\input texinfo    @c -*- texinfo -*-
@c %**start of header
@setfilename org-roam.info
@settitle Org-roam User Manual
@documentencoding UTF-8
@documentlanguage en
@c %**end of header

@copying
@quotation
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.

@end quotation
@end copying

@dircategory Emacs
@direntry
* Org-roam: (org-roam). Roam Research for Emacs.
@end direntry

@finalout
@titlepage
@title Org-roam User Manual
@subtitle for version 2.2.2
@author Jethro Kuan
@page
@vskip 0pt plus 1filll
@insertcopying
@end titlepage

@ifnottex
@node Top
@top Org-roam User Manual

@noindent

This manual is for Org-roam version 2.2.2.

@quotation
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.

@end quotation

@end ifnottex

@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::

@detailmenu
--- The Detailed Node Listing ---

Installation

* Installing from MELPA::
* Installing from Source::

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?::

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::

@end detailmenu
@end menu

@node Introduction
@chapter Introduction

Org-roam is a tool for networked thought. It reproduces some of @uref{https://roamresearch.com/, Roam
Research's} @footnote{To understand more about Roam, a collection of links are available in @ref{Note-taking Workflows}.} key features within @uref{https://orgmode.org/, Org-mode}.

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 @uref{https://github.com/jkitchin/org-ref, 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:

@itemize
@item
@strong{Privacy and Security:} Your personal wiki belongs only to you, entirely
offline and in your control. Encrypt your notes with GPG@.
@item
@strong{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.
@item
@strong{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.
@item
@strong{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.
@item
@strong{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.
@end itemize

@node Target Audience
@chapter 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.

@quotation
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)

@end quotation

@node A Brief Introduction to the Zettelkasten Method
@chapter 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.

@strong{Fleeting notes}

A slip-box requires a method for quickly capturing ideas. These are called
@strong{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
@code{org-capture} (see @ref{Capture,,,org,}), or using Org-roam's daily notes
functionality (see @ref{org-roam-dailies}). This provides a central inbox for collecting
thoughts, to be processed later into permanent notes.

@strong{Permanent notes}

Permanent notes are further split into two categories: @strong{literature notes} and
@strong{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.

@node Installation
@chapter Installation

Org-roam can be installed using Emacs' package manager or manually from its
development repository.

@menu
* Installing from MELPA::
* Installing from Source::
@end menu

@node Installing from MELPA
@section 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 @ref{Packages,,,emacs,}. Then, add one of the
archives to @samp{package-archives}:

@itemize
@item
To use Melpa:
@end itemize

@lisp
(require 'package)
(add-to-list 'package-archives
             '("melpa" . "http://melpa.org/packages/") t)
@end lisp

@itemize
@item
To use Melpa-Stable:
@end itemize

@lisp
(require 'package)
(add-to-list 'package-archives
             '("melpa-stable" . "http://stable.melpa.org/packages/") t)
@end lisp

Org-roam also depends on a recent version of Org, which can be obtained in Org's
package repository (see @ref{Installation,,,org,}).

Once you have done that, you can install Org-roam and its dependencies
using:

@example
M-x package-install RET org-roam RET
@end example

@node Installing from Source
@section Installing from Source

You may install Org-roam directly from the repository on @uref{https://github.com/org-roam/org-roam, GitHub} 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:

@example
git clone https://github.com/org-roam/org-roam.git /path/to/org/roam
@end example

where @code{./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 @code{require} the
Org-roam library. Add the following code to your @code{.emacs}:

@lisp
(add-to-list 'load-path "/path/to/org/roam")
(require 'org-roam)
@end lisp

You now have Org-roam installed. However, you don't necessarily have the
dependencies that it requires. These include:

@itemize
@item
dash
@item
f
@item
s
@item
org
@item
emacsql
@item
magit-section
@end itemize

You can install this manually as well, or get the latest version from MELPA@. You
may wish to use @uref{https://github.com/jwiegley/use-package, use-package}, @uref{https://github.com/raxod502/straight.el, 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 @code{/doc}
subdirectory of the Org-roam repository, and run the following:

@example
make infodir=/path/to/my/info/files install-info
@end example

Where @code{/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 @code{.emacs} file:

@lisp
(require 'info)
(add-to-list 'Info-default-directory-list
             "/path/to/my/info/files")
@end lisp

You can also use one of the default locations, such as:

@itemize
@item
@emph{usr/local/share/info}
@item
@emph{usr/share/info}
@item
@emph{usr/local/share/info}
@end itemize

If you do this, you'll need to make sure you have write-access to that location,
or run the above @code{make} command as root.

Now that the info file is ready, you need to add it to the corresponding @code{dir}
file:

@example
install-info /path/to/my/info/files/org-roam.info /path/to/my/info/files/dir
@end example

@node Getting Started
@chapter Getting Started

@menu
* The Org-roam Node::
* Links between Nodes::
* Setting up Org-roam::
* Creating and Linking Nodes::
* Customizing Node Completions::
@end menu

@node The Org-roam Node
@section 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:

@quotation
A node is any headline or top level file with an ID@.

@end quotation

For example, with this example file content:

@example
:PROPERTIES:
:ID:       foo
:END:
#+title: Foo

* Bar
:PROPERTIES:
:ID:       bar
:END:
@end example

We create two nodes:

@enumerate
@item
A file node ``Foo'' with id @code{foo}.
@item
A headline node ``Bar'' with id @code{bar}.
@end enumerate

Headlines without IDs will not be considered Org-roam nodes. Org IDs can be
added to files or headlines via the interactive command @code{M-x org-id-get-create}.

@node Links between Nodes
@section Links between Nodes

We link between nodes using Org's standard ID link (e.g. @code{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.

@node Setting up Org-roam
@section Setting up Org-roam

Org-roam's capabilities stem from its aggressive caching: it crawls all files
within @code{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
@code{org-roam-directory}. Org-roam searches recursively within @code{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 @code{org-roam-directory}:

@lisp
(make-directory "~/org-roam")
(setq org-roam-directory (file-truename "~/org-roam"))
@end lisp

The @code{file-truename} function is only necessary when you use symbolic links
inside @code{org-roam-directory}: Org-roam does not resolve symbolic links. One can
however instruct Emacs to always resolve symlinks, at a performance cost:

@lisp
(setq find-file-visit-truename t)
@end lisp

Next, we setup Org-roam to run functions on file changes to maintain cache
consistency. This is achieved by running @code{M-x org-roam-db-autosync-mode}. To
ensure that Org-roam is available on startup, place this in your Emacs
configuration:

@lisp
(org-roam-db-autosync-mode)
@end lisp

To build the cache manually, run @code{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.

@node Creating and Linking Nodes
@section Creating and Linking Nodes

Org-roam makes it easy to create notes and link them together. There are 2 main
functions for creating nodes:

@itemize
@item
@code{org-roam-node-insert}: creates a node if it does not exist, and inserts a
link to the node at point.
@item
@code{org-roam-node-find}: creates a node if it does not exist, and visits the
node.
@item
@code{org-roam-capture}: creates a node if it does not exist, and restores the
current window configuration upon completion.
@end itemize

Let's first try @code{org-roam-node-find}. Calling @code{M-x org-roam-node-find} will
show a list of titles for nodes that reside in @code{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 @code{RET}. This begins the note
creation process. This process uses @code{org-capture}'s templating system, and can
be customized (see @ref{The Templating System}). Using the default template, pressing
@code{C-c C-c} finishes the note capture.

Now that we have a node, we can try inserting a link to the node using @code{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 @code{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 @ref{Completion}).

@node Customizing Node Completions
@section Customizing Node Completions

Node selection is achieved via the @code{completing-read} interface, typically
through @code{org-roam-node-read}. The presentation of these nodes are governed by
@code{org-roam-node-display-template}.

@itemize
@item
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.
@end itemize

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 @code{org-roam-node-display-template} as such:

@lisp
(setq org-roam-node-display-template
      (concat "$@{title:*@} "
              (propertize "$@{tags:10@}" 'face 'org-tag)))
@end lisp

@node Customizing Node Caching
@chapter Customizing Node Caching

@menu
* How to cache::
* What to cache::
* When to cache::
@end menu

@node How to cache
@section How to cache

Org-roam uses a SQLite database to perform caching.  This integration is
managed by the @uref{https://github.com/magit/emacsql, emacsql} library.  It should ``just work''.

@node What to cache
@section 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 @code{ROAM_EXCLUDE}
property to a non-nil value. For example:

@example
* Foo
  :PROPERTIES:
  :ID:       foo
  :ROAM_EXCLUDE: t
  :END:
@end example

One can also set @code{org-roam-db-node-include-function}. For example, to exclude
all headlines with the @code{ATTACH} tag from the Org-roam database, one can set:

@lisp
(setq org-roam-db-node-include-function
      (lambda ()
        (not (member "ATTACH" (org-get-tags)))))
@end lisp

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
@code{org-roam-db-extra-links-elements} to specify which additional Org AST element
types to consider.

@itemize
@item
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).
@end itemize

Additionally, one may want to ignore certain keys from being excluded within
property drawers. For example, we would not want @code{ROAM_REFS} links to be
self-referential. Hence, to exclude specific keys, we use
@code{org-roam-db-extra-links-exclude-keys}.

@itemize
@item
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.
@end itemize

@node When to cache
@section 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 @code{org-roam-db-update-on-save} to @code{nil}.

@itemize
@item
Variable: org-roam-db-update-on-save
@end itemize

If t, update the Org-roam database upon saving the file. Disable this if your
files are large and updating the database is slow.

@node The Org-roam Buffer
@chapter 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:

@itemize
@item
@code{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.
@item
@code{org-roam-buffer-display-dedicated}: Launch an Org-roam buffer for a specific
node without visiting its file. Unlike @code{org-roam-buffer-toggle} you can have
multiple such buffers and their content won't be automatically replaced with a
new node at point.
@end itemize

To bring up a buffer that tracks the current node at point, call @code{M-x
org-roam-buffer-toggle}.

@itemize
@item
Function: org-roam-buffer-toggle

Toggle display of the @code{org-roam-buffer}.
@end itemize

To bring up a buffer that's dedicated for a specific node, call @code{M-x
org-roam-buffer-display-dedicated}.

@itemize
@item
Function: org-roam-buffer-display-dedicated

Launch node dedicated Org-roam buffer without visiting the node itself.
@end itemize

@menu
* Navigating the Org-roam Buffer::
* Configuring what is displayed in the buffer::
* Configuring the Org-roam buffer display::
* Styling the Org-roam buffer::
@end menu

@node Navigating the Org-roam Buffer
@section Navigating the Org-roam Buffer

The Org-roam buffer uses @code{magit-section}, making the typical @code{magit-section}
keybindings available. Here are several of the more useful ones:

@itemize
@item
@code{M-@{N@}}: @code{magit-section-show-level-@{N@}-all}
@item
@code{n}: @code{magit-section-forward}
@item
@code{<TAB>}: @code{magit-section-toggle}
@item
@code{<RET>}: @code{org-roam-buffer-visit-thing}
@end itemize

@code{org-roam-buffer-visit-thing} is a placeholder command, that is replaced by
section-specific commands such as @code{org-roam-node-visit}.

@node Configuring what is displayed in the buffer
@section Configuring what is displayed in the buffer

There are currently 3 provided widget types:

@table @asis
@item Backlinks
View (preview of) nodes that link to this node
@item Reference Links
Nodes that reference this node (see @ref{Refs})
@item Unlinked references
View nodes that contain text that match the nodes
title/alias but are not linked
@end table

To configure what sections are displayed in the buffer, set @code{org-roam-mode-sections}.

@lisp
(setq org-roam-mode-sections
      (list #'org-roam-backlinks-section
            #'org-roam-reflinks-section
            ;; #'org-roam-unlinked-references-section
            ))
@end lisp

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 @code{org-roam-mode-sections} as follows:

@lisp
(setq org-roam-mode-sections
      '((org-roam-backlinks-section :unique t)
        org-roam-reflinks-section))
@end lisp

The backlinks section @code{org-roam-backlinks-section} also supports a
predicate to filter backlinks, @code{:show-backlink-p}.  This can be used
as follows:

@lisp
(defun my-org-roam-show-backlink-p (backlink)
  (not (member "daily" (org-roam-node-tags (org-roam-backlink-source-node backlink)))))

(setq org-roam-mode-sections
      '((org-roam-backlinks-section :unique t :show-backlink-p my-org-roam-show-backlink-p)
        org-roam-reflinks-section))
@end lisp

@node Configuring the Org-roam buffer display
@section 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:

@lisp
(add-to-list 'display-buffer-alist
             '("\\*org-roam\\*"
               (display-buffer-in-direction)
               (direction . right)
               (window-width . 0.33)
               (window-height . fit-window-to-buffer)))
@end lisp

Crucially, the window is a regular window (not a side-window), and this allows
for predictable navigation:

@itemize
@item
@code{RET} navigates to thing-at-point in the current window, replacing the
Org-roam buffer.
@item
@code{C-u RET} navigates to thing-at-point in the other window.
@end itemize

For users that prefer using a side-window for the org-roam buffer, the following
example configuration should provide a good starting point:

@lisp
(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)))))
@end lisp

@node Styling the Org-roam buffer
@section @strong{TODO} Styling the Org-roam buffer

@node Node Properties
@chapter Node Properties

@menu
* Standard Org properties::
* Titles and Aliases::
* Tags::
* Refs::
@end menu

@node Standard Org properties
@section Standard Org properties

Org-roam caches most of the standard Org properties. The full list now includes:

@itemize
@item
outline level
@item
todo state
@item
priority
@item
scheduled
@item
deadline
@item
tags
@end itemize

@node Titles and Aliases
@section 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@math{_ALIASES}'' property to the node:

@example
* Artificial Intelligence
:PROPERTIES:
:ROAM_ALIASES: AI
:END:
@end example

Alternatively, Org-roam provides some functions to add or remove aliases.

@itemize
@item
Function: org-roam-alias-add alias

Add ALIAS to the node at point. When called interactively, prompt for the
alias to add.

@item
Function: org-roam-alias-remove

Remove an alias from the node at point.
@end itemize

@node Tags
@section Tags

Tags for top-level (file) nodes are pulled from the variable @code{org-file-tags},
which is set by the @code{#+filetags} keyword, as well as other tags the file may
have inherited. Tags for headline level nodes are regular Org tags.

Note that the @code{#+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.

@node Refs
@section 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@math{_REFS}'' property as follows:

@example
* Google
:PROPERTIES:
:ROAM_REFS: https://www.google.com/
:END:
@end example

With the above example, if another node links to @uref{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
 @code{roam-ref} protocol (see @ref{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.

@itemize
@item
Function: org-roam-ref-add ref

Add REF to the node at point. When called interactively, prompt for the
ref to add.

@item
Function: org-roam-ref-remove

Remove a ref from the node at point.
@end itemize

@node Citations
@chapter 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 @code{[cite:@@key]}) and @uref{https://github.com/jkitchin/org-ref, org-ref}
citations (of form cite:key).

Org-roam attempts to load both the @code{org-ref} and @code{org-cite} package when
indexing files, so no further setup from the user is required for citation
support.

@menu
* Using the Cached Information::
@end menu

@node Using the Cached Information
@section 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:

@example
* Probabilistic Robotics
:PROPERTIES:
:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
:ROAM_REFS: @@thrun2005probabilistic
:END:
@end example

or

@example
* Probabilistic Robotics
:PROPERTIES:
:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
:ROAM_REFS: [cite:@@thrun2005probabilistic]
:END:
@end example

for @code{org-cite}, or:

@example
* Probabilistic Robotics
:PROPERTIES:
:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
:ROAM_REFS: cite:thrun2005probabilistic
:END:
@end example

for @code{org-ref}.

When another node has a citation for that key, we can see it using the
@code{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 @code{citation} table of the Org-roam
database.

@node Completion
@chapter Completion

Completions for Org-roam are provided via @code{completion-at-point}. Org-roam
currently provides completions in two scenarios:

@itemize
@item
When within an Org bracket link
@item
Anywhere
@end itemize

Completions are installed locally in all Org-roam files. To trigger completions,
call @code{M-x completion-at-point}. If using @code{company-mode}, add @code{company-capf} to
@code{company-backends}.

Completions respect @code{completion-styles}: the user is free to choose how
candidates are matched. An example of a completion style that has grown in
popularity is @uref{https://github.com/oantolin/orderless, orderless}.

@menu
* Completing within Link Brackets::
* Completing anywhere::
@end menu

@node Completing within Link Brackets
@section Completing within Link Brackets

Completions within link brackets are provided by
@code{org-roam-complete-link-at-point}.

The completion candidates are the titles and aliases for all Org-roam nodes.
Upon choosing a candidate, a @code{roam:Title} link will be inserted, linking to node
of choice.

@node Completing anywhere
@section Completing anywhere

The same completions can be triggered anywhere for the symbol at point if not
within a bracketed link. This is provided by @code{org-roam-complete-everywhere}.
Similarly, the completion candidates are the titles and aliases for all Org-roam
nodes, and upon choosing a candidate a @code{roam:Title} link will be inserted
linking to the node of choice.

This is disabled by default. To enable it, set @code{org-roam-completion-everywhere}
to @code{t}:

@lisp
(setq org-roam-completion-everywhere t)
@end lisp

@itemize
@item
Variable: org-roam-completion-everywhere
@end itemize

When non-nil, provide link completion matching outside of Org links.

@node Encryption
@chapter 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 @code{.gpg}
extension in your Org-roam capture templates. For example:

@lisp
(setq org-roam-capture-templates '(("d" "default" plain "%?"
     :target (file+head "$@{slug@}.org.gpg"
                        "#+title: $@{title@}\n")
     :unnarrowed t)))
@end lisp

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.

@node The Templating System
@chapter The Templating System

Org-roam extends the @code{org-capture} system, providing a smoother note-taking
experience. However, these extensions mean Org-roam capture templates are
incompatible with @code{org-capture} templates.

Org-roam's templates are specified by @code{org-roam-capture-templates}. Just like
@code{org-capture-templates}, @code{org-roam-capture-templates} can contain multiple
templates. If @code{org-roam-capture-templates} only contains one template, there
will be no prompt for template selection.

@menu
* Template Walkthrough::
* Org-roam Template Expansion::
@end menu

@node Template Walkthrough
@section 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 @code{org-capture} templates.

@lisp
(("d" "default" plain "%?"
  :target (file+head "%<%Y%m%d%H%M%S>-$@{slug@}.org"
                     "#+title: $@{title@}\n")
  :unnarrowed t))
@end lisp

@enumerate
@item
The template has short key @code{"d"}. If you have only one template, org-roam
automatically chooses this template for you.
@item
The template is given a description of @code{"default"}.
@item
@code{plain} text is inserted. Other options include Org headings via
@code{entry}.
@item
Notice that the @code{target} that's usually in Org-capture templates is missing
here.
@item
@code{"%?"} is the template inserted on each call to @code{org-roam-capture-}.
This template means don't insert any content, but place the cursor here.
@item
@code{: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.
@item
@code{: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.
@end enumerate

See the @code{org-roam-capture-templates} documentation for more details and
customization options.

@node Org-roam Template Expansion
@section 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 @ref{Template Walkthrough, , Template
Walkthrough}.

Org-roam provides the @code{$@{foo@}} syntax for substituting variables with known
strings. @code{$@{foo@}}'s substitution is performed as follows:

@enumerate
@item
If @code{foo} is a function, @code{foo} is called with the current node as its
argument.
@item
Else if @code{org-roam-node-foo} is a function, @code{foo} is called with the current node
as its argument. The @code{org-roam-node-} prefix defines many of Org-roam's node
accessors such as @code{org-roam-node-title} and @code{org-roam-node-level}.
@item
Else look up @code{org-roam-capture--info} for @code{foo}. This is an internal variable
that is set before the capture process begins.
@item
If none of the above applies, read a string using @code{completing-read}.
@enumerate
@item
Org-roam also provides the @code{$@{foo=default_val@}} syntax, where if a default
value is provided, will be the initial value for the @code{foo} key during
minibuffer completion.
@end enumerate
@end enumerate

One can check the list of available keys for nodes by inspecting the
@code{org-roam-node} struct. At the time of writing, it is:

@lisp
(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)
@end lisp

This makes @code{$@{file@}}, @code{$@{file-hash@}} etc. all valid substitutions.

@node Extensions
@chapter Extensions

@menu
* org-roam-protocol::
* org-roam-graph::
* org-roam-dailies::
* org-roam-export::
@end menu

@node org-roam-protocol
@section org-roam-protocol

Org-roam provides extensions for capturing content from external applications
such as the browser, via @code{org-protocol}. Org-roam extends @code{org-protocol} with 2
protocols: the @code{roam-node} and @code{roam-ref} protocols.

@menu
* Installation: Installation (1). 
* The roam-node protocol::
* The roam-ref protocol::
@end menu

@node Installation (1)
@subsection Installation

To enable Org-roam's protocol extensions, simply add the following to your init
file:

@lisp
(require 'org-roam-protocol)
@end lisp

We also need to set up @code{org-protocol}: the instructions for setting up
@code{org-protocol} are reproduced here.

On a high-level, external calls are passed to Emacs via @code{emacsclient}.
@code{org-protocol} intercepts these and runs custom actions based on the protocols
registered. Hence, to use @code{org-protocol}, once must:

@enumerate
@item
launch the @code{emacsclient} process
@item
Register @code{org-protocol://} as a valid scheme-handler
@end enumerate

The instructions for the latter for each operating system is detailed below.

@menu
* Linux::
* Mac OS::
* Windows::
@end menu

@node Linux
@unnumberedsubsubsec Linux

For Linux users, create a desktop application in
@code{~/.local/share/applications/org-protocol.desktop}:

@example
[Desktop Entry]
Name=Org-Protocol
Exec=emacsclient %u
Icon=emacs-icon
Type=Application
Terminal=false
MimeType=x-scheme-handler/org-protocol
@end example

Associate @code{org-protocol://} links with the desktop application by
running in your shell:

@example
xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
@end example

To disable the ``confirm'' prompt in Chrome, you can also make Chrome show a
checkbox to tick, so that the @code{Org-Protocol Client} app will be used without
confirmation. To do this, run in a shell:

@example
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
@end example

and then restart Chrome (for example, by navigating to <chrome://restart>) to
make the new policy take effect.

See @uref{https://www.chromium.org/administrators/linux-quick-start, here} for more info on the @code{/etc/opt/chrome/policies/managed} directory and
@uref{https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox, here} for information on the @code{ExternalProtocolDialogShowAlwaysOpenCheckbox} policy.

@node Mac OS
@unnumberedsubsubsec Mac OS

For Mac OS, we need to create our own application.

@enumerate
@item
Launch Script Editor
@item
Use the following script, paying attention to the path to @code{emacsclient}:
@end enumerate

@lisp
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 & " &> /dev/null &"
    tell application "Emacs" to activate
end open location
@end lisp

@enumerate
@item
Save the script in @code{/Applications/OrgProtocolClient.app}, changing the script type to
``Application'', rather than ``Script''.
@item
Edit @code{/Applications/OrgProtocolClient.app/Contents/Info.plist}, adding the
following before the last @code{</dict>} tag:
@end enumerate

@example
<key>CFBundleURLTypes</key>
<array>
  <dict>
    <key>CFBundleURLName</key>
    <string>org-protocol handler</string>
    <key>CFBundleURLSchemes</key>
    <array>
      <string>org-protocol</string>
    </array>
  </dict>
</array>
@end example

@enumerate
@item
Save the file, and run the @code{OrgProtocolClient.app} to register the protocol.
@end enumerate

To disable the ``confirm'' prompt in Chrome, you can also make Chrome
show a checkbox to tick, so that the @code{OrgProtocol} app will be used
without confirmation. To do this, run in a shell:

@example
defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
@end example

If you're using @uref{https://github.com/railwaycat/homebrew-emacsmacport, Emacs Mac Port}, it registered its `Emacs.app` as the default
handler for the URL scheme `org-protocol`. To make @code{OrgProtocol.app}
the default handler instead, run:

@example
defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
'@{"LSHandlerPreferredVersions" = @{ "LSHandlerRoleAll" = "-"; @}; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";@}'
@end example

Then restart your computer.

If you're using the @uref{https://formulae.brew.sh/formula/emacs, Emacs Homebrew formula}, you may need one of the following additional configurations:

@enumerate
@item
Add option `-c` to `emacsclient` in the script, and start emacs from command line with `emacs --daemon`
@end enumerate

@lisp
on open location this_URL
    set EC to "/usr/local/bin/emacsclient -c --no-wait "
    set filePath to quoted form of this_URL
    do shell script EC & filePath & " &> /dev/null &"
    tell application "Emacs" to activate
end open location
@end lisp

@enumerate
@item
Add `(server-start)` in .emacs (in this case you do not need option `-c` for `emacsclient` in the script, and you do not need to start emacs with `emacs --daemon`
@end enumerate

@itemize
@item
@anchor{Testing org-protocol}Testing org-protocol


To test that you have the handler setup and registered properly from the command
line you can run:

@example
open org-protocol://roam-ref\?template=r\&ref=test\&title=this
@end example

If you get an error similar too this or the wrong handler is run:

@quotation
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=@{@math{_LSLine}=1489, _LSFunction=runEvaluator@}).

@end quotation

You may need to manually register your handler, like this:

@example
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
@end example

Here is a link to the lsregister command that is really useful: @uref{https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/}
@end itemize

@node Windows
@unnumberedsubsubsec Windows

For Windows, create a temporary @code{org-protocol.reg} file:

@example
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\""
@end example

The above will forward the protocol to WSL@. If you run Emacs natively on
Windows, replace the last line with:

@example
@@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
@end example

After executing the .reg file, the protocol is registered and you can delete the
file.

@node The roam-node protocol
@subsection The roam-node protocol

The roam-node protocol opens the node with ID specified by the @code{node} key (e.g.
@code{org-protocol://roam-node?node=node-id}). @code{org-roam-graph} uses this to make the
graph navigable.

@node The roam-ref protocol
@subsection The roam-ref protocol

This protocol finds or creates a new note with a given @code{ROAM_REFS}:

@image{images/roam-ref,,,,gif}

To use this, create the following @uref{https://en.wikipedia.org/wiki/Bookmarklet, bookmarklet} in your browser:

@example
javascript:location.href =
    'org-protocol://roam-ref?template=r&ref='
    + encodeURIComponent(location.href)
    + '&title='
    + encodeURIComponent(document.title)
    + '&body='
    + encodeURIComponent(window.getSelection())
@end example

or as a keybinding in @code{qutebrowser} in , using the @code{config.py} file (see
@uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}):

@example
config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
@end example

where @code{template} is the template key for a template in
@code{org-roam-capture-ref-templates} (see @ref{The Templating System}).

@node org-roam-graph
@section org-roam-graph

Org-roam provides basic graphing capabilities to explore interconnections
between notes, in @code{org-roam-graph}. This is done by performing SQL queries and
generating images using @uref{https://graphviz.org/, Graphviz}. The graph can also be navigated: see @ref{org-roam-protocol}.

The entry point to graph creation is @code{org-roam-graph}.

@itemize
@item
Function: org-roam-graph & optional arg node
@end itemize

Build and display a graph for NODE@.
ARG may be any of the following values:

@itemize
@item
@code{nil}       show the full graph.
@item
@code{integer}   an integer argument @code{N} will show the graph for the connected
components to node up to @code{N} steps away.
@end itemize

@itemize
@item
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 @code{neato} in place of @code{dot}, which generates a more
compact graph layout.

@item
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:

@enumerate
@item
A string, which is a path to the program used
@item
a function accepting a single argument: the graph file path.
@end enumerate

@code{nil} uses @code{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:

@lisp
(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)))))
@end lisp
@end itemize

@menu
* Graph Options::
@end menu

@node Graph Options
@subsection Graph Options

Graphviz provides many options for customizing the graph output, and Org-roam
supports some of them. See @uref{https://graphviz.gitlab.io/_pages/doc/info/attrs.html}
for customizable options.

@itemize
@item
User Option: org-roam-graph-filetype

The file type to generate for graphs. This defaults to @code{"svg"}.

@item
User Option: org-roam-graph-extra-config

Extra options passed to graphviz for the digraph (The ``G'' attributes).
Example: @code{'~(("rankdir" . "LR"))}

@item
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 @code{"id"}, or @code{"http"}. The cdr of the
list is another alist of Graphviz node options (the ``N'' attributes).

@item
User Option: org-roam-graph-edge-extra-config

Extra options for edges in the graphviz output (The ``E'' attributes).
Example: @code{'(("dir" . "back"))}
@end itemize

@node org-roam-dailies
@section org-roam-dailies

Org-roam provides journaling capabilities akin to
Org-journal with @code{org-roam-dailies}.

@menu
* Configuration::
* Usage::
@end menu

@node Configuration
@subsection Configuration

For @code{org-roam-dailies} to work, you need to define two variables:

@itemize
@item
Variable: @code{org-roam-dailies-directory}

Path to daily-notes. This path is relative to @code{org-roam-directory}.

@item
Variable: @code{org-roam-dailies-capture-templates}

Capture templates for daily-notes in Org-roam.
@end itemize

Here is a sane default configuration:

@lisp
(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"))))
@end lisp

See @ref{The Templating System} for creating new templates.

@node Usage
@subsection Usage

@code{org-roam-dailies} provides these interactive functions:

@itemize
@item
Function: @code{org-roam-dailies-capture-today} &optional goto

Create an entry in the daily note for today.

When @code{goto} is non-nil, go to the note without creating an entry.

@item
Function: @code{org-roam-dailies-goto-today}

Find the daily note for today, creating it if necessary.
@end itemize

There are variants of those commands for @code{-yesterday} and @code{-tomorrow}:

@itemize
@item
Function: @code{org-roam-dailies-capture-yesterday} n &optional goto

Create an entry in the daily note for yesterday.

With numeric argument @code{n}, use the daily note @code{n} days in the past.

@item
Function: @code{org-roam-dailies-goto-yesterday}

With numeric argument N, use the daily-note N days in the future.
@end itemize

There are also commands which allow you to use Emacs’s @code{calendar} to find the date

@itemize
@item
Function: @code{org-roam-dailies-capture-date}

Create an entry in the daily note for a date using the calendar.

Prefer past dates, unless @code{prefer-future} is non-nil.

With a 'C-u' prefix or when @code{goto} is non-nil, go the note without
creating an entry.

@item
Function: @code{org-roam-dailies-goto-date}

Find the daily note for a date using the calendar, creating it if necessary.

Prefer past dates, unless @code{prefer-future} is non-nil.

@item
Function: @code{org-roam-dailies-find-directory}

Find and open @code{org-roam-dailies-directory}.

@item
Function: @code{org-roam-dailies-goto-previous-note}

When in an daily-note, find the previous one.

@item
Function: @code{org-roam-dailies-goto-next-note}

When in an daily-note, find the next one.
@end itemize

@node org-roam-export
@section org-roam-export

Because Org-roam files are plain org files, they can be exported easily using
@code{org-export} to a variety of formats, including @code{html} and @code{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:

@lisp
(require 'org-roam-export)
@end lisp

@node Performance Optimization
@chapter Performance Optimization

@menu
* Garbage Collection::
@end menu

@node Garbage Collection
@section 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 @ref{Garbage Collection,info:elisp#Garbage Collection,,elisp,}).

Org-roam provides the option @code{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
@code{org-roam-db-gc-threshold} to a high value (such as @code{most-positive-fixnum}):

@lisp
(setq org-roam-db-gc-threshold most-positive-fixnum)
@end lisp

@node The Org-mode Ecosystem
@chapter 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::
@end menu

@node Browsing History with winner-mode
@section Browsing History with winner-mode

@code{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.

@code{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
@code{winner-mode}. To use @code{winner-mode}, simply enable it, and bind the appropriate
interactive functions:

@lisp
(winner-mode +1)
(define-key winner-mode-map (kbd "<M-left>") #'winner-undo)
(define-key winner-mode-map (kbd "<M-right>") #'winner-redo)

@end lisp

@node Versioning Notes
@section 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 @uref{https://git-scm.com/, Git}. Simply initialize
@code{org-roam-directory} as a Git repository, and commit your files at regular or
appropriate intervals. @uref{https://magit.vc/, Magit} 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. @uref{https://gitlab.com/pidu/git-timemachine, Git-timemachine} allows you to visit historic
versions of a tracked Org-roam note.

@node Full-text search with Deft
@section Full-text search with Deft

@uref{https://jblevins.org/projects/deft/, Deft} provides a nice interface for browsing and filtering org-roam notes.

@lisp
(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))
@end lisp

The Deft interface can slow down quickly when the number of files get huge.
@uref{https://github.com/hasu/notdeft, Notdeft} is a fork of Deft that uses an external search engine and indexer.

@node Org-journal
@section Org-journal

@uref{https://github.com/bastibe/org-journal, Org-journal} provides journaling capabilities to Org-mode. A lot of its
functionalities have been incorporated into Org-roam under the name
@ref{org-roam-dailies, , @code{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.

@lisp
(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"))
@end lisp

@node Org-download
@section Org-download

@uref{https://github.com/abo-abo/org-download, Org-download} lets you screenshot and yank images from the web into your notes:

@float Figure
@image{images/org-download,,,,gif}
@caption{org-download}
@end float

@lisp
(use-package org-download
  :after org
  :bind
  (:map org-mode-map
        (("s-Y" . org-download-screenshot)
         ("s-y" . org-download-yank))))
@end lisp

@node mathpixel
@section mathpix.el

@uref{https://github.com/jethrokuan/mathpix.el, mathpix.el} uses @uref{https://mathpix.com/, Mathpix's} API to convert clips into latex equations:

@float Figure
@image{images/mathpix,,,,gif}
@caption{mathpix}
@end float

@lisp
(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))
@end lisp

@node Org-noter / Interleave
@section Org-noter / Interleave

@uref{https://github.com/weirdNox/org-noter, Org-noter} and @uref{https://github.com/rudolfochrist/interleave, Interleave} are both projects that allow synchronised annotation of
documents (PDF, EPUB etc.) within Org-mode.

@node Bibliography
@section Bibliography

Org 9.5 added native citation and bibliography functionality, called ``org-cite'',
which org-roam supports.

@uref{https://github.com/org-roam/org-roam-bibtex, org-roam-bibtex} offers tight integration between @uref{https://github.com/jkitchin/org-ref, org-ref}, @uref{https://github.com/tmalsburg/helm-bibtex, helm-bibtex} and
@code{org-roam}. This helps you manage your bibliographic notes under @code{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 @code{ROAM_REFS}.

@node Spaced Repetition
@section Spaced Repetition

@uref{https://www.leonrische.me/fc/index.html, Org-fc} is a spaced repetition system that scales well with a large number of
files. Other alternatives include @uref{https://orgmode.org/worg/org-contrib/org-drill.html, org-drill}, and @uref{https://github.com/abo-abo/pamparam, pamparam}.

To use Anki for spaced repetition, @uref{https://github.com/louietan/anki-editor, anki-editor} allows you to write your cards in
Org-mode, and sync your cards to Anki via @uref{https://github.com/FooSoft/anki-connect#installation, anki-connect}.

@node FAQ
@chapter 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?::
@end menu

@node How do I have more than one Org-roam directory?
@section How do I have more than one Org-roam directory?

Emacs supports directory-local variables, allowing the value of
@code{org-roam-directory} to be different in different directories. It does this by
checking for a file named @code{.dir-locals.el}.

To add support for multiple directories, override the @code{org-roam-directory}
variable using directory-local variables. This is what @code{.dir-locals.el} may
contain:

@lisp
((nil . ((org-roam-directory . "/path/to/alt/org-roam-dir")
         (org-roam-db-location . "/path/to/alt/org-roam-dir/org-roam.db"))))
@end lisp

Note @code{org-roam-directory} and @code{org-roam-db-location} should be an absolute path, not relative.

Alternatively, use @code{eval} if you wish to call functions:

@lisp
((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))))))
@end lisp

All files within that directory will be treated as their own separate set of
Org-roam files. Remember to run @code{org-roam-db-sync} from a file within
that directory, at least once.

@node How do I create a note whose title already matches one of the candidates?
@section 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:

@table @asis
@item Ivy
call @code{ivy-immediate-done}, typically bound to @code{C-M-j}. Alternatively,
set @code{ivy-use-selectable-prompt} to @code{t}, so that ``bar'' is now selectable.
@item Helm
Org-roam should provide a selectable ``[?] bar'' candidate at the top of
the candidate list.
@end table

@node How can I stop Org-roam from creating IDs everywhere?
@section 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 @code{org-id-link-to-org-use-id}: setting it to @code{'create-if-interactive}
is a popular option.

@node How do I migrate from Roam Research?
@section 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 @uref{https://github.com/fabioberger/roam-migration, in the repository}.

@node How to migrate from Org-roam v1?
@section 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 @samp{M-x org-roam-migrate-wizard}.
@uref{https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html, This blog post}
provides a good overview of what's new in v2 and how to migrate.

Essentially, to migrate notes from v1 to v2, one must:

@enumerate
@item
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).
@item
Update the Org-roam database to conform to the new schema.
@item
Replace @code{#+ROAM_KEY} into the @code{ROAM_REFS} property
@item
Replace @code{#+ROAM_ALIAS} into the @code{ROAM_ALIASES} property
@item
Move @code{#+ROAM_TAGS} into the @code{#+FILETAGS} property for file-level nodes,
and the @code{ROAM_TAGS} property for headline nodes
@item
Replace existing file links with ID links.
@end enumerate

@node How do I publish my notes with an Internet-friendly graph?
@section How do I publish my notes with an Internet-friendly graph?

The default graph builder creates a graph with an @uref{https://orgmode.org/worg/org-contrib/org-protocol.html, org-protocol}
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 @uref{https://orgmode.org/manual/Publishing.html, publishing} capability:

@enumerate
@item
configure org-mode to publish your org-roam notes as a project.
@item
create a function that overrides the default org-protocol link
creation function(@samp{org-roam-default-link-builder}).
@item
create a hook that's called at the end of graph creation to copy
the generated graph to the appropriate place.
@end enumerate

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::
@end menu

@node Configure org-mode for publishing
@subsection Configure org-mode for publishing

This has two steps:
@enumerate
@item
Setting of a @emph{roam} project that publishes your notes.
@item
Configuring the @emph{sitemap.html} generation.
@item
Setting up @samp{org-publish} to generate the graph.
@end enumerate

This will require code like the following:
@lisp
(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\">")))
@end lisp

@node Overriding the default link creation function
@subsection 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.
@lisp
(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)
@end lisp

@node Copying the generated file to the export directory
@subsection Copying the generated file to the export directory

The default behavior of @samp{org-roam-graph} is to generate the graph and
display it in Emacs.  There is an @samp{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:

@lisp
(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)))))
@end lisp

@node Developer's Guide to Org-roam
@chapter Developer's Guide to Org-roam

@menu
* Org-roam's Design Principle::
* Building Extensions and Advanced Customization of Org-roam::
@end menu

@node Org-roam's Design Principle
@section 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:

@itemize
@item
link graph traversal and visualization
@item
Instantaneous SQL-like queries on headlines
@itemize
@item
What are my TODOs, scheduled for X, or due by Y@?
@end itemize
@item
Accessing the properties of a node, such as its tags, refs, TODO state or
priority
@end itemize

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.

@node Building Extensions and Advanced Customization of Org-roam
@section 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 use one or more of
the following functionalities:

@itemize
@item
Access to Org-roam's database
@item
Usage/modification of Org-roam's interactive commands
@end itemize

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.

@enumerate
@item
Extensions should not modify the database schema. Any extension that requires
the caching of additional data should make a request upstream to Org-roam.
@item
Extensions requiring access to the database should explicitly state support
for the database version (@code{org-roam-db-version}), and only conditionally
load when support is available.
@end enumerate

@menu
* Accessing the Database::
* Accessing and Modifying Nodes::
* Extending the Capture System::
@end menu

@node Accessing the Database
@subsection Accessing the Database

Access to the database is provided singularly by @code{org-roam-db-query}, for
example:

@lisp
(org-roam-db-query [:select * :from nodes])
@end lisp

One can refer to the database schema by looking up
@code{org-roam-db--table-schemata}. There are multiple helper functions within
Org-roam that call @code{org-roam-db-query}, these are subject to change. To ensure
that extensions/customizations are robust to change, extensions should only use
@code{org-roam-db-query}, and perhaps replicate the SQL query if necessary.

@node Accessing and Modifying Nodes
@subsection Accessing and Modifying Nodes

The node interface is cleanly defined using @code{cl-defstruct}. The primary
method to access nodes is @code{org-roam-node-at-point} and @code{org-roam-node-read}:

@itemize
@item
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.

@item
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
@code{org-roam-node}), and when nil is returned the node will be
filtered out.
SORT-FN is a function to sort nodes. See @code{org-roam-node-read-sort-by-file-mtime}
for an example sort function.
If REQUIRE-MATCH, the minibuffer prompt will require a match.
@end itemize

Once you obtain the node, you can use the accessors for the node, e.g.
@code{org-roam-node-id} or @code{org-roam-node-todo}.

It is possible to define (or override existing) properties on nodes. This is
simply done using a @code{cl-defmethod} on the @code{org-roam-node} struct:

@lisp
(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)))))
@end lisp

The snippet above defines a new property @code{namespace} on @code{org-roam-node}, which
making it available for use in capture templates.

@node Extending the Capture System
@subsection 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 @code{org-roam-capture-}:

@itemize
@item
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.
@end itemize

An example of an extension using @code{org-roam-capture-} is @code{org-roam-dailies}
itself:

@lisp
(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)))
@end lisp

@node Appendix
@chapter Appendix

@menu
* Note-taking Workflows::
* Ecosystem::
@end menu

@node Note-taking Workflows
@section Note-taking Workflows

@table @asis
@item Books
@itemize
@item
@uref{https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes, How To Take Smart Notes}
@end itemize
@item Articles
@itemize
@item
@uref{https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1, The Zettelkasten Method - LessWrong 2.0}
@item
@uref{https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might, Building a Second Brain in Roam@dots{}And Why You Might Want To : RoamResearch}
@item
@uref{https://www.nateliason.com/blog/roam, Roam Research: Why I Love It and How I Use It - Nat Eliason}
@item
@uref{https://twitter.com/adam_keesling/status/1196864424725774336?s=20, Adam Keesling's Twitter Thread}
@item
@uref{https://blog.jethro.dev/posts/how_to_take_smart_notes_org/, How To Take Smart Notes With Org-mode · Jethro Kuan}
@end itemize
@item Threads
@itemize
@item
@uref{https://news.ycombinator.com/item?id=22473209, Ask HN: How to Take Good Notes}
@end itemize
@item Videos
@itemize
@item
@uref{https://www.youtube.com/watch?v=RvWic15iXjk, How to Use Roam to Outline a New Article in Under 20 Minutes}
@end itemize
@end table

@node Ecosystem
@section Ecosystem

@node Keystroke Index
@appendix Keystroke Index

@printindex ky

@node Command Index
@appendix Command Index

@printindex cp

@node Function Index
@appendix Function Index

@printindex fn

@node Variable Index
@appendix Variable Index

@printindex vr

Emacs 29.4 (Org mode 9.7.19)
@bye
