regenerate texi

PATH needs to be manually set on Windows. Previously, it was explicitly
mentioned that it was unnecessary. More recent experience is that it's necessary.

.dir-locals.el

@@ -4,9 +4,6 @@
   (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
   (elisp-lint-indent-specs . ((describe . 1)
                               (it . 1)
-                              (thread-first . 0)
-                              (cl-flet . 1)
-                              (cl-flet* . 1)
                               (org-element-map . defun)
                               (org-roam-dolist-with-progress . 2)
                               (org-roam-with-temp-buffer . 1)

.github/workflows/test.yml

@@ -46,7 +46,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Install Eldev
-        run: curl -fsSL https://raw.github.com/org-roam/org-roam/master/github-eldev | sh
+        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
 
       - name: Install dependencies
         run: make prepare

CHANGELOG.md

@@ -1,45 +1,8 @@
 # Changelog
-## 2.2.1
-### Breaking
-- [#2054](https://github.com/org-roam/org-roam/pull/2054) node: simplify default `org-roam-node-display-template`.
-  This was done so completions work fine by default on all completion systems. To restore the tabular vertical completion interface, set this in your configuration:
-
-  ```emacs-lisp
-  (setq org-roam-node-display-template
-        (concat "${title:*} "
-                (propertize "${tags:10}" 'face 'org-tag)))
-  ```
 
+## TBD
 ### Added
-- [#2042](https://github.com/org-roam/org-roam/pull/2042) db: add `org-roam-db-extra-links-elements` and `org-roam-db-extra-links-exclude-keys` for fine-grained control over additional link parsing
-- [#2049](https://github.com/org-roam/org-roam/pull/2049) capture: allow ID to be used as part of `org-roam-capture-templates`
-- [#2050](https://github.com/org-roam/org-roam/pull/2050) core: add `FILTER-FN` to `org-roam-node-random`
-- [#2065](https://github.com/org-roam/org-roam/pull/2065) dailies: add `keys` argument to the remaining dailies functions `org-roam-dailies-goto-yesterday`/`-today`/`-tomorrow`/`-date` and `org-roam-dailies-capture-yesterday`/`-tomorrow`/`-date` to give the abilty to get into a capture buffer bypassing the selection screen in all dailies commands. Extension of #2055
-- [#2079](https://github.com/org-roam/org-roam/pull/2079) capture: ensure that `:ref` info captured in all cases.
-- [#2121](https://github.com/org-roam/org-roam/pull/2121) buffer: add unique option to `org-roam-backlinks-section`
-
-### Removed
-### Fixed
-- [#2086](https://github.com/org-roam/org-roam/pull/2086) capture: correctly update org-id-locations on capture
-- [#2082](https://github.com/org-roam/org-roam/pull/2082) buffer: don't destroy window if `org-roam-node-toggle` reuses window
-- [#2080](https://github.com/org-roam/org-roam/pull/2080) dailies: prevent multiple "dailies/" subdir expansions
-- [#2055](https://github.com/org-roam/org-roam/pull/2055) dailies: removed stray f require, which was causing require and compilation errors
-- [#2117](https://github.com/org-roam/org-roam/pull/2117) capture: preserve trailing whitespace content in capture templates
-
-### Changed
-- [#2060](https://github.com/org-roam/org-roam/pull/2060) node: added double acute accent normalization for Unicode characters in titles
-- [#2040](https://github.com/org-roam/org-roam/pull/2040) completions: fix completions display-width for Helm users
-- [#2025](https://github.com/org-roam/org-roam/pull/2025) chore: removed the dependencies on f.el and s.el
-- [#2109](https://github.com/org-roam/org-roam/pull/2109) capture: `org-roam-node-insert` places cursor after inserted link where appropriate
-- [#2123](https://github.com/org-roam/org-roam/pull/2123), [#2124](https://github.com/org-roam/org-roam/pull/2124) buffer: `org-roam-mode-section-functions` renamed to `org-roam-mode-sections`, supports passing args into the section-rendering function
-
-## 2.2.0
-### Added
-- [#1806](https://github.com/org-roam/org-roam/pull/1806), [#2017](https://github.com/org-roam/org-roam/pull/2017) db: support caching and usage of Org 9.5's in-built citations
-- [#1963](https://github.com/org-roam/org-roam/pull/1963) db: cache file title into files table
-- [#1977](https://github.com/org-roam/org-roam/pull/1977) db: support Org-ref v3 citations
-- [#1907](https://github.com/org-roam/org-roam/pull/1907), [#2009](https://github.com/org-roam/org-roam/pull/2009), [#2018](https://github.com/org-roam/org-roam/pull/2018) db: support sqlite3
-- [#2028](https://github.com/org-roam/org-roam/pull/2028) dailies: add `keys` argument to `org-roam-dailies-capture-today` and `org-roam-dailies--capture` functions to give the abilty to get into a capture buffer bypassing the selection screen
+- [#1806](https://github.com/org-roam/org-roam/pull/1806) db: support caching and usage of Org 9.5's in-built citations
 
 ### Removed
 ### Changed
@@ -47,22 +10,12 @@
 - [#1809](https://github.com/org-roam/org-roam/pull/1809) capture: the mandatory `:if-new` property of each capture template is now renamed to `:target`
 - [#1829](https://github.com/org-roam/org-roam/pull/1829) perf: file sql updates are now wrapped in a transaction
 - [#1877](https://github.com/org-roam/org-roam/pull/1877) dailies: stop asking for time, only date
-- [#1949](https://github.com/org-roam/org-roam/pull/1949) db: check for property drawers are now case-insensitive
 
 ### Fixed
 - [#1798](https://github.com/org-roam/org-roam/pull/1798) org-roam-node-at-point: do not skip invisible headings
 - [#1807](https://github.com/org-roam/org-roam/pull/1807) capture: always trigger `:if-new` template for existing nodes
 - [#1813](https://github.com/org-roam/org-roam/pull/1813) db: prevent empty ROAM_ALIASES from crashing db updates
 - [#1816](https://github.com/org-roam/org-roam/pull/1816) db: prevent invalid ROAM_REFS from crashing db updates
-- [#1893](https://github.com/org-roam/org-roam/pull/1893), [#1896](https://github.com/org-roam/org-roam/pull/1896), [#1901](https://github.com/org-roam/org-roam/pull/1901), [#1895](https://github.com/org-roam/org-roam/pull/1895), [#1904](https://github.com/org-roam/org-roam/pull/1904) completions: various mini-buffer related completion fixes
-- [#1931](https://github.com/org-roam/org-roam/pull/1931) utils: org-roam-set-keyword now skips over all drawers
-- [#1947](https://github.com/org-roam/org-roam/pull/1947) db: links in ROAM_REFS are no longer considered as links
-- [#1948](https://github.com/org-roam/org-roam/pull/1948) completions: fix same-line completions
-- [#1953](https://github.com/org-roam/org-roam/pull/1953) db: refresh CATEGORY before writing to db
-- [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1946](https://github.com/org-roam/org-roam/pull/1946), [#1958](https://github.com/org-roam/org-roam/pull/1958) various performance improvements
-- [#1980](https://github.com/org-roam/org-roam/pull/1980) utils: fix org-roam-with-file changing the minor-mode
-- [#2016](https://github.com/org-roam/org-roam/pull/2016) db: fix node caching being affected by agenda variables
-- [#2033](https://github.com/org-roam/org-roam/pull/2023) db: respect local variables during db parsing
 
 ## 2.1.0
 ### Added

README.md

@@ -47,6 +47,30 @@ Stable](https://stable.melpa.org/) using `package.el`:
 ```
 M-x package-install RET org-roam RET
 ```
+
+Here's a very basic sample for configuration of `org-roam` using `use-package`:
+
+```emacs-lisp
+(use-package org-roam
+  :ensure t
+  :custom
+  (org-roam-directory (file-truename "/path/to/org-files/"))
+  :bind (("C-c n l" . org-roam-buffer-toggle)
+         ("C-c n f" . org-roam-node-find)
+         ("C-c n g" . org-roam-graph)
+         ("C-c n i" . org-roam-node-insert)
+         ("C-c n c" . org-roam-capture)
+         ;; Dailies
+         ("C-c n j" . org-roam-dailies-capture-today))
+  :config
+  (org-roam-db-autosync-mode)
+  ;; If using org-roam-protocol
+  (require 'org-roam-protocol))
+```
+
+Note that the `file-truename` function is only necessary when you use symbolic
+link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
+to the directory.
 </details>
 
 ### Using `straight.el`
@@ -174,33 +198,6 @@ Org-roam also comes with `.texi` files to integrate with Emacs' built-in Info
 system. Read the manual to find more details for how to install them manually.
 </details>
 
-## Configuration
-
-Here's a very basic sample for configuration of `org-roam` using `use-package`:
-
-```emacs-lisp
-(use-package org-roam
-  :ensure t
-  :custom
-  (org-roam-directory (file-truename "/path/to/org-files/"))
-  :bind (("C-c n l" . org-roam-buffer-toggle)
-         ("C-c n f" . org-roam-node-find)
-         ("C-c n g" . org-roam-graph)
-         ("C-c n i" . org-roam-node-insert)
-         ("C-c n c" . org-roam-capture)
-         ;; Dailies
-         ("C-c n j" . org-roam-dailies-capture-today))
-  :config
-  ;; If you're using a vertical completion framework, you might want a more informative completion interface
-  (setq org-roam-node-display-template (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag)))
-  (org-roam-db-autosync-mode)
-  ;; If using org-roam-protocol
-  (require 'org-roam-protocol))
-```
-
-Note that the `file-truename` function is only necessary when you use symbolic
-link to `org-roam-directory`. Org-roam won't automatically resolve symbolic link
-to the directory.
 ## Getting Started
 
 [David Wilson](https://github.com/daviwil) of [System
@@ -228,7 +225,7 @@ it has not already been addressed on [GitHub][issues] or on
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-- [Alexey Shmalko](https://www.alexeyshmalko.com/)
+- [Alexey Shmalko](https://braindump.rasen.dev/)
 - [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
 
 ## Contributing

doc/org-roam.org

@@ -1,20 +1,20 @@
 #+title: Org-roam User Manual
 #+author: Jethro Kuan
 #+email: jethrokuan95@gmail.com
-#+date: 2020-2022
+#+date: 2020-2021
 #+language: en
 
 #+texinfo_deffn: t
 #+texinfo_dir_category: Emacs
 #+texinfo_dir_title: Org-roam: (org-roam).
 #+texinfo_dir_desc: Roam Research for Emacs.
-#+subtitle: for version 2.2.1
+#+subtitle: for version 2.1.0
 
 #+options: H:4 num:3 toc:nil creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent
 
-This manual is for Org-roam version 2.2.1.
+This manual is for Org-roam version 2.1.0.
 
 #+BEGIN_QUOTE
 Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
@@ -369,12 +369,7 @@ For this tutorial, create an empty directory, and set ~org-roam-directory~:
 #+END_SRC
 
 The ~file-truename~ function is only necessary when you use symbolic links
-inside ~org-roam-directory~: Org-roam does not resolve symbolic links. One can
-however instruct Emacs to always resolve symlinks, at a performance cost:
-
-#+begin_src emacs-lisp
-  (setq find-file-visit-truename t)
-#+end_src
+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
@@ -418,59 +413,8 @@ brought through the node creation process.
 One can also conveniently insert links via the completion-at-point functions
 Org-roam provides (see [[*Completion][Completion]]).
 
-** Customizing Node Completions
-
-Node selection is achieved via the ~completing-read~ interface, typically
-through `org-roam-node-read`. The presentation of these nodes are governed by
-~org-roam-node-display-template~.
-
-- Variable: org-roam-node-display-template
-
-  Configures display formatting for Org-roam node.
-
-  Patterns of form "${field-name:length}" are interpolated based
-  on the current node.
-
-  Each "field-name" is replaced with the return value of each
-  corresponding accessor function for org-roam-node, e.g.
-  "${title}" will be interpolated by the result of
-  org-roam-node-title. You can also define custom accessors using
-  cl-defmethod. For example, you can define:
-
-    (cl-defmethod org-roam-node-my-title ((node org-roam-node))
-      (concat "My " (org-roam-node-title node)))
-
-  and then reference it here or in the capture templates as
-  "${my-title}".
-
-  "length" is an optional specifier and declares how many
-  characters can be used to display the value of the corresponding
-  field. If it's not specified, the field will be inserted as is,
-  i.e. it won't be aligned nor trimmed. If it's an integer, the
-  field will be aligned accordingly and all the exceeding
-  characters will be trimmed out. If it's "*", the field will use
-  as many characters as possible and will be aligned accordingly.
-
-  A closure can also be assigned to this variable in which case the
-  closure is evaluated and the return value is used as the
-  template. The closure must evaluate to a valid template string.
-
-If you're using a vertical completion framework, such as Ivy and Selectrum,
-Org-roam supports the generation of an aligned, tabular completion interface.
-For example, to include a column for tags up to 10 character widths wide, one
-can set ~org-roam-node-display-template~ as such:
-
-#+begin_src emacs-lisp
-  (setq org-roam-node-display-template
-        (concat "${title:*} "
-                (propertize "${tags:10}" 'face 'org-tag)))
-#+end_src
-
 * Customizing Node Caching
 ** How to cache
-:PROPERTIES:
-:ID:       280bfca8-83f3-4371-bc3a-25478d25129c
-:END:
 
 Org-roam uses a sqlite database to perform caching, but there are multiple Emacs
 libraries that can be used. The default used by Org-roam is ~emacs-sqlite~.
@@ -541,35 +485,6 @@ all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
         (not (member "ATTACH" (org-get-tags)))))
 #+end_src
 
-Org-roam relied on the obtained Org AST for the buffer to parse links. However,
-links appearing in some places (e.g. within property drawers) are not considered
-by the Org AST to be links. Therefore, Org-roam takes special care of
-additionally trying to process these links. Use
-~org-roam-db-extra-links-elements~ to specify which additional Org AST element
-types to consider.
-
-- Variable: org-roam-db-extra-links-elements
-
-  The list of Org element types to include for parsing by Org-roam.
-
-  By default, when parsing Org's AST, links within keywords and
-  property drawers are not parsed as links. Sometimes however, it
-  is desirable to parse and cache these links (e.g. hiding links in
-  a property drawer).
-
-Additionally, one may want to ignore certain keys from being excluded within
-property drawers. For example, we would not want ~ROAM_REFS~ links to be
-self-referential. Hence, to exclude specific keys, we use
-~org-roam-db-extra-links-exclude-keys~.
-
-- Variable: org-roam-db-extra-links-exclude-keys
-
-  Keys to ignore when mapping over links.
-
-  The car of the association list is the Org element type (e.g. keyword). The
-  cdr is a list of case-insensitive strings to exclude from being treated as
-  links.
-
 ** When to cache
 
 By default, Org-roam is eager in caching: each time an Org-roam file is modified
@@ -636,10 +551,10 @@ There are currently 3 provided widget types:
 - Unlinked references :: View 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-sections.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-section-functions~.
 
 #+begin_src emacs-lisp
-  (setq org-roam-mode-sections
+  (setq org-roam-mode-section-functions
         (list #'org-roam-backlinks-section
               #'org-roam-reflinks-section
               ;; #'org-roam-unlinked-references-section
@@ -648,16 +563,6 @@ To configure what sections are displayed in the buffer, set ~org-roam-mode-secti
 
 Note that computing unlinked references may be slow, and has not been added in by default.
 
-For each section function, you can pass args along to modify its behaviour. For
-example, if you want to render unique sources for backlinks (and also keep
-rendering reference links), set ~org-roam-mode-sections~ as follows:
-
-#+begin_src emacs-lisp
-  (setq org-roam-mode-sections
-        '((org-roam-backlinks-section :unique t)
-          org-roam-reflinks-section))
-#+end_src
-
 ** Configuring the Org-roam buffer display
 
 Org-roam does not control how the pop-up buffer is displayed: this is left to
@@ -806,16 +711,6 @@ citation key:
 :END:
 #+end_src
 
-or
-
-#+begin_src org
-,* Probabilistic Robotics
-:PROPERTIES:
-:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
-:ROAM_REFS: [cite:@thrun2005probabilistic]
-:END:
-#+end_src
-
 for ~org-cite~, or:
 
 #+begin_src org
@@ -912,16 +807,7 @@ file:
 #+END_SRC
 
 We also need to set up ~org-protocol~: the instructions for setting up
-~org-protocol~ are reproduced here.
-
-On a high-level, external calls are passed to Emacs via ~emacsclient~.
-~org-protocol~ intercepts these and runs custom actions based on the protocols
-registered. Hence, to use ~org-protocol~, once must:
-
-1. launch the ~emacsclient~ process
-2. Register ~org-protocol://~ as a valid scheme-handler
-
-The instructions for the latter for each operating system is detailed below.
+~org-protocol~ are reproduced below.
 
 *** Linux
 For Linux users, create a desktop application in
@@ -1465,9 +1351,6 @@ documents (PDF, EPUB etc.) within Org-mode.
 
 ** Bibliography
 
-Org 9.5 added native citation and bibliography functionality, called "org-cite",
-which org-roam supports.
-
 [[https://github.com/org-roam/org-roam-bibtex][org-roam-bibtex]] offers tight integration between [[https://github.com/jkitchin/org-ref][org-ref]], [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
 ~org-roam~. This helps you manage your bibliographic notes under ~org-roam~.
 
@@ -1640,20 +1523,6 @@ to the publishing directory.  Example code follows:
                                          (kill-buffer (file-name-nondirectory svg))
                                          (setq my-publish-time 0)))))
 #+end_src
-** I'm seeing this "Selecting deleted buffer" error. What do I do?
-
-The "selecting deleted buffer" error usually occurs when you don't have a
-working ~emacsql-sqlite~ executable. Org-roam relies on this executable to
-function properly, and doesn't catch this error. This issue is most commonly
-seen on Windows setups. You can browse through the various GitHub issues posted
-about this [[https://github.com/org-roam/org-roam/issues?q=is%3Aissue+selecting+deleted][here]].
-
-To fix this, you can try the following:
-
-1. If on Windows, try replacing your system binary with [[https://github.com/nobiot/emacsql-sqlite.exe][this one]] that has been proven
-   to work
-2. Use the ~emacsql-sqlite3~ option rather than compiling your own emacsql
-   binary (see [[id:280bfca8-83f3-4371-bc3a-25478d25129c][How to cache]]).
 
 * Developer's Guide to Org-roam
 ** Org-roam's Design Principle

doc/org-roam.texi

@@ -31,7 +31,7 @@ General Public License for more details.
 @finalout
 @titlepage
 @title Org-roam User Manual
-@subtitle for version 2.2.1
+@subtitle for version 2.1.0
 @author Jethro Kuan
 @page
 @vskip 0pt plus 1filll
@@ -44,7 +44,7 @@ General Public License for more details.
 
 @noindent
 
-This manual is for Org-roam version 2.2.1.
+This manual is for Org-roam version 2.1.0.
 
 @quotation
 Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@@gmail.com>
@@ -110,7 +110,6 @@ Getting Started
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
-* Customizing Node Completions::
 
 Customizing Node Caching
 
@@ -195,7 +194,6 @@ FAQ
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
-* I'm seeing this ``Selecting deleted buffer'' error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?. 
 
 How do I publish my notes with an Internet-friendly graph?
 
@@ -588,7 +586,6 @@ your Emacs configuration folder like this:
 * Links between Nodes::
 * Setting up Org-roam::
 * Creating and Linking Nodes::
-* Customizing Node Completions::
 @end menu
 
 @node The Org-roam Node
@@ -655,12 +652,7 @@ For this tutorial, create an empty directory, and set @code{org-roam-directory}:
 @end lisp
 
 The @code{file-truename} function is only necessary when you use symbolic links
-inside @code{org-roam-directory}: Org-roam does not resolve symbolic links. One can
-however instruct Emacs to always resolve symlinks, at a performance cost:
-
-@lisp
-(setq find-file-visit-truename t)
-@end lisp
+inside @code{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 @code{M-x org-roam-db-autosync-mode}. To
@@ -712,56 +704,6 @@ brought through the node creation process.
 One can also conveniently insert links via the completion-at-point functions
 Org-roam provides (see @ref{Completion}).
 
-@node Customizing Node Completions
-@section Customizing Node Completions
-
-Node selection is achieved via the @code{completing-read} interface, typically
-through `org-roam-node-read`. The presentation of these nodes are governed by
-@code{org-roam-node-display-template}.
-
-@defvar org-roam-node-display-template
-
-Configures display formatting for Org-roam node.
-
-Patterns of form ``$@{field-name:length@}'' are interpolated based
-on the current node.
-
-Each ``field-name'' is replaced with the return value of each
-corresponding accessor function for org-roam-node, e.g.
-``$@{title@}'' will be interpolated by the result of
-org-roam-node-title. You can also define custom accessors using
-cl-defmethod. For example, you can define:
-
-(cl-defmethod org-roam-node-my-title ((node org-roam-node))
-  (concat ``My '' (org-roam-node-title node)))
-
-and then reference it here or in the capture templates as
-``$@{my-title@}''.
-
-``length'' is an optional specifier and declares how many
-characters can be used to display the value of the corresponding
-field. If it's not specified, the field will be inserted as is,
-i.e. it won't be aligned nor trimmed. If it's an integer, the
-field will be aligned accordingly and all the exceeding
-characters will be trimmed out. If it's ``*'', the field will use
-as many characters as possible and will be aligned accordingly.
-
-A closure can also be assigned to this variable in which case the
-closure is evaluated and the return value is used as the
-template. The closure must evaluate to a valid template string.
-@end defvar
-
-If you're using a vertical completion framework, such as Ivy and Selectrum,
-Org-roam supports the generation of an aligned, tabular completion interface.
-For example, to include a column for tags up to 10 character widths wide, one
-can set @code{org-roam-node-display-template} as such:
-
-@lisp
-(setq org-roam-node-display-template
-      (concat "$@{title:*@} "
-              (propertize "$@{tags:10@}" 'face 'org-tag)))
-@end lisp
-
 @node Customizing Node Caching
 @chapter Customizing Node Caching
 
@@ -844,37 +786,6 @@ all headlines with the @code{ATTACH} tag from the Org-roam database, one can set
         (not (member "ATTACH" (org-get-tags)))))
 @end example
 
-Org-roam relied on the obtained Org AST for the buffer to parse links. However,
-links appearing in some places (e.g. within property drawers) are not considered
-by the Org AST to be links. Therefore, Org-roam takes special care of
-additionally trying to process these links. Use
-@code{org-roam-db-extra-links-elements} to specify which additional Org AST element
-types to consider.
-
-@defvar org-roam-db-extra-links-elements
-
-The list of Org element types to include for parsing by Org-roam.
-
-By default, when parsing Org's AST, links within keywords and
-property drawers are not parsed as links. Sometimes however, it
-is desirable to parse and cache these links (e.g. hiding links in
-a property drawer).
-@end defvar
-
-Additionally, one may want to ignore certain keys from being excluded within
-property drawers. For example, we would not want @code{ROAM_REFS} links to be
-self-referential. Hence, to exclude specific keys, we use
-@code{org-roam-db-extra-links-exclude-keys}.
-
-@defvar org-roam-db-extra-links-exclude-keys
-
-Keys to ignore when mapping over links.
-
-The car of the association list is the Org element type (e.g. keyword). The
-cdr is a list of case-insensitive strings to exclude from being treated as
-links.
-@end defvar
-
 @node When to cache
 @section When to cache
 
@@ -976,10 +887,10 @@ There are currently 3 provided widget types:
 title/alias but are not linked
 @end itemize
 
-To configure what sections are displayed in the buffer, set ~org-roam-mode-sections.
+To configure what sections are displayed in the buffer, set @code{org-roam-mode-section-functions}.
 
 @lisp
-(setq org-roam-mode-sections
+(setq org-roam-mode-section-functions
       (list #'org-roam-backlinks-section
             #'org-roam-reflinks-section
             ;; #'org-roam-unlinked-references-section
@@ -988,16 +899,6 @@ To configure what sections are displayed in the buffer, set ~org-roam-mode-secti
 
 Note that computing unlinked references may be slow, and has not been added in by default.
 
-For each section function, you can pass args along to modify its behaviour. For
-example, if you want to render unique sources for backlinks (and also keep
-rendering reference links), set @code{org-roam-mode-sections} as follows:
-
-@lisp
-(setq org-roam-mode-sections
-      '((org-roam-backlinks-section :unique t)
-        org-roam-reflinks-section))
-@end lisp
-
 @node Configuring the Org-roam buffer display
 @section Configuring the Org-roam buffer display
 
@@ -1165,7 +1066,7 @@ Remove a ref from the node at point.
 
 Since version 9.5, Org has first-class support for citations. Org-roam supports
 the caching of both these in-built citations (of form @code{[cite:@@key]}) and @uref{https://github.com/jkitchin/org-ref, org-ref}
-citations (of form cite:key).
+citations (of form @uref{key}).
 
 Org-roam attempts to load both the @code{org-ref} and @code{org-cite} package when
 indexing files, so no further setup from the user is required for citation
@@ -1190,16 +1091,6 @@ citation key:
 :END:
 @end example
 
-or
-
-@example
-* Probabilistic Robotics
-:PROPERTIES:
-:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
-:ROAM_REFS: [cite:@@thrun2005probabilistic]
-:END:
-@end example
-
 for @code{org-cite}, or:
 
 @example
@@ -1319,21 +1210,7 @@ file:
 @end lisp
 
 We also need to set up @code{org-protocol}: the instructions for setting up
-@code{org-protocol} are reproduced here.
-
-On a high-level, external calls are passed to Emacs via @code{emacsclient}.
-@code{org-protocol} intercepts these and runs custom actions based on the protocols
-registered. Hence, to use @code{org-protocol}, once must:
-
-@itemize
-@item
-launch the @code{emacsclient} process
-
-@item
-Register @code{org-protocol://} as a valid scheme-handler
-@end itemize
-
-The instructions for the latter for each operating system is detailed below.
+@code{org-protocol} are reproduced below.
 
 @menu
 * Linux::
@@ -2019,9 +1896,6 @@ documents (PDF, EPUB etc.) within Org-mode.
 @node Bibliography
 @section Bibliography
 
-Org 9.5 added native citation and bibliography functionality, called ``org-cite'',
-which org-roam supports.
-
 @uref{https://github.com/org-roam/org-roam-bibtex, org-roam-bibtex} offers tight integration between @uref{https://github.com/jkitchin/org-ref, org-ref}, @uref{https://github.com/tmalsburg/helm-bibtex, helm-bibtex} and
 @code{org-roam}. This helps you manage your bibliographic notes under @code{org-roam}.
 
@@ -2048,7 +1922,6 @@ Org-mode, and sync your cards to Anki via @uref{https://github.com/FooSoft/anki-
 * How do I migrate from Roam Research?::
 * How to migrate from Org-roam v1?::
 * How do I publish my notes with an Internet-friendly graph?::
-* I'm seeing this ``Selecting deleted buffer'' error. What do I do?: I'm seeing this ``Selecting deleted buffer'' error What do I do?. 
 @end menu
 
 @node How do I have more than one Org-roam directory?
@@ -2259,27 +2132,6 @@ to the publishing directory.  Example code follows:
                                        (setq my-publish-time 0)))))
 @end lisp
 
-@node I'm seeing this ``Selecting deleted buffer'' error What do I do?
-@section I'm seeing this ``Selecting deleted buffer'' error. What do I do?
-
-The ``selecting deleted buffer'' error usually occurs when you don't have a
-working @code{emacsql-sqlite} executable. Org-roam relies on this executable to
-function properly, and doesn't catch this error. This issue is most commonly
-seen on Windows setups. You can browse through the various GitHub issues posted
-about this @uref{https://github.com/org-roam/org-roam/issues?q=is%3Aissue+selecting+deleted, here}.
-
-To fix this, you can try the following:
-
-@itemize
-@item
-If on Windows, try replacing your system binary with @uref{https://github.com/nobiot/emacsql-sqlite.exe, this one} that has been proven
-to work
-
-@item
-Use the @code{emacsql-sqlite3} option rather than compiling your own emacsql
-binary (see @ref{How to cache}).
-@end itemize
-
 @node Developer's Guide to Org-roam
 @chapter Developer's Guide to Org-roam
 

extensions/org-roam-dailies.el

@@ -7,8 +7,8 @@
 ;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,9 +34,10 @@
 ;; each file named after certain date and stored in `org-roam-dailies-directory'.
 ;;
 ;; One can use dailies for various purposes, e.g. journaling, fleeting notes,
-;; scratch notes or whatever else you can think of.
+;; scratch notes and whatever else you can came up with.
 ;;
 ;;; Code:
+(require 'f)
 (require 'dash)
 (require 'org-roam)
 
@@ -129,103 +130,79 @@ See `org-roam-capture-templates' for the template documentation."
 ;;; Commands
 ;;;; Today
 ;;;###autoload
-(defun org-roam-dailies-capture-today (&optional goto keys)
+(defun org-roam-dailies-capture-today (&optional goto)
   "Create an entry in the daily-note for today.
-When GOTO is non-nil, go the note without creating an entry.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+When GOTO is non-nil, go the note without creating an entry."
   (interactive "P")
-  (org-roam-dailies--capture (current-time) goto keys))
+  (org-roam-dailies--capture (current-time) goto))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-today (&optional keys)
-  "Find the daily-note for today, creating it if necessary.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+(defun org-roam-dailies-goto-today ()
+  "Find the daily-note for today, creating it if necessary."
   (interactive)
-  (org-roam-dailies-capture-today t keys))
+  (org-roam-dailies-capture-today t))
 
 ;;;; Tomorrow
 ;;;###autoload
-(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
   "Create an entry in the daily-note for tomorrow.
 
 With numeric argument N, use the daily-note N days in the future.
 
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+creating an entry."
   (interactive "p")
-  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto keys))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-tomorrow (n &optional keys)
+(defun org-roam-dailies-goto-tomorrow (n)
   "Find the daily-note for tomorrow, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+future."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow n t keys))
+  (org-roam-dailies-capture-tomorrow n t))
 
 ;;;; Yesterday
 ;;;###autoload
-(defun org-roam-dailies-capture-yesterday (n &optional goto keys)
+(defun 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.
 
-When GOTO is non-nil, go the note without creating an entry.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+When GOTO is non-nil, go the note without creating an entry."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) goto keys))
+  (org-roam-dailies-capture-tomorrow (- n) goto))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-yesterday (n &optional keys)
+(defun org-roam-dailies-goto-yesterday (n)
   "Find the daily-note for yesterday, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+future."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) t keys))
+  (org-roam-dailies-capture-tomorrow (- n) t))
 
 ;;;; Date
 ;;;###autoload
-(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
   "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.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+creating an entry."
   (interactive "P")
   (let ((time (let ((org-read-date-prefer-future prefer-future))
                 (org-read-date nil t nil (if goto
                                              "Find daily-note: "
                                            "Capture to daily-note: ")))))
-    (org-roam-dailies--capture time goto keys)))
+    (org-roam-dailies--capture time goto)))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-date (&optional prefer-future keys)
+(defun org-roam-dailies-goto-date (&optional prefer-future)
   "Find the daily-note for a date using the calendar, creating it if necessary.
-Prefer past dates, unless PREFER-FUTURE is non-nil.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
+Prefer past dates, unless PREFER-FUTURE is non-nil."
   (interactive)
-  (org-roam-dailies-capture-date t prefer-future keys))
+  (org-roam-dailies-capture-date t prefer-future))
 
 ;;;; Navigation
 (defun org-roam-dailies-goto-next-note (&optional n)
@@ -289,7 +266,7 @@ If FILE is not specified, use the current buffer's file-path."
     (save-match-data
       (and
        (org-roam-file-p path)
-       (org-roam-descendant-of-p path directory)))))
+       (f-descendant-of-p path directory)))))
 
 ;;;###autoload
 (defun org-roam-dailies-find-directory ()
@@ -323,16 +300,11 @@ Return (MONTH DAY YEAR) or nil if not an Org time-string."
 ;;; Capture implementation
 (add-to-list 'org-roam-capture--template-keywords :override-default-time)
 
-(defun org-roam-dailies--capture (time &optional goto keys)
+(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.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
-  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory))
-        (org-roam-dailies-directory "./"))
+When GOTO is non-nil, go the note without creating an entry."
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
     (org-roam-capture- :goto (when goto '(4))
-                       :keys keys
                        :node (org-roam-node-create)
                        :templates org-roam-dailies-capture-templates
                        :props (list :override-default-time time)))

extensions/org-roam-graph.el

@@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -266,7 +266,7 @@ Handles both Org-roam nodes, and string nodes (e.g. urls)."
                 (org-roam-quote-string
                  (pcase org-roam-graph-shorten-titles
                    (`truncate (truncate-string-to-width title org-roam-graph-max-title-length nil nil "..."))
-                   (`wrap (org-roam-word-wrap org-roam-graph-max-title-length title))
+                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
                    (_ title)))))
           (setq node-id (org-roam-node-id node)
                 node-properties `(("label"   . ,shortened-title)

extensions/org-roam-overlay.el

@@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.

extensions/org-roam-protocol.el

@@ -4,7 +4,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -169,6 +169,25 @@ org-protocol://roam-node?node=uuid"
 (push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
       org-protocol-protocol-alist)
 
+;;; Capture implementation
+(add-hook 'org-roam-capture-preface-hook #'org-roam-protocol--try-capture-to-ref-h)
+(defun org-roam-protocol--try-capture-to-ref-h ()
+  "Try to capture to an existing node that match the ref."
+  (when-let ((node (and (plist-get org-roam-capture--info :ref)
+                        (org-roam-node-from-ref
+                         (plist-get org-roam-capture--info :ref)))))
+    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+    (goto-char (org-roam-node-point node))
+    (widen)
+    (org-roam-node-id node)))
+
+(add-hook 'org-roam-capture-new-node-hook #'org-roam-protocol--insert-captured-ref-h)
+(defun org-roam-protocol--insert-captured-ref-h ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
+
 (provide 'org-roam-protocol)
 
 ;;; org-roam-protocol.el ends here

github-eldev

@@ -1,11 +0,0 @@
-#! /bin/sh
-set -e
-
-ELDEV_BIN_DIR=~/.local/bin
-
-# `$GITHUB_PATH' is a magic file which contents is translated to environment variable `$PATH'.
-echo "$ELDEV_BIN_DIR" >> $GITHUB_PATH
-
-mkdir -p $ELDEV_BIN_DIR
-curl -fsSL https://raw.githubusercontent.com/doublep/eldev/f111d19cda305e5e8fcb70a5675b87173041cb68/bin/eldev > $ELDEV_BIN_DIR/eldev
-chmod a+x $ELDEV_BIN_DIR/eldev

org-roam-capture.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -407,8 +407,6 @@ TEMPLATES is a list of org-roam templates."
           (mapcar (lambda (template)
                     (org-roam-capture--convert-template template props))
                   (or templates org-roam-capture-templates)))
-         (_ (setf (org-roam-node-id node) (or (org-roam-node-id node)
-                                              (org-id-new))))
          (org-roam-capture--node node)
          (org-roam-capture--info info))
     (when (and (not keys)
@@ -505,7 +503,7 @@ Return the ID of the location."
        (set-buffer (org-capture-target-buffer path))
        (when new-file-p
          (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+         (insert (org-roam-capture--fill-template head t)))
        (widen)
        (setq p (goto-char (point-min))))
       (`(file+head+olp ,path ,head ,olp)
@@ -515,7 +513,7 @@ Return the ID of the location."
        (widen)
        (when new-file-p
          (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+         (insert (org-roam-capture--fill-template head t)))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m)))
@@ -574,11 +572,11 @@ Return the ID of the location."
     ;; caller.
     (save-excursion
       (goto-char p)
-      (if-let ((id (org-entry-get p "ID")))
-          (setf (org-roam-node-id org-roam-capture--node) id)
-        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
+      (when-let* ((node org-roam-capture--node)
+                  (id (org-roam-node-id node)))
+        (org-entry-put p "ID" id))
       (prog1
-          (org-id-get)
+          (org-id-get-create)
         (run-hooks 'org-roam-capture-new-node-hook)))))
 
 (defun org-roam-capture--get-target ()
@@ -591,9 +589,8 @@ Return the ID of the location."
 PATH is a string that can optionally contain templated text in
 it."
   (or (org-roam-node-file org-roam-capture--node)
-      (thread-first
-        path
-        (org-roam-capture--fill-template)
+      (thread-first path
+        (org-roam-capture--fill-template t)
         (string-trim)
         (expand-file-name org-roam-directory))))
 
@@ -618,7 +615,7 @@ you can catch it with `condition-case'."
     (org-with-wide-buffer
      (goto-char start)
      (dolist (heading olp)
-       (setq heading (org-roam-capture--fill-template heading))
+       (setq heading (org-roam-capture--fill-template heading t))
        (let ((re (format org-complex-heading-regexp-format
                          (regexp-quote heading)))
              (cnt 0))
@@ -680,24 +677,6 @@ the current value of `point'."
             (goto-char (org-entry-end-position))))))))
   (point))
 
-;;; Capture implementation
-(add-hook 'org-roam-capture-preface-hook #'org-roam-capture--try-capture-to-ref-h)
-(defun org-roam-capture--try-capture-to-ref-h ()
-  "Try to capture to an existing node that match the ref."
-  (when-let ((node (and (plist-get org-roam-capture--info :ref)
-                        (org-roam-node-from-ref
-                         (plist-get org-roam-capture--info :ref)))))
-    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-    (goto-char (org-roam-node-point node))
-    (widen)
-    (org-roam-node-id node)))
-
-(add-hook 'org-roam-capture-new-node-hook #'org-roam-capture--insert-captured-ref-h)
-(defun org-roam-capture--insert-captured-ref-h ()
-  "Insert the ref if any."
-  (when-let ((ref (plist-get org-roam-capture--info :ref)))
-    (org-roam-ref-add ref)))
-
 ;;;; Finalizers
 (add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize-h)
 (defun org-roam-capture--install-finalize-h ()
@@ -710,14 +689,11 @@ the current value of `point'."
   (when-let ((region (org-roam-capture--get :region)))
     (org-roam-unshield-region (car region) (cdr region)))
   (if org-note-abort
-      (when-let ((new-file (org-roam-capture--get :new-file))
-                 (_ (yes-or-no-p "Delete file for aborted capture?")))
+      (when-let ((new-file (org-roam-capture--get :new-file)))
+        (org-roam-message "Deleting file for aborted capture %s" new-file)
         (when (find-buffer-visiting new-file)
           (kill-buffer (find-buffer-visiting new-file)))
         (delete-file new-file))
-    (when-let* ((buffer (plist-get org-capture-plist :buffer))
-                (file (buffer-file-name buffer)))
-      (org-id-add-location (org-roam-capture--get :id) file))
     (when-let* ((finalize (org-roam-capture--get :finalize))
                 (org-roam-finalize-fn (intern (concat "org-roam-capture--finalize-"
                                                       (symbol-name finalize)))))
@@ -744,53 +720,48 @@ This function is to be called in the Org-capture finalization process."
         (delete-region (car region) (cdr region))
         (set-marker (car region) nil)
         (set-marker (cdr region) nil))
-      (let* ((id (org-roam-capture--get :id))
-             (description (org-roam-capture--get :link-description))
-             (link (org-link-make-string (concat "id:" id)
-                                         description)))
-        (if (eq (point) (marker-position mkr))
-            (insert link)
-          (org-with-point-at mkr
-            (insert link)))
-        (run-hook-with-args 'org-roam-post-node-insert-hook
-                            id
-                            description)))))
+      (org-with-point-at mkr
+        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
+                                      (org-roam-capture--get :link-description)))))))
 
 ;;;; Processing of the capture templates
-(defun org-roam-capture--fill-template (template &optional ensure-newline)
+(defun org-roam-capture--fill-template (template &optional org-capture-p newline)
   "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE, and then runs
-org-capture's template expansion.
-When ENSURE-NEWLINE, always ensure there's a newline behind."
-  (let ((template-whitespace-content (org-roam-whitespace-content template)))
+It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+also run Org-capture's template expansion.
+If NEWLINE, ensure that the template returned ends with a newline."
+  (setq template (org-roam-format-template
+                  template
+                  (lambda (key default-val)
+                    (let ((fn (intern key))
+                          (node-fn (intern (concat "org-roam-node-" key)))
+                          (ksym (intern (concat ":" key))))
+                      (cond
+                       ((fboundp fn)
+                        (funcall fn org-roam-capture--node))
+                       ((fboundp node-fn)
+                        (funcall node-fn org-roam-capture--node))
+                       ((plist-get org-roam-capture--info ksym)
+                        (plist-get org-roam-capture--info ksym))
+                       (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
+                            (plist-put org-roam-capture--info ksym r)
+                            r)))))))
+  ;; WARNING:
+  ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
+  ;; template does not start with any whitespace, and only ends with a single newline
+  ;;
+  ;; In most cases where we rely on `org-capture-fill-template' to populate non-org-capture-related templates,
+  ;; (e.g. in OLPs), we strip the final newline, obtaining a template that seems to be string-trimmed.
+  ;;
+  ;; This means that if the original passed template has newlines, and ORG-CAPTURE-P is true, then the extra
+  ;; whitespace specified in the template will be ignored.
+  (when org-capture-p
     (setq template
-          (org-roam-format-template
-           template
-           (lambda (key default-val)
-             (let ((fn (intern key))
-                   (node-fn (intern (concat "org-roam-node-" key)))
-                   (ksym (intern (concat ":" key))))
-               (cond
-                ((fboundp fn)
-                 (funcall fn org-roam-capture--node))
-                ((fboundp node-fn)
-                 (funcall node-fn org-roam-capture--node))
-                ((plist-get org-roam-capture--info ksym)
-                 (plist-get org-roam-capture--info ksym))
-                (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
-                     (plist-put org-roam-capture--info ksym r)
-                     r)))))))
-    ;; WARNING:
-    ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
-    ;; template does not start with any whitespace, and only ends with a single newline
-    ;;
-    ;; Instead, we restore the whitespace in the original template.
-    (setq template (replace-regexp-in-string "\n$" "" (org-capture-fill-template template)))
-    (when (and ensure-newline
-               (string-equal template-whitespace-content ""))
-      (setq template-whitespace-content "\n"))
-    (setq template (concat template template-whitespace-content))
-    template))
+          (replace-regexp-in-string "\n$" "" (org-capture-fill-template template))))
+  (when (and newline
+             (not (string-suffix-p "\n" template)))
+    (setq template (concat template "\n")))
+  template)
 
 (defun org-roam-capture--convert-template (template &optional props)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.

org-roam-compat.el

@@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -229,10 +229,6 @@ nodes." org-id-locations-file)
   'org-roam-remove-property
   'org-roam-property-remove "org-roam 2.1")
 
-(define-obsolete-variable-alias
-  'org-roam-mode-section-functions
-  'org-roam-mode-sections "org-roam 2.2.0")
-
 ;;; Obsolete functions
 (make-obsolete 'org-roam-get-keyword 'org-collect-keywords "org-roam 2.0")
 

org-roam-db.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -54,7 +54,7 @@ a compiler. See https://nullprogram.com/blog/2014/02/06/."
                  (const sqlite3)
                  (symbol :tag "other")))
 
-(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
   "The path to file where the Org-roam database is stored.
 
 It is the user's responsibility to set this correctly, especially
@@ -98,35 +98,15 @@ slow."
   :type 'boolean
   :group 'org-roam)
 
-(defcustom org-roam-db-extra-links-elements '(node-property keyword)
-  "The list of Org element types to include for parsing by Org-roam.
-
-By default, when parsing Org's AST, links within keywords and
-property drawers are not parsed as links. Sometimes however, it
-is desirable to parse and cache these links (e.g. hiding links in
-a property drawer)."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
-  :type '(set (const :tag "keywords" keyword)
-              (const :tag "property drawers" node-property)))
-
-(defcustom org-roam-db-extra-links-exclude-keys '((node-property . ("ROAM_REFS"))
-                                                  (keyword . ("transclude")))
-  "Keys to ignore when mapping over links.
-
-The car of the association list is the Org element type (e.g.
-keyword). The cdr is a list of case-insensitive strings to
-exclude from being treated as links.
-
-For example, we use this to prevent self-referential links in
-ROAM_REFS."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
-  :type '(alist))
-
 ;;; Variables
 (defconst org-roam-db-version 18)
 
+;; TODO Rename this
+(defconst org-roam--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))
+
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
@@ -165,7 +145,6 @@ Performs a database upgrade when required."
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
       (let ((conn (funcall (org-roam-db--conn-fn) org-roam-db-location)))
-        (emacsql conn [:pragma (= foreign_keys ON)])
         (when-let ((process (emacsql-process conn)))
           (set-process-query-on-exit-flag process nil))
         (puthash (expand-file-name (file-name-as-directory org-roam-directory))
@@ -264,6 +243,7 @@ The query is expected to be able to fail, in this situation, run HANDLER."
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
+  (emacsql db [:pragma (= foreign_keys ON)])
   (emacsql-with-transaction db
     (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
       (emacsql db [:create-table $i1 $S2] table schema))
@@ -379,12 +359,15 @@ If UPDATE-P is non-nil, first remove the file in the database."
          ;; Links correctly recognized by Org Mode
          ((eq type 'link)
           (setq link element))
+         ;; Prevent self-referencing links in ROAM_REFS
+         ((and (eq type 'node-property)
+               (org-roam-string-equal (org-element-property :key element) "ROAM_REFS"))
+          nil)
          ;; Links in property drawers and lines starting with #+. Recall that, as for Org Mode v9.4.4, the
          ;; org-element-type of links within properties drawers is "node-property" and for lines starting with
          ;; #+ is "keyword".
-         ((and (member type org-roam-db-extra-links-elements)
-               (not (member-ignore-case (org-element-property :key element)
-                                        (cdr (assoc type org-roam-db-extra-links-exclude-keys))))
+         ((and (or (eq type 'node-property)
+                   (eq type 'keyword))
                (setq bounds (org-in-regexp org-link-any-re))
                (setq link (buffer-substring-no-properties
                            (car bounds)
@@ -499,24 +482,9 @@ INFO is the org-element parsed buffer."
     (let (rows)
       (dolist (ref refs)
         (save-match-data
-          (cond (;; @citeKey
-                 (string-prefix-p "@" ref)
+          (cond ((string-prefix-p "@" ref)
                  (push (vector node-id (substring ref 1) "cite") rows))
-                (;; [cite:@citeKey]
-                 (string-prefix-p "[cite:" ref)
-                 (condition-case nil
-                     (let ((cite-obj (org-cite-parse-objects ref)))
-                       (org-element-map cite-obj 'citation-reference
-                         (lambda (cite)
-                           (let ((key (org-element-property :key cite)))
-                             (push (vector node-id key "cite") rows)))))
-                   (error
-                    (lwarn '(org-roam) :warning
-                           "%s:%s\tInvalid cite %s, skipping..." (buffer-file-name) (point) ref))))
-                (;; https://google.com, cite:citeKey
-                 ;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
-                 ;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
-                 (string-match org-link-plain-re ref)
+                ((string-match org-link-plain-re ref)
                  (let ((link-type (match-string 1 ref))
                        (path (match-string 2 ref)))
                    (if (and (boundp 'org-ref-cite-types)

org-roam-id.el

@@ -1,117 +0,0 @@
-;;; org-roam-id.el --- ID-related utilities for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program 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.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This module provides ID-related facilities using the Org-roam database.
-;;
-;;; Code:
-(require 'org-id)
-
-(defun org-roam-id-at-point ()
-  "Return the ID at point, if any.
-Recursively traverses up the headline tree to find the
-first encapsulating ID."
-  (org-with-wide-buffer
-   (org-back-to-heading-or-point-min t)
-   (while (and (not (org-roam-db-node-p))
-               (not (bobp)))
-     (org-roam-up-heading-or-point-min))
-   (when (org-roam-db-node-p)
-     (org-id-get))))
-
-(defun org-roam-id-find (id &optional markerp)
-  "Return the location of the entry with the id ID using the Org-roam db.
-The return value is a cons cell (file-name . position), or nil
-if there is no entry with that ID.
-With optional argument MARKERP, return the position as a new marker."
-  (cond
-   ((symbolp id) (setq id (symbol-name id)))
-   ((numberp id) (setq id (number-to-string id))))
-  (let ((node (org-roam-populate (org-roam-node-create :id id))))
-    (when-let ((file (org-roam-node-file node)))
-      (if markerp
-          (unwind-protect
-              (let ((buffer (or (find-buffer-visiting file)
-                                (find-file-noselect file))))
-                (with-current-buffer buffer
-                  (move-marker (make-marker) (org-roam-node-point node) buffer))))
-        (cons (org-roam-node-file node)
-              (org-roam-node-point node))))))
-
-(defun org-roam-id-open (id _)
-  "Go to the entry with id ID.
-Like `org-id-open', but additionally uses the Org-roam database."
-  (org-mark-ring-push)
-  (let ((m (or (org-roam-id-find id 'marker)
-               (org-id-find id 'marker)))
-        cmd)
-    (unless m
-      (error "Cannot find entry with ID \"%s\"" id))
-    ;; Use a buffer-switching command in analogy to finding files
-    (setq cmd
-          (or
-           (cdr
-            (assq
-             (cdr (assq 'file org-link-frame-setup))
-             '((find-file . switch-to-buffer)
-               (find-file-other-window . switch-to-buffer-other-window)
-               (find-file-other-frame . switch-to-buffer-other-frame))))
-           'switch-to-buffer-other-window))
-    (if (not (equal (current-buffer) (marker-buffer m)))
-        (funcall cmd (marker-buffer m)))
-    (goto-char m)
-    (move-marker m nil)
-    (org-show-context)))
-
-(org-link-set-parameters "id" :follow #'org-roam-id-open)
-
-;;;###autoload
-(defun org-roam-update-org-id-locations (&rest directories)
-  "Scan Org-roam files to update `org-id' related state.
-This is like `org-id-update-id-locations', but will automatically
-use the currently bound `org-directory' and `org-roam-directory'
-along with DIRECTORIES (if any), where the lookup for files in
-these directories will be always recursive.
-
-Note: Org-roam doesn't have hard dependency on
-`org-id-locations-file' to lookup IDs for nodes that are stored
-in the database, but it still tries to properly integrates with
-`org-id'. This allows the user to cross-reference IDs outside of
-the current `org-roam-directory', and also link with \"id:\"
-links to headings/files within the current `org-roam-directory'
-that are excluded from identification in Org-roam as
-`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
-  (interactive)
-  (cl-loop for dir in (cons org-roam-directory directories)
-           for org-roam-directory = dir
-           nconc (org-roam-list-files) into files
-           finally (org-id-update-id-locations files org-roam-verbose)))
-
-(provide 'org-roam-id)
-
-;;; org-roam-id.el ends here

org-roam-migrate.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-mode.el

@@ -1,12 +1,12 @@
 ;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
 
-;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -39,28 +39,14 @@
 (defvar org-ref-buffer-hacked)
 
 ;;; Options
-(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
-                                        #'org-roam-reflinks-section)
-  "A list of sections for the `org-roam-mode' based buffers.
-Each section is a function that is passed the an `org-roam-node'
-for which the section will be constructed for as the first
-argument. Normally this node is `org-roam-buffer-current-node'.
-The function may also accept other optional arguments. Each item
-in the list is either:
-
-1. A function, which is called only with the `org-roam-node' as the argument
-2. A list, containing the function and the optional arguments.
-
-For example, one can add
-
-    (org-roam-backlinks-section :unique t)
-
-to the list to pass :unique t to the section-rendering function."
+(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
+                                                 #'org-roam-reflinks-section)
+  "Functions that insert sections in the `org-roam-mode' based buffers.
+Each function is called with one argument, which is an
+`org-roam-node' for which the buffer will be constructed for.
+Normally this node is `org-roam-buffer-current-node'."
   :group 'org-roam
-  :type `(repeat (choice (symbol :tag "Function")
-                         (list :tag "Function with arguments"
-                               (symbol :tag "Function")
-                               (repeat :tag "Arguments" :inline t (sexp :tag "Arg"))))))
+  :type 'hook)
 
 (defcustom org-roam-buffer-postrender-functions (list)
   "Functions to run after the Org-roam buffer is rendered.
@@ -182,7 +168,7 @@ This mode is used by special Org-roam buffers, such as persistent
 `org-roam-buffer' and dedicated Org-roam buffers
 \(`org-roam-buffer-display-dedicated'), which render the
 information in a section-like manner (see
-`org-roam-mode-sections'), with which the user can
+`org-roam-mode-section-functions'), with which the user can
 interact with."
   :group 'org-roam
   (face-remap-add-relative 'header-line 'org-roam-header-line))
@@ -242,14 +228,7 @@ buffer."
      (org-roam-node-title org-roam-buffer-current-node))
     (magit-insert-section (org-roam)
       (magit-insert-heading)
-      (dolist (section org-roam-mode-sections)
-        (pcase section
-          ((pred functionp)
-           (funcall section org-roam-buffer-current-node))
-          (`(,fn . ,args)
-           (apply fn (cons org-roam-buffer-current-node args)))
-          (_
-           (user-error "Invalid `org-roam-mode-sections' specification")))))
+      (run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node))
     (run-hooks 'org-roam-buffer-postrender-functions)
     (goto-char 0)))
 
@@ -310,7 +289,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
   (pcase (org-roam-buffer--visibility)
     ('visible
      (progn
-       (quit-window nil (get-buffer-window org-roam-buffer))
+       (delete-window (get-buffer-window org-roam-buffer))
        (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
     ((or 'exists 'none)
      (progn
@@ -480,23 +459,14 @@ headline, up to the next headline."
         (org-roam-populate (org-roam-backlink-target-node backlink)))
   backlink)
 
-(cl-defun org-roam-backlinks-get (node &key unique)
-  "Return the backlinks for NODE.
-
- When UNIQUE is nil, show all positions where references are found.
- When UNIQUE is t, limit to unique sources."
-  (let* ((sql (if unique
-                  [:select :distinct [source dest pos properties]
-                   :from links
-                   :where (= dest $s1)
-                   :and (= type "id")
-                   :group :by source
-                   :having (funcall min pos)]
-                [:select [source dest pos properties]
-                 :from links
-                 :where (= dest $s1)
-                 :and (= type "id")]))
-         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
+(defun org-roam-backlinks-get (node)
+  "Return the backlinks for NODE."
+  (let ((backlinks (org-roam-db-query
+                    [:select [source dest pos properties]
+                     :from links
+                     :where (= dest $s1)
+                     :and (= type "id")]
+                    (org-roam-node-id node))))
     (cl-loop for backlink in backlinks
              collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                        (org-roam-populate
@@ -512,12 +482,9 @@ Sorts by title."
   (string< (org-roam-node-title (org-roam-backlink-source-node a))
            (org-roam-node-title (org-roam-backlink-source-node b))))
 
-(cl-defun org-roam-backlinks-section (node &key (unique nil))
-  "The backlinks section for NODE.
-
-When UNIQUE is nil, show all positions where references are found.
-When UNIQUE is t, limit to unique sources."
-  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
+(defun org-roam-backlinks-section (node)
+  "The backlinks section for NODE."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
     (magit-insert-section (org-roam-backlinks)
       (magit-insert-heading "Backlinks:")
       (dolist (backlink backlinks)
@@ -676,7 +643,7 @@ References from FILE are excluded."
                     col (string-to-number (match-string 3 line))
                     match (match-string 4 line))
               (when (and match
-                         (not (file-equal-p (org-roam-node-file node) f))
+                         (not (f-equal-p (org-roam-node-file node) f))
                          (member (downcase match) (mapcar #'downcase titles)))
                 (magit-insert-section section (org-roam-grep-section)
                   (oset section file f)

org-roam-node.el

@@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -36,7 +36,8 @@
 
 ;;; Options
 ;;;; Completing-read
-(defcustom org-roam-node-display-template "${title}"
+(defcustom org-roam-node-display-template
+  (concat "${title:*} " (propertize "${tags:10}" 'face 'org-tag))
   "Configures display formatting for Org-roam node.
 Patterns of form \"${field-name:length}\" are interpolated based
 on the current node.
@@ -131,8 +132,7 @@ It takes a single argument REF, which is a propertized string."
   :type 'boolean)
 
 (defcustom org-roam-extract-new-file-path "%<%Y%m%d%H%M%S>-${slug}.org"
-  "The file path template to use when a node is extracted to its own file.
-This path is relative to `org-roam-directory'."
+  "The file path to use when a node is extracted to its own file."
   :group 'org-roam
   :type 'string)
 
@@ -175,7 +175,6 @@ This path is relative to `org-roam-directory'."
                            776 ; U+0308 COMBINING DIAERESIS
                            777 ; U+0309 COMBINING HOOK ABOVE
                            778 ; U+030A COMBINING RING ABOVE
-                           779 ; U+030B COMBINING DOUBLE ACUTE ACCENT
                            780 ; U+030C COMBINING CARON
                            795 ; U+031B COMBINING HORN
                            803 ; U+0323 COMBINING DOT BELOW
@@ -187,12 +186,14 @@ This path is relative to `org-roam-directory'."
                            816 ; U+0330 COMBINING TILDE BELOW
                            817 ; U+0331 COMBINING MACRON BELOW
                            )))
-    (cl-flet* ((nonspacing-mark-p (char) (memq char slug-trim-chars))
-               (strip-nonspacing-marks (s) (string-glyph-compose
-                                            (apply #'string
-                                                   (seq-remove #'nonspacing-mark-p
-                                                               (string-glyph-decompose s)))))
-               (cl-replace (title pair) (replace-regexp-in-string (car pair) (cdr pair) title)))
+    (cl-flet* ((nonspacing-mark-p (char)
+                                  (memq char slug-trim-chars))
+               (strip-nonspacing-marks (s)
+                                       (string-glyph-compose
+                                        (apply #'string (seq-remove #'nonspacing-mark-p
+                                                                    (string-glyph-decompose s)))))
+               (cl-replace (title pair)
+                           (replace-regexp-in-string (car pair) (cdr pair) title)))
       (let* ((pairs `(("[^[:alnum:][:digit:]]" . "_") ;; convert anything not alphanumeric
                       ("__*" . "_")                   ;; remove sequential underscores
                       ("^_" . "")                     ;; remove starting underscore
@@ -425,41 +426,19 @@ GROUP BY id")))
                               all-titles)))))
 
 ;;;; Finders
-(defun org-roam-node-marker (node)
-  "Get the marker for NODE."
-  (unwind-protect
-      (let* ((file (org-roam-node-file node))
-             (buffer (or (find-buffer-visiting file)
-                         (find-file-noselect file))))
-        (with-current-buffer buffer
-          (move-marker (make-marker) (org-roam-node-point node) buffer)))))
-
-(defun org-roam-node-open (node &optional cmd force)
-  "Go to the node NODE.
-CMD is the command used to display the buffer. If not provided,
-`org-link-frame-setup' is respected. Assumes that the node is
-fully populated, with file and point. If NODE is already visited,
-this won't automatically move the point to the beginning of the
-NODE, unless FORCE is non-nil."
-  (interactive (list (org-roam-node-at-point) current-prefix-arg))
-  (org-mark-ring-push)
-  (let ((m (org-roam-node-marker node))
-        (cmd (or cmd
-                 (cdr
-                  (assq
-                   (cdr (assq 'file org-link-frame-setup))
-                   '((find-file . switch-to-buffer)
-                     (find-file-other-window . switch-to-buffer-other-window)
-                     (find-file-other-frame . switch-to-buffer-other-frame))))
-                 'switch-to-buffer-other-window)))
-    (if (not (equal (current-buffer) (marker-buffer m)))
-        (funcall cmd (marker-buffer m)))
-    (when (or force
-              (not (equal (org-roam-node-id node)
-                          (org-roam-id-at-point))))
-      (goto-char m))
-    (move-marker m nil))
-  (org-show-context))
+(defun org-roam-node-find-noselect (node &optional force)
+  "Navigate to the point for NODE, and return the buffer.
+If NODE is already visited, this won't automatically move the
+point to the beginning of the NODE, unless FORCE is non-nil."
+  (unless (org-roam-node-file node)
+    (user-error "Node does not have corresponding file"))
+  (let ((buf (find-file-noselect (org-roam-node-file node))))
+    (with-current-buffer buf
+      (when (or force
+                (not (equal (org-roam-node-id node)
+                            (org-roam-id-at-point))))
+        (goto-char (org-roam-node-point node))))
+    buf))
 
 (defun org-roam-node-visit (node &optional other-window force)
   "From the current buffer, visit NODE. Return the visited buffer.
@@ -471,10 +450,13 @@ If NODE is already visited, this won't automatically move the
 point to the beginning of the NODE, unless FORCE is non-nil. In
 interactive calls FORCE always set to t."
   (interactive (list (org-roam-node-at-point t) current-prefix-arg t))
-  (org-roam-node-open node (if other-window
+  (let ((buf (org-roam-node-find-noselect node force))
+        (display-buffer-fn (if other-window
                                #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)
-                      force))
+                             #'pop-to-buffer-same-window)))
+    (funcall display-buffer-fn buf)
+    (when (org-invisible-p) (org-show-context))
+    buf))
 
 ;;;###autoload
 (cl-defun org-roam-node-find (&optional other-window initial-input filter-fn &key templates)
@@ -495,16 +477,16 @@ The TEMPLATES, if provided, override the list of capture templates (see
        :props '(:finalize find-file)))))
 
 ;;;###autoload
-(defun org-roam-node-random (&optional other-window filter-fn)
+(defun org-roam-node-random (&optional other-window)
   "Find and open a random Org-roam node.
 With prefix argument OTHER-WINDOW, visit the node in another
-window instead.
-FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
-and when nil is returned the node will be filtered out."
+window instead."
   (interactive current-prefix-arg)
-  (org-roam-node-visit
-   (cdr (seq-random-elt (org-roam-node-read--completions filter-fn)))
-   other-window))
+  (let ((random-row (seq-random-elt (org-roam-db-query [:select [id file pos] :from nodes]))))
+    (org-roam-node-visit (org-roam-node-create :id (nth 0 random-row)
+                                               :file (nth 1 random-row)
+                                               :point (nth 2 random-row))
+                         other-window)))
 
 ;;;; Completing-read interface
 (defun org-roam-node-read (&optional initial-input filter-fn sort-fn require-match prompt)
@@ -516,7 +498,17 @@ 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.
 PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"Node: \""
-  (let* ((nodes (org-roam-node-read--completions filter-fn sort-fn))
+  (let* ((nodes (org-roam-node-read--completions))
+         (nodes (if filter-fn
+                    (cl-remove-if-not
+                     (lambda (n) (funcall filter-fn (cdr n)))
+                     nodes)
+                  nodes))
+         (sort-fn (or sort-fn
+                      (when org-roam-node-default-sort
+                        (intern (concat "org-roam-node-read-sort-by-"
+                                        (symbol-name org-roam-node-default-sort))))))
+         (_ (when sort-fn (setq nodes (seq-sort sort-fn nodes))))
          (prompt (or prompt "Node: "))
          (node (completing-read
                 prompt
@@ -537,31 +529,15 @@ PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"
     (or (cdr (assoc node nodes))
         (org-roam-node-create :title node))))
 
-(defun org-roam-node-read--completions (&optional filter-fn sort-fn)
+(defun org-roam-node-read--completions ()
   "Return an alist for node completion.
 The car is the displayed title or alias for the node, and the cdr
 is the `org-roam-node'.
-FILTER-FN is a function to filter out nodes: it takes 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.
 The displayed title is formatted according to `org-roam-node-display-template'."
-  (let* ((template (org-roam-node--process-display-format org-roam-node-display-template))
-         (nodes (org-roam-node-list))
-         (nodes (mapcar (lambda (node)
-                          (org-roam-node-read--to-candidate node template)) nodes))
-         (nodes (if filter-fn
-                    (cl-remove-if-not
-                     (lambda (n) (funcall filter-fn (cdr n)))
-                     nodes)
-                  nodes))
-         (sort-fn (or sort-fn
-                      (when org-roam-node-default-sort
-                        (intern (concat "org-roam-node-read-sort-by-"
-                                        (symbol-name org-roam-node-default-sort))))))
-         (nodes (if sort-fn (seq-sort sort-fn nodes)
-                  nodes)))
-    nodes))
+  (let ((template (org-roam-node--process-display-format org-roam-node-display-template))
+        (nodes (org-roam-node-list)))
+    (mapcar (lambda (node)
+              (org-roam-node-read--to-candidate node template)) nodes)))
 
 (defun org-roam-node-read--to-candidate (node template)
   "Return a minibuffer completion candidate given NODE.
@@ -569,8 +545,7 @@ TEMPLATE is the processed template used to format the entry."
   (let ((candidate-main (org-roam-node--format-entry
                          template
                          node
-                         (1- (if (bufferp (current-buffer))
-                                 (window-width) (frame-width))))))
+                         (1- (frame-width)))))
     (cons (propertize candidate-main 'node node) node)))
 
 (defun org-roam-node--format-entry (template node &optional width)
@@ -688,13 +663,9 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
                   (delete-region beg end)
                   (set-marker beg nil)
                   (set-marker end nil))
-                (let ((id (org-roam-node-id node)))
-                  (insert (org-link-make-string
-                           (concat "id:" id)
-                           description))
-                  (run-hook-with-args 'org-roam-post-node-insert-hook
-                                      id
-                                      description)))
+                (insert (org-link-make-string
+                         (concat "id:" (org-roam-node-id node))
+                         description)))
             (org-roam-capture-
              :node node
              :info info
@@ -702,10 +673,31 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
              :props (append
                      (when (and beg end)
                        (list :region (cons beg end)))
-                     (list :link-description description
+                     (list :insert-at (point-marker)
+                           :link-description description
                            :finalize 'insert-link))))))
     (deactivate-mark)))
 
+(add-hook 'org-roam-find-file-hook #'org-roam-open-id-with-org-roam-db-h)
+(defun org-roam-open-id-with-org-roam-db-h ()
+  "Try to open \"id:\" links at point by querying them to the database."
+  (add-hook 'org-open-at-point-functions #'org-roam-open-id-at-point nil t))
+
+(defun org-roam-open-id-at-point ()
+  "Navigate to \"id:\" link at point using the Org-roam database."
+  (when (org-in-regexp org-link-any-re)
+    (let ((link (match-string 2))
+          id)
+      (when (string-prefix-p "id:" link)
+        (setq id (substring-no-properties link 3))
+        (let ((node (org-roam-populate (org-roam-node-create :id id))))
+          (cond
+           ((org-roam-node-file node)
+            (org-mark-ring-push)
+            (org-roam-node-visit node nil 'force)
+            t)
+           (t nil)))))))
+
 ;;;;; [roam:] link
 (org-link-set-parameters "roam" :follow #'org-roam-link-follow-link)
 (defun org-roam-link-follow-link (title-or-alias)
@@ -819,8 +811,7 @@ Any tags declared on #+FILETAGS: are transferred to tags on the new top heading.
 Any top level properties drawers are incorporated into the new heading."
   (interactive)
   (org-with-point-at 1
-    (org-map-region #'org-do-demote
-                    (point-min) (point-max))
+    (org-map-entries 'org-do-demote)
     (insert "* "
             (org-roam--get-keyword "title")
             "\n")
@@ -835,11 +826,9 @@ Converts a file containing a headline node at the top to a file
 node."
   (interactive)
   (org-with-point-at 1
-    (org-map-region
-     (lambda ()
-       (when (> (org-outline-level) 1)
-         (org-do-promote)))
-     (point-min) (point-max))
+    (org-map-entries (lambda ()
+                       (when (> (org-outline-level) 1)
+                         (org-do-promote))))
     (let ((title (nth 4 (org-heading-components)))
           (tags (nth 5 (org-heading-components))))
       (beginning-of-line)
@@ -931,11 +920,8 @@ If region is active, then use it instead of the node at point."
                            (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
                                 (plist-put template-info ksym r)
                                 r)))))))
-           (file-path
-            (expand-file-name
-             (read-file-name "Extract node to: "
-                             (file-name-as-directory org-roam-directory) template nil template)
-             org-roam-directory)))
+           (file-path (read-file-name "Extract node to: "
+                                      (file-name-as-directory org-roam-directory) template nil template)))
       (when (file-exists-p file-path)
         (user-error "%s exists. Aborting" file-path))
       (org-cut-subtree)
@@ -945,6 +931,42 @@ If region is active, then use it instead of the node at point."
         (org-roam-promote-entire-buffer)
         (save-buffer)))))
 
+;;; IDs
+;;;; Getters
+(defun org-roam-id-at-point ()
+  "Return the ID at point, if any.
+Recursively traverses up the headline tree to find the
+first encapsulating ID."
+  (org-with-wide-buffer
+   (org-back-to-heading-or-point-min t)
+   (while (and (not (org-roam-db-node-p))
+               (not (bobp)))
+     (org-roam-up-heading-or-point-min))
+   (when (org-roam-db-node-p)
+     (org-id-get))))
+
+;;;###autoload
+(defun org-roam-update-org-id-locations (&rest directories)
+  "Scan Org-roam files to update `org-id' related state.
+This is like `org-id-update-id-locations', but will automatically
+use the currently bound `org-directory' and `org-roam-directory'
+along with DIRECTORIES (if any), where the lookup for files in
+these directories will be always recursive.
+
+Note: Org-roam doesn't have hard dependency on
+`org-id-locations-file' to lookup IDs for nodes that are stored
+in the database, but it still tries to properly integrates with
+`org-id'. This allows the user to cross-reference IDs outside of
+the current `org-roam-directory', and also link with \"id:\"
+links to headings/files within the current `org-roam-directory'
+that are excluded from identification in Org-roam as
+`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
+  (interactive)
+  (cl-loop for dir in (cons org-roam-directory directories)
+           for org-roam-directory = dir
+           nconc (org-roam-list-files) into files
+           finally (org-id-update-id-locations files org-roam-verbose)))
+
 ;;; Refs
 ;;;; Completing-read interface
 (defun org-roam-ref-read (&optional initial-input filter-fn)

org-roam-utils.el

@@ -1,11 +1,11 @@
 ;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
 
-;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
+;; Version: 2.1.0
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -52,16 +52,6 @@
        (org-roam-replace-string "\\" "\\\\")
        (org-roam-replace-string "\"" "\\\"")))
 
-(defun org-roam-word-wrap (len s)
-  "If S is longer than LEN, wrap the words with newlines."
-  (declare (side-effect-free t))
-  (save-match-data
-    (with-temp-buffer
-      (insert s)
-      (let ((fill-column len))
-        (fill-region (point-min) (point-max)))
-      (buffer-substring (point-min) (point-max)))))
-
 (defun org-roam-string-equal (s1 s2)
   "Return t if S1 and S2 are equal.
 Like `string-equal', but case-insensitive."
@@ -69,15 +59,6 @@ Like `string-equal', but case-insensitive."
        (or (string-equal s1 s2)
            (string-equal (downcase s1) (downcase s2)))))
 
-(defun org-roam-whitespace-content (s)
-  "Return the whitespace content at the end of S."
-  (with-temp-buffer
-    (let ((c 0))
-      (insert s)
-      (skip-chars-backward " \t\n")
-      (buffer-substring-no-properties
-       (point) (point-max)))))
-
 (defun org-roam-strip-comments (s)
   "Strip Org comments from string S."
   (with-temp-buffer
@@ -118,12 +99,6 @@ SPEC is a list, as per `dolist'."
     `(dolist ,spec ,@body)))
 
 ;;; File utilities
-(defun org-roam-descendant-of-p (a b)
-  "Return t if A is descendant of B."
-  (unless (equal (file-truename a) (file-truename b))
-    (string-prefix-p (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name b) t t)
-                     (replace-regexp-in-string "^\\([A-Za-z]\\):" 'downcase (expand-file-name a) t t))))
-
 (defmacro org-roam-with-file (file keep-buf-p &rest body)
   "Execute BODY within FILE.
 If FILE is nil, execute BODY in the current buffer.
@@ -144,8 +119,7 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
          (delay-mode-hooks
            (let ((org-inhibit-startup t)
                  (org-agenda-files nil))
-             (org-mode)
-             (hack-local-variables))))
+             (org-mode))))
        (setq res (progn ,@body))
        (unless (and new-buf (not ,keep-buf-p))
          (save-buffer)))

org-roam.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.2.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+;; Version: 2.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -71,6 +71,7 @@
 ;; majority of them can be found at https://github.com/org-roam and MELPA.
 ;;
 ;;; Code:
+(require 'f)
 (require 'dash)
 
 (require 'rx)
@@ -122,12 +123,6 @@ All Org files, at any level of nesting, are considered part of the Org-roam."
   :group 'org-roam
   :type 'hook)
 
-(defcustom org-roam-post-node-insert-hook nil
-  "Hook run when an Org-roam node is inserted as an Org link.
-Each function takes two arguments: the id of the node, and the link description."
-  :group 'org-roam
-  :type 'hook)
-
 (defcustom org-roam-file-extensions '("org")
   "List of file extensions to be included by Org-Roam.
 While a file extension different from \".org\" may be used, the
@@ -200,7 +195,7 @@ FILE is an Org-roam file if:
        (member ext org-roam-file-extensions)
        (not (and org-roam-file-exclude-regexp
                  (string-match-p org-roam-file-exclude-regexp path)))
-       (org-roam-descendant-of-p path (expand-file-name org-roam-directory))))))
+       (f-descendant-of-p path (expand-file-name org-roam-directory))))))
 
 (defun org-roam-list-files ()
   "Return a list of all Org-roam files under `org-roam-directory'.
@@ -265,8 +260,7 @@ If no files are found, an empty list is returned."
        (shell-command-to-string it)
        (ansi-color-filter-apply it)
        (split-string it "\n")
-       (seq-filter (lambda (s)
-                     (not (or (null s) (string= "" s)))) it)))
+       (seq-filter #'s-present? it)))
 
 (defun org-roam--list-files-search-globs (exts)
   "Given EXTS, return a list of search globs.
@@ -285,8 +279,8 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
 (defun org-roam--list-files-fd (executable dir)
   "Return all Org-roam files under DIR, using \"fd\", provided as EXECUTABLE."
   (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
-         (extensions (string-join (mapcar (lambda (glob) (concat "-e " (substring glob 2 -1))) globs) " "))
-         (command (string-join `(,executable "-L" "--type file" ,extensions "." ,dir) " ")))
+         (extensions (string-join (mapcar (lambda (glob) (substring glob 2 -1)) globs) " -e "))
+         (command (string-join `(,executable "-L" ,dir "--type file" ,extensions) " ")))
     (org-roam--shell-command-files command)))
 
 (defalias 'org-roam--list-files-fdfind #'org-roam--list-files-fd)
@@ -319,7 +313,6 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
   (require 'org-roam-utils)
   (require 'org-roam-db)
   (require 'org-roam-node)
-  (require 'org-roam-id)
   (require 'org-roam-capture)
   (require 'org-roam-mode)
   (require 'org-roam-migrate))

tests/test-org-roam-capture.el

@@ -1,51 +0,0 @@
-;;; test-org-roam-capture.el --- Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it 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 program 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.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(describe "org-roam-capture--fill-template"
-  (it "fills template without newline"
-    (expect
-     (org-roam-capture--fill-template "foo")
-     :to-equal "foo"))
-
-  (it "fills template ensuring newline"
-    (expect
-     (org-roam-capture--fill-template "foo" 'ensure-newline)
-     :to-equal "foo\n"))
-
-  (it "fills template with newline"
-    (expect
-     (org-roam-capture--fill-template "foo\n")
-     :to-equal "foo\n"))
-
-  (it "fills template with two newlines"
-    (expect
-     (org-roam-capture--fill-template "foo\n\n")
-     :to-equal "foo\n\n")
-    (expect
-     (org-roam-capture--fill-template "foo\n\t\n")
-     :to-equal "foo\n\t\n")))
-
-(provide 'test-org-roam-capture)

tests/test-org-roam-utils.el

@@ -1,39 +0,0 @@
-;;; test-org-roam-utils.el --- Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it 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 program 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.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(describe "org-roam-whitespace-content"
-  (it "extracts whitespace correctly"
-    (expect
-     (org-roam-whitespace-content "foo")
-     :to-equal "")
-    (expect
-     (org-roam-whitespace-content "foo\n")
-     :to-equal "\n")
-    (expect
-     (org-roam-whitespace-content "foo\n\t\n")
-     :to-equal "\n\t\n")))
-
-(provide 'test-org-roam-utils)