     Copyright (C) 2020-2021 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 2.1.0.

     Copyright (C) 2020-2021 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 tool for networked thought. It reproduces some of Roam Research's (https://roamresearch.com/)  (To understand more about Roam, a collection of links are available in Note-taking Workflows.) key features within Org-mode (https://orgmode.org/).

Org-roam allows for effortless non-hierarchical note-taking: with Org-roam, notes flow naturally, making note-taking fun and easy. Org-roam augments the Org-mode syntax, and will work for anyone already using Org-mode for their personal wiki.

Org-roam leverages the mature ecosystem around Org-mode. For example, it has first-class support for org-ref (https://github.com/jkitchin/org-ref) for citation management, and is able to piggyback off Org's excellent LaTeX and source-block evaluation capabilities.

Org-roam provides these benefits over other tooling:

  * Privacy and Security: Your personal wiki belongs only to you, entirely offline and in your control. Encrypt your notes with GPG.

  * Longevity of Plain Text: Unlike web solutions like Roam Research, the notes are first and foremost plain Org-mode files -- Org-roam simply builds an auxiliary database to give the personal wiki superpowers. Having your notes in plain-text is crucial for the longevity of your wiki. Never have to worry about proprietary web solutions being taken down. The notes are still functional even if Org-roam ceases to exist.

  * Free and Open Source: Org-roam is free and open-source, which means that if you feel unhappy with any part of Org-roam, you may choose to extend Org-roam, or open a pull request.

  * Leverage the Org-mode ecosystem: Over the decades, Emacs and Org-mode has developed into a mature system for plain-text organization. Building upon Org-mode already puts Org-roam light-years ahead of many other solutions.

  * Built on Emacs: Emacs is also a fantastic interface for editing text, and Org-roam inherits many of the powerful text-navigation and editing packages available to Emacs.

Target Audience
***************

Org-roam is a tool that will appear unfriendly to anyone unfamiliar with Emacs and Org-mode, but it is also extremely powerful to those willing to put effort in mastering the intricacies. Org-roam stands on the shoulders of giants. Emacs was first created in 1976, and remains the tool of choice for many for editing text and designing textual interfaces. The malleability of Emacs allowed the creation of Org-mode, an all-purpose plain-text system for maintaining TODO lists, planning projects, and authoring documents. Both of these tools are incredibly vast and require significant time investment to master.

Org-roam assumes only basic familiarity with these tools. It is not difficult to get up and running with basic text-editing functionality, but one will only fully appreciate the power of building Roam functionality into Emacs and Org-mode when the usage of these tools become more advanced.

One key advantage to Org-roam is that building on top of Emacs gives it malleability. This is especially important for note-taking workflows. It is our belief that note-taking workflows are extremely personal, and there is no one tool that's perfect for you. Org-mode and Org-roam allows you to discover what works for you, and build that perfect tool for yourself.

If you are new to the software, and choose to take this leap of faith, I hope you find yourself equally entranced as Neal Stephenson was.

     Emacs outshines all other editing software in approximately the same way that the noonday sun does the stars. It is not just bigger and brighter; it simply makes everything else vanish. – Neal Stephenson, In the Beginning was the Command Line (1998)

A Brief Introduction to the Zettelkasten Method
***********************************************

Org-roam provides utilities for maintaining a digital slip-box. This section aims to provide a brief introduction to the ``slip-box'', or ``Zettelkasten'' method. By providing some background on the method, we hope that the design decisions of Org-roam will become clear, and that will aid in using Org-roam appropriately. In this section we will introduce terms commonly used within the Zettelkasten community and the Org-roam forums.

The Zettelkasten is a personal tool for thinking and writing. It places heavy emphasis on connecting ideas, building up a web of thought. Hence, it is well suited for knowledge workers and intellectual tasks, such as conducting research. The Zettelkasten can act as a research partner, where conversations with it may produce new and surprising lines of thought.

This method is attributed to German sociologist Niklas Luhmann, who using the method had produced volumes of written works. Luhmann's slip-box was simply a box of cards. These cards are small -- often only large enough to fit a single concept. The size limitation encourages ideas to be broken down into individual concepts. These ideas are explicitly linked together. The breakdown of ideas encourages tangential exploration of ideas, increasing the surface for thought. Making linking explicit between notes also encourages one to think about the connections between concepts.

At the corner of each note, Luhmann ascribed each note with an ordered ID, allowing him to link and jump between notes. In Org-roam, we simply use hyperlinks.

Org-roam is the slip-box, digitalized in Org-mode. Every zettel (card) is a plain-text, Org-mode file. In the same way one would maintain a paper slip-box, Org-roam makes it easy to create new zettels, pre-filling boilerplate content using a powerful templating system.

Fleeting notes

A slip-box requires a method for quickly capturing ideas. These are called fleeting notes: they are simple reminders of information or ideas that will need to be processed later on, or trashed. This is typically accomplished using org-capture (see Capture (org)), or using Org-roam's daily notes functionality (see Org-roam Dailies). This provides a central inbox for collecting thoughts, to be processed later into permanent notes.

Permanent notes

Permanent notes are further split into two categories: literature notes and concept notes. Literature notes can be brief annotations on a particular source (e.g. book, website or paper), that you'd like to access later on. Concept notes require much more care in authoring: they need to be self-explanatory and detailed. Org-roam's templating system supports the addition of different templates to facilitate the creation of these notes.

For further reading on the Zettelkasten method, ``How to Take Smart Notes'' by Sonke Ahrens is a decent guide.

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

Installing from Source
======================

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

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

Installing from GitHub requires that you clone the repository:

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

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

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

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

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

  * dash

  * f

  * s

  * org

  * emacsql

  * emacsql-sqlite

  * magit-section

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

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

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

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

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

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

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

  * usr/local/share/info

  * usr/share/info

  * usr/local/share/info

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

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

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

Installation Troubleshooting
============================

C Compiler
----------

Org-roam relies on an Emacs package called emacsql and emacsql-sqlite to work with the sqlite database. Both of them should be installed automatically in your Emacs environment as a prerequisite for Org-roam when you install it.

emacsql-sqlite requires a C compiler (e.g. gcc or clang) to be present in your computer. How to install a C compiler depends on the OS that you use.

  * For Windows:

There are various ways to install one, depending on how you have installed Emacs. If you use Emacs within a Cygwin or MinGW environment, then you should install a compiler using their respective package manager.

If you have installed your Emacs from the GNU Emacs website (https://www.gnu.org/software/emacs/), then the easiest way is to use MSYS2 (https://www.msys2.org/) as at the time of this writing:

  * Use the installer in the official website and install MSYS2

  * Run MSYS2

  * In the command-line tool, type the following and answer ``Y'' to proceed:

          pacman -S gcc

     Note that you do not need to manually set the PATH for MSYS2; the

installer automatically takes care of it for you.

  * Open Emacs and call M-x org-roam-db-autosync-mode

     This will automatically start compiling emacsql-sqlite; you should see a

message in minibuffer. It may take a while until compilation completes. Once complete, you should see a new file emacsql-sqlite.exe created in a subfolder named sqlite under emacsql-sqlite installation folder. It's typically in your Emacs configuration folder like this: /.config/emacs/elpa/emacsql-sqlite-20190727.1710/sqlite

Getting Started
***************

The Org-roam Node
=================

We first begin with some terminology we'll use throughout the manual. We term the basic denomination in Org-roam a node. We define a node as follows:

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

For example, with this example file content:

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

     * Bar
     :PROPERTIES:
     :ID:       bar
     :END:

We create two nodes:

  * A file node ``Foo'' with id foo.

  * A headline node ``Bar'' with id bar.

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

Links between Nodes
===================

We link between nodes using Org's standard ID link (e.g. id:foo). While only ID links will be considered during the computation of links between nodes, Org-roam caches all other links in the documents for external use.

Setting up Org-roam
===================

Org-roam's capabilities stem from its aggressive caching: it crawls all files within org-roam-directory, and maintains a cache of all links and nodes.

