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(docs): add docs for Org-roam unlinked references (#1144)

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Jethro Kuan
2020-09-27 15:21:49 +08:00
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2 changed files with 122 additions and 93 deletions
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doc/org-roam.org
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@ -1023,6 +1023,20 @@ 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 ~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 window displaying the error message, as well as the list of actions that can be
taken provided in ~:actions~. 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 [[https://github.com/BurntSushi/ripgrep][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 * Performance Optimization
** TODO Profiling Key Operations ** TODO Profiling Key Operations
** Garbage Collection ** Garbage Collection

201
doc/org-roam.texi
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@ -80,6 +80,7 @@ General Public License for more details.
* Roam Protocol:: * Roam Protocol::
* Daily Notes:: * Daily Notes::
* Diagnosing and Repairing Files:: * Diagnosing and Repairing Files::
* Finding Unlinked References::
* Performance Optimization:: * Performance Optimization::
* Appendix:: * Appendix::
* FAQ:: * FAQ::
@ -294,9 +295,9 @@ To use Melpa:
@end itemize @end itemize
@lisp @lisp
(require 'package) (require 'package)
(add-to-list 'package-archives (add-to-list 'package-archives
'("melpa" . "http://melpa.org/packages/") t) '("melpa" . "http://melpa.org/packages/") t)
@end lisp @end lisp
@itemize @itemize
@ -305,9 +306,9 @@ To use Melpa-Stable:
@end itemize @end itemize
@lisp @lisp
(require 'package) (require 'package)
(add-to-list 'package-archives (add-to-list 'package-archives
'("melpa-stable" . "http://stable.melpa.org/packages/") t) '("melpa-stable" . "http://stable.melpa.org/packages/") t)
@end lisp @end lisp
Org-roam also depends on a recent version of Org, which can be obtained in Org's Org-roam also depends on a recent version of Org, which can be obtained in Org's
@ -321,14 +322,14 @@ Once you have added your preferred archive, you need to update the
local package list using: local package list using:
@example @example
M-x package-refresh-contents RET M-x package-refresh-contents RET
@end example @end example
Once you have done that, you can install Org-roam and its dependencies Once you have done that, you can install Org-roam and its dependencies
using: using:
@example @example
M-x package-install RET org-roam RET M-x package-install RET org-roam RET
@end example @end example
Now see @ref{Post-Installation Tasks}. Now see @ref{Post-Installation Tasks}.
@ -340,7 +341,7 @@ Users of Debian 11 or later or Ubuntu 20.10 or later can simply install Org-roam
using Apt: using Apt:
@example @example
apt-get install elpa-org-roam apt-get install elpa-org-roam
@end example @end example
Org-roam will then be autoloaded into Emacs. Org-roam will then be autoloaded into Emacs.
@ -399,7 +400,7 @@ Where @code{/path/to/my/info/files} is the location where you keep info files. T
@lisp @lisp
(require 'info) (require 'info)
(add-to-list 'Info-default-directory-list (add-to-list 'Info-default-directory-list
"/path/to/my/info/files") "/path/to/my/info/files")
@end lisp @end lisp
You can also use one of the default locations, such as: You can also use one of the default locations, such as:
@ -429,7 +430,7 @@ Org-roam uses @code{emacsql-sqlite3}, which requires @code{sqlite3} to be locate
operating system. You can verify that this is the case by executing: operating system. You can verify that this is the case by executing:
@lisp @lisp
(executable-find "sqlite3") (executable-find "sqlite3")
@end lisp @end lisp
If you have @code{sqlite3} installed, and @code{executable-find} still reports @code{nil}, then If you have @code{sqlite3} installed, and @code{executable-find} still reports @code{nil}, then
@ -438,7 +439,7 @@ variable @code{exec-path}. You may rectify this by manually adding the path with
your Emacs configuration: your Emacs configuration:
@lisp @lisp
(add-to-list 'exec-path "path/to/sqlite3") (add-to-list 'exec-path "path/to/sqlite3")
@end lisp @end lisp
@node Getting Started @node Getting Started
@ -551,10 +552,10 @@ The aliases are space-delimited, and can be multi-worded using quotes
Take for example the following org file: Take for example the following org file:
@example @example
#+title: World War 2 #+title: World War 2
#+roam_alias: "WWII" "World War II" #+roam_alias: "WWII" "World War II"
* Headline * Headline
@end example @end example
@multitable {aaaaaaaaaaa} {aaaaaaaaaaaaaaaaaaaaaaaa} @multitable {aaaaaaaaaaa} {aaaaaaaaaaaaaaaaaaaaaaaa}
@ -625,8 +626,8 @@ Refs are unique identifiers for files. Each note can only have 1 ref.
For example, a note for a website may contain a ref: For example, a note for a website may contain a ref:
@example @example
#+title: Google #+title: Google
#+roam_key: https://www.google.com/ #+roam_key: https://www.google.com/
@end example @end example
These keys come in useful for when taking website notes, using the These keys come in useful for when taking website notes, using the
@ -636,8 +637,8 @@ Alternatively, add a ref for notes for a specific paper, using its
@uref{https://github.com/jkitchin/org-ref, org-ref} citation key: @uref{https://github.com/jkitchin/org-ref, org-ref} citation key:
@example @example
#+title: Neural Ordinary Differential Equations #+title: Neural Ordinary Differential Equations
#+roam_key: cite:chen18_neural_ordin_differ_equat #+roam_key: cite:chen18_neural_ordin_differ_equat
@end example @end example
The backlinks buffer will show any cites of this key: e.g. The backlinks buffer will show any cites of this key: e.g.
@ -690,11 +691,11 @@ To demonstrate the additions made to org-capture templates. Here, we walkthrough
the default template, reproduced below. the default template, reproduced below.
@lisp @lisp
("d" "default" plain (function org-roam--capture-get-point) ("d" "default" plain (function org-roam--capture-get-point)
"%?" "%?"
:file-name "%<%Y%m%d%H%M%S>-$@{slug@}" :file-name "%<%Y%m%d%H%M%S>-$@{slug@}"
:head "#+title: $@{title@}\n" :head "#+title: $@{title@}\n"
:unnarrowed t) :unnarrowed t)
@end lisp @end lisp
@enumerate @enumerate
@ -760,11 +761,11 @@ advantage of org-mode's @code{%(EXP)} template expansion to call @code{format-ti
directly to provide its third argument to specify UTC@. directly to provide its third argument to specify UTC@.
@lisp @lisp
("d" "default" plain (function org-roam--capture-get-point) ("d" "default" plain (function org-roam--capture-get-point)
"%?" "%?"
:file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--$@{slug@}\" (current-time) t)" :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--$@{slug@}\" (current-time) t)"
:head "#+title: $@{title@}\n" :head "#+title: $@{title@}\n"
:unnarrowed t) :unnarrowed t)
@end lisp @end lisp
@node Concepts and Configuration @node Concepts and Configuration
@ -1029,10 +1030,10 @@ a function accepting a single argument: the graph file path.
If you are using WSL2 and would like to open the graph in Windows, you can use the second option to set the browser and network file path: If you are using WSL2 and would like to open the graph in Windows, you can use the second option to set the browser and network file path:
@lisp @lisp
(setq org-roam-graph-viewer (setq org-roam-graph-viewer
(lambda (file) (lambda (file)
(let ((org-roam-graph-viewer "/mnt/c/Program Files/Mozilla Firefox/firefox.exe")) (let ((org-roam-graph-viewer "/mnt/c/Program Files/Mozilla Firefox/firefox.exe"))
(org-roam-graph--open (concat "file://///wsl$/Ubuntu" file))))) (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))
@end lisp @end lisp
@end itemize @end itemize
@ -1091,7 +1092,7 @@ are excluded.
@end itemize @end itemize
@example @example
(setq org-roam-graph-exclude-matcher '("private" "dailies")) (setq org-roam-graph-exclude-matcher '("private" "dailies"))
@end example @end example
This setting excludes all files whose path contain ``private'' or ``dailies''. This setting excludes all files whose path contain ``private'' or ``dailies''.
@ -1104,7 +1105,7 @@ its interactive commands. The default setting uses Emacs' standard
@code{completing-read} mechanism. @code{completing-read} mechanism.
@lisp @lisp
(setq org-roam-completion-system 'default) (setq org-roam-completion-system 'default)
@end lisp @end lisp
If you have installed Helm or Ivy, and have their modes enabled, under the If you have installed Helm or Ivy, and have their modes enabled, under the
@ -1114,7 +1115,7 @@ In the rare scenario where you use Ivy globally, but prefer @uref{https://emacs-
commands, set: commands, set:
@lisp @lisp
(setq org-roam-completion-system 'helm) (setq org-roam-completion-system 'helm)
@end lisp @end lisp
Other options include @code{'ido}, and @code{'ivy}. Other options include @code{'ido}, and @code{'ivy}.
@ -1307,7 +1308,7 @@ or as a keybinding in @code{qutebrowser} in , using the @code{config.py} file (s
@uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}): @uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}):
@example @example
config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)") config.bind("<Ctrl-r>", "open javascript:location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title)")
@end example @end example
where @code{template} is the template key for a template in where @code{template} is the template key for a template in
@ -1355,6 +1356,20 @@ checker, to perform autofixes for the errors. For each error detected,
window displaying the error message, as well as the list of actions that can be window displaying the error message, as well as the list of actions that can be
taken provided in @code{:actions}. taken provided in @code{:actions}.
@node Finding Unlinked References
@chapter 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 @code{M-x org-roam-unlinked-references} from within
an Org-roam note. Org-roam uses @uref{https://github.com/BurntSushi/ripgrep, 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.
@node Performance Optimization @node Performance Optimization
@chapter Performance Optimization @chapter Performance Optimization
@ -1378,7 +1393,7 @@ operations. To reduce the number of garbage collection processes, one may set
@code{org-roam-db-gc-threshold} to a high value (such as @code{most-positive-fixnum}): @code{org-roam-db-gc-threshold} to a high value (such as @code{most-positive-fixnum}):
@lisp @lisp
(setq org-roam-db-gc-threshold most-positive-fixnum) (setq org-roam-db-gc-threshold most-positive-fixnum)
@end lisp @end lisp
@node Appendix @node Appendix
@ -1442,9 +1457,9 @@ operations. To reduce the number of garbage collection processes, one may set
@code{winner-mode} can be used as a simple version of browser history for Org-roam. Each click through org-roam links (from both Org files and the backlinks buffer) causes changes in window configuration, which can be undone and redone using @code{winner-mode}. To use @code{winner-mode}, simply enable it, and bind the appropriate interactive functions: @code{winner-mode} can be used as a simple version of browser history for Org-roam. Each click through org-roam links (from both Org files and the backlinks buffer) causes changes in window configuration, which can be undone and redone using @code{winner-mode}. To use @code{winner-mode}, simply enable it, and bind the appropriate interactive functions:
@lisp @lisp
(winner-mode +1) (winner-mode +1)
(define-key winner-mode-map (kbd "<M-left>") #'winner-undo) (define-key winner-mode-map (kbd "<M-left>") #'winner-undo)
(define-key winner-mode-map (kbd "<M-right>") #'winner-redo) (define-key winner-mode-map (kbd "<M-right>") #'winner-redo)
@end lisp @end lisp
@ -1466,15 +1481,15 @@ versions of a tracked Org-roam note.
@uref{https://jblevins.org/projects/deft/, Deft} provides a nice interface for browsing and filtering org-roam notes. @uref{https://jblevins.org/projects/deft/, Deft} provides a nice interface for browsing and filtering org-roam notes.
@lisp @lisp
(use-package deft (use-package deft
:after org :after org
:bind :bind
("C-c n d" . deft) ("C-c n d" . deft)
:custom :custom
(deft-recursive t) (deft-recursive t)
(deft-use-filter-string-for-filename t) (deft-use-filter-string-for-filename t)
(deft-default-extension "org") (deft-default-extension "org")
(deft-directory "/path/to/org-roam-files/")) (deft-directory "/path/to/org-roam-files/"))
@end lisp @end lisp
If the title of the Org file is not the first line, you might not get If the title of the Org file is not the first line, you might not get
@ -1483,29 +1498,29 @@ functionality. Here I'm using
@uref{https://github.com/raxod502/el-patch, el-patch}: @uref{https://github.com/raxod502/el-patch, el-patch}:
@lisp @lisp
(use-package el-patch (use-package el-patch
:straight (:host github :straight (:host github
:repo "raxod502/el-patch" :repo "raxod502/el-patch"
:branch "develop")) :branch "develop"))
(eval-when-compile (eval-when-compile
(require 'el-patch)) (require 'el-patch))
(use-package deft (use-package deft
;; same as above... ;; same as above...
:config/el-patch :config/el-patch
(defun deft-parse-title (file contents) (defun deft-parse-title (file contents)
"Parse the given FILE and CONTENTS and determine the title. "Parse the given FILE and CONTENTS and determine the title.
If `deft-use-filename-as-title' is nil, the title is taken to 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 be the first non-empty line of the FILE. Else the base name of the FILE is
used as title." used as title."
(el-patch-swap (if deft-use-filename-as-title (el-patch-swap (if deft-use-filename-as-title
(deft-base-filename file) (deft-base-filename file)
(let ((begin (string-match "^.+$" contents))) (let ((begin (string-match "^.+$" contents)))
(if begin (if begin
(funcall deft-parse-title-function (funcall deft-parse-title-function
(substring contents begin (match-end 0)))))) (substring contents begin (match-end 0))))))
(org-roam--get-title-or-slug file)))) (org-roam--get-title-or-slug file))))
@end lisp @end lisp
The Deft interface can slow down quickly when the number of files get The Deft interface can slow down quickly when the number of files get
@ -1521,14 +1536,14 @@ provides better journaling capabilities, and a nice calendar interface
to see all dated entries. to see all dated entries.
@lisp @lisp
(use-package org-journal (use-package org-journal
:bind :bind
("C-c n j" . org-journal-new-entry) ("C-c n j" . org-journal-new-entry)
:custom :custom
(org-journal-date-prefix "#+title: ") (org-journal-date-prefix "#+title: ")
(org-journal-file-format "%Y-%m-%d.org") (org-journal-file-format "%Y-%m-%d.org")
(org-journal-dir "/path/to/org-roam-files/") (org-journal-dir "/path/to/org-roam-files/")
(org-journal-date-format "%A, %d %B %Y")) (org-journal-date-format "%A, %d %B %Y"))
@end lisp @end lisp
@node Note-taking Add-ons @node Note-taking Add-ons
@ -1555,12 +1570,12 @@ These are some plugins that make note-taking in Org-mode more enjoyable.
@end float @end float
@lisp @lisp
(use-package org-download (use-package org-download
:after org :after org
:bind :bind
(:map org-mode-map (:map org-mode-map
(("s-Y" . org-download-screenshot) (("s-Y" . org-download-screenshot)
("s-y" . org-download-yank)))) ("s-y" . org-download-yank))))
@end lisp @end lisp
@node mathpixel @node mathpixel
@ -1574,12 +1589,12 @@ These are some plugins that make note-taking in Org-mode more enjoyable.
@end float @end float
@lisp @lisp
(use-package mathpix.el (use-package mathpix.el
:straight (:host github :repo "jethrokuan/mathpix.el") :straight (:host github :repo "jethrokuan/mathpix.el")
:custom ((mathpix-app-id "app-id") :custom ((mathpix-app-id "app-id")
(mathpix-app-key "app-key")) (mathpix-app-key "app-key"))
:bind :bind
("C-x m" . mathpix-screenshot)) ("C-x m" . mathpix-screenshot))
@end lisp @end lisp
@node Org-noter / Interleave @node Org-noter / Interleave
@ -1626,8 +1641,8 @@ variable using directory-local variables. This is what @code{.dir-locals.el} may
contain: contain:
@lisp @lisp
((nil . ((org-roam-directory . ".") ((nil . ((org-roam-directory . ".")
(org-roam-db-location . "./org-roam.db")))) (org-roam-db-location . "./org-roam.db"))))
@end lisp @end lisp
All files within that directory will be treated as their own separate All files within that directory will be treated as their own separate