     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.

Org-roam User Manual
********************

This manual is for Org-roam version 1.2.1.

     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.

Introduction
************

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

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.

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.

     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)

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 capture (org)), or using Org-roam's daily notes functionality (see 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 Packages (emacs). Then, add one of the archives to package-archives:

  * To use Melpa:

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

  * To use Melpa-Stable:

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

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

     (add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)

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

     M-x package-refresh-contents RET

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

     M-x package-install RET org-roam RET

Now see 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:

     apt-get install elpa-org-roam

Org-roam will then be autoloaded into Emacs.

Installing from the Git Repository
==================================

You may install Org-roam directly from the repository on GitHub (https://github.com/org-roam/org-roam) if you like. This will give you access to the latest version hours or days before it appears on MELPA, and months (or more) before it is added to the Debian or Ubuntu repositories. This will also give you access to various developmental branches that may be available.

Note, however, that development version, and especially any feature branches, may not always be in working order. You'll need to be prepared to do some debugging, or to manually roll-back to working versions, if you install from GitHub.

Installing from GitHub requires that you clone the repository:

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

where ./path/to/org/roam is the location you will store your copy of the code.

Next, you need to add this location to your load path, and require the Org-roam library. Add the following code to your .emacs:

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

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

  * dash

  * f

  * s

  * org

  * emacsql

  * emacsql-sqlite3

You can install this manually as well, or get the latest version from MELPA. You may wish to use use-package (https://github.com/jwiegley/use-package), straight.el (https://github.com/raxod502/straight.el), or some other tool or tools to help manage this.

If you would like to install the manual for access from Emacs' built-in Info system, you'll need to compile the .texi source file, and install it in an appropriate location.

To compile the .texi source file, from a terminal navigate to the /doc subdirectory of the Org-roam repository, and run the following:

     make infodir=/path/to/my/info/files install-info

Where /path/to/my/info/files is the location where you keep info files. This target directory needs to be stored in the variable `Info-default-directory-list`. If you aren't using one of the default info locations, you can configure this with the following in your .emacs file:

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

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

  * usr/local/share/info

  * usr/share/info

  * usr/local/share/info

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

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

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

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:

     (executable-find "sqlite3")

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:

     (add-to-list 'exec-path "path/to/sqlite3")

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 Zettelkasten Method (https://zettelkasten.de/), and many of Roam Research's (https://roamresearch.com) 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.

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:

     (make-directory "~/org-roam")
     (setq org-roam-directory "~/org-roam")

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:

     (add-hook 'after-init-hook 'org-roam-mode)

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). 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).

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:

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

     * Headline

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:

     (setq org-roam-tag-sources '(prop last-directory))

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:

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

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

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

     #+title: Neural Ordinary Differential Equations
     #+roam_key: cite:chen18_neural_ordin_differ_equat

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

Figure: org-ref-citelink

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 capture (org)). 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.

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

 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.

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 org-capture's documentation page (https://orgmode.org/manual/Template-expansion.html#Template-expansion).

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.

     ("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)

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.

  * Variable: org-roam-file-exclude-regexp

     Files matching this regular expression are excluded from the Org-roam.

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 Files
==============

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

Inserting Links
***************

The preferred mode of linking is via file links to files, and id links for headlines. This maintains the strongest compatibility with Org-mode, ensuring that the links still function without Org-roam, and work well exporting to other backends.

file links can be inserted via org-roam-insert. Links to headlines can be inserted by navigating to the desired headline and calling org-store-link. This will create an ID for the headline if it does not already exist, and populate the Org-roam database. The link can then be inserted via org-insert-link.

An alternative mode of insertion is using Org-roam's roam links. Org-roam registers this link type, and interprets the path as follows:

[[roam:title]]
     links to an Org-roam file with title or alias ``title''

[[roam:*headline]]
     links to the headline ``headline'' in the current Org-roam file

[[roam:title*headline]]
     links to the headline ``headline'' in the Org-roam file with title or alias ``title''

roam links support auto-completion via completion-at-point: simply call completion-at-point within a roam link. Users of company-mode may want to prepend company-capf to the beginning of variable company-backends.

To easily insert roam links, one may wish to use a package like key-chord (https://github.com/emacsorphanage/key-chord/). In the following example, typing ``[['' will insert a stub roam link:

     (key-chord-define org-mode-map "[[" #'my/insert-roam-link)

     (defun my/insert-roam-link ()
         "Inserts an Org-roam link."
         (interactive)
         (insert "[[roam:]]")
         (backward-char 2))

  * 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.

  * User Option: org-roam-completion-ignore-case

     When non-nil, the roam link completions are ignore case. For example, calling completion-at-point within [[roam:fo]] will present a completion for a file with title ``Foo''. Defaults to t.

  * User Option: org-roam-link-auto-replace

     When non-nil, roam links will be replaced with file or id links when they are navigated to, and on file save, when a match is found. This is desirable to maintain compatibility with vanilla Org, but resolved links are harder to edit. Defaults to t.

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 Graphviz (https://graphviz.org/). The graph can also be navigated: see 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:

          (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)))))

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.

     (setq org-roam-graph-exclude-matcher '("private" "dailies"))

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.

     (setq org-roam-completion-system 'default)

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 Helm (https://emacs-helm.github.io/helm/) for org-roam commands, set:

     (setq org-roam-completion-system 'helm)

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:

     (require 'org-roam-protocol)

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:

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

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

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

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

     sudo mkdir -p /etc/opt/chrome/policies/managed/
     sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
     {
       "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
     }
     EOF
     sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json

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

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

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

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

     brew cask install platypus

 1. Create a script launch_emacs.sh:

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

 1. Create a Platypus app with the following settings:

     | 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                     |

Inside Settings:

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

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

     defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true

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

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

Then restart your computer.

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

     REGEDIT4

     [HKEY_CLASSES_ROOT\org-protocol]
     @="URL:Org Protocol"
     "URL Protocol"=""
     [HKEY_CLASSES_ROOT\org-protocol\shell]
     [HKEY_CLASSES_ROOT\org-protocol\shell\open]
     [HKEY_CLASSES_ROOT\org-protocol\shell\open\command]
     @="\"C:\\Windows\\System32\\wsl.exe\" emacsclient \"%1\""

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

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

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

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):

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

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

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

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

where template is the template key for a template in org-roam-capture-ref-templates (see 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:

     (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))))

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.

Finding Unlinked References
***************************

Unlinked references are occurrences of strings of text that exactly match the title or alias of an existing note in the Org-roam database. Org-roam provides facilities for discovering these unlinked references, so one may decide whether to convert them into links.

To use this feature, simply call M-x org-roam-unlinked-references from within an Org-roam note. Org-roam uses ripgrep (https://github.com/BurntSushi/ripgrep), specifically a clever PCRE regex to find occurrences of the title or aliases of the currently open note in all Org-roam files. This thus requires a version of ripgrep that is compiled with PCRE support.

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 (elisp)).

Org-roam provides the option org-roam-db-gc-threshold to temporarily change the threshold value for GC to be triggered during these memory-intensive operations. To reduce the number of garbage collection processes, one may set org-roam-db-gc-threshold to a high value (such as most-positive-fixnum):

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

Appendix
********

Note-taking Workflows
=====================

Books

       * How To Take Smart Notes (https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes)

Articles

       * The Zettelkasten Method - LessWrong 2.0 (https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1)

       * Building a Second Brain in Roam...And Why You Might Want To : RoamResearch (https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)

       * Roam Research: Why I Love It and How I Use It - Nat Eliason (https://www.nateliason.com/blog/roam)

       * Adam Keesling's Twitter Thread (https://twitter.com/adam_keesling/status/1196864424725774336?s=20)

       * How To Take Smart Notes With Org-mode · Jethro Kuan (https://blog.jethro.dev/posts/how_to_take_smart_notes_org/)

Threads

       * Ask HN: How to Take Good Notes (https://news.ycombinator.com/item?id=22473209)

Videos

       * How to Use Roam to Outline a New Article in Under 20 Minutes (https://www.youtube.com/watch?v=RvWic15iXjk)

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:

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

Versioning Notes
----------------

Since Org-roam notes are just plain text, it is trivial to track changes in your notes database using version control systems such as Git (https://git-scm.com/). Simply initialize org-roam-directory as a Git repository, and commit your files at regular or appropriate intervals. Magit (https://magit.vc/) is a great interface to Git within Emacs.

In addition, it may be useful to observe how a particular note has evolved, by looking at the file history. Git-timemachine (https://gitlab.com/pidu/git-timemachine) allows you to visit historic versions of a tracked Org-roam note.

Full-text search interface with Deft
------------------------------------

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

     (use-package deft
       :after org
       :bind
       ("C-c n d" . deft)
       :custom
       (deft-recursive t)
       (deft-use-filter-string-for-filename t)
       (deft-default-extension "org")
       (deft-directory "/path/to/org-roam-files/"))

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 el-patch (https://github.com/raxod502/el-patch):

     (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))))

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

Org-journal
-----------

Org-journal (https://github.com/bastibe/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.

     (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"))

Note-taking Add-ons
-------------------

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

Org-download
............

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

Figure: org-download

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

mathpix.el
..........

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

Figure: mathpix

     (use-package mathpix.el
       :straight (:host github :repo "jethrokuan/mathpix.el")
       :custom ((mathpix-app-id "app-id")
                (mathpix-app-key "app-key"))
       :bind
       ("C-x m" . mathpix-screenshot))

Org-noter / Interleave
......................

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

Bibliography
............

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

Spaced Repetition
.................

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

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:

     ((nil . ((org-roam-directory . ".")
              (org-roam-db-location . "./org-roam.db"))))

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 in the repository (https://github.com/fabioberger/roam-migration).

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:

Ivy
     call ivy-immediate-done, typically bound to C-M-j. Alternatively, set ivy-use-selectable-prompt to t, so that ``bar'' is now selectable.

Helm
     Org-roam should provide a selectable ``[?] bar'' candidate at the top of the candidate list.

Emacs 28.0.50 (Org mode 9.4)