#+title: Org-roam User Manual
:PREAMBLE:
#+author: Jethro Kuan
#+email: jethrokuan95@gmail.com
#+date: 2020-2020
#+language: en

#+texinfo_dir_category: Emacs
#+texinfo_dir_title: Org-roam: (org-roam).
#+texinfo_dir_desc: Rudimentary Roam Replica for Emacs.
#+subtitle: for version 1.2.1

#+options: H:4 num:3 toc:2 creator:t
#+property: header-args :eval never
#+texinfo: @noindent

This manual is for Org-roam version 1.2.1.

#+BEGIN_QUOTE
Copyright (C) 2020-2020 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_QUOTE

:END:

* Introduction

Org-roam is a [[https://roamresearch.com/][Roam Research]] replica built around the
all-powerful [[https://orgmode.org/][Org-mode]].

Org-roam is a solution for effortless non-hierarchical note-taking
with Org-mode. With Org-roam, notes flow naturally, making note-taking
fun and easy. Org-roam should also work as a plug-and-play solution
for anyone already using Org-mode for their personal wiki.

To understand more about Roam, a collection of links are available in
[[*Note-taking Workflows][Note-taking Workflows]].

Org-roam aims to implement the core features of Roam, leveraging the
mature ecosystem around Org-mode where possible. Eventually, we hope
to further introduce features enabled by the Emacs ecosystem.

Org-roam provides several benefits over other tooling:

- Privacy and Security :: Edit your personal wiki completely offline, entirely 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 up an auxilliary 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. Edit your plain-text notes in notepad if all other editors cease 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 PR.
- Leverages the Org-mode ecosystem :: Over the years, 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 we can inherit many of the powerful text-navigation and editing packages available to Emacs.

* Target Audience

Org-roam is a tool that will appear unfriendly to anyone unfamiliar with Emacs
and Org-mode, but is also extremely powerful to those willing to put effort in
mastering the intricacies of the tools. Org-roam stands on the shoulders on
giants. Emacs was first created in 1976, and remains a top tier tool 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 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.

#+BEGIN_QUOTE
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_QUOTE

* 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 also introduce terms commonly used within
the Zettelkasten community, which will also commonly appear in the Org-roam
forums and channels of discussion.

The Zettelkasten method of note-taking is designed to increase research
productivity: in particular, it acts 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.

In its paper form, the slip-box is 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.

Org-roam is the slip-box, digitalized in Org-mode. Every zettel (card) is a
plain-text, Org-mode file. These files are often placed in the same directory.
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. Org-roam also facilitates the linking of zettels using Org-mode ~file:~
links.

A slip-box requires a method of 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 info:org#capture), or using Org-roam's daily notes
functionality (see [[*Daily Notes][Daily Notes]]). This provides a central inbox for collecting
thoughts, to be processed later into 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.

* Installation

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

** 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 info:emacs#Packages. Then, add one of the
archives to =package-archives=:

- To use Melpa:

#+BEGIN_SRC emacs-lisp
  (require 'package)
  (add-to-list 'package-archives
               '("melpa" . "http://melpa.org/packages/") t)
#+END_SRC

- To use Melpa-Stable:

#+BEGIN_SRC emacs-lisp
  (require 'package)
  (add-to-list 'package-archives
               '("melpa-stable" . "http://stable.melpa.org/packages/") t)
#+END_SRC

Org-roam also depends on a recent version of Org, which can be obtained in Org's
package repository (see info:org#Installation). To use Org's ELPA archive:

#+BEGIN_SRC emacs-lisp
(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)
#+END_SRC

Once you have added your preferred archive, you need to update the
local package list using:

#+BEGIN_EXAMPLE
  M-x package-refresh-contents RET
#+END_EXAMPLE

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

#+BEGIN_EXAMPLE
  M-x package-install RET org-roam RET
#+END_EXAMPLE

Now see [[*Post-Installation Tasks][Post-Installation Tasks]].

** Installing from Apt

Users of Debian 11 or later or Ubuntu 20.10 or later can simply install Org-roam
using Apt:

#+BEGIN_SRC bash
  apt-get install elpa-org-roam
#+END_SRC

Org-roam will then be autoloaded into Emacs.

** TODO Installing from the Git Repository

** Post-Installation Tasks

Org-roam uses ~emacsql-sqlite3~, which requires ~sqlite3~ to be located on
~exec-path~. Please ensure that ~sqlite3~ is installed appropriately on your
operating system. You can verify that this is the case by executing:

#+BEGIN_SRC emacs-lisp
  (executable-find "sqlite3")
#+END_SRC

If you have ~sqlite3~ installed, and ~executable-find~ still reports ~nil~, then
it is likely that the path to the executable is not a member of the Emacs
variable ~exec-path~. You may rectify this by manually adding the path within
your Emacs configuration:

#+BEGIN_SRC emacs-lisp
  (add-to-list 'exec-path "path/to/sqlite3")
#+END_SRC

* Getting Started

This short tutorial describes the essential commands used in Org-roam, to help
you get started.

First, it is important to understand how Org-roam was designed. Org-roam was
built to support a workflow that was not possible with vanilla Org-mode. This
flow is modelled after the [[https://zettelkasten.de/][Zettelkasten Method]], and many of [[https://roamresearch.com][Roam Research's]]
workflows. Org-roam does not magically make note-taking better -- this often
requires a radical change in your current note-taking workflow. To understand
more about the methods and madness, see [[*Note-taking Workflows][Note-taking Workflows]].

To first start using Org-roam, one needs to pick a location to store the
Org-roam files. The directory that will contain your notes, and database index
is specified by the variable ~org-roam-directory~. This variable needs to be set
before any calls to Org-roam functions, including enabling ~org-roam-mode~. For
this tutorial, create an empty directory, and set ~org-roam-directory~:

#+BEGIN_SRC emacs-lisp
(make-directory "~/org-roam")
(setq org-roam-directory "~/org-roam")
#+END_SRC

We encourage using a flat hierarchy for storing notes, but some prefer using
folders for storing specific kinds of notes (e.g. websites, papers). This is
fine; Org-roam searches recursively within ~org-roam-directory~ for any notes.
Instead of relying on the file hierarchy for any form of categorization, we
solely rely on links between files to establish connections between notes.

Next, we need to enable the global minor mode ~org-roam-mode~. This sets up Emacs
with several hooks, builds a cache and keeps it consistent. We recommend
starting ~org-roam-mode~ on startup:

#+BEGIN_SRC emacs-lisp
(add-hook 'after-init-hook 'org-roam-mode)
#+END_SRC

To build the cache manually, one can run ~M-x org-roam-db-build-cache~. The
cache is a sqlite database named ~org-roam.db~, which defaults to residing in
the root ~org-roam-directory~. Cache builds may take a while the first time, but
is often instantaneous in subsequent runs.

Let us now create our first note. Call ~M-x org-roam-find-file~. This shows a list
of titles for notes that reside in ~org-roam-directory~. It should show nothing
right now, since there are no notes in the directory. Entering the title of the
note you wish to create, and pressing ~RET~ should begin the note creation
process. This process uses ~org-capture~'s templating system, and can be freely
customized (see [[*The Templating System][The Templating System]]). Using the default template, pressing ~C-c
C-c~ finishes the note capture. Running ~M-x org-roam-find-file~ again should show
the note you have created, and selecting that entry will bring you to that note.

The crux of Org-roam is making it easy to create notes, and link them together.
To link notes together, we call ~M-x org-roam-insert~. This brings up a prompt
with a list of title for existing notes. Selecting an existing entry will create
and insert a link to the current file. Entering a non-existent title will create
a new note with that title. Good usage of Org-roam requires liberally linking
files: this facilitates building up a dense knowledge graph of inter-connected
notes.

Org-roam provides an interface to view backlinks. It shows backlinks for the
currently active Org-roam note, along with some surrounding context. To toggle
the visibility of this buffer, call ~M-x org-roam~.

For a visual representation of the notes and their connections, Org-roam also
provides graphing capabilities, using Graphviz. It generates graphs with notes
as nodes, and links between them as edges. The generated graph can be used to
navigate to the files, but this requires some additional setup (see [[*Roam Protocol][Roam
Protocol]]).

* Anatomy of an Org-roam File

The bulk of Org-roam's functionality is built on top of vanilla
Org-mode. However, to support additional functionality, Org-roam adds
several Org-roam-specific keywords. These functionality are not crucial
to effective use of Org-roam.

** Titles

To easily find a note, a title needs to be prescribed to a note. A note can have
many titles: this allows a note to be referred to by different names, which is
especially useful for topics or concepts with acronyms. For example, for a note
like "World War 2", it may be desirable to also refer to it using the acronym
"WWII".

Org-roam calls ~org-roam--extract-titles~ to extract titles. It uses the
variable ~org-roam-title-sources~, to control how the titles are extracted. The
title extraction methods supported are:

1. ~'title~: This extracts the title using the file ~#+title~ property
2. ~'headline~: This extracts the title from the first headline in the Org file
3. ~'alias~: This extracts a list of titles using the ~#+roam_alias~ property.
   The aliases are space-delimited, and can be multi-worded using quotes

Take for example the following org file:

#+BEGIN_SRC org
  #+title: World War 2
  #+roam_alias: "WWII" "World War II"

  * Headline
#+END_SRC

| Method      | Titles                   |
|-------------+--------------------------|
| ~'title~    | '("World War 2")         |
| ~'headline~ | '("Headline")            |
| ~'alias~    | '("WWII" "World War II") |

One can freely control which extraction methods to use by customizing
~org-roam-title-sources~: see the doc-string for the variable for more
information. If all methods of title extraction return no results, the file-name
is used in place of the titles for completions.

If you wish to add your own title extraction method, you may push a symbol
~'foo~ into ~org-roam-title-sources~, and define a
~org-roam--extract-titles-foo~ which accepts no arguments. See
~org-roam--extract-titles-title~ for an example.

** Tags

Tags are used as meta-data for files: they facilitate interactions with notes
where titles are insufficient. For example, tags allow for categorization of
notes: differentiating between bibliographical and structure notes during interactive commands.

Org-roam calls ~org-roam--extract-tags~ to extract tags from files. It uses the
variable ~org-roam-tag-sources~, to control how tags are extracted. The tag
extraction methods supported are:

1. ~'prop~: This extracts tags from the ~#+roam_tags~ property. Tags are space delimited, and can be multi-word using double quotes.
2. ~'all-directories~: All sub-directories relative to ~org-roam-directory~ are
   extracted as tags. That is, if a file is located at relative path
   ~foo/bar/file.org~, the file will have tags ~foo~ and ~bar~.
3. ~'last-directory~: Extracts the last directory relative to
   ~org-roam-directory~ as the tag. That is, if a file is located at relative
   path ~foo/bar/file.org~, the file will have tag ~bar~.
4. ~'first-directory~: Extracts the first directory relative to
   ~org-roam-directory~ as the tag. That is, if a file is located at relative
   path ~foo/bar/file.org~, the file will have tag ~foo~.

By default, only the ~'prop~ extraction method is enabled. To enable the other
extraction methods, you may modify ~org-roam-tag-sources~:

#+BEGIN_SRC emacs-lisp
(setq org-roam-tag-sources '(prop last-directory))
#+END_SRC

If you wish to add your own tag extraction method, you may push a symbol ~'foo~
into ~org-roam-tag-sources~, and define a ~org-roam--extract-tags-foo~ which
accepts the absolute file path as its argument. See
~org-roam--extract-tags-prop~ for an example.

** File Refs

Refs are unique identifiers for files. Each note can only have 1 ref.
For example, a note for a website may contain a ref:

#+BEGIN_SRC org
  #+title: Google
  #+roam_key: https://www.google.com/
#+END_SRC

These keys come in useful for when taking website notes, using the
~roam-ref~ protocol (see [[*Roam Protocol][Roam Protocol]]).

