org-roam/doc/org-roam.org

#+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 1.1.1

#+OPTIONS: H:4 num:3 toc:2 creator:t
#+PROPERTY: header-args :eval never
#+TEXINFO: @noindent

This manual is for Org-roam version 1.1.1.

#+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.
* Installation
** _ :ignore:
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

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]].

** TODO Installing from the Git Repository

** TODO Post-Installation Tasks

* 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 begin using Org-roam, one should set the =org-roam-directory= to the directory
containing your notes. For this tutorial, create an empty directory, and set the
=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.

** File Aliases

Suppose you want a note to be referred to by different names (e.g.
"World War 2", "WWII"). You may specify such aliases using the
=#+ROAM_ALIAS= attribute:

#+BEGIN_SRC org
  #+TITLE: World War 2
  #+ROAM_ALIAS: "WWII" "World War II"
#+END_SRC

** 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=. However, org-capture was not designed for such use.
Org-roam abuses =org-capture=, extending its syntax. To first understand how
org-roam's templating system works, it may be useful to look into basic usage of
=org-capture=.

Org-roam's templates can be customized by modifying the variable
=org-roam-capture-templates=.

** 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=.
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-window

  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.

** 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 offers completion when choosing note titles etc. The completion
system is configurable. The default setting,

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

uses Emacs' standard =completing-read=. If you prefer
[[https://emacs-helm.github.io/helm/][Helm]], use

#+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.


** 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 a Firefox bookmarklet as follows:

#+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=, adding the following to the =autoconfig.yml= file:

#+BEGIN_SRC yaml
settings:
  bindings.commands:
    global:
      normal:
        gc: open javascript:void(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.

* 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 across all Org-roam
files, and this can take some time. To run the check only for the current file,
run =C-u M-x org-roam-doctor=.

- 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=.

* _ 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
A number of packages work well combined with Org-Roam:

*** 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/zaeph/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://github.com/l3kn/org-fc/][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 . "/path/to/here/"))))
#+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.

* _ :ignore:
# Local Variables:
# 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: