of these notes.
 
    For further reading on the Zettelkasten method, “How to Take Smart
 Notes” by Sonke Ahrens is a decent guide.
 
 
 File: org-roam.info,  Node: Installation,  Next: Getting Started,  Prev: A Brief Introduction to the Zettelkasten Method,  Up: Top
 
 4 Installation
 **************
 
 Org-roam can be installed using Emacs’ package manager or manually from
 its development repository.
 
 * Menu:
 
 * Installing from MELPA::
 * Installing from Source::
 * Installation Troubleshooting::
 
 
 File: org-roam.info,  Node: Installing from MELPA,  Next: Installing from Source,  Up: Installation
 
 4.1 Installing from MELPA
 =========================
 
 Org-roam is available from Melpa and Melpa-Stable.  If you haven’t used
 Emacs’ package manager before, you may familiarize yourself with it by
 reading the documentation in the Emacs manual, see *note
 (emacs)Packages::.  Then, add one of the archives to ‘package-archives’:
 
    • To use Melpa:
 
      (require 'package)
      (add-to-list 'package-archives
                   '("melpa" . "http://melpa.org/packages/") t)
 
    • To use Melpa-Stable:
 
      (require 'package)
      (add-to-list 'package-archives
                   '("melpa-stable" . "http://stable.melpa.org/packages/") t)
 
    Org-roam also depends on a recent version of Org, which can be
 obtained in Org’s package repository (see *note (org)Installation::).
 
    Once you have done that, you can install Org-roam and its
 dependencies using:
 
      M-x package-install RET org-roam RET
 
 
 File: org-roam.info,  Node: Installing from Source,  Next: Installation Troubleshooting,  Prev: Installing from MELPA,  Up: Installation
 
 4.2 Installing from Source
 ==========================
 
 You may install Org-roam directly from the repository on GitHub
 (https://github.com/org-roam/org-roam) if you like.  This will give you
 access to the latest version hours or days before it appears on MELPA,
 and months (or more) before it is added to the Debian or Ubuntu
 repositories.  This will also give you access to various developmental
 branches that may be available.
 
    Note, however, that development version, and especially any feature
 branches, may not always be in working order.  You’ll need to be
 prepared to do some debugging, or to manually roll-back to working
 versions, if you install from GitHub.
 
    Installing from GitHub requires that you clone the repository:
 
      git clone https://github.com/org-roam/org-roam.git /path/to/org/roam
 
    where ‘./path/to/org/roam’ is the location you will store your copy
 of the code.
 
    Next, you need to add this location to your load path, and ‘require’
 the Org-roam library.  Add the following code to your ‘.emacs’:
 
      (add-to-list 'load-path "/path/to/org/roam")
      (require 'org-roam)
 
    You now have Org-roam installed.  However, you don’t necessarily have
 the dependencies that it requires.  These include:
 
    • dash
 
    • f
 
    • s
 
    • org
 
    • emacsql
 
    • emacsql-sqlite
 
    • magit-section
 
    You can install this manually as well, or get the latest version from
 MELPA.  You may wish to use use-package
 (https://github.com/jwiegley/use-package), straight.el
 (https://github.com/raxod502/straight.el) to help manage this.
 
    If you would like to install the manual for access from Emacs’
 built-in Info system, you’ll need to compile the .texi source file, and
 install it in an appropriate location.
 
    To compile the .texi source file, from a terminal navigate to the
 ‘/doc’ subdirectory of the Org-roam repository, and run the following:
 
      make infodir=/path/to/my/info/files install-info
 
    Where ‘/path/to/my/info/files’ is the location where you keep info
 files.  This target directory needs to be stored in the variable
 ‘Info-default-directory-list‘.  If you aren’t using one of the default
 info locations, you can configure this with the following in your
 ‘.emacs’ file:
 
      (require 'info)
      (add-to-list 'Info-default-directory-list
                   "/path/to/my/info/files")
 
    You can also use one of the default locations, such as:
 
    • _usr/local/share/info_
 
    • _usr/share/info_
 
    • _usr/local/share/info_
 
    If you do this, you’ll need to make sure you have write-access to
 that location, or run the above ‘make’ command as root.
 
    Now that the info file is ready, you need to add it to the
 corresponding ‘dir’ file:
 
      install-info /path/to/my/info/files/org-roam.info /path/to/my/info/files/dir
 
 
 File: org-roam.info,  Node: Installation Troubleshooting,  Prev: Installing from Source,  Up: Installation
 
 4.3 Installation Troubleshooting
 ================================
 
 * Menu:
 
 * C Compiler::
 
 
 File: org-roam.info,  Node: C Compiler,  Up: Installation Troubleshooting
 
 4.3.1 C Compiler
 ----------------
 
 Org-roam relies on an Emacs package called ‘emacsql’ and
 ‘emacsql-sqlite’ to work with the ‘sqlite’ database.  Both of them
 should be installed automatically in your Emacs environment as a
 prerequisite for Org-roam when you install it.
 
    ‘emacsql-sqlite’ requires a C compiler (e.g.  ‘gcc’ or ‘clang’) to be
 present in your computer.  How to install a C compiler depends on the OS
 that you use.
 
 * Menu:
 
 * C Compiler for Windows::
 
 
 File: org-roam.info,  Node: C Compiler for Windows,  Up: C Compiler
 
 C Compiler for Windows
 ......................
 
 One of the easiest ways to install a C compiler in Windows is to use
 MSYS2 (https://www.msys2.org/) as at the time of this writing:
 
    • Download and use the installer in the official MSYS2 website
 
    • Run MSYS2 and in its terminal, type the following and answer “Y” to
      proceed – this will install ‘gcc’ in your PC:
 
           pacman -S gcc
 
    • On Windows, add ‘C:\msys64\usr\bin’ (command ‘where gcc’ in MSYS2
      terminal can tell you the correct path) to ‘PATH’ in your
      environmental variables
 
    • Launch Emacs and call ‘M-x org-roam-db-autosync-mode’ (launch Emacs
      after defining the path, so that Emacs can recognize it)
 
    This will automatically start compiling ‘emacsql-sqlite’; you should
 see a message in minibuffer.  It may take a while until compilation
 completes.  Once complete, you should see a new file
 ‘emacsql-sqlite.exe’ created in a subfolder named ‘sqlite’ under
 ‘emacsql-sqlite’ installation folder.  It’s typically in your Emacs
 configuration folder like this:
 ‘/.config/emacs/elpa/emacsql-sqlite-20190727.1710/sqlite’
 
 
 File: org-roam.info,  Node: Getting Started,  Next: Customizing Node Caching,  Prev: Installation,  Up: Top
 
 5 Getting Started
 *****************
 
 * Menu:
 
 * The Org-roam Node::
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
 * Customizing Node Completions::
 
 
 File: org-roam.info,  Node: The Org-roam Node,  Next: Links between Nodes,  Up: Getting Started
 
 5.1 The Org-roam Node
 =====================
 
 We first begin with some terminology we’ll use throughout the manual.
 We term the basic denomination in Org-roam a node.  We define a node as
 follows:
 
      A node is any headline or top level file with an ID.
 
    For example, with this example file content:
 
      :PROPERTIES:
      :ID:       foo
      :END:
      #+title: Foo
 
      * Bar
      :PROPERTIES:
      :ID:       bar
      :END:
 
    We create two nodes:
 
    • A file node “Foo” with id ‘foo’.
 
    • A headline node “Bar” with id ‘bar’.
 
    Headlines without IDs will not be considered Org-roam nodes.  Org IDs
 can be added to files or headlines via the interactive command ‘M-x
 org-id-get-create’.
 
 
 File: org-roam.info,  Node: Links between Nodes,  Next: Setting up Org-roam,  Prev: The Org-roam Node,  Up: Getting Started
 
 5.2 Links between Nodes
 =======================
 
 We link between nodes using Org’s standard ID link (e.g.  ‘id:foo’).
 While only ID links will be considered during the computation of links
 between nodes, Org-roam caches all other links in the documents for
 external use.
 
 
 File: org-roam.info,  Node: Setting up Org-roam,  Next: Creating and Linking Nodes,  Prev: Links between Nodes,  Up: Getting Started
 
 5.3 Setting up Org-roam
 =======================
 
 Org-roam’s capabilities stem from its aggressive caching: it crawls all
 files within ‘org-roam-directory’, and maintains a cache of all links
 and nodes.
 
    To start using Org-roam, pick a location to store the Org-roam files.
 The directory that will contain your notes is specified by the variable
 ‘org-roam-directory’.  Org-roam searches recursively within
 ‘org-roam-directory’ for notes.  This variable needs to be set before
 any calls to Org-roam functions.
 
    For this tutorial, create an empty directory, and set
 ‘org-roam-directory’:
 
      (make-directory "~/org-roam")
      (setq org-roam-directory (file-truename "~/org-roam"))
 
    The ‘file-truename’ function is only necessary when you use symbolic
 links inside ‘org-roam-directory’: Org-roam does not resolve symbolic
 links.  One can however instruct Emacs to always resolve symlinks, at a
 performance cost:
 
      (setq find-file-visit-truename t)
 
    Next, we setup Org-roam to run functions on file changes to maintain
 cache consistency.  This is achieved by running ‘M-x
 org-roam-db-autosync-mode’.  To ensure that Org-roam is available on
 startup, place this in your Emacs configuration:
 
      (org-roam-db-autosync-mode)
 
    To build the cache manually, run ‘M-x org-roam-db-sync’.  Cache
 builds may take a while the first time, but subsequent builds are often
 instantaneous because they only reprocess modified files.
 
 
 File: org-roam.info,  Node: Creating and Linking Nodes,  Next: Customizing Node Completions,  Prev: Setting up Org-roam,  Up: Getting Started
 
 5.4 Creating and Linking Nodes
 ==============================
 
 Org-roam makes it easy to create notes and link them together.  There
 are 2 main functions for creating nodes:
 
    • ‘org-roam-node-insert’: creates a node if it does not exist, and
      inserts a link to the node at point.
 
    • ‘org-roam-node-find’: creates a node if it does not exist, and
      visits the node.
 
    • ‘org-roam-capture’: creates a node if it does not exist, and
      restores the current window configuration upon completion.
 