Alternatively, add a ref for notes for a specific paper, using its
[[https://github.com/jkitchin/org-ref][org-ref]] citation key:

#+BEGIN_SRC org
  #+title: Neural Ordinary Differential Equations
  #+roam_key: cite:chen18_neural_ordin_differ_equat
#+END_SRC

The backlinks buffer will show any cites of this key: e.g.

#+CAPTION: org-ref-citelink
[[file:images/org-ref-citelink.png]]
* The Templating System

Rather than creating blank files on ~org-roam-insert~ and ~org-roam-find-file~,
it may be desirable to prefill the file with templated content. This may
include:

- Time of creation
- File it was created from
- Clipboard content
- Any other data you may want to input manually

This requires a complex template insertion system. Fortunately, Org ships with a
powerful one: ~org-capture~ (see info:org#capture). However, org-capture was not
designed for such use. Org-roam abuses ~org-capture~, extending its syntax and
capabilities. To first understand how org-roam's templating system works, it may
be useful to look into basic usage of ~org-capture~.

For these reasons, Org-roam capture templates are not compatible with regular
~org-capture~. Hence, Org-roam's templates can be customized by instead
modifying the variable ~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.

** Template Walkthrough

To demonstrate the additions made to org-capture templates. Here, we walkthrough
the default template, reproduced below.

#+BEGIN_SRC emacs-lisp
  ("d" "default" plain (function org-roam--capture-get-point)
       "%?"
       :file-name "%<%Y%m%d%H%M%S>-${slug}"
       :head "#+title: ${title}\n"
       :unnarrowed t)
#+END_SRC

1. The template has short key ~"d"~. If you have only one template,
   org-roam automatically chooses this template for you.
2. The template is given a description of ~"default"~.
3. ~plain~ text is inserted. Other options include Org headings via
   ~entry~.
4. ~(function org-roam--capture-get-point)~ should not be changed.
5. ~"%?"~ is the template inserted on each call to ~org-roam-capture--capture~.
   This template means don't insert any content, but place the cursor
   here.
6. ~:file-name~ is the file-name template for a new note, if it doesn't yet
   exist. This creates a file at path that looks like
   ~/path/to/org-roam-directory/20200213032037-foo.org~. This template also
   allows you to specify if you want the note to go into a subdirectory. For
   example, the template ~private/${slug}~ will create notes in
   ~/path/to/org-roam-directory/private~.
7. ~:head~ contains the initial template to be inserted (once only), at
   the beginning of the file. Here, the title global attribute is
   inserted.
8. ~:unnarrowed t~ tells org-capture to show the contents for the whole
   file, rather than narrowing to just the entry.

Other options you may want to learn about include ~:immediate-finish~.

** 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 [[*Template Walkthrough][Template
Walkthrough]].

In org-roam templates, the ~${var}~ syntax allows for the expansion of
variables, stored in ~org-roam-capture--info~. For example, during
~org-roam-insert~, the user is prompted for a title. Upon entering a
non-existent title, the ~title~ key in ~org-roam-capture--info~ is set to the
provided title. ~${title}~ is then expanded into the provided title during the
org-capture process. Any variables that do not contain strings, are prompted for
values using ~completing-read~.

After doing this expansion, the org-capture's template expansion system
is used to fill up the rest of the template. You may read up more on
this on [[https://orgmode.org/manual/Template-expansion.html#Template-expansion][org-capture's documentation page]].

To illustrate this dual expansion process, take for example the template string:
~"%<%Y%m%d%H%M%S>-${title}"~, with the title ~"Foo"~. The template is first
expanded into ~%<%Y%m%d%H%M%S>-Foo~. Then org-capture expands ~%<%Y%m%d%H%M%S>~
with timestamp: e.g. ~20200213032037-Foo~.

All of the flexibility afforded by Emacs and Org-mode are available. For
example, if you want to encode a UTC timestamp in the filename, you can take
advantage of org-mode's ~%(EXP)~ template expansion to call ~format-time-string~
directly to provide its third argument to specify UTC.

#+BEGIN_SRC emacs-lisp
  ("d" "default" plain (function org-roam--capture-get-point)
       "%?"
       :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
       :head "#+title: ${title}\n"
       :unnarrowed t)
#+END_SRC

* Concepts and Configuration
The number of configuration options is deliberately kept small, to keep
the Org-roam codebase manageable. However, we attempt to accommodate as
many usage styles as possible.

All of Org-roam's customization options can be viewed via
~M-x customize-group org-roam~.

** Directories and Files

This section concerns the placement and creation of files.

- Variable: org-roam-directory

  This is the default path to Org-roam files. All Org files, at any level of
  nesting, are considered part of the Org-roam.

- Variable: org-roam-db-location

  Location of the Org-roam database. If this is non-nil, the Org-roam sqlite
  database is saved here.

  It is the user’s responsibility to set this correctly, especially when used
  with multiple Org-roam instances.

** The Org-roam Buffer

The Org-roam buffer displays backlinks for the currently active Org-roam note.

- User Option: org-roam-buffer

  The name of the org-roam buffer. Defaults to ~*org-roam*~.

- User Option: org-roam-buffer-position

  The position of the Org-roam buffer side window. Valid values are ~'left~,
  ~'right~, ~'top~, ~'bottom~.

- User Option: org-roam-buffer-width

  Width of ~org-roam-buffer~. Has an effect only if ~org-roam-buffer-position~ is
  ~'left~ or ~'right~.

- User Option: org-roam-buffer-height

  Height of ~org-roam-buffer~. Has an effect only if ~org-roam-buffer-position~ is
  ~'top~ or ~'bottom~.

- User Option: org-roam-buffer-no-delete-other-windows

  The ~no-delete-window~ parameter for the org-roam buffer. Setting it to ~'t~ prevents the window from being deleted when calling ~delete-other-windows~.

** Org-roam Links

Org-roam links are regular ~file:~ links in Org-mode. By default, links are
inserted with the title as the link description with ~org-roam-insert~.

- User Option: org-roam-link-title-format

  To distinguish between org-roam links and regular links, one may choose to use
  special indicators for Org-roam links. Defaults to ~"%s"~.

  If your version of Org is at least ~9.2~, consider styling the link differently,
  by customizing the ~org-roam-link~, and ~org-roam-link-current~ faces.

** Org-roam Files

Org-roam files are created and prefilled using Org-roam's templating
system. The templating system is customizable (see [[*The Templating System][The Templating System]]).

* Navigating Around

** Index File

As your collection grows, you might want to create an index where you keep links
to your main files.

In Org-roam, you can define the path to your index file by setting
~org-roam-index-file~.

- Variable: org-roam-index-file

  Path to the Org-roam index file.

  The path can be a string or a function. If it is a string, it should be the
  path (absolute or relative to ~org-roam-directory~) to the index file. If it
  is is a function, the function should return the path to the index file.
  Otherwise, the index is assumed to be a note in ~org-roam-index~ whose
  title is ~"Index"~.

- Function: org-roam-find-index

  Opens the Index file in the current ~org-roam-directory~.

* Encryption

One may wish to keep private, encrypted files. Org-roam supports encryption (via
GPG), which can be enabled for all new files by setting ~org-roam-encrypt-files~
to ~t~. When enabled, new files are created with the ~.org.gpg~ extension and
decryption are handled automatically by EasyPG.

Note that Emacs will prompt for a password for encrypted files during
cache updates if it requires reading the encrypted file. To reduce the
number of password prompts, you may wish to cache the password.

- Variable: org-roam-encrypt-files

  Whether to encrypt new files.  If true, create files with .org.gpg extension.
* Graphing

Org-roam provides graphing capabilities to explore interconnections between
notes. This is done by performing SQL queries and generating images using
[[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Roam Protocol][Roam Protocol]].

The entry point to graph creation is ~org-roam-graph~.

- Function: org-roam-graph & optional arg file node-query

  Build and possibly display a graph for FILE from NODE-QUERY.
  If FILE is nil, default to current buffer’s file name.
  ARG may be any of the following values:

  - ~nil~       show the graph.
  - ~C-u~       show the graph for FILE.
  - ~C-u N~     show the graph for FILE limiting nodes to N steps.
  - ~C-u C-u~   build the graph.
  - ~C-u -~     build the graph for FILE.
  - ~C-u -N~    build the graph for FILE limiting nodes to N steps.

- 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:

  1. A string, which is a path to the program used
  2. 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:
  
  #+BEGIN_SRC emacs-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_SRC

** 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-extra-config

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

- User Option: org-roam-graph-node-extra-config

  Extra options for nodes in the graphviz output (The "N" attributes).
  Example: ~'(("color" . "skyblue"))~

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

  Extra options for edges in the graphviz output (The "E" attributes).
  Example: ~'(("dir" . "back"))~

- User Option: org-roam-graph-edge-cites-extra-config

  Extra options for citation edges in the graphviz output.
  Example: ~'(("color" . "red"))~

** Excluding Nodes and Edges

One may want to exclude certain files to declutter the graph.

- User Option: org-roam-graph-exclude-matcher

  Matcher for excluding nodes from the generated graph. Any nodes and links for
  file paths matching this string is excluded from the graph.

  If value is a string, the string is the only matcher.

  If value is a list, all file paths matching any of the strings
  are excluded.

#+BEGIN_EXAMPLE
    (setq org-roam-graph-exclude-matcher '("private" "dailies"))
#+END_EXAMPLE

This setting excludes all files whose path contain "private" or "dailies".

* Org-roam Completion System

Org-roam allows customization of which minibuffer completion system to use for
its interactive commands. The default setting uses Emacs' standard
~completing-read~ mechanism.

#+BEGIN_SRC emacs-lisp
  (setq org-roam-completion-system 'default)
#+END_SRC

If you have installed Helm or Ivy, and have their modes enabled, under the
~'default~ setting they will be used.

In the rare scenario where you use Ivy globally, but prefer [[https://emacs-helm.github.io/helm/][Helm]] for org-roam
commands, set:

#+BEGIN_SRC emacs-lisp
  (setq org-roam-completion-system 'helm)
#+END_SRC

Other options include ~'ido~, and ~'ivy~.

* Roam Protocol
** _ :ignore:
Org-roam extending ~org-protocol~ with 2 protocols: the ~roam-file~
and ~roam-ref~ protocol.

** Installation

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

#+BEGIN_SRC emacs-lisp
(require 'org-roam-protocol)
#+END_SRC

The instructions for setting up ~org-protocol~ are reproduced below.

We will also need to create a desktop application for ~emacsclient~. The
instructions for various platforms are shown below.

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

#+begin_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 ~org-protocol://~ links with the desktop application by
running in your shell:

#+BEGIN_SRC bash
xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
#+END_SRC

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:

#+BEGIN_SRC bash
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_SRC

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

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

For MacOS, one solution is to use [[https://github.com/sveinbjornt/Platypus][Platypus]]. Here are the instructions for
setting up with Platypus and Chrome:

1. Install and launch Platypus (with [[https://brew.sh/][Homebrew]]):

#+BEGIN_SRC bash
brew cask install platypus
#+END_SRC

2. Create a script ~launch_emacs.sh~:

#+BEGIN_SRC bash
#!/usr/bin/env bash
/usr/local/bin/emacsclient --no-wait $1
#+END_SRC

3. Create a Platypus app with the following settings:

#+begin_example
| Setting                        | Value                     |
|--------------------------------+---------------------------|
| App Name                       | "OrgProtocol"             |
| Script Type                    | "env" · "/usr/bin/env"    |
| Script Path                    | "path/to/launch-emacs.sh" |
| Interface                      | None                      |
| Accept dropped items           | true                      |
| Remain running after execution | false                     |
#+end_example


Inside ~Settings~:

#+begin_example
| Setting                        | Value          |
|--------------------------------+----------------|
| Accept dropped files           | true           |
| Register as URI scheme handler | true           |
| Protocol                       | "org-protocol" |
#+end_example

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:

#+BEGIN_SRC bash
defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
#+END_SRC


If you're using [[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 ~OrgProtocol.app~
the default handler instead, run:

#+BEGIN_SRC bash
defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
#+END_SRC

Then restart your computer.

For Windows, create a temporary ~org-protocol.reg~ file:

#+BEGIN_SRC text
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_SRC

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

#+BEGIN_SRC text
@="\"c:\\path\\to\\emacs\\bin\\emacsclientw.exe\"  \"%1\""
#+END_SRC

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

** The roam-file protocol

This is a simple protocol that opens the path specified by the ~file~
key (e.g. ~org-protocol://roam-file?file=/tmp/file.org~). This is used
in the generated graph.

** The roam-ref protocol

This protocol finds or creates a new note with a given ~roam_key~ (see [[*Anatomy of an Org-roam File][Anatomy of an Org-roam File]]):

[[file:images/roam-ref.gif]]

To use this, create the following [[https://en.wikipedia.org/wiki/Bookmarklet][bookmarklet]] in your browser:

#+BEGIN_SRC javascript
javascript:location.href =
'org-protocol://roam-ref?template=r&ref='
+ encodeURIComponent(location.href)
+ '&title='
+ encodeURIComponent(document.title)
#+END_SRC

or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):

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

where ~template~ is the template key for a template in
~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]). These templates
should contain a ~#+roam_key: ${ref}~ in it.

* TODO Daily Notes

* Diagnosing and Repairing Files

Org-roam provides a utility for diagnosing and repairing problematic files via
~org-roam-doctor~. By default, ~org-roam-doctor~ runs the check on the current
Org-roam file. To run the check only for the current file, run ~C-u M-x
org-roam-doctor~, but note that this may take some time.

- Function: org-roam-doctor &optional this-buffer

  Perform a check on Org-roam files to ensure cleanliness. If THIS-BUFFER, run
  the check only for the current buffer.

The checks run are defined in ~org-roam-doctor--checkers~. Each checker is an
instance of ~org-roam-doctor-checker~. To define a checker, use
~make-org-roam-doctor-checker~. Here is a sample definition:

#+BEGIN_SRC emacs-lisp
(make-org-roam-doctor-checker
    :name 'org-roam-doctor-broken-links
    :description "Fix broken links."
    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
               ("r" . ("Replace link" . org-roam-doctor--replace-link))
               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
#+END_SRC

The ~:name~ property is the name of the function run. The function takes in the
Org parse tree, and returns a list of ~(point error-message)~. ~:description~ is a
short description of what the checker does. ~:actions~ is an alist containing
elements of the form ~(char . (prompt . function))~. These actions are defined per
checker, to perform autofixes for the errors. For each error detected,
~org-roam-doctor~ will move the point to the current error, and pop-up a help
window displaying the error message, as well as the list of actions that can be
taken provided in ~:actions~.
* Performance Optimization
** TODO Profiling Key Operations
** 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 [[info:elisp#Garbage Collection][info: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~):

#+BEGIN_SRC emacs-lisp
  (setq org-roam-db-gc-threshold most-positive-fixnum)
#+END_SRC

* _ Copying
:PROPERTIES:
:COPYING:    t
:END:

#+BEGIN_QUOTE
Copyright (C) 2020-2020 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_QUOTE

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

*** 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:

#+BEGIN_SRC emacs-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_SRC
*** 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 [[https://git-scm.com/][Git]]. Simply initialize
~org-roam-directory~ as a Git repository, and commit your files at regular or
appropriate intervals. [[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. [[https://gitlab.com/pidu/git-timemachine][Git-timemachine]] allows you to visit historic
versions of a tracked Org-roam note.

*** Full-text search interface with Deft
   :PROPERTIES:
   :CUSTOM_ID: deft
   :END:

[[https://jblevins.org/projects/deft/][Deft]] provides a nice interface for browsing and filtering org-roam notes.