To start using Org-roam, pick a location to store the Org-roam files. The directory that will contain your notes is specified by the variable org-roam-directory. Org-roam searches recursively within org-roam-directory for notes. This variable needs to be set before any calls to Org-roam functions.

For this tutorial, create an empty directory, and set org-roam-directory:

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

The file-truename function is only necessary when you use symbolic links inside org-roam-directory: Org-roam does not resolve symbolic links.

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

     (org-roam-db-autosync-mode)

To build the cache manually, run M-x org-roam-db-sync. Cache builds may take a while the first time, but subsequent builds are often instantaneous because they only reprocess modified files.

Creating and Linking Nodes
==========================

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

  * org-roam-node-insert: creates a node if it does not exist, and inserts a link to the node at point.

  * org-roam-node-find: creates a node if it does not exist, and visits the node.

  * org-roam-capture: creates a node if it does not exist, and restores the current window configuration upon completion.

Let's first try org-roam-node-find. Calling M-x org-roam-node-find will show a list of titles for nodes that reside in org-roam-directory. It should show nothing right now, since there are no notes in the directory. Enter the title of the note you wish to create, and press RET. This begins the note creation process. This process uses org-capture's templating system, and can be customized (see The Templating System). Using the default template, pressing C-c C-c finishes the note capture.

Now that we have a node, we can try inserting a link to the node using M-x org-roam-node-insert. This brings up the list of nodes, which should contain the node you just created. Selecting the node will insert an id: link to the node. If you instead entered a title that does not exist, you will once again be brought through the node creation process.

One can also conveniently insert links via the completion-at-point functions Org-roam provides (see Completion).

Customizing Node Caching
************************

What to cache
=============

By default, all nodes (any headline or file with an ID) are cached by Org-roam. There are instances where you may want to have headlines with ID, but not have them cached by Org-roam.

To exclude a headline from the Org-roam database, set the ROAM_EXCLUDE property to a non-nil value. For example:

     * Foo
       :PROPERTIES:
       :ID:       foo
       :ROAM_EXCLUDE: t
       :END:

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

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

When to cache
=============

By default, Org-roam is eager in caching: each time an Org-roam file is modified and saved, it updates the database for the corresponding file. This keeps the database up-to-date, causing the least surprise when using the interactive commands.

However, depending on how large your Org files are, database updating can be a slow operation. You can disable the automatic updating of the database by setting org-roam-db-update-on-save to nil.

 -- Variable: org-roam-db-update-on-save

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

The Org-roam Buffer
*******************

Org-roam provides the Org-roam buffer: an interface to view relationships with other notes (backlinks, reference links, unlinked references etc.). There are two main commands to use here:

  * org-roam-buffer-toggle: Launch an Org-roam buffer that tracks the node currently at point. This means that the content of the buffer changes as the point is moved, if necessary.

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

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

 -- Function: org-roam-buffer-toggle

     Toggle display of the org-roam-buffer.

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

 -- Function: org-roam-buffer-display-dedicated

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

Navigating the Org-roam Buffer
==============================

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

  * M-{N}: magit-section-show-level-{N}-all

  * n: magit-section-forward

-<TAB>: magit-section-toggle

  * <RET>: org-roam-buffer-visit-thing

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

Configuring what is displayed in the buffer
===========================================

There are currently 3 provided widget types:

  * BacklinksView (preview of) nodes that link to this node

  * Reference LinksNodes that reference this node (see Refs)

  * Unlinked referencesView nodes that contain text that match the nodes title/alias but are not linked

To configure what sections are displayed in the buffer, set org-roam-mode-section-functions.

     (setq org-roam-mode-section-functions
           (list #'org-roam-backlinks-section
                 #'org-roam-reflinks-section
                 ;; #'org-roam-unlinked-references-section
                 ))

Note that computing unlinked references may be slow, and has not been added in by default.

Configuring the Org-roam buffer display
=======================================

Org-roam does not control how the pop-up buffer is displayed: this is left to the user. The author's recommended configuration is as follows:

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

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

  * RET navigates to thing-at-point in the current window, replacing the Org-roam buffer.

  * C-u RET navigates to thing-at-point in the other window.

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

     (add-to-list 'display-buffer-alist
                  '("\\*org-roam\\*"
                    (display-buffer-in-side-window)
                    (side . right)
                    (slot . 0)
                    (window-width . 0.33)
                    (window-parameters . ((no-other-window . t)
                                          (no-delete-other-windows . t)))))

TODO Styling the Org-roam buffer
================================

Node Properties
***************

Standard Org properties
=======================

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

  * outline level

  * todo state

  * priority

  * scheduled

  * deadline

  * tags

Titles and Aliases
==================

Each node has a single title. For file nodes, this is specified with the `#+title` property for the file. For headline nodes, this is the main text.

Nodes can also have multiple aliases. Aliases allow searching for nodes via an alternative name. For example, one may want to assign a well-known acronym (AI) to a node titled ``Artificial Intelligence''.

To assign an alias to a node, add the ``ROAM_ALIASES'' property to the node:

     * Artificial Intelligence
     :PROPERTIES:
     :ROAM_ALIASES: AI
     :END:

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

 -- Function: org-roam-alias-add alias

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

 -- Function: org-roam-alias-remove

     Remove an alias from the node at point.

Tags
====

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

Note that the #+filetags keyword results in tags being inherited by headers within the file. This makes it impossible for selective tag inheritance: i.e. either tag inheritance is turned off, or all headline nodes will inherit the tags from the file node. This is a design compromise of Org-roam.

Refs
====

Refs are unique identifiers for nodes. These keys allow references to the key to show up in the Org-roam buffer. For example, a node for a website may use the URL as the ref, and a node for a paper may use an Org-ref citation key.

To add a ref, add to the ``ROAM_REFS'' property as follows:

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

With the above example, if another node links to https://www.google.com/, it will show up as a “reference backlink”.

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

You may assign multiple refs to a single node, for example when you want multiple papers in a series to share the same note, or an article has a citation key and a URL at the same time.

Org-roam also provides some functions to add or remove refs.

 -- Function: org-roam-ref-add ref

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

 -- Function: org-roam-ref-remove

     Remove a ref from the node at point.

Citations
*********

Since version 9.5, Org has first-class support for citations. Org-roam supports the caching of both these in-built citations (of form [cite:@key]) and org-ref (https://github.com/jkitchin/org-ref) citations (of form (NO_ITEM_DATA:key)).

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

Using the Cached Information
============================

It is common to use take reference notes for academic papers. To designate the node to be the canonical node for the academic paper, we can use its unique citation key:

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

for org-cite, or:

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

for org-ref.

When another node has a citation for that key, we can see it using the Reflinks section of the Org-roam buffer.

Extension developers may be interested in retrieving the citations within their notes. This information can be found within the citation table of the Org-roam database.

Completion
**********

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

  * When within an Org bracket link

  * Anywhere

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

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

Completing within Link Brackets
===============================

Completions within link brackets are provided by org-roam-complete-link-at-point.

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

Completing anywhere
===================

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

This is disable by default. To enable it, set org-roam-completion-everywhere to t:

     (setq org-roam-completion-everywhere t)

 -- Variable: org-roam-completion-everywhere

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

Encryption
**********

Emacs has support for creating and editing encrypted gpg files, and Org-roam need not provide additional tooling. To create encrypted files, simply add the .gpg extension in your Org-roam capture templates. For example:

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

Note that the Org-roam database stores metadata information in plain-text (headline text, for example), so if this information is private to you then you should also ensure the database is encrypted.

Org-roam Protocol
*****************

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

Installation
============

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

     (require 'org-roam-protocol)

We also need to set up org-protocol: the instructions for setting up org-protocol are reproduced below.

Linux
-----

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

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

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

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

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

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

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

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

Mac OS
------

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

  * Launch Script Editor

  * Use the following script, paying attention to the path to emacsclient:

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

  * Save the script in /Applications/OrgProtocolClient.app, changing the script type to ``Application'', rather than ``Script''.

  * Edit /Applications/OrgProtocolClient.app/Contents/Info.plist, adding the following before the last </dict> tag:

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

  * Save the file, and run the OrgProtocolClient.app to register the protocol.

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

     defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true

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

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

Then restart your computer.

Windows
-------

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

     REGEDIT4

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

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

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

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

The roam-node protocol
======================

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

The roam-ref protocol
=====================

This protocol finds or creates a new note with a given ROAM_REFS:

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

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

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

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

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

The Templating System
*********************

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

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

Template Walkthrough
====================

To demonstrate the additions made to org-capture templates. Here, we explain the default template, reproduced below. You will find most of the elements of the template are similar to org-capture templates.

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

  * The template has short key "d". If you have only one template, org-roam automatically chooses this template for you.

  * The template is given a description of "default".

  * plain text is inserted. Other options include Org headings via entry.

  * Notice that the target that's usually in Org-capture templates is missing here.

  * "%?" is the template inserted on each call to org-roam-capture-. This template means don't insert any content, but place the cursor here.

  * :target is a compulsory specification in the Org-roam capture template. The first element of the list indicates the type of the target, the second element indicates the location of the captured node, and the rest of the elements indicate prefilled template that will be inserted and the position of the point will be adjusted for. The latter behavior varies from type to type of the capture target.

  * :unnarrowed t tells org-capture to show the contents for the whole file, rather than narrowing to just the entry. This is part of the Org-capture templates.

See the org-roam-capture-templates documentation for more details and customization options.

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.

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

  * If foo is a function, foo is called with the current node as its argument.

  * Else if org-roam-node-foo is a function, foo is called with the current node as its argument. The org-roam-node- prefix defines many of Org-roam's node accessors such as org-roam-node-title and org-roam-node-level.

  * Else look up org-roam-capture--info for foo. This is an internal variable that is set before the capture process begins.

  * If none of the above applies, read a string using completing-read.

       * Org-roam also provides the ${foo=default_val} syntax, where if a default value is provided, will be the initial value for the foo key during minibuffer completion.

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

     (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
                                  (:copier nil))
       "A heading or top level file with an assigned ID property."
       file file-hash file-atime file-mtime
       id level point todo priority scheduled deadline title properties olp
       tags aliases refs)

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

Graphing
********

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

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

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

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

  * nil       show the full graph.

  * integer   an integer argument N will show the graph for the connected components to node up to N steps away.

 -- User Option: org-roam-graph-executable

     Path to the graphing executable (in this case, Graphviz). Set this if Org-roam is unable to find the Graphviz executable on your system.

     You may also choose to use neato in place of dot, which generates a more compact graph layout.

 -- User Option: org-roam-graph-viewer

     Org-roam defaults to using Firefox (located on PATH) to view the SVG, but you may choose to set it to:

       * A string, which is a path to the program used

       * a function accepting a single argument: the graph file path.

     nil uses view-file to view the graph.

     If you are using WSL2 and would like to open the graph in Windows, you can use the second option to set the browser and network file path:

          (setq org-roam-graph-viewer
              (lambda (file)
                (let ((org-roam-graph-viewer "/mnt/c/Program Files/Mozilla Firefox/firefox.exe"))
                  (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))

Graph Options
=============

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

 -- User Option: org-roam-graph-filetype

     The file type to generate for graphs. This defaults to "svg".

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

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

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

     An alist of options to style the nodes. The car of the alist node type such as "id", or "http". The cdr of the list is another alist of Graphviz node options (the ``N'' attributes).

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

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

Org-roam Dailies
****************

Org-roam provides journaling capabilities akin to Org-journal with org-roam-dailies.

Configuration
=============

For org-roam-dailies to work, you need to define two variables:

 -- Variable: org-roam-dailies-directory

     Path to daily-notes. This path is relative to org-roam-directory.

 -- Variable: org-roam-dailies-capture-templates

     Capture templates for daily-notes in Org-roam.

Here is a sane default configuration:

     (setq org-roam-dailies-directory "daily/")

     (setq org-roam-dailies-capture-templates
           '(("d" "default" entry
              "* %?"
              :target (file+head "%<%Y-%m-%d>.org"
                                 "#+title: %<%Y-%m-%d>\n"))))

See The Templating System for creating new templates.

Usage
=====

org-roam-dailies provides these interactive functions:

 -- Function: org-roam-dailies-capture-today &optional goto

     Create an entry in the daily note for today.

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

 -- Function: org-roam-dailies-goto-today

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

There are variants of those commands for -yesterday and -tomorrow:

 -- Function: org-roam-dailies-capture-yesterday n &optional goto

     Create an entry in the daily note for yesteday.

     With numeric argument n, use the daily note n days in the past.

 -- Function: org-roam-dailies-goto-yesterday

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

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

 -- Function: org-roam-dailies-capture-date

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

     Prefer past dates, unless prefer-future is non-nil.

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

 -- Function: org-roam-dailies-goto-date

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

     Prefer past dates, unless prefer-future is non-nil.

 -- Function: org-roam-dailies-find-directory

     Find and open org-roam-dailies-directory.

 -- Function: org-roam-dailies-goto-previous-note

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

 -- Function: org-roam-dailies-goto-next-note

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

Performance Optimization
************************

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)

The Org-mode Ecosystem
**********************

Because Org-roam is built on top of Org-mode, it benefits from the vast number of packages already available.

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 with Deft
==========================

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

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

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

Org-journal
===========

Org-journal (https://github.com/bastibe/org-journal) provides journaling capabilities to Org-mode. A lot of its functionalities have been incorporated into Org-roam under the name org-roam-dailies. It remains a good tool if you want to isolate your verbose journal entries from the ideas you would write on a scratchpad.

     (use-package org-journal
       :bind
       ("C-c n j" . org-journal-new-entry)
       :custom
       (org-journal-date-prefix "#+title: ")
       (org-journal-file-format "%Y-%m-%d.org")
       (org-journal-dir "/path/to/journal/files/")
       (org-journal-date-format "%A, %d %B %Y"))

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.

For example, though helm-bibtex provides the ability to visit notes for bibliographic entries, org-roam-bibtex extends it with the ability to visit the file with the right ROAM_REFS.

Spaced Repetition
=================

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

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

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 . (expand-file-name "."))
              (org-roam-db-location . (expand-file-name "./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-sync 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:

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

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

How can I stop Org-roam from creating IDs everywhere?
=====================================================

Other than the interactive commands that Org-roam provides, Org-roam does not create IDs everywhere. If you are noticing that IDs are being created even when you don't want them to be (e.g. when tangling an Org file), check the value you have set for org-id-link-to-org-use-id: setting it to 'create-if-interactive is a popular option.

Migrating from Org-roam v1
**************************

Those coming from Org-roam v1 will do well treating v2 as entirely new software. V2 has a smaller core and fewer moving parts, while retaining the bulk of its functionality. It is recommended to read the documentation above about nodes.

It is still desirable to migrate notes collected in v1 to v2. To migrate your v1 notes to v2, you may use the migration script provided in this gist (https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4), or this gist (https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4#gistcomment-3737019), the latter being better tested. This blog post (https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html) provides a good overview of what's new in v2 and how to migrate.

Simply put, to migrate notes from v1 to v2, one must:

  * Add IDs to all existing notes. These are located in top-level property drawers (Although note that in v2, not all files need to have IDs)

  * Update the Org-roam database to conform to the new schema.

  * Replace #+ROAM_KEY into the ROAM_REFS property

  * Replace #+ROAM_ALIAS into the ROAM_ALIASES property

  * Move #+ROAM_TAGS into the #+FILETAGS property for file-level nodes, and the ROAM_TAGS property for headline nodes

  * Replace existing file links with ID links.

Developer's Guide to Org-roam
*****************************

Org-roam's Design Principle
===========================

Org-roam is primarily motivated by the need for a dual representation. We (humans) love operating in a plain-text environment. The syntax rules of Org-mode are simple and fit snugly within our brain. This also allows us to use the tools and packages we love to explore and edit our notes. Org-mode is simply the most powerful plain-text format available, with support for images, LaTeX, TODO planning and much more.

But this plain-text format is simply ill-suited for exploration of these notes: plain-text is simply not amenable for answering large-scale, complex queries (e.g. how many tasks do I have that are due by next week?). Interfaces such as Org-agenda slow to a crawl when the number of files becomes unwieldy, which can quickly become the case.

At its core, Org-roam provides a database abstraction layer, providing a dual representation of what's already available in plain-text. This allows us (humans) to continue working with plain-text, while programs can utilize the database layer to perform complex queries. These capabilities include, but are not limited to:

  * link graph traversal and visualization

  * Instantaneous SQL-like queries on headlines

       * What are my TODOs, scheduled for X, or due by Y?

  * Accessing the properties of a node, such as its tags, refs, TODO state or priority

All of these functionality is powered by this database abstraction layer. Hence, at its core Org-roam's primary goal is to provide a resilient dual representation that is cheap to maintain, easy to understand, and is as up-to-date as it possibly can. Org-roam also then exposes an API to this database abstraction layer for users who would like to perform programmatic queries on their Org files.

Building Extensions and Advanced Customization of Org-roam
==========================================================

Because Org-roam's core functionality is small, it is possible and sometimes desirable to build extensions on top of it. These extensions may one or more of the following functionalities:

  * Access to Org-roam's database

  * Usage/modification of Org-roam's interactive commands

Org-roam provides no guarantees that extensions will continue to function as Org-roam evolves, but by following these simple rules, extensions can be made robust to local changes in Org-roam.

  * Extensions should not modify the database schema. Any extension that requires the caching of additional data should make a request upstream to Org-roam.

  * Extensions requiring access to the database should explicitly state support for the database version (org-roam-db-version), and only conditionally load when support is available.

Accessing the Database
----------------------

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

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

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

Accessing and Modifying Nodes
-----------------------------

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

 -- Function: org-roam-node-at-point &optional assert

     Return the node at point. If ASSERT, throw an error if there is no node at point.

 -- Function: org-roam-node-read &optional initial-input filter-fn sort-fn
     require-match

     Read and return an `org-roam-node'. INITIAL-INPUT is the initial minibuffer prompt value. FILTER-FN is a function to filter out nodes: it takes a single argument (an org-roam-node), and when nil is returned the node will be filtered out. SORT-FN is a function to sort nodes. See org-roam-node-read-sort-by-file-mtime for an example sort function. If REQUIRE-MATCH, the minibuffer prompt will require a match.

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

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

     (cl-defmethod org-roam-node-namespace ((node org-roam-node))
       "Return the namespace for NODE.
     The namespace is the final directory of the file for the node."
       (file-name-nondirectory
        (directory-file-name
         (file-name-directory (org-roam-node-file node)))))

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

Extending the Capture System
----------------------------

Org-roam applies some patching over Org's capture system to smooth out the user experience, and sometimes it is desirable to use Org-roam's capturing system instead. The exposed function to be used in extensions is org-roam-capture-:

 -- Function: org-roam-capture- &key goto keys node info props templates

     Main entry point. GOTO and KEYS correspond to `org-capture' arguments. INFO is a plist for filling up Org-roam's capture templates. NODE is an `org-roam-node' construct containing information about the node. PROPS is a plist containing additional Org-roam properties for each template. TEMPLATES is a list of org-roam templates.

An example of an extension using org-roam-capture- is org-roam-dailies itself:

     (defun org-roam-dailies--capture (time &optional goto)
       "Capture an entry in a daily-note for TIME, creating it if necessary.

     When GOTO is non-nil, go the note without creating an entry."
       (org-roam-capture- :goto (when goto '(4))
                          :node (org-roam-node-create)
                          :templates org-roam-dailies-capture-templates
                          :props (list :override-default-time time))
       (when goto (run-hooks 'org-roam-dailies-find-file-hook)))

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
=========

Bibliography
************

NO_ITEM_DATA:key

Emacs 28.0.50 (Org mode 9.5)