    Let’s first try ‘org-roam-node-find’.  Calling ‘M-x
 org-roam-node-find’ will show a list of titles for nodes that reside in
 ‘org-roam-directory’.  It should show nothing right now, since there are
 no notes in the directory.  Enter the title of the note you wish to
 create, and press ‘RET’.  This begins the note creation process.  This
 process uses ‘org-capture’’s templating system, and can be customized
 (see *note The Templating System::).  Using the default template,
 pressing ‘C-c C-c’ finishes the note capture.
 
    Now that we have a node, we can try inserting a link to the node
 using ‘M-x org-roam-node-insert’.  This brings up the list of nodes,
 which should contain the node you just created.  Selecting the node will
 insert an ‘id:’ link to the node.  If you instead entered a title that
 does not exist, you will once again be brought through the node creation
 process.
 
    One can also conveniently insert links via the completion-at-point
 functions Org-roam provides (see *note Completion::).
 
 
 File: org-roam.info,  Node: Customizing Node Completions,  Prev: Creating and Linking Nodes,  Up: Getting Started
 
 5.5 Customizing Node Completions
 ================================
 
 Node selection is achieved via the ‘completing-read’ interface,
 typically through ‘org-roam-node-read‘.  The presentation of these nodes
 are governed by ‘org-roam-node-display-template’.
 
  -- Variable: org-roam-node-display-template
 
      Configures display formatting for Org-roam node.
 
      Patterns of form “${field-name:length}” are interpolated based on
      the current node.
 
      Each “field-name” is replaced with the return value of each
      corresponding accessor function for org-roam-node, e.g.  “${title}”
      will be interpolated by the result of org-roam-node-title.  You can
      also define custom accessors using cl-defmethod.  For example, you
      can define:
 
      (cl-defmethod org-roam-node-my-title ((node org-roam-node)) (concat
      “My ” (org-roam-node-title node)))
 
      and then reference it here or in the capture templates as
      “${my-title}”.
 
      “length” is an optional specifier and declares how many characters
      can be used to display the value of the corresponding field.  If
      it’s not specified, the field will be inserted as is, i.e.  it
      won’t be aligned nor trimmed.  If it’s an integer, the field will
      be aligned accordingly and all the exceeding characters will be
      trimmed out.  If it’s “*”, the field will use as many characters as
      possible and will be aligned accordingly.
 
      A closure can also be assigned to this variable in which case the
      closure is evaluated and the return value is used as the template.
      The closure must evaluate to a valid template string.
 
    If you’re using a vertical completion framework, such as Ivy and
 Selectrum, Org-roam supports the generation of an aligned, tabular
 completion interface.  For example, to include a column for tags up to
 10 character widths wide, one can set ‘org-roam-node-display-template’
 as such:
 
      (setq org-roam-node-display-template
            (concat "${title:*} "
                    (propertize "${tags:10}" 'face 'org-tag)))
 
 
 File: org-roam.info,  Node: Customizing Node Caching,  Next: The Org-roam Buffer,  Prev: Getting Started,  Up: Top
 
 6 Customizing Node Caching
 **************************
 
 * Menu:
 
 * How to cache::
 * What to cache::
 * When to cache::
 
 
 File: org-roam.info,  Node: How to cache,  Next: What to cache,  Up: Customizing Node Caching
 
 6.1 How to cache
 ================
 
 Org-roam uses a sqlite database to perform caching, but there are
 multiple Emacs libraries that can be used.  The default used by Org-roam
 is ‘emacs-sqlite’.  Below the pros and cons of each package is used:
 
    **emacs-sqlite** (https://github.com/skeeto/emacsql)
 
    The default option used by Org-roam.  This library is the most mature
 and well-supported and is imported by default in Org-roam.
 
    One downside of using ‘emacs-sqlite’ is that using it requires
 compilation and can cause issues in some environments (especially
 Windows).  If you have issues producing the customized binary required
 by ‘emacs-sqlite’, consider using ‘emacs-sqlite3’.
 
    **emacs-sqlite3** (https://github.com/cireu/emacsql-sqlite3)
 
    ‘emacs-sqlite3’ uses the official sqlite3 binary that can be obtained
 from your system’s package manager.  This is useful if you have issues
 producing the ‘sqlite3’ binary required by the other packages.  However,
 it is not recommended because it has some compatibility issues with
 Emacs, but should work for most regular cases.  See Chris Wellon’s blog
 post (https://nullprogram.com/blog/2014/02/06/) for more information.
 
    To use ‘emacsql-sqlite3’, ensure that the package is installed, and
 set:
 
      (setq org-roam-database-connector 'sqlite3)
 
    **emacssql-sqlite-module**
 (https://melpa.org/#/emacsql-sqlite-module) (previously
 emacsql-libsqlite3)
 
    ‘emacs-sqlite-module’ is a relatively young package which uses an
 Emacs module that exposes parts of the SQLite C API to Emacs Lisp,
 instead of using subprocess as ‘emacsql-sqlite’ does.  It is expected to
 be a more performant drop-in replacement for ‘emacs-sqlite’.
 
      (setq org-roam-database-connector 'sqlite-module)
 
    **emacsql-sqlite-builtin**
 (https://melpa.org/#/emacsql-sqlite-builtin)
 
    ‘emacsql-sqlite-builtin’ uses the in-built SQLite support for Emacs
 29 and later.  This is the recommended option if you are using a version
 of Emacs that supports it.
 
      (setq org-roam-database-connector 'sqlite-builtin)
 
 
 File: org-roam.info,  Node: What to cache,  Next: When to cache,  Prev: How to cache,  Up: Customizing Node Caching
 
 6.2 What to cache
 =================
 
 By default, all nodes (any headline or file with an ID) are cached by
 Org-roam.  There are instances where you may want to have headlines with
 ID, but not have them cached by Org-roam.
 
    To exclude a headline from the Org-roam database, set the
 ‘ROAM_EXCLUDE’ property to a non-nil value.  For example:
 
      * Foo
        :PROPERTIES:
        :ID:       foo
        :ROAM_EXCLUDE: t
        :END:
 
    One can also set ‘org-roam-db-node-include-function’.  For example,
 to exclude all headlines with the ‘ATTACH’ tag from the Org-roam
 database, one can set:
 
      (setq org-roam-db-node-include-function
            (lambda ()
              (not (member "ATTACH" (org-get-tags)))))
 
    Org-roam relied on the obtained Org AST for the buffer to parse
 links.  However, links appearing in some places (e.g.  within property
 drawers) are not considered by the Org AST to be links.  Therefore,
 Org-roam takes special care of additionally trying to process these
 links.  Use ‘org-roam-db-extra-links-elements’ to specify which
 additional Org AST element types to consider.
 
  -- Variable: org-roam-db-extra-links-elements
 
      The list of Org element types to include for parsing by Org-roam.
 
      By default, when parsing Org’s AST, links within keywords and
      property drawers are not parsed as links.  Sometimes however, it is
      desirable to parse and cache these links (e.g.  hiding links in a
      property drawer).
 
    Additionally, one may want to ignore certain keys from being excluded
 within property drawers.  For example, we would not want ‘ROAM_REFS’
 links to be self-referential.  Hence, to exclude specific keys, we use
 ‘org-roam-db-extra-links-exclude-keys’.
 
  -- Variable: org-roam-db-extra-links-exclude-keys
 
      Keys to ignore when mapping over links.
 
      The car of the association list is the Org element type (e.g.
      keyword).  The cdr is a list of case-insensitive strings to exclude
      from being treated as links.
 
 
 File: org-roam.info,  Node: When to cache,  Prev: What to cache,  Up: Customizing Node Caching
 
 6.3 When to cache
 =================
 
 By default, Org-roam is eager in caching: each time an Org-roam file is
 modified and saved, it updates the database for the corresponding file.
 This keeps the database up-to-date, causing the least surprise when
 using the interactive commands.
 
    However, depending on how large your Org files are, database updating
 can be a slow operation.  You can disable the automatic updating of the
 database by setting ‘org-roam-db-update-on-save’ to ‘nil’.
 
  -- Variable: org-roam-db-update-on-save
 
    If t, update the Org-roam database upon saving the file.  Disable
 this if your files are large and updating the database is slow.
 
 
 File: org-roam.info,  Node: The Org-roam Buffer,  Next: Node Properties,  Prev: Customizing Node Caching,  Up: Top
 
 7 The Org-roam Buffer
 *********************
 
 Org-roam provides the Org-roam buffer: an interface to view
 relationships with other notes (backlinks, reference links, unlinked
 references etc.).  There are two main commands to use here:
 
    • ‘org-roam-buffer-toggle’: Launch an Org-roam buffer that tracks the
      node currently at point.  This means that the content of the buffer
      changes as the point is moved, if necessary.
 
    • ‘org-roam-buffer-display-dedicated’: Launch an Org-roam buffer for
      a specific node without visiting its file.  Unlike
      ‘org-roam-buffer-toggle’ you can have multiple such buffers and
      their content won’t be automatically replaced with a new node at
      point.
 
    To bring up a buffer that tracks the current node at point, call ‘M-x
 org-roam-buffer-toggle’.
 
  -- Function: org-roam-buffer-toggle
 
      Toggle display of the ‘org-roam-buffer’.
 
    To bring up a buffer that’s dedicated for a specific node, call ‘M-x
 org-roam-buffer-display-dedicated’.
 
  -- Function: org-roam-buffer-display-dedicated
 
      Launch node dedicated Org-roam buffer without visiting the node
      itself.
 
 * Menu:
 
 * Navigating the Org-roam Buffer::
 * Configuring what is displayed in the buffer::
 * Configuring the Org-roam buffer display::
 * Styling the Org-roam buffer::
 
 
 File: org-roam.info,  Node: Navigating the Org-roam Buffer,  Next: Configuring what is displayed in the buffer,  Up: The Org-roam Buffer
 
 7.1 Navigating the Org-roam Buffer
 ==================================
 
 The Org-roam buffer uses ‘magit-section’, making the typical
 ‘magit-section’ keybindings available.  Here are several of the more
 useful ones:
 
    • ‘M-{N}’: ‘magit-section-show-level-{N}-all’
 
    • ‘n’: ‘magit-section-forward’
 
    • ‘<TAB>’: ‘magit-section-toggle’
 
    • ‘<RET>’: ‘org-roam-buffer-visit-thing’
 
    ‘org-roam-buffer-visit-thing’ is a placeholder command, that is
 replaced by section-specific commands such as ‘org-roam-node-visit’.
 
 
 File: org-roam.info,  Node: Configuring what is displayed in the buffer,  Next: Configuring the Org-roam buffer display,  Prev: Navigating the Org-roam Buffer,  Up: The Org-roam Buffer
 
 7.2 Configuring what is displayed in the buffer
 ===============================================
 
 There are currently 3 provided widget types:
 
    • BacklinksView (preview of) nodes that link to this node
 
    • Reference LinksNodes that reference this node (see *note Refs::)
 
    • Unlinked referencesView nodes that contain text that match the
      nodes title/alias but are not linked
 
    To configure what sections are displayed in the buffer, set
 ~org-roam-mode-sections.
 
      (setq org-roam-mode-sections
            (list #'org-roam-backlinks-section
                  #'org-roam-reflinks-section
                  ;; #'org-roam-unlinked-references-section
                  ))
 
    Note that computing unlinked references may be slow, and has not been
 added in by default.
 
    For each section function, you can pass args along to modify its
 behaviour.  For example, if you want to render unique sources for
 backlinks (and also keep rendering reference links), set
 ‘org-roam-mode-sections’ as follows:
 
      (setq org-roam-mode-sections
            '((org-roam-backlinks-section :unique t)
              org-roam-reflinks-section))
 
 
 File: org-roam.info,  Node: Configuring the Org-roam buffer display,  Next: Styling the Org-roam buffer,  Prev: Configuring what is displayed in the buffer,  Up: The Org-roam Buffer
 
 7.3 Configuring the Org-roam buffer display
 ===========================================
 
 Org-roam does not control how the pop-up buffer is displayed: this is
 left to the user.  The author’s recommended configuration is as follows:
 
      (add-to-list 'display-buffer-alist
                   '("\\*org-roam\\*"
                     (display-buffer-in-direction)
                     (direction . right)
                     (window-width . 0.33)
                     (window-height . fit-window-to-buffer)))
 
    Crucially, the window is a regular window (not a side-window), and
 this allows for predictable navigation:
 
    • ‘RET’ navigates to thing-at-point in the current window, replacing
      the Org-roam buffer.
 
    • ‘C-u RET’ navigates to thing-at-point in the other window.
 
    For users that prefer using a side-window for the org-roam buffer,
 the following example configuration should provide a good starting
 point:
 
      (add-to-list 'display-buffer-alist
                   '("\\*org-roam\\*"
                     (display-buffer-in-side-window)
                     (side . right)
                     (slot . 0)
                     (window-width . 0.33)
                     (window-parameters . ((no-other-window . t)
                                           (no-delete-other-windows . t)))))
 
 
 File: org-roam.info,  Node: Styling the Org-roam buffer,  Prev: Configuring the Org-roam buffer display,  Up: The Org-roam Buffer
 
 7.4 *TODO* Styling the Org-roam buffer
 ======================================
 
 
 File: org-roam.info,  Node: Node Properties,  Next: Citations,  Prev: The Org-roam Buffer,  Up: Top
 
 8 Node Properties
 *****************
 
 * Menu:
 
 * Standard Org properties::
 * Titles and Aliases::
 * Tags::
 * Refs::
 
 
 File: org-roam.info,  Node: Standard Org properties,  Next: Titles and Aliases,  Up: Node Properties
 
 8.1 Standard Org properties
 ===========================
 
 Org-roam caches most of the standard Org properties.  The full list now
 includes:
 
    • outline level
 
    • todo state
 
    • priority
 
    • scheduled
 
    • deadline
 
    • tags
 
 
 File: org-roam.info,  Node: Titles and Aliases,  Next: Tags,  Prev: Standard Org properties,  Up: Node Properties
 
 8.2 Titles and Aliases
 ======================
 
 Each node has a single title.  For file nodes, this is specified with
 the ‘#+title‘ property for the file.  For headline nodes, this is the
 main text.
 
    Nodes can also have multiple aliases.  Aliases allow searching for
 nodes via an alternative name.  For example, one may want to assign a
 well-known acronym (AI) to a node titled “Artificial Intelligence”.
 
    To assign an alias to a node, add the “ROAM_ALIASES” property to the
 node:
 
      * Artificial Intelligence
      :PROPERTIES:
      :ROAM_ALIASES: AI
      :END:
 
    Alternatively, Org-roam provides some functions to add or remove
 aliases.
 
  -- Function: org-roam-alias-add alias
 
      Add ALIAS to the node at point.  When called interactively, prompt
      for the alias to add.
 
  -- Function: org-roam-alias-remove
 
      Remove an alias from the node at point.
 
 
 File: org-roam.info,  Node: Tags,  Next: Refs,  Prev: Titles and Aliases,  Up: Node Properties
 
 8.3 Tags
 ========
 
 Tags for top-level (file) nodes are pulled from the variable
 ‘org-file-tags’, which is set by the ‘#+filetags’ keyword, as well as
 other tags the file may have inherited.  Tags for headline level nodes
 are regular Org tags.
 
    Note that the ‘#+filetags’ keyword results in tags being inherited by
 headers within the file.  This makes it impossible for selective tag
 inheritance: i.e.  either tag inheritance is turned off, or all headline
 nodes will inherit the tags from the file node.  This is a design
 compromise of Org-roam.
 
 
 File: org-roam.info,  Node: Refs,  Prev: Tags,  Up: Node Properties
 
 8.4 Refs
 ========
 
 Refs are unique identifiers for nodes.  These keys allow references to
 the key to show up in the Org-roam buffer.  For example, a node for a
 website may use the URL as the ref, and a node for a paper may use an
 Org-ref citation key.
 
    To add a ref, add to the “ROAM_REFS” property as follows:
 
      * Google
      :PROPERTIES:
      :ROAM_REFS: https://www.google.com/
      :END:
 
    With the above example, if another node links to
 <https://www.google.com/>, it will show up as a “reference backlink”.
 
    These keys also come in useful for when taking website notes, using
 the ‘roam-ref’ protocol (see *note org-roam-protocol::).
 
    You may assign multiple refs to a single node, for example when you
 want multiple papers in a series to share the same note, or an article
 has a citation key and a URL at the same time.
 
    Org-roam also provides some functions to add or remove refs.
 
  -- Function: org-roam-ref-add ref
 
      Add REF to the node at point.  When called interactively, prompt
      for the ref to add.
 
  -- Function: org-roam-ref-remove
 
      Remove a ref from the node at point.
 
 
 File: org-roam.info,  Node: Citations,  Next: Completion,  Prev: Node Properties,  Up: Top
 
 9 Citations
 ***********
 
 Since version 9.5, Org has first-class support for citations.  Org-roam
 supports the caching of both these in-built citations (of form
 ‘[cite:@key]’) and org-ref (https://github.com/jkitchin/org-ref)
 citations (of form cite:key).
 
    Org-roam attempts to load both the ‘org-ref’ and ‘org-cite’ package
 when indexing files, so no further setup from the user is required for
 citation support.
 
 * Menu:
 
 * Using the Cached Information::
 
 
 File: org-roam.info,  Node: Using the Cached Information,  Up: Citations
 
 9.1 Using the Cached Information
 ================================
 
 It is common to use take reference notes for academic papers.  To
 designate the node to be the canonical node for the academic paper, we
 can use its unique citation key:
 
      * Probabilistic Robotics
      :PROPERTIES:
      :ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
      :ROAM_REFS: @thrun2005probabilistic
      :END:
 
    or
 
      * Probabilistic Robotics
      :PROPERTIES:
      :ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
      :ROAM_REFS: [cite:@thrun2005probabilistic]
      :END:
 
    for ‘org-cite’, or:
 
      * Probabilistic Robotics
      :PROPERTIES:
      :ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
      :ROAM_REFS: cite:thrun2005probabilistic
      :END:
 
    for ‘org-ref’.
 
    When another node has a citation for that key, we can see it using
 the ‘Reflinks’ section of the Org-roam buffer.
 
    Extension developers may be interested in retrieving the citations
 within their notes.  This information can be found within the ‘citation’
 table of the Org-roam database.
 
 
 File: org-roam.info,  Node: Completion,  Next: Encryption,  Prev: Citations,  Up: Top
 
 10 Completion
 *************
 
 Completions for Org-roam are provided via ‘completion-at-point’.
 Org-roam currently provides completions in two scenarios:
 
    • When within an Org bracket link
 
    • Anywhere
 
    Completions are installed locally in all Org-roam files.  To trigger
 completions, call ‘M-x completion-at-point’.  If using ‘company-mode’,
 add ‘company-capf’ to ‘company-backends’.
 
    Completions respect ‘completion-styles’: the user is free to choose
 how candidates are matched.  An example of a completion style that has
 grown in popularity is orderless
 (https://github.com/oantolin/orderless).
 
 * Menu:
 
 * Completing within Link Brackets::
 * Completing anywhere::
 
 
 File: org-roam.info,  Node: Completing within Link Brackets,  Next: Completing anywhere,  Up: Completion
 
 10.1 Completing within Link Brackets
 ====================================
 
 Completions within link brackets are provided by
 ‘org-roam-complete-link-at-point’.
 
    The completion candidates are the titles and aliases for all Org-roam
 nodes.  Upon choosing a candidate, a ‘roam:Title’ link will be inserted,
 linking to node of choice.
 
 
 File: org-roam.info,  Node: Completing anywhere,  Prev: Completing within Link Brackets,  Up: Completion
 
 10.2 Completing anywhere
 ========================
 
 The same completions can be triggered anywhere for the symbol at point
 if not within a bracketed link.  This is provided by
 ‘org-roam-complete-everywhere’.  Similarly, the completion candidates
 are the titles and aliases for all Org-roam nodes, and upon choosing a
 candidate a ‘roam:Title’ link will be inserted linking to the node of
 choice.
 
    This is disable by default.  To enable it, set
 ‘org-roam-completion-everywhere’ to ‘t’:
 
      (setq org-roam-completion-everywhere t)
 
  -- Variable: org-roam-completion-everywhere
 
    When non-nil, provide link completion matching outside of Org links.
 
 
 File: org-roam.info,  Node: Encryption,  Next: The Templating System,  Prev: Completion,  Up: Top
 
 11 Encryption
 *************
 
 Emacs has support for creating and editing encrypted gpg files, and
 Org-roam need not provide additional tooling.  To create encrypted
 files, simply add the ‘.gpg’ extension in your Org-roam capture
 templates.  For example:
 
      (setq org-roam-capture-templates '(("d" "default" plain "%?"
           :target (file+head "${slug}.org.gpg"
                              "#+title: ${title}\n")
           :unnarrowed t)))
 
    Note that the Org-roam database stores metadata information in
 plain-text (headline text, for example), so if this information is
 private to you then you should also ensure the database is encrypted.
 
 
 File: org-roam.info,  Node: The Templating System,  Next: Extensions,  Prev: Encryption,  Up: Top
 
 12 The Templating System
 ************************
 
 Org-roam extends the ‘org-capture’ system, providing a smoother
 note-taking experience.  However, these extensions mean Org-roam capture
 templates are incompatible with ‘org-capture’ templates.
 
    Org-roam’s templates are specified by ‘org-roam-capture-templates’.
 Just like ‘org-capture-templates’, ‘org-roam-capture-templates’ can
 contain multiple templates.  If ‘org-roam-capture-templates’ only
 contains one template, there will be no prompt for template selection.
 
 * Menu:
 
 * Template Walkthrough::
 * Org-roam Template Expansion::
 
 
 File: org-roam.info,  Node: Template Walkthrough,  Next: Org-roam Template Expansion,  Up: The Templating System
 
 12.1 Template Walkthrough
 =========================
 
 To demonstrate the additions made to org-capture templates.  Here, we
 explain the default template, reproduced below.  You will find most of
 the elements of the template are similar to ‘org-capture’ templates.
 
      (("d" "default" plain "%?"
        :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                           "#+title: ${title}\n")
        :unnarrowed t))
 
    • The template has short key ‘"d"’.  If you have only one template,
      org-roam automatically chooses this template for you.
 
    • The template is given a description of ‘"default"’.
 
    • ‘plain’ text is inserted.  Other options include Org headings via
      ‘entry’.
 
    • Notice that the ‘target’ that’s usually in Org-capture templates is
      missing here.
 
    • ‘"%?"’ is the template inserted on each call to
      ‘org-roam-capture-’.  This template means don’t insert any content,
      but place the cursor here.
 
    • ‘:target’ is a compulsory specification in the Org-roam capture
      template.  The first element of the list indicates the type of the
      target, the second element indicates the location of the captured
      node, and the rest of the elements indicate prefilled template that
      will be inserted and the position of the point will be adjusted
      for.  The latter behavior varies from type to type of the capture
      target.
 
    • ‘:unnarrowed t’ tells org-capture to show the contents for the
      whole file, rather than narrowing to just the entry.  This is part
      of the Org-capture templates.
 
    See the ‘org-roam-capture-templates’ documentation for more details
 and customization options.
 
 
 File: org-roam.info,  Node: Org-roam Template Expansion,  Prev: Template Walkthrough,  Up: The Templating System
 
 12.2 Org-roam Template Expansion
 ================================
 
 Org-roam’s template definitions also extend org-capture’s template
 syntax, to allow prefilling of strings.  We have seen a glimpse of this
 in *note Template Walkthrough: Template Walkthrough.
 
    Org-roam provides the ‘${foo}’ syntax for substituting variables with
 known strings.  ‘${foo}’’s substitution is performed as follows:
 
    • If ‘foo’ is a function, ‘foo’ is called with the current node as
      its argument.
 
    • Else if ‘org-roam-node-foo’ is a function, ‘foo’ is called with the
      current node as its argument.  The ‘org-roam-node-’ prefix defines
      many of Org-roam’s node accessors such as ‘org-roam-node-title’ and
      ‘org-roam-node-level’.
 
    • Else look up ‘org-roam-capture--info’ for ‘foo’.  This is an
      internal variable that is set before the capture process begins.
 
    • If none of the above applies, read a string using
      ‘completing-read’.
         • Org-roam also provides the ‘${foo=default_val}’ syntax, where
           if a default value is provided, will be the initial value for
           the ‘foo’ key during minibuffer completion.
 
    One can check the list of available keys for nodes by inspecting the
 ‘org-roam-node’ struct.  At the time of writing, it is:
 
      (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
                                   (:copier nil))
        "A heading or top level file with an assigned ID property."
        file file-hash file-atime file-mtime
        id level point todo priority scheduled deadline title properties olp
        tags aliases refs)
 
    This makes ‘${file}’, ‘${file-hash}’ etc.  all valid substitutions.
 
 
 File: org-roam.info,  Node: Extensions,  Next: Performance Optimization,  Prev: The Templating System,  Up: Top
 
 13 Extensions
 *************
 
 * Menu:
 
 * org-roam-protocol::
 * org-roam-graph::
 * org-roam-dailies::
 * org-roam-export::
 
 
 File: org-roam.info,  Node: org-roam-protocol,  Next: org-roam-graph,  Up: Extensions
 
 13.1 org-roam-protocol
 ======================
 
 Org-roam provides extensions for capturing content from external
 applications such as the browser, via ‘org-protocol’.  Org-roam extends
 ‘org-protocol’ with 2 protocols: the ‘roam-node’ and ‘roam-ref’
 protocols.
 
 * Menu:
 
 * Installation: Installation (1).
 * The roam-node protocol::
 * The roam-ref protocol::
 
 
 File: org-roam.info,  Node: Installation (1),  Next: The roam-node protocol,  Up: org-roam-protocol
 
 13.1.1 Installation
 -------------------
 
 To enable Org-roam’s protocol extensions, simply add the following to
 your init file:
 
      (require 'org-roam-protocol)
 
    We also need to set up ‘org-protocol’: the instructions for setting
 up ‘org-protocol’ are reproduced here.
 
    On a high-level, external calls are passed to Emacs via
 ‘emacsclient’.  ‘org-protocol’ intercepts these and runs custom actions
 based on the protocols registered.  Hence, to use ‘org-protocol’, once
 must:
 
    • launch the ‘emacsclient’ process
 
    • Register ‘org-protocol://’ as a valid scheme-handler
 
    The instructions for the latter for each operating system is detailed
 below.
 
 * Menu:
 
 * Linux::
 * Mac OS::
 * Windows::
 
 
 File: org-roam.info,  Node: Linux,  Next: Mac OS,  Up: Installation (1)
 
 Linux
 .....
 
 For Linux users, create a desktop application in
 ‘~/.local/share/applications/org-protocol.desktop’:
 
      [Desktop Entry]
      Name=Org-Protocol
      Exec=emacsclient %u
      Icon=emacs-icon
      Type=Application
      Terminal=false
      MimeType=x-scheme-handler/org-protocol
 
    Associate ‘org-protocol://’ links with the desktop application by
 running in your shell:
 
      xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
 
    To disable the “confirm” prompt in Chrome, you can also make Chrome
 show a checkbox to tick, so that the ‘Org-Protocol Client’ app will be
 used without confirmation.  To do this, run in a shell:
 
      sudo mkdir -p /etc/opt/chrome/policies/managed/
      sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
      {
        "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
      }
      EOF
      sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
 
    and then restart Chrome (for example, by navigating to
 <chrome://restart>) to make the new policy take effect.
 
    See here (https://www.chromium.org/administrators/linux-quick-start)
 for more info on the ‘/etc/opt/chrome/policies/managed’ directory and
 here
 (https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox)
 for information on the ‘ExternalProtocolDialogShowAlwaysOpenCheckbox’
 policy.
 
 
 File: org-roam.info,  Node: Mac OS,  Next: Windows,  Prev: Linux,  Up: Installation (1)
 
 Mac OS
 ......
 
 For Mac OS, we need to create our own application.
 
    • Launch Script Editor
 
    • Use the following script, paying attention to the path to
      ‘emacsclient’:
 
      on open location this_URL
          set EC to "/usr/local/bin/emacsclient --no-wait "
          set filePath to quoted form of this_URL
          do shell script EC & filePath
          tell application "Emacs" to activate
      end open location
 
    • Save the script in ‘/Applications/OrgProtocolClient.app’, changing
      the script type to “Application”, rather than “Script”.
 
    • Edit ‘/Applications/OrgProtocolClient.app/Contents/Info.plist’,
      adding the following before the last ‘</dict>’ tag:
 
      <key>CFBundleURLTypes</key>
      <array>
        <dict>
          <key>CFBundleURLName</key>
          <string>org-protocol handler</string>
          <key>CFBundleURLSchemes</key>
          <array>
            <string>org-protocol</string>
          </array>
        </dict>
      </array>
 
    • Save the file, and run the ‘OrgProtocolClient.app’ to register the
      protocol.
 
    To disable the “confirm” prompt in Chrome, you can also make Chrome
 show a checkbox to tick, so that the ‘OrgProtocol’ app will be used
 without confirmation.  To do this, run in a shell:
 
      defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
 
    If you’re using Emacs Mac Port
 (https://github.com/railwaycat/homebrew-emacsmacport), it registered its
 ‘Emacs.app‘ as the default handler for the URL scheme ‘org-protocol‘.
 To make ‘OrgProtocol.app’ the default handler instead, run:
 
      defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
      '{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
 
    Then restart your computer.
 
    • Testing org-protocol
 
      To test that you have the handler setup and registered properly
      from the command line you can run:
 
           open org-protocol://roam-ref\?template=r\&ref=test\&title=this
 
      If you get an error similar too this or the wrong handler is run:
 
           No application knows how to open URL
           org-protocol://roam-ref?template=r&ref=test&title=this (Error
           Domain=NSOSStatusErrorDomain Code=-10814
           “kLSApplicationNotFoundErr: E.g.  no application claims the
           file” UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
 
      You may need to manually register your handler, like this:
 
           /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
 
      Here is a link to the lsregister command that is really useful:
      <https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/>
 
 
 File: org-roam.info,  Node: Windows,  Prev: Mac OS,  Up: Installation (1)
 
 Windows
 .......
 
 For Windows, create a temporary ‘org-protocol.reg’ file:
 
      REGEDIT4
 
      [HKEY_CLASSES_ROOT\org-protocol]
      @="URL:Org Protocol"
      "URL Protocol"=""
      [HKEY_CLASSES_ROOT\org-protocol\shell]
      [HKEY_CLASSES_ROOT\org-protocol\shell\open]
      [HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
      @="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""
 
    The above will forward the protocol to WSL.  If you run Emacs
 natively on Windows, replace the last line with:
 
      @="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
 
    After executing the .reg file, the protocol is registered and you can
 delete the file.
 
 
 File: org-roam.info,  Node: The roam-node protocol,  Next: The roam-ref protocol,  Prev: Installation (1),  Up: org-roam-protocol
 
 13.1.2 The roam-node protocol
 -----------------------------
 
 The roam-node protocol opens the node with ID specified by the ‘node’
 key (e.g.  ‘org-protocol://roam-node?node=node-id’).  ‘org-roam-graph’
 uses this to make the graph navigable.
 
 
 File: org-roam.info,  Node: The roam-ref protocol,  Prev: The roam-node protocol,  Up: org-roam-protocol
 
 13.1.3 The roam-ref protocol
 ----------------------------
 
 This protocol finds or creates a new note with a given ‘ROAM_REFS’:
 
  
    To use this, create the following bookmarklet
 (https://en.wikipedia.org/wiki/Bookmarklet) in your browser:
 
      javascript:location.href =
          'org-protocol://roam-ref?template=r&ref='
          + encodeURIComponent(location.href)
          + '&title='
          + encodeURIComponent(document.title)
          + '&body='
          + encodeURIComponent(window.getSelection())
 
    or as a keybinding in ‘qutebrowser’ in , using the ‘config.py’ file
 (see Configuring qutebrowser
 (https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc)):
 
      config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
 
    where ‘template’ is the template key for a template in
 ‘org-roam-capture-ref-templates’ (see *note The Templating System::).
 
 
 File: org-roam.info,  Node: org-roam-graph,  Next: org-roam-dailies,  Prev: org-roam-protocol,  Up: Extensions
 
 13.2 org-roam-graph
 ===================
 
 Org-roam provides basic graphing capabilities to explore
 interconnections between notes, in ‘org-roam-graph’.  This is done by
 performing SQL queries and generating images using Graphviz
 (https://graphviz.org/).  The graph can also be navigated: see *note
 org-roam-protocol::.
 
    The entry point to graph creation is ‘org-roam-graph’.
 
  -- Function: org-roam-graph & optional arg node
 
    Build and display a graph for NODE.  ARG may be any of the following
 values:
 
    • ‘nil’ show the full graph.
 
    • ‘integer’ an integer argument ‘N’ will show the graph for the
      connected components to node up to ‘N’ steps away.
  -- User Option: org-roam-graph-executable
 
      Path to the graphing executable (in this case, Graphviz).  Set this
      if Org-roam is unable to find the Graphviz executable on your
      system.
 
      You may also choose to use ‘neato’ in place of ‘dot’, which
      generates a more compact graph layout.
 
  -- User Option: org-roam-graph-viewer
 
      Org-roam defaults to using Firefox (located on PATH) to view the
      SVG, but you may choose to set it to:
 
         • A string, which is a path to the program used
 
         • a function accepting a single argument: the graph file path.
 
      ‘nil’ uses ‘view-file’ to view the graph.
 
      If you are using WSL2 and would like to open the graph in Windows,
      you can use the second option to set the browser and network file
      path:
 
           (setq org-roam-graph-viewer
               (lambda (file)
                 (let ((org-roam-graph-viewer "/mnt/c/Program Files/Mozilla Firefox/firefox.exe"))
                   (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))
 
 * Menu:
 
 * Graph Options::
 
 
 File: org-roam.info,  Node: Graph Options,  Up: org-roam-graph
 
 13.2.1 Graph Options
 --------------------
 
 Graphviz provides many options for customizing the graph output, and
 Org-roam supports some of them.  See
 <https://graphviz.gitlab.io/_pages/doc/info/attrs.html> for customizable
 options.
 
  -- User Option: org-roam-graph-filetype
 
      The file type to generate for graphs.  This defaults to ‘"svg"’.
 
  -- User Option: org-roam-graph-extra-config
 
      Extra options passed to graphviz for the digraph (The “G”
      attributes).  Example: ‘'~(("rankdir" . "LR"))’
 
  -- User Option: org-roam-graph-node-extra-config
 
      An alist of options to style the nodes.  The car of the alist node
      type such as ‘"id"’, or ‘"http"’.  The cdr of the list is another
      alist of Graphviz node options (the “N” attributes).
 
  -- User Option: org-roam-graph-edge-extra-config
 
      Extra options for edges in the graphviz output (The “E”
      attributes).  Example: ‘'(("dir" . "back"))’
 
 
 File: org-roam.info,  Node: org-roam-dailies,  Next: org-roam-export,  Prev: org-roam-graph,  Up: Extensions
 
 13.3 org-roam-dailies
 =====================
 
 Org-roam provides journaling capabilities akin to Org-journal with
 ‘org-roam-dailies’.
 
 * Menu:
 
 * Configuration::
 * Usage::
 
 
 File: org-roam.info,  Node: Configuration,  Next: Usage,  Up: org-roam-dailies
 
 13.3.1 Configuration
 --------------------
 
 For ‘org-roam-dailies’ to work, you need to define two variables:
 
  -- Variable: ‘org-roam-dailies-directory’
 
      Path to daily-notes.  This path is relative to
      ‘org-roam-directory’.
 
  -- Variable: ‘org-roam-dailies-capture-templates’
 
      Capture templates for daily-notes in Org-roam.
 
    Here is a sane default configuration:
 
      (setq org-roam-dailies-directory "daily/")
 
      (setq org-roam-dailies-capture-templates
            '(("d" "default" entry
               "* %?"
               :target (file+head "%<%Y-%m-%d>.org"
                                  "#+title: %<%Y-%m-%d>\n"))))
 
    See *note The Templating System:: for creating new templates.
 
 
 File: org-roam.info,  Node: Usage,  Prev: Configuration,  Up: org-roam-dailies
 
 13.3.2 Usage
 ------------
 
 ‘org-roam-dailies’ provides these interactive functions:
 
  -- Function: ‘org-roam-dailies-capture-today’ &optional goto
 
      Create an entry in the daily note for today.
 
      When ‘goto’ is non-nil, go to the note without creating an entry.
 
  -- Function: ‘org-roam-dailies-goto-today’
 
      Find the daily note for today, creating it if necessary.
 
    There are variants of those commands for ‘-yesterday’ and
 ‘-tomorrow’:
 
  -- Function: ‘org-roam-dailies-capture-yesterday’ n &optional goto
 
      Create an entry in the daily note for yesterday.
 
      With numeric argument ‘n’, use the daily note ‘n’ days in the past.
 
  -- Function: ‘org-roam-dailies-goto-yesterday’
 
      With numeric argument N, use the daily-note N days in the future.
 
    There are also commands which allow you to use Emacs’s ‘calendar’ to
 find the date
 
  -- Function: ‘org-roam-dailies-capture-date’
 
      Create an entry in the daily note for a date using the calendar.
 
      Prefer past dates, unless ‘prefer-future’ is non-nil.
 
      With a ’C-u’ prefix or when ‘goto’ is non-nil, go the note without
      creating an entry.
 
  -- Function: ‘org-roam-dailies-goto-date’
 
      Find the daily note for a date using the calendar, creating it if
      necessary.
 
      Prefer past dates, unless ‘prefer-future’ is non-nil.
 
  -- Function: ‘org-roam-dailies-find-directory’
 
      Find and open ‘org-roam-dailies-directory’.
 
  -- Function: ‘org-roam-dailies-goto-previous-note’
 
      When in an daily-note, find the previous one.
 
  -- Function: ‘org-roam-dailies-goto-next-note’
 
      When in an daily-note, find the next one.
 
 
 File: org-roam.info,  Node: org-roam-export,  Prev: org-roam-dailies,  Up: Extensions
 
 13.4 org-roam-export
 ====================
 
 Because Org-roam files are plain org files, they can be exported easily
 using ‘org-export’ to a variety of formats, including ‘html’ and ‘pdf’.
 However, Org-roam relies heavily on ID links, which Org’s html export
 has poor support of.  To fix this, Org-roam provides a bunch of
 overrides to better support export.  To use them, simply run:
 
      (require 'org-roam-export)
 
 
 File: org-roam.info,  Node: Performance Optimization,  Next: The Org-mode Ecosystem,  Prev: Extensions,  Up: Top
 
 14 Performance Optimization
 ***************************
 
 * Menu:
 
 * Garbage Collection::
 
 
 File: org-roam.info,  Node: Garbage Collection,  Up: Performance Optimization
 
 14.1 Garbage Collection
 =======================
 
 During the cache-build process, Org-roam generates a lot of in-memory
 data-structures (such as the Org file’s AST), which are discarded after
 use.  These structures are garbage collected at regular intervals (see
 *note info:elisp#Garbage Collection: (elisp)Garbage Collection.).
 
    Org-roam provides the option ‘org-roam-db-gc-threshold’ to
 temporarily change the threshold value for GC to be triggered during
 these memory-intensive operations.  To reduce the number of garbage
 collection processes, one may set ‘org-roam-db-gc-threshold’ to a high
 value (such as ‘most-positive-fixnum’):
 
      (setq org-roam-db-gc-threshold most-positive-fixnum)
 
 
 File: org-roam.info,  Node: The Org-mode Ecosystem,  Next: FAQ,  Prev: Performance Optimization,  Up: Top
 
 15 The Org-mode Ecosystem
 *************************
 
 Because Org-roam is built on top of Org-mode, it benefits from the vast
 number of packages already available.
 
 * Menu:
 
 * Browsing History with winner-mode::
 * Versioning Notes::
 * Full-text search with Deft::
 * Org-journal::
 * Org-download::
 * mathpix.el: mathpixel.
 * Org-noter / Interleave::
 * Bibliography::
 * Spaced Repetition::
 
 
 File: org-roam.info,  Node: Browsing History with winner-mode,  Next: Versioning Notes,  Up: The Org-mode Ecosystem
 
 15.1 Browsing History with winner-mode
 ======================================
 
 ‘winner-mode’ is a global minor mode that allows one to undo and redo
 changes in the window configuration.  It is included with GNU Emacs
 since version 20.
 
    ‘winner-mode’ can be used as a simple version of browser history for
 Org-roam.  Each click through org-roam links (from both Org files and
 the backlinks buffer) causes changes in window configuration, which can
 be undone and redone using ‘winner-mode’.  To use ‘winner-mode’, simply
 enable it, and bind the appropriate interactive functions:
 
      (winner-mode +1)
      (define-key winner-mode-map (kbd "<M-left>") #'winner-undo)
      (define-key winner-mode-map (kbd "<M-right>") #'winner-redo)
 
 
 
 File: org-roam.info,  Node: Versioning Notes,  Next: Full-text search with Deft,  Prev: Browsing History with winner-mode,  Up: The Org-mode Ecosystem
 
 15.2 Versioning Notes
 =====================
 
 Since Org-roam notes are just plain text, it is trivial to track changes
 in your notes database using version control systems such as Git
 (https://git-scm.com/).  Simply initialize ‘org-roam-directory’ as a Git
 repository, and commit your files at regular or appropriate intervals.
 Magit (https://magit.vc/) is a great interface to Git within Emacs.
 
    In addition, it may be useful to observe how a particular note has
 evolved, by looking at the file history.  Git-timemachine
 (https://gitlab.com/pidu/git-timemachine) allows you to visit historic
 versions of a tracked Org-roam note.
 
 
 File: org-roam.info,  Node: Full-text search with Deft,  Next: Org-journal,  Prev: Versioning Notes,  Up: The Org-mode Ecosystem
 
 15.3 Full-text search with Deft
 ===============================
 
 Deft (https://jblevins.org/projects/deft/) provides a nice interface for
 browsing and filtering org-roam notes.
 
      (use-package deft
        :after org
        :bind
        ("C-c n d" . deft)
        :custom
        (deft-recursive t)
        (deft-use-filter-string-for-filename t)
        (deft-default-extension "org")
        (deft-directory org-roam-directory))
 
    The Deft interface can slow down quickly when the number of files get
 huge.  Notdeft (https://github.com/hasu/notdeft) is a fork of Deft that
 uses an external search engine and indexer.
 
 
 File: org-roam.info,  Node: Org-journal,  Next: Org-download,  Prev: Full-text search with Deft,  Up: The Org-mode Ecosystem
 
 15.4 Org-journal
 ================
 
 Org-journal (https://github.com/bastibe/org-journal) provides journaling
 capabilities to Org-mode.  A lot of its functionalities have been
 incorporated into Org-roam under the name *note ‘org-roam-dailies’:
 org-roam-dailies.  It remains a good tool if you want to isolate your
 verbose journal entries from the ideas you would write on a scratchpad.
 
      (use-package org-journal
        :bind
        ("C-c n j" . org-journal-new-entry)
        :custom
        (org-journal-date-prefix "#+title: ")
        (org-journal-file-format "%Y-%m-%d.org")
        (org-journal-dir "/path/to/journal/files/")
        (org-journal-date-format "%A, %d %B %Y"))
 
 
 File: org-roam.info,  Node: Org-download,  Next: mathpixel,  Prev: Org-journal,  Up: The Org-mode Ecosystem
 
 15.5 Org-download
 =================
 
 Org-download (https://github.com/abo-abo/org-download) lets you
 screenshot and yank images from the web into your notes:
 
  
 Figure: org-download
 
      (use-package org-download
        :after org
        :bind
        (:map org-mode-map
              (("s-Y" . org-download-screenshot)
               ("s-y" . org-download-yank))))
 
 
 File: org-roam.info,  Node: mathpixel,  Next: Org-noter / Interleave,  Prev: Org-download,  Up: The Org-mode Ecosystem
 
 15.6 mathpix.el
 ===============
 
 mathpix.el (https://github.com/jethrokuan/mathpix.el) uses Mathpix’s
 (https://mathpix.com/) API to convert clips into latex equations:
 
  
 Figure: mathpix
 
      (use-package mathpix.el
        :straight (:host github :repo "jethrokuan/mathpix.el")
        :custom ((mathpix-app-id "app-id")
                 (mathpix-app-key "app-key"))
        :bind
        ("C-x m" . mathpix-screenshot))
 
 
 File: org-roam.info,  Node: Org-noter / Interleave,  Next: Bibliography,  Prev: mathpixel,  Up: The Org-mode Ecosystem
 
 15.7 Org-noter / Interleave
 ===========================
 
 Org-noter (https://github.com/weirdNox/org-noter) and Interleave
 (https://github.com/rudolfochrist/interleave) are both projects that
 allow synchronised annotation of documents (PDF, EPUB etc.)  within
 Org-mode.
 
 
 File: org-roam.info,  Node: Bibliography,  Next: Spaced Repetition,  Prev: Org-noter / Interleave,  Up: The Org-mode Ecosystem
 
 15.8 Bibliography
 =================
 
 Org 9.5 added native citation and bibliography functionality, called
 “org-cite”, which org-roam supports.
 
    org-roam-bibtex (https://github.com/org-roam/org-roam-bibtex) offers
 tight integration between org-ref (https://github.com/jkitchin/org-ref),
 helm-bibtex (https://github.com/tmalsburg/helm-bibtex) and ‘org-roam’.
 This helps you manage your bibliographic notes under ‘org-roam’.
 
    For example, though helm-bibtex provides the ability to visit notes
 for bibliographic entries, org-roam-bibtex extends it with the ability
 to visit the file with the right ‘ROAM_REFS’.
 
 
 File: org-roam.info,  Node: Spaced Repetition,  Prev: Bibliography,  Up: The Org-mode Ecosystem
 
 15.9 Spaced Repetition
 ======================
 
 Org-fc (https://www.leonrische.me/fc/index.html) is a spaced repetition
 system that scales well with a large number of files.  Other
 alternatives include org-drill
 (https://orgmode.org/worg/org-contrib/org-drill.html), and pamparam
 (https://github.com/abo-abo/pamparam).
 
    To use Anki for spaced repetition, anki-editor
 (https://github.com/louietan/anki-editor) allows you to write your cards
 in Org-mode, and sync your cards to Anki via anki-connect
 (https://github.com/FooSoft/anki-connect#installation).
 
 
 File: org-roam.info,  Node: FAQ,  Next: Developer's Guide to Org-roam,  Prev: The Org-mode Ecosystem,  Up: Top
 
 16 FAQ
 ******
 
 * Menu:
 
 * How do I have more than one Org-roam directory?::
 * How do I create a note whose title already matches one of the candidates?::
 * How can I stop Org-roam from creating IDs everywhere?::
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
 * I’m seeing this “Selecting deleted buffer” error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?.
 
 
 File: org-roam.info,  Node: How do I have more than one Org-roam directory?,  Next: How do I create a note whose title already matches one of the candidates?,  Up: FAQ
 
 16.1 How do I have more than one Org-roam directory?
 ====================================================
 
 Emacs supports directory-local variables, allowing the value of
 ‘org-roam-directory’ to be different in different directories.  It does
 this by checking for a file named ‘.dir-locals.el’.
 
    To add support for multiple directories, override the
 ‘org-roam-directory’ variable using directory-local variables.  This is
 what ‘.dir-locals.el’ may contain:
 
      ((nil . ((org-roam-directory . "/path/to/alt/org-roam-dir")
               (org-roam-db-location . "/path/to/alt/org-roam-dir/org-roam.db"))))
 
    Note ‘org-roam-directory’ and ‘org-roam-db-location’ should be an
 absolute path, not relative.
 
    Alternatively, use ‘eval’ if you wish to call functions:
 
      ((nil . ((eval . (setq-local
                        org-roam-directory (expand-file-name (locate-dominating-file
                                                              default-directory ".dir-locals.el"))))
               (eval . (setq-local
                        org-roam-db-location (expand-file-name "org-roam.db"
                                                               org-roam-directory))))))
 
    All files within that directory will be treated as their own separate
 set of Org-roam files.  Remember to run ‘org-roam-db-sync’ from a file
 within that directory, at least once.
 
 
 File: org-roam.info,  Node: How do I create a note whose title already matches one of the candidates?,  Next: How can I stop Org-roam from creating IDs everywhere?,  Prev: How do I have more than one Org-roam directory?,  Up: FAQ
 
 16.2 How do I create a note whose title already matches one of the candidates?
 ==============================================================================
 
 This situation arises when, for example, one would like to create a note
 titled “bar” when “barricade” already exists.
 
    The solution is dependent on the mini-buffer completion framework in
 use.  Here are the solutions:
 
    • Ivycall ‘ivy-immediate-done’, typically bound to ‘C-M-j’.
      Alternatively, set ‘ivy-use-selectable-prompt’ to ‘t’, so that
      “bar” is now selectable.
 
    • HelmOrg-roam should provide a selectable “[?]  bar” candidate at
      the top of the candidate list.
 
 
 File: org-roam.info,  Node: How can I stop Org-roam from creating IDs everywhere?,  Next: How do I migrate from Roam Research?,  Prev: How do I create a note whose title already matches one of the candidates?,  Up: FAQ
 
 16.3 How can I stop Org-roam from creating IDs everywhere?
 ==========================================================
 
 Other than the interactive commands that Org-roam provides, Org-roam
 does not create IDs everywhere.  If you are noticing that IDs are being
 created even when you don’t want them to be (e.g.  when tangling an Org
 file), check the value you have set for ‘org-id-link-to-org-use-id’:
 setting it to ‘'create-if-interactive’ is a popular option.
 
 
 File: org-roam.info,  Node: How do I migrate from Roam Research?,  Next: How to migrate from Org-roam v1?,  Prev: How can I stop Org-roam from creating IDs everywhere?,  Up: FAQ
 
 16.4 How do I migrate from Roam Research?
 =========================================
 
 Fabio has produced a command-line tool that converts markdown files
 exported from Roam Research into Org-roam compatible markdown.  More
 instructions are provided in the repository
 (https://github.com/fabioberger/roam-migration).
 
 
 File: org-roam.info,  Node: How to migrate from Org-roam v1?,  Next: How do I publish my notes with an Internet-friendly graph?,  Prev: How do I migrate from Roam Research?,  Up: FAQ
 
 16.5 How to migrate from Org-roam v1?
 =====================================
 
 Those coming from Org-roam v1 will do well treating v2 as entirely new
 software.  V2 has a smaller core and fewer moving parts, while retaining
 the bulk of its functionality.  It is recommended to read the
 documentation above about nodes.
 
    It is still desirable to migrate notes collected in v1 to v2.  To
 migrate your v1 notes to v2, use ‘M-x org-roam-migrate-wizard’.  This
 blog post
 (https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html)
 provides a good overview of what’s new in v2 and how to migrate.
 
    Essentially, to migrate notes from v1 to v2, one must:
 
    • Add IDs to all existing notes.  These are located in top-level
      property drawers (Although note that in v2, not all files need to
      have IDs).
 
    • Update the Org-roam database to conform to the new schema.
 
    • Replace ‘#+ROAM_KEY’ into the ‘ROAM_REFS’ property
 
    • Replace ‘#+ROAM_ALIAS’ into the ‘ROAM_ALIASES’ property
 
    • Move ‘#+ROAM_TAGS’ into the ‘#+FILETAGS’ property for file-level
      nodes, and the ‘ROAM_TAGS’ property for headline nodes
 
    • Replace existing file links with ID links.
 
 
 File: org-roam.info,  Node: How do I publish my notes with an Internet-friendly graph?,  Next: I'm seeing this ``Selecting deleted buffer'' error What do I do?,  Prev: How to migrate from Org-roam v1?,  Up: FAQ
 
 16.6 How do I publish my notes with an Internet-friendly graph?
 ===============================================================
 
 The default graph builder creates a graph with an org-protocol
 (https://orgmode.org/worg/org-contrib/org-protocol.html) handler which
 is convenient when you’re working locally but inconvenient when you want
 to publish your notes for remote access.  Likewise, it defaults to
 displaying the graph in Emacs which has the exact same caveats.  This
 problem is solvable in the following way using org-mode’s native
 publishing (https://orgmode.org/manual/Publishing.html) capability:
 
    • configure org-mode to publish your org-roam notes as a project.
 
    • create a function that overrides the default org-protocol link
      creation function(‘org-roam-default-link-builder’).
 
    • create a hook that’s called at the end of graph creation to copy
      the generated graph to the appropriate place.
 
    The example code below is used to publish to a local directory where
 a separate shell script copies the files to the remote site.
 
 * Menu:
 
 * Configure org-mode for publishing::
 * Overriding the default link creation function::
 * Copying the generated file to the export directory::
 
 
 File: org-roam.info,  Node: Configure org-mode for publishing,  Next: Overriding the default link creation function,  Up: How do I publish my notes with an Internet-friendly graph?
 
 16.6.1 Configure org-mode for publishing
 ----------------------------------------
 
 This has two steps:
    • Setting of a _roam_ project that publishes your notes.
 
    • Configuring the _sitemap.html_ generation.
 
    • Setting up ‘org-publish’ to generate the graph.
 
    This will require code like the following:
      (defun roam-sitemap (title list)
        (concat "#+OPTIONS: ^:nil author:nil html-postamble:nil\n"
                "#+SETUPFILE: ./simple_inline.theme\n"
                "#+TITLE: " title "\n\n"
                (org-list-to-org list) "\nfile:sitemap.svg"))
 
      (setq my-publish-time 0)   ; see the next section for context
      (defun roam-publication-wrapper (plist filename pubdir)
        (org-roam-graph)
        (org-html-publish-to-html plist filename pubdir)
        (setq my-publish-time (cadr (current-time))))
 
      (setq org-publish-project-alist
        '(("roam"
           :base-directory "~/roam"
           :auto-sitemap t
           :sitemap-function roam-sitemap
           :sitemap-title "Roam notes"
           :publishing-function roam-publication-wrapper
           :publishing-directory "~/roam-export"
           :section-number nil
           :table-of-contents nil
           :style "<link rel=\"stylesheet\" href=\"../other/mystyle.cs\" type=\"text/css\">")))
 
 
 File: org-roam.info,  Node: Overriding the default link creation function,  Next: Copying the generated file to the export directory,  Prev: Configure org-mode for publishing,  Up: How do I publish my notes with an Internet-friendly graph?
 
 16.6.2 Overriding the default link creation function
 ----------------------------------------------------
 
 The code below will generate a link to the generated html file instead
 of the default org-protocol link.
      (defun org-roam-custom-link-builder (node)
        (let ((file (org-roam-node-file node)))
          (concat (file-name-base file) ".html")))
 
      (setq org-roam-graph-link-builder 'org-roam-custom-link-builder)
 
 
 File: org-roam.info,  Node: Copying the generated file to the export directory,  Prev: Overriding the default link creation function,  Up: How do I publish my notes with an Internet-friendly graph?
 
 16.6.3 Copying the generated file to the export directory
 ---------------------------------------------------------
 
 The default behavior of ‘org-roam-graph’ is to generate the graph and
 display it in Emacs.  There is an ‘org-roam-graph-generation-hook’
 available that provides access to the file names so they can be copied
 to the publishing directory.  Example code follows:
 
      (add-hook 'org-roam-graph-generation-hook
                (lambda (dot svg) (if (< (- (cadr (current-time)) my-publish-time) 5)
                                      (progn (copy-file svg "~/roam-export/sitemap.svg" 't)
                                             (kill-buffer (file-name-nondirectory svg))
                                             (setq my-publish-time 0)))))
 
 
 File: org-roam.info,  Node: I'm seeing this ``Selecting deleted buffer'' error What do I do?,  Prev: How do I publish my notes with an Internet-friendly graph?,  Up: FAQ
 
 16.7 I’m seeing this “Selecting deleted buffer” error. What do I do?
 ====================================================================
 
 The “selecting deleted buffer” error usually occurs when you don’t have
 a working ‘emacsql-sqlite’ executable.  Org-roam relies on this
 executable to function properly, and doesn’t catch this error.  This
 issue is most commonly seen on Windows setups.  You can browse through
 the various GitHub issues posted about this here
 (https://github.com/org-roam/org-roam/issues?q=is%3Aissue+selecting+deleted).
 
    To fix this, you can try the following:
 
    • If on Windows, try replacing your system binary with this one
      (https://github.com/nobiot/emacsql-sqlite.exe) that has been proven
      to work
 
    • Use the ‘emacsql-sqlite3’ option rather than compiling your own
      emacsql binary (see *note How to cache::).
 
 
 File: org-roam.info,  Node: Developer's Guide to Org-roam,  Next: Appendix,  Prev: FAQ,  Up: Top
 
 17 Developer’s Guide to Org-roam
 ********************************
 
 * Menu:
 
 * Org-roam's Design Principle::
 * Building Extensions and Advanced Customization of Org-roam::
 
 
 File: org-roam.info,  Node: Org-roam's Design Principle,  Next: Building Extensions and Advanced Customization of Org-roam,  Up: Developer's Guide to Org-roam
 
 17.1 Org-roam’s Design Principle
 ================================
 
 Org-roam is primarily motivated by the need for a dual representation.
 We (humans) love operating in a plain-text environment.  The syntax
 rules of Org-mode are simple and fit snugly within our brain.  This also
 allows us to use the tools and packages we love to explore and edit our
 notes.  Org-mode is simply the most powerful plain-text format
 available, with support for images, LaTeX, TODO planning and much more.
 
    But this plain-text format is simply ill-suited for exploration of
 these notes: plain-text is simply not amenable for answering
 large-scale, complex queries (e.g.  how many tasks do I have that are
 due by next week?).  Interfaces such as Org-agenda slow to a crawl when
 the number of files becomes unwieldy, which can quickly become the case.
 
    At its core, Org-roam provides a database abstraction layer,
 providing a dual representation of what’s already available in
 plain-text.  This allows us (humans) to continue working with
 plain-text, while programs can utilize the database layer to perform
 complex queries.  These capabilities include, but are not limited to:
 
    • link graph traversal and visualization
 
    • Instantaneous SQL-like queries on headlines
         • What are my TODOs, scheduled for X, or due by Y?
 
    • Accessing the properties of a node, such as its tags, refs, TODO
      state or priority
 
    All of these functionality is powered by this database abstraction
 layer.  Hence, at its core Org-roam’s primary goal is to provide a
 resilient dual representation that is cheap to maintain, easy to
 understand, and is as up-to-date as it possibly can.  Org-roam also then
 exposes an API to this database abstraction layer for users who would
 like to perform programmatic queries on their Org files.
 
 
 File: org-roam.info,  Node: Building Extensions and Advanced Customization of Org-roam,  Prev: Org-roam's Design Principle,  Up: Developer's Guide to Org-roam
 
 17.2 Building Extensions and Advanced Customization of Org-roam
 ===============================================================
 
 Because Org-roam’s core functionality is small, it is possible and
 sometimes desirable to build extensions on top of it.  These extensions
 may one or more of the following functionalities:
 
    • Access to Org-roam’s database
 
    • Usage/modification of Org-roam’s interactive commands
 
    Org-roam provides no guarantees that extensions will continue to
 function as Org-roam evolves, but by following these simple rules,
 extensions can be made robust to local changes in Org-roam.
 
    • Extensions should not modify the database schema.  Any extension
      that requires the caching of additional data should make a request
      upstream to Org-roam.
 
    • Extensions requiring access to the database should explicitly state
      support for the database version (‘org-roam-db-version’), and only
      conditionally load when support is available.
 
 * Menu:
 
 * Accessing the Database::
 * Accessing and Modifying Nodes::
 * Extending the Capture System::
 
 
 File: org-roam.info,  Node: Accessing the Database,  Next: Accessing and Modifying Nodes,  Up: Building Extensions and Advanced Customization of Org-roam
 
 17.2.1 Accessing the Database
 -----------------------------
 
 Access to the database is provided singularly by ‘org-roam-db-query’,
 for example:
 
      (org-roam-db-query [:select * :from nodes])
 
    One can refer to the database schema by looking up
 ‘org-roam-db--table-schemata’.  There are multiple helper functions
 within Org-roam that call ‘org-roam-db-query’, these are subject to
 change.  To ensure that extensions/customizations are robust to change,
 extensions should only use ‘org-roam-db-query’, and perhaps replicate
 the SQL query if necessary.
 
 
 File: org-roam.info,  Node: Accessing and Modifying Nodes,  Next: Extending the Capture System,  Prev: Accessing the Database,  Up: Building Extensions and Advanced Customization of Org-roam
 
 17.2.2 Accessing and Modifying Nodes
 ------------------------------------
 
 The node interface is cleanly defined using ‘cl-defstruct’.  The primary
 method to access nodes is ‘org-roam-node-at-point’ and
 ‘org-roam-node-read’:
 
  -- Function: org-roam-node-at-point &optional assert
 
      Return the node at point.  If ASSERT, throw an error if there is no
      node at point.
 
  -- Function: org-roam-node-read &optional initial-input filter-fn
           sort-fn
      require-match
 
      Read and return an ‘org-roam-node’.  INITIAL-INPUT is the initial
      minibuffer prompt value.  FILTER-FN is a function to filter out
      nodes: it takes a single argument (an ‘org-roam-node’), and when
      nil is returned the node will be filtered out.  SORT-FN is a
      function to sort nodes.  See
      ‘org-roam-node-read-sort-by-file-mtime’ for an example sort
      function.  If REQUIRE-MATCH, the minibuffer prompt will require a
      match.
 
    Once you obtain the node, you can use the accessors for the node,
 e.g.  ‘org-roam-node-id’ or ‘org-roam-node-todo’.
 
    It is possible to define (or override existing) properties on nodes.
 This is simply done using a ‘cl-defmethod’ on the ‘org-roam-node’
 struct:
 
      (cl-defmethod org-roam-node-namespace ((node org-roam-node))
        "Return the namespace for NODE.
      The namespace is the final directory of the file for the node."
        (file-name-nondirectory
         (directory-file-name
          (file-name-directory (org-roam-node-file node)))))
 
    The snippet above defines a new property ‘namespace’ on
 ‘org-roam-node’, which making it available for use in capture templates.
 
 
 File: org-roam.info,  Node: Extending the Capture System,  Prev: Accessing and Modifying Nodes,  Up: Building Extensions and Advanced Customization of Org-roam
 
 17.2.3 Extending the Capture System
 -----------------------------------
 
 Org-roam applies some patching over Org’s capture system to smooth out
 the user experience, and sometimes it is desirable to use Org-roam’s
 capturing system instead.  The exposed function to be used in extensions
 is ‘org-roam-capture-’:
 
  -- Function: org-roam-capture- &key goto keys node info props templates
 
      Main entry point.  GOTO and KEYS correspond to ‘org-capture’
      arguments.  INFO is a plist for filling up Org-roam’s capture
      templates.  NODE is an ‘org-roam-node’ construct containing
      information about the node.  PROPS is a plist containing additional
      Org-roam properties for each template.  TEMPLATES is a list of
      org-roam templates.
 
    An example of an extension using ‘org-roam-capture-’ is
 ‘org-roam-dailies’ itself:
 
      (defun org-roam-dailies--capture (time &optional goto)
        "Capture an entry in a daily-note for TIME, creating it if necessary.
 
      When GOTO is non-nil, go the note without creating an entry."
        (org-roam-capture- :goto (when goto '(4))
                           :node (org-roam-node-create)
                           :templates org-roam-dailies-capture-templates
                           :props (list :override-default-time time))
        (when goto (run-hooks 'org-roam-dailies-find-file-hook)))
 
 
 File: org-roam.info,  Node: Appendix,  Next: Keystroke Index,  Prev: Developer's Guide to Org-roam,  Up: Top
 
 18 Appendix
 ***********
 
 * Menu:
 
 * Note-taking Workflows::
 * Ecosystem::
 
 
 File: org-roam.info,  Node: Note-taking Workflows,  Next: Ecosystem,  Up: Appendix
 
 18.1 Note-taking Workflows
 ==========================
 
    • Books
         • How To Take Smart Notes
           (https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes)
 
    • Articles
         • The Zettelkasten Method - LessWrong 2.0
           (https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1)
 
         • Building a Second Brain in Roam...And Why You Might Want To :
           RoamResearch
           (https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)
 
         • Roam Research: Why I Love It and How I Use It - Nat Eliason
           (https://www.nateliason.com/blog/roam)
 
         • Adam Keesling’s Twitter Thread
           (https://twitter.com/adam_keesling/status/1196864424725774336?s=20)
 
         • How To Take Smart Notes With Org-mode · Jethro Kuan
           (https://blog.jethro.dev/posts/how_to_take_smart_notes_org/)
 
    • Threads
         • Ask HN: How to Take Good Notes
           (https://news.ycombinator.com/item?id=22473209)
 
    • Videos
         • How to Use Roam to Outline a New Article in Under 20 Minutes
           (https://www.youtube.com/watch?v=RvWic15iXjk)
 
 
 File: org-roam.info,  Node: Ecosystem,  Prev: Note-taking Workflows,  Up: Appendix
 
 18.2 Ecosystem
 ==============
 
 
 File: org-roam.info,  Node: Keystroke Index,  Next: Command Index,  Prev: Appendix,  Up: Top
 
 Appendix A Keystroke Index
 **************************
 
 
 File: org-roam.info,  Node: Command Index,  Next: Function Index,  Prev: Keystroke Index,  Up: Top
 
 Appendix B Command Index
 ************************
 
 
 File: org-roam.info,  Node: Function Index,  Next: Variable Index,  Prev: Command Index,  Up: Top
 
 Appendix C Function Index
 *************************
 
  * Menu:
 
 * org-roam-alias-add:                    Titles and Aliases.   (line 25)
 * org-roam-alias-remove:                 Titles and Aliases.   (line 30)
 * org-roam-buffer-display-dedicated:     The Org-roam Buffer.  (line 30)
 * org-roam-buffer-toggle:                The Org-roam Buffer.  (line 23)
 * org-roam-capture-:                     Extending the Capture System.
                                                                (line 11)
 * org-roam-dailies-capture-date:         Usage.                (line 34)
 * org-roam-dailies-capture-today:        Usage.                (line  8)
 * org-roam-dailies-capture-yesterday:    Usage.                (line 21)
 * org-roam-dailies-find-directory:       Usage.                (line 50)
 * org-roam-dailies-goto-date:            Usage.                (line 43)
 * org-roam-dailies-goto-next-note:       Usage.                (line 58)
 * org-roam-dailies-goto-previous-note:   Usage.                (line 54)
 * org-roam-dailies-goto-today:           Usage.                (line 14)
 * org-roam-dailies-goto-yesterday:       Usage.                (line 27)
 * org-roam-graph:                        org-roam-graph.       (line 14)
 * org-roam-node-at-point:                Accessing and Modifying Nodes.
                                                                (line 10)
 * org-roam-node-read:                    Accessing and Modifying Nodes.
                                                                (line 15)
 * org-roam-ref-add:                      Refs.                 (line 30)
 * org-roam-ref-remove:                   Refs.                 (line 35)
 
 
 File: org-roam.info,  Node: Variable Index,  Prev: Function Index,  Up: Top
 
 Appendix D Variable Index
 *************************
 
  * Menu:
 
 * org-roam-completion-everywhere:        Completing anywhere.  (line 18)
 * org-roam-dailies-capture-templates:    Configuration.        (line 13)
 * org-roam-dailies-directory:            Configuration.        (line  8)
 * org-roam-db-extra-links-elements:      What to cache.        (line 34)
 * org-roam-db-extra-links-exclude-keys:  What to cache.        (line 48)
 * org-roam-db-update-on-save:            When to cache.        (line 15)
 * org-roam-graph-edge-extra-config:      Graph Options.        (line 26)
 * org-roam-graph-executable:             org-roam-graph.       (line 23)
 * org-roam-graph-extra-config:           Graph Options.        (line 15)
 * org-roam-graph-filetype:               Graph Options.        (line 11)
 * org-roam-graph-node-extra-config:      Graph Options.        (line 20)
 * org-roam-graph-viewer:                 org-roam-graph.       (line 32)
 * org-roam-node-display-template:        Customizing Node Completions.
                                                                (line 10)
 
 Emacs 29.0.50 (Org mode 9.6)
 
 
 Tag Table:
 Node: Top754
 Node: Introduction4514
 Ref: Introduction-Footnote-16659
 Node: Target Audience6768
 Node: A Brief Introduction to the Zettelkasten Method8644
 Node: Installation11802
 Node: Installing from MELPA12166
 Node: Installing from Source13181
 Node: Installation Troubleshooting16164
 Node: C Compiler16366
 Node: C Compiler for Windows16937
 Node: Getting Started18178
 Node: The Org-roam Node18470
 Node: Links between Nodes19298
 Node: Setting up Org-roam19703
 Node: Creating and Linking Nodes21310
 Node: Customizing Node Completions23030
 Node: Customizing Node Caching25250
 Node: How to cache25486
 Node: What to cache27679
 Node: When to cache29807
 Node: The Org-roam Buffer30576
 Node: Navigating the Org-roam Buffer32032
 Node: Configuring what is displayed in the buffer32748
 Node: Configuring the Org-roam buffer display34079
 Node: Styling the Org-roam buffer35580
 Node: Node Properties35792
 Node: Standard Org properties36011
 Node: Titles and Aliases36361
 Node: Tags37362
 Node: Refs38022
 Node: Citations39222
 Node: Using the Cached Information39788
 Node: Completion40935
 Node: Completing within Link Brackets41731
 Node: Completing anywhere42181
 Node: Encryption42957
 Node: The Templating System43713
 Node: Template Walkthrough44430
 Node: Org-roam Template Expansion46274
 Node: Extensions48161
 Node: org-roam-protocol48397
 Node: Installation (1)48859
 Node: Linux49701
 Node: Mac OS51227
 Ref: Testing org-protocol53265
 Node: Windows54278
 Node: The roam-node protocol55021
 Node: The roam-ref protocol55408
 Node: org-roam-graph56586
 Node: Graph Options58483
 Node: org-roam-dailies59505
 Node: Configuration59792
 Node: Usage60601
 Node: org-roam-export62397
 Node: Performance Optimization62917
 Node: Garbage Collection63123
 Node: The Org-mode Ecosystem63917
 Node: Browsing History with winner-mode64414
 Node: Versioning Notes65286
 Node: Full-text search with Deft66077
 Node: Org-journal66828
 Node: Org-download67640
 Node: mathpixel68157
 Node: Org-noter / Interleave68736
 Node: Bibliography69128
 Node: Spaced Repetition69889
 Node: FAQ70545
 Node: How do I have more than one Org-roam directory?71152
 Node: How do I create a note whose title already matches one of the candidates?72723
 Node: How can I stop Org-roam from creating IDs everywhere?73643
 Node: How do I migrate from Roam Research?74337
 Node: How to migrate from Org-roam v1?74834
 Node: How do I publish my notes with an Internet-friendly graph?76243
 Node: Configure org-mode for publishing77685
 Node: Overriding the default link creation function79171
 Node: Copying the generated file to the export directory79843
 Node: I'm seeing this ``Selecting deleted buffer'' error What do I do?80814
 Node: Developer's Guide to Org-roam81872
 Node: Org-roam's Design Principle82146
 Node: Building Extensions and Advanced Customization of Org-roam84136
 Node: Accessing the Database85398
 Node: Accessing and Modifying Nodes86127
 Node: Extending the Capture System88003
 Node: Appendix89545
 Node: Note-taking Workflows89732
 Node: Ecosystem91014
 Node: Keystroke Index91131
 Node: Command Index91282
 Node: Function Index91435
 Node: Variable Index93213
 
 End Tag Table
 
 
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