#+BEGIN_SRC emacs-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 "/path/to/org-roam-files/"))
#+END_SRC

If the title of the Org file is not the first line, you might not get
nice titles. You may choose to patch this to use ~org-roam~'s
functionality. Here I'm using
[[https://github.com/raxod502/el-patch][el-patch]]:

#+BEGIN_SRC emacs-lisp
  (use-package el-patch
    :straight (:host github
                     :repo "raxod502/el-patch"
                     :branch "develop"))

  (eval-when-compile
    (require 'el-patch))

  (use-package deft
    ;; same as above...
    :config/el-patch
    (defun deft-parse-title (file contents)
      "Parse the given FILE and CONTENTS and determine the title.
  If `deft-use-filename-as-title' is nil, the title is taken to
  be the first non-empty line of the FILE.  Else the base name of the FILE is
  used as title."
      (el-patch-swap (if deft-use-filename-as-title
                         (deft-base-filename file)
                       (let ((begin (string-match "^.+$" contents)))
                         (if begin
                             (funcall deft-parse-title-function
                                      (substring contents begin (match-end 0))))))
                     (org-roam--get-title-or-slug file))))
#+END_SRC

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

*** Org-journal
   :PROPERTIES:
   :CUSTOM_ID: org-journal
   :END:

[[https://github.com/bastibe/org-journal][Org-journal]] is a more
powerful alternative to the simple function ~org-roam-dailies-today~. It
provides better journaling capabilities, and a nice calendar interface
to see all dated entries.

#+BEGIN_SRC emacs-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/org-roam-files/")
    (org-journal-date-format "%A, %d %B %Y"))
#+END_SRC

*** Note-taking Add-ons
   :PROPERTIES:
   :CUSTOM_ID: note-taking-add-ons
   :END:

These are some plugins that make note-taking in Org-mode more enjoyable.

**** Org-download
    :PROPERTIES:
    :CUSTOM_ID: org-download
    :END:

[[https://github.com/abo-abo/org-download][Org-download]] lets you screenshot and yank images from the web into your notes:

#+CAPTION: org-download
[[file:images/org-download.gif]]

#+BEGIN_SRC emacs-lisp
  (use-package org-download
    :after org
    :bind
    (:map org-mode-map
          (("s-Y" . org-download-screenshot)
           ("s-y" . org-download-yank))))
#+END_SRC

**** mathpix.el
    :PROPERTIES:
    :CUSTOM_ID: mathpix.el
    :END:

[[https://github.com/jethrokuan/mathpix.el][mathpix.el]] uses [[https://mathpix.com/][Mathpix's]] API to convert clips into latex equations:

#+CAPTION: mathpix
[[file:images/mathpix.gif]]

#+BEGIN_SRC emacs-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_SRC

**** Org-noter / Interleave
    :PROPERTIES:
    :CUSTOM_ID: org-noter-interleave
    :END:

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

**** Bibliography
    :PROPERTIES:
    :CUSTOM_ID: bibliography
    :END:

[[https://github.com/org-roam/org-roam-bibtex][org-roam-bibtex]] offers
tight integration between
[[https://github.com/jkitchin/org-ref][org-ref]],
[[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
~org-roam~. This helps you manage your bibliographic notes under
~org-roam~.

**** Spaced Repetition
    :PROPERTIES:
    :CUSTOM_ID: spaced-repetition
    :END:

[[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 [[https://orgmode.org/worg/org-contrib/org-drill.html][org-drill]], and [[https://github.com/abo-abo/pamparam][pamparam]].

* FAQ
** 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:

#+BEGIN_SRC emacs-lisp
    ((nil . ((org-roam-directory . ".")
             (org-roam-db-location . "./org-roam.db"))))
#+END_SRC

All files within that directory will be treated as their own separate
set of Org-roam files. Remember to run ~org-roam-db-build-cache~ from a
file within that directory, at least once.

** 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 [[https://github.com/fabioberger/roam-migration][in the repository]].

# Local Variables:
# eval: (require 'ol-info)
# before-save-hook: org-make-toc
# after-save-hook: (lambda nil (progn (require 'ox-texinfo nil t) (org-texinfo-export-to-info)))
# indent-tabs-mode: nil
# org-src-preserve-indentation: nil
# End: