release 2.3.0

Not all links to a node come from another node.  Persisting OLP data
allows us to build backlinks with information about these non-node
headings.

Revert: db4170a459.

.dir-locals.el

@@ -4,10 +4,13 @@
   (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)
                               (org-with-point-at . 1)
                               (magit-insert-section . defun)
                               (magit-section-case . 0)
-                              (->> . 1)
                               (org-roam-with-file . 2)))))

.github/FUNDING.yml

@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: [jethrokuan, zaeph]
+github: [jethrokuan]
 patreon: # Replace with a single Patreon username
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username

.github/ISSUE_TEMPLATE/bug_report.md

@@ -39,5 +39,3 @@ Example:
 ### Environment
 
 <!-- Please M-x org-roam-diagnostics and paste results here -->
-
-- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere

.github/workflows/docs.yml

@@ -4,7 +4,7 @@ name: "Docs"
 on:
   push:
     branches:
-      - master
+      - main
 
 jobs:
   build:

.github/workflows/test.yml

@@ -28,7 +28,7 @@ on:
   pull_request:
   push:
     branches:
-      - master
+      - main
 
 jobs:
   build:
@@ -36,7 +36,11 @@ jobs:
     strategy:
       matrix:
         emacs_version:
-          - 27.1
+          # REVIEW: we do not yet have the bootstrapping in place to test
+          #         versions of emacs without built-in sqlite (pre 29.1)
+          # - 27.2
+          # - 28.2
+          - 29.4
           - snapshot
     steps:
       - uses: purcell/setup-emacs@master
@@ -46,7 +50,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Install Eldev
-        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
+        run: curl -fsSL https://raw.github.com/org-roam/org-roam/master/github-eldev | sh
 
       - name: Install dependencies
         run: make prepare

CHANGELOG.md

@@ -1,7 +1,176 @@
 # Changelog
 
-## 2.1.0
+## 2.3.0 (2025-05-24)
+
+* (perf)node-read: filter before map to candidate by @russmatney in https://github.com/org-roam/org-roam/pull/2168
+* (chore): remove extraneous changelog line by @jethrokuan in https://github.com/org-roam/org-roam/pull/2172
+* (fix)org-roam-file-p: don't exclude org-roam-directory by @toregilhk in https://github.com/org-roam/org-roam/pull/2178
+* (chore) fix version numbers by @jethrokuan in https://github.com/org-roam/org-roam/pull/2182
+* (fix) org-roam-file-p handle opening a buffer with no path by @jethrokuan in https://github.com/org-roam/org-roam/pull/2185
+* (fix)db: update atime on file access by @jethrokuan in https://github.com/org-roam/org-roam/pull/2174
+* Fix org-roam-extract-subtree by @ralfdoering in https://github.com/org-roam/org-roam/pull/2191
+* (node): fix org-roam-node-at-point check by @jethrokuan in https://github.com/org-roam/org-roam/pull/2195
+* (chore): reapply #2178 by @jethrokuan in https://github.com/org-roam/org-roam/pull/2197
+* Solved issue #2192 (Respect blank lines in capture templates) by @alopezrivera in https://github.com/org-roam/org-roam/pull/2203
+* (chore)ci: /s/master/main by @jethrokuan in https://github.com/org-roam/org-roam/pull/2204
+* support custom minibuffer matching function by @cuttlefisch in https://github.com/org-roam/org-roam/pull/2177
+* (db)fix: org-roam-db-connector group by @jethrokuan in https://github.com/org-roam/org-roam/pull/2209
+* ensure unique candidates in `org-roam-ref-find` by @bdarcus in https://github.com/org-roam/org-roam/pull/2208
+* (db)fix: FOREIGN KEY error in narrowed buffer by @psii in https://github.com/org-roam/org-roam/pull/2215
+* (feat): org-roam-property-* code duplication removed (#2217) by @clanghans in https://github.com/org-roam/org-roam/pull/2218
+* (db)fix: file modification detection failing in some edge cases by @kisaragi-hiu in https://github.com/org-roam/org-roam/pull/2221
+* (fix): autoload org-roam-list-files by @jethrokuan in https://github.com/org-roam/org-roam/pull/2226
+* (fix): links not displayed properly in org-roam-buffer by @ntharim in https://github.com/org-roam/org-roam/pull/2236
+* (fix): remove use of deprecated org-font-lock-ensure by @jethrokuan in https://github.com/org-roam/org-roam/pull/2238
+* was missing the FULL parameter to `org-end-of-meta-data` - fixes #2242 by @jmay in https://github.com/org-roam/org-roam/pull/2246
+* (Docs): Fixed typos in the docs by @hnvy in https://github.com/org-roam/org-roam/pull/2256
+* Fix space chars in roam refs by @hwiorn in https://github.com/org-roam/org-roam/pull/2285
+* org-roam-tag-add: use tags separator as crm-separator by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2282
+* Support multi-line org titles by @FelixBrendel in https://github.com/org-roam/org-roam/pull/2264
+* (Docs): orgmode.org/elpa has been shut down by @aviad in https://github.com/org-roam/org-roam/pull/2258
+* Minor typo in the commented text of the definition of `org-roam-refile` by @apc in https://github.com/org-roam/org-roam/pull/2263
+* fix outline of link in properties by @bhuztez in https://github.com/org-roam/org-roam/pull/2230
+* (fix): update `org-roam-unlinked-references-section` check by @Elilif in https://github.com/org-roam/org-roam/pull/2254
+* Add support for filtering backlinks. by @swflint in https://github.com/org-roam/org-roam/pull/2247
+* (docs): update documentation on database-connectors by @jethrokuan in https://github.com/org-roam/org-roam/pull/2298
+* (db): default to sqlite-builtin when possible by @jethrokuan in https://github.com/org-roam/org-roam/pull/2299
+* don't complete org-roam nodes in source blocks by @ParetoOptimalDev in https://github.com/org-roam/org-roam/pull/2292
+* (core): add org-roam-node-category by @jethrokuan in https://github.com/org-roam/org-roam/pull/2300
+* add discoverability support for age encrypted org files by @anticomputer in https://github.com/org-roam/org-roam/pull/2302
+* (minor): fix lints on main by @jethrokuan in https://github.com/org-roam/org-roam/pull/2320
+* utils: descendant-of-p: Defend against nils by @qzdl in https://github.com/org-roam/org-roam/pull/2319
+* Add customisable function for prompting when adding refs by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2317
+* Fix org-fold-core-style in org-roam-buffer by @hwiorn in https://github.com/org-roam/org-roam/pull/2325
+* depend on snapshot of emacsql by @jethrokuan in https://github.com/org-roam/org-roam/pull/2327
+* (node): org-roam-node-at-point: don't error in non-org buffers by @Hugo-Heagren in https://github.com/org-roam/org-roam/pull/2329
+* (node) add optional NOCASE parameter to org-roam-node-from-title-or-alias by @nuthub in https://github.com/org-roam/org-roam/pull/2403
+* (docs): update org-protocol instructions by @benthamite in https://github.com/org-roam/org-roam/pull/2401
+* Fix some typos by @feltcat in https://github.com/org-roam/org-roam/pull/2430
+* (docs): fix name of my-org-roam-show-backlink-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2447
+* Link Martin Edström's knowledge base by @meedstrom in https://github.com/org-roam/org-roam/pull/2394
+* Update org-roam.org by @marcosbodio in https://github.com/org-roam/org-roam/pull/2441
+* (chore): fix indent blocking ci lint execution by @Delapouite in https://github.com/org-roam/org-roam/pull/2448
+* Fix Issue #2410 - Unlinked References doesnt work if the org-roam-directory has a space in it.  by @vikram-mandyam in https://github.com/org-roam/org-roam/pull/2411
+* (test): add "org-roam--list-files-search-globs" by @Delapouite in https://github.com/org-roam/org-roam/pull/2449
+* Backlink heading by @toregilhk in https://github.com/org-roam/org-roam/pull/2333
+* (test): add org-roam-id-find by @Delapouite in https://github.com/org-roam/org-roam/pull/2450
+* (test): add org-roam-id-at-point by @Delapouite in https://github.com/org-roam/org-roam/pull/2451
+* (test): add org-roam--buffer-promoteable-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2452
+* (test): add org-roam--get-titles by @Delapouite in https://github.com/org-roam/org-roam/pull/2453
+* (test): add org-roam-node-from-{id|title-or-alias} by @Delapouite in https://github.com/org-roam/org-roam/pull/2454
+* (test): add org-roam-alias-{add|remove} by @Delapouite in https://github.com/org-roam/org-roam/pull/2455
+* (docs): add missing versions dates and obsolete notice by @Delapouite in https://github.com/org-roam/org-roam/pull/2456
+* (docs): explain org-roam-file-exclude-regexp by @adamoudad in https://github.com/org-roam/org-roam/pull/2458
+* (test): add org-roam-demote-entire-buffer by @Delapouite in https://github.com/org-roam/org-roam/pull/2459
+* (test): add org-roam-file-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2460
+* (test): add org-roam-buffer-p by @Delapouite in https://github.com/org-roam/org-roam/pull/2461
+* (fix): remove dead-code about org-roam-shield feature by @Delapouite in https://github.com/org-roam/org-roam/pull/2462
+* (test): add org-roam-db--file-hash by @Delapouite in https://github.com/org-roam/org-roam/pull/2464
+* (test): add org-roam-db-get-{scheduled|deadline}-time by @Delapouite in https://github.com/org-roam/org-roam/pull/2465
+* Doc formatting: 2 fixes by @kevinrineer in https://github.com/org-roam/org-roam/pull/2475
+* Take org-roam-node as argument to #'org-roam-refile by @pestctrl in https://github.com/org-roam/org-roam/pull/2388
+* Compatibility with latest org-id version: advise org-id-find rather than overwriting id link by @ricklupton in https://github.com/org-roam/org-roam/pull/2432
+* Depend on emacsql 4.0.0 by @bcc32 in https://github.com/org-roam/org-roam/pull/2466
+* Use regexp match to replace hard-coded path equal test by @manphiz in https://github.com/org-roam/org-roam/pull/2497
+* Align sqlite integration with emacsql 4.0 by @dustinfarris in https://github.com/org-roam/org-roam/pull/2503
+* fix #2425 Prevent data loss when user has called org-roam-extract-subtree on folded org headline by @akashpal-21 in https://github.com/org-roam/org-roam/pull/2444
+* Rely on emacsql-sqlite-open to pick the best available back-end by @tarsius in https://github.com/org-roam/org-roam/pull/2486
+* Set org-roam-directory to a non-existent path to ensure robust test by @manphiz in https://github.com/org-roam/org-roam/pull/2499
+* (perf): Deprecate link :outline properties by @meedstrom in https://github.com/org-roam/org-roam/pull/2509
+* Bump DB version to avoid error by @meedstrom in https://github.com/org-roam/org-roam/pull/2514
+
+
+## 2.2.2 (2022-04-25)
+
+### Breaking
 ### Added
+- [#2138](https://github.com/org-roam/org-roam/pull/2138) export: add new module
+- [#2170](https://github.com/org-roam/org-roam/pull/2170) log: add new module for working with org logs
+- [#2158](https://github.com/org-roam/org-roam/pull/2158) db: support emacsql-sqlite-builtin and emacsql-sqlite-module
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: support a list of `org-roam-file-exclude-regexp`
+
+### Removed
+### Fixed
+- [#2091](https://github.com/org-roam/org-roam/pull/2091) node: fix org-roam-promote-entire-buffer structural errors
+- [#2130](https://github.com/org-roam/org-roam/pull/2130) buffer: unlinked-references section now also searches within symlinked directories
+- [#2152](https://github.com/org-roam/org-roam/pull/2152) org-roam-preview-default-function: doesn't copy copy content of next heading node when current node's content is empty
+- [#2159](https://github.com/org-roam/org-roam/pull/2159) db: fix db syncs on narrowed buffers
+- [#2156](https://github.com/org-roam/org-roam/pull/2157) capture: templates with functions are handled correctly to avoid signaling `char-or-string-p`
+
+### Changed
+- [#2160](https://github.com/org-roam/org-roam/pull/2160) core: ignore files in `org-attach-id-dir` by default
+
+## 2.2.1 (2022-03-15)
+
+### 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)))
+  ```
+
+### 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 (2022-01-14)
+
+### 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
+
+### Removed
+### Changed
+- [#1795](https://github.com/org-roam/org-roam/pull/1795) buffer: optimized reflinks fetch
+- [#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 (2021-08-20)
+
+### Added
+- [#1693](https://github.com/org-roam/org-roam/pull/1693) added `filter-fn` and `templates` parameter to `org-roam-capture`, `org-roam-node-find`, and `org-roam-node-insert`
 - [#1709](https://github.com/org-roam/org-roam/pull/1709) added ability to specify default value in org-roam capture templates
 - [#1710](https://github.com/org-roam/org-roam/pull/1710) added `org-roam-extract-subtree`
 - [#1720](https://github.com/org-roam/org-roam/pull/1720) added `org-roam-db-update-on-save`
@@ -29,7 +198,10 @@
 - [#1713](https://github.com/org-roam/org-roam/pull/1713) capture: check for file-existence before template insertion
 - [#1725](https://github.com/org-roam/org-roam/pull/1725) db: always compute hash of encrypted file to prevent re-processing of encrypted files
 
-## 2.0.0
+## 2.0.0 (2021-07-17)
+
+A few symbols have been marked as obsolete. Have a look at the content of [org-roam-compat.el](https://github.com/org-roam/org-roam/blob/f819720c510185af713522c592833ec9f2934251/org-roam-compat.el#L159)
+
 ### Added
 - [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
 - [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
@@ -56,7 +228,7 @@
 - [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
 - [#1542](https://github.com/org-roam/org-roam/issues/1542) fix files not excluded when `org-roam-list-files-commands` is nil
 
-## 1.2.3 (13-11-2020)
+## 1.2.3 (2020-11-13)
 
 Primarily a stabilization and bug-fix release.
 
@@ -87,7 +259,7 @@ Org-roam-dailies has also been revamped to include new features, see [this video
 - [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
 - [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
 
-## 1.2.2 (06-10-2020)
+## 1.2.2 (2020-10-06)
 
 In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
 
@@ -125,7 +297,7 @@ This change requires you to set `org-roam-directory` to the resolved path of a f
 - [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
 - [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
 
-## 1.2.1 (27-07-2020)
+## 1.2.1 (2020-07-27)
 
 This release consisted of a big deal of refactoring and bug fixes. Notably, we fixed several catastrophic failures on db builds with bad setups (#854), and modularized tag and title extractions.
 
@@ -158,7 +330,7 @@ We also added some new features that had been a long time coming:
 - [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
 - [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
 
-## 1.2.0 (12-06-2020)
+## 1.2.0 (2020-06-12)
 
 In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
 
@@ -186,7 +358,7 @@ We also add `org-roam-unlinked-references`, which naively finds text that could
 - [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
 - [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
 
-## 1.1.1 (18-05-2020)
+## 1.1.1 (2020-05-18)
 
 In this release, we added two new features:
 
@@ -226,7 +398,7 @@ As usual, this release comes with a multitude of bug-fixes and refactorings.
 - [#606](https://github.com/org-roam/org-roam/pull/606) Added `org-roam-dev.el` for developer coding standards
 - [#622](https://github.com/org-roam/org-roam/pull/622) Online documentation now points to the Org-based documentation
 
-## 1.1.0 (21-04-2020)
+## 1.1.0 (2020-04-21)
 
 To the average user, this release is mainly a bugfix release with additional options to customize. However, the changes made to the source is significant. Most notably, in this release:
 
@@ -264,7 +436,7 @@ In the coming months, you can expect work on bigger projects (e.g. revamping the
 - [#363](https://github.com/org-roam/org-roam/pull/363), [#473](https://github.com/org-roam/org-roam/pull/473) Modularize org-roam features.
 - [#497](https://github.com/org-roam/org-roam/pull/497) Simplify `org-roam--list-files` implementation
 
-## 1.0.0 (23-03-2020)
+## 1.0.0 (2020-03-23)
 
 Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
 been stable for the most part.
@@ -283,7 +455,7 @@ been stable for the most part.
 - [#293](https://github.com/org-roam/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
 - [#275](https://github.com/org-roam/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
 
-## 1.0.0-rc1 (06-03-2020)
+## 1.0.0-rc1 (2020-03-06)
 
 This is a pre-release before the push to MELPA. It contains large
 internal changes, with little user-facing changes. Most notably, the

README.md

@@ -39,7 +39,7 @@ detailed information, please read the [manual][docs].
 
 ### Using `package.el`
 <details>
-<summary>Toggle instuctions</summary>
+<summary>Toggle instructions</summary>
 
 You can install `org-roam` from [MELPA](https://melpa.org/) or [MELPA
 Stable](https://stable.melpa.org/) using `package.el`:
@@ -47,35 +47,11 @@ 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`
 <details>
-<summary>Toggle instuctions</summary>
+<summary>Toggle instructions</summary>
 
 Installation from MELPA or MELPA Stable using `straight.el`:
 
@@ -115,7 +91,7 @@ next sample will get you there:
 
 ### Using Doom Emacs
 <details>
-<summary>Toggle instuctions</summary>
+<summary>Toggle instructions</summary>
 
 Doom's `:lang org` module comes with support for `org-roam`, but it's not
 enabled by default. To activate it pass `+roam2` flag to `org` module in your
@@ -177,9 +153,8 @@ dependencies. These include:
 - dash
 - f
 - s
-- org (9.4 is the minimal required version!)
+- org (9.6 is the minimum required version!)
 - emacsql
-- emacsql-sqlite
 - magit-section
 - filenotify-recursive
 
@@ -198,6 +173,33 @@ 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
@@ -225,8 +227,9 @@ 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://braindump.rasen.dev/)
+- [Alexey Shmalko](https://www.alexeyshmalko.com/)
 - [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
+- [Martin Edström](https://edstrom.dev/)
 
 ## Contributing
 
@@ -249,6 +252,6 @@ General Public License, Version 3.
 [release]: https://github.com/org-roam/org-roam/releases
 [docs]: https://www.orgroam.com/manual.html
 [discourse]: https://org-roam.discourse.group/
-[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
+[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ
 [issues]: https://github.com/org-roam/org-roam/issues
 [faq]: https://www.orgroam.com/manual.html#FAQ

doc/index.html

@@ -95,7 +95,7 @@
         <ul>
             <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual.html">Online Manual</a></li>
             <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
-            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
+            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ">Slack</a></li>
           </ul>
       </div>
     </section>
@@ -151,7 +151,7 @@
         <div class="row">
           <a
             class="content footer-links"
-            href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ"
             >Slack</a
           >
         </div>

doc/org-roam.org

@@ -1,23 +1,23 @@
 #+title: Org-roam User Manual
 #+author: Jethro Kuan
 #+email: jethrokuan95@gmail.com
-#+date: 2020-2021
+#+date: 2020-2025
 #+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 2.1.0
+#+subtitle: for version 2.3.0
 
 #+options: H:4 num:3 toc:nil creator:t ':t
 #+property: header-args :eval never
 #+texinfo: @noindent
 
-This manual is for Org-roam version 2.1.0.
+This manual is for Org-roam version 2.3.0.
 
 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 You can redistribute this document and/or modify it under the terms of the GNU
 General Public License as published by the Free Software Foundation, either
@@ -134,7 +134,7 @@ A slip-box requires a method for quickly capturing ideas. These are called
 *fleeting notes*: they are simple reminders of information or ideas that will
 need to be processed later on, or trashed. This is typically accomplished using
 ~org-capture~ (see info:org#Capture), or using Org-roam's daily notes
-functionality (see [[*Org-roam Dailies][Org-roam Dailies]]). This provides a central inbox for collecting
+functionality (see [[*org-roam-dailies][org-roam-dailies]]). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
 *Permanent notes*
@@ -178,18 +178,7 @@ archives to =package-archives=:
 #+END_SRC
 
 Org-roam also depends on a recent version of Org, which can be obtained in Org's
-package repository (see info:org#Installation). To use Org's ELPA archive:
+package repository (see info:org#Installation).
-
-#+BEGIN_SRC emacs-lisp
-(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)
-#+END_SRC
-
-Once you have added your preferred archive, you need to update the
-local package list using:
-
-#+BEGIN_EXAMPLE
-  M-x package-refresh-contents RET
-#+END_EXAMPLE
 
 Once you have done that, you can install Org-roam and its dependencies
 using:
@@ -235,7 +224,6 @@ dependencies that it requires. These include:
 - s
 - org
 - emacsql
-- emacsql-sqlite
 - magit-section
 
 You can install this manually as well, or get the latest version from MELPA. You
@@ -279,44 +267,6 @@ file:
 install-info /path/to/my/info/files/org-roam.info /path/to/my/info/files/dir
 #+end_src
 
-** Installation Troubleshooting
-*** C Compiler
-Org-roam relies on an Emacs package called ~emacsql~ and ~emacsql-sqlite~ to
-work with the ~sqlite~ database. Both of them should be installed automatically
-in your Emacs environment as a prerequisite for Org-roam when you install it.
-
-~emacsql-sqlite~ requires a C compiler (e.g. ~gcc~ or ~clang~) to be present in
-your computer. How to install a C compiler depends on the OS that you use.
-
-- For Windows:
-
-There are various ways to install one, depending on how you have installed
-Emacs. If you use Emacs within a Cygwin or MinGW environment, then you should
-install a compiler using their respective package manager.
-
-If you have installed your Emacs from the [[https://www.gnu.org/software/emacs/][GNU Emacs website]], then the easiest way
-is to use [[https://www.msys2.org/][MSYS2]] as at the time of this writing:
-
-1. Use the installer in the official website and install MSYS2
-2. Run MSYS2
-3. In the command-line tool, type the following and answer "Y" to proceed:
-
-   #+BEGIN_SRC bash
-     pacman -S gcc
-   #+END_SRC
-
-   Note that you do not need to manually set the PATH for MSYS2; the
-installer automatically takes care of it for you.
-
-4. Open Emacs and call ~M-x org-roam-db-autosync-mode~
-
-   This will automatically start compiling ~emacsql-sqlite~; you should see a
-message in minibuffer. It may take a while until compilation completes. Once
-complete, you should see a new file ~emacsql-sqlite.exe~ created in a subfolder
-named ~sqlite~ under ~emacsql-sqlite~ installation folder. It's typically in
-your Emacs configuration folder like this:
-~/.config/emacs/elpa/emacsql-sqlite-20190727.1710/sqlite~
-
 * Getting Started
 ** The Org-roam Node
 
@@ -373,7 +323,12 @@ 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.
+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
 
 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
@@ -417,7 +372,59 @@ 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
+Org-roam uses a SQLite database to perform caching.  This integration is
+managed by the [[https://github.com/magit/emacsql][emacsql]] library.  It should "just work".
+
 ** What to cache
 
 By default, all nodes (any headline or file with an ID) are cached by Org-roam.
@@ -438,12 +445,41 @@ property to a non-nil value. For example:
 One can also set ~org-roam-db-node-include-function~. For example, to exclude
 all headlines with the ~ATTACH~ tag from the Org-roam database, one can set:
 
-#+begin_src org
+#+begin_src emacs-lisp
 (setq org-roam-db-node-include-function
       (lambda ()
         (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
@@ -510,10 +546,10 @@ 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-section-functions~.
+To configure what sections are displayed in the buffer, set ~org-roam-mode-sections~.
 
 #+begin_src emacs-lisp
-  (setq org-roam-mode-section-functions
+  (setq org-roam-mode-sections
         (list #'org-roam-backlinks-section
               #'org-roam-reflinks-section
               ;; #'org-roam-unlinked-references-section
@@ -522,6 +558,29 @@ 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
+
+The backlinks section ~org-roam-backlinks-section~ also supports a
+predicate to filter backlinks, ~:show-backlink-p~.  This can be used
+as follows:
+
+#+begin_src emacs-lisp
+  (defun my-org-roam-show-backlink-p (backlink)
+    (not (member "daily" (org-roam-node-tags (org-roam-backlink-source-node backlink)))))
+
+  (setq org-roam-mode-sections
+        '((org-roam-backlinks-section :unique t :show-backlink-p my-org-roam-show-backlink-p)
+          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
@@ -629,7 +688,7 @@ With the above example, if another node links to https://www.google.com/, it
 will show up as a “reference backlink”.
 
 These keys also come in useful for when taking website notes, using the
- ~roam-ref~ protocol (see [[*Org-roam Protocol][Roam Protocol]]).
+ ~roam-ref~ protocol (see [[*org-roam-protocol][org-roam-protocol]]).
 
 You may assign multiple refs to a single node, for example when you want
 multiple papers in a series to share the same note, or an article has a citation
@@ -646,6 +705,59 @@ Org-roam also provides some functions to add or remove refs.
 
   Remove a ref from the node at point.
 
+* Citations
+
+Since version 9.5, Org has first-class support for citations. Org-roam supports
+the caching of both these in-built citations (of form ~[cite:@key]~) and [[https://github.com/jkitchin/org-ref][org-ref]]
+citations (of form cite:key).
+
+Org-roam attempts to load both the ~org-ref~ and ~org-cite~ package when
+indexing files, so no further setup from the user is required for citation
+support.
+
+** Using the Cached Information
+
+It is common to use take reference notes for academic papers. To designate the
+node to be the canonical node for the academic paper, we can use its unique
+citation key:
+
+#+begin_src org
+,* Probabilistic Robotics
+:PROPERTIES:
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: @thrun2005probabilistic
+: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
+,* Probabilistic Robotics
+:PROPERTIES:
+:ID:       51b7b82c-bbb4-4822-875a-ed548cffda10
+:ROAM_REFS: cite:thrun2005probabilistic
+:END:
+#+end_src
+
+for ~org-ref~.
+
+When another node has a citation for that key, we can see it using the
+~Reflinks~ section of the Org-roam buffer.
+
+Extension developers may be interested in retrieving the citations within their
+notes. This information can be found within the ~citation~ table of the Org-roam
+database.
+
 * Completion
 
 Completions for Org-roam are provided via ~completion-at-point~. Org-roam
@@ -679,7 +791,7 @@ Similarly, the completion candidates are the titles and aliases for all Org-roam
 nodes, and upon choosing a candidate a ~roam:Title~ link will be inserted
 linking to the node of choice.
 
-This is disable by default. To enable it, set ~org-roam-completion-everywhere~
+This is disabled by default. To enable it, set ~org-roam-completion-everywhere~
 to ~t~:
 
 #+begin_src emacs-lisp
@@ -698,7 +810,7 @@ extension in your Org-roam capture templates. For example:
 
 #+begin_src emacs-lisp
 (setq org-roam-capture-templates '(("d" "default" plain "%?"
-     :if-new (file+head "${slug}.org.gpg"
+     :target (file+head "${slug}.org.gpg"
                         "#+title: ${title}\n")
      :unnarrowed t)))
 #+end_src
@@ -707,13 +819,95 @@ Note that the Org-roam database stores metadata information in plain-text
 (headline text, for example), so if this information is private to you then you
 should also ensure the database is encrypted.
 
-* Org-roam Protocol
+* The Templating System
+
+Org-roam extends the ~org-capture~ system, providing a smoother note-taking
+experience. However, these extensions mean Org-roam capture templates are
+incompatible with ~org-capture~ templates.
+
+Org-roam's templates are specified by ~org-roam-capture-templates~. Just like
+~org-capture-templates~, ~org-roam-capture-templates~ can contain multiple
+templates. If ~org-roam-capture-templates~ only contains one template, there
+will be no prompt for template selection.
+
+** Template Walkthrough
+
+To demonstrate the additions made to org-capture templates. Here, we explain
+the default template, reproduced below. You will find most of the elements
+of the template are similar to ~org-capture~ templates.
+
+#+BEGIN_SRC emacs-lisp
+(("d" "default" plain "%?"
+  :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                     "#+title: ${title}\n")
+  :unnarrowed t))
+#+END_SRC
+
+1. The template has short key ~"d"~. If you have only one template, org-roam
+   automatically chooses this template for you.
+2. The template is given a description of ~"default"~.
+3. ~plain~ text is inserted. Other options include Org headings via
+   ~entry~.
+4. Notice that the ~target~ that's usually in Org-capture templates is missing
+   here.
+5. ~"%?"~ is the template inserted on each call to ~org-roam-capture-~.
+   This template means don't insert any content, but place the cursor here.
+6. ~:target~ is a compulsory specification in the Org-roam capture template. The
+   first element of the list indicates the type of the target, the second
+   element indicates the location of the captured node, and the rest of the
+   elements indicate prefilled template that will be inserted and the position
+   of the point will be adjusted for. The latter behavior varies from type to
+   type of the capture target.
+7. ~:unnarrowed t~ tells org-capture to show the contents for the whole file,
+   rather than narrowing to just the entry. This is part of the Org-capture
+   templates.
+
+See the ~org-roam-capture-templates~ documentation for more details and
+customization options.
+
+** Org-roam Template Expansion
+
+Org-roam's template definitions also extend org-capture's template syntax, to
+allow prefilling of strings. We have seen a glimpse of this in [[*Template Walkthrough][Template
+Walkthrough]].
+
+Org-roam provides the ~${foo}~ syntax for substituting variables with known
+strings. ~${foo}~'s substitution is performed as follows:
+
+1. If ~foo~ is a function, ~foo~ is called with the current node as its
+   argument.
+2. Else if ~org-roam-node-foo~ is a function, ~foo~ is called with the current node
+   as its argument. The ~org-roam-node-~ prefix defines many of Org-roam's node
+   accessors such as ~org-roam-node-title~ and ~org-roam-node-level~.
+3. Else look up ~org-roam-capture--info~ for ~foo~. This is an internal variable
+   that is set before the capture process begins.
+4. If none of the above applies, read a string using ~completing-read~.
+   a. Org-roam also provides the ~${foo=default_val}~ syntax, where if a default
+      value is provided, will be the initial value for the ~foo~ key during
+      minibuffer completion.
+
+One can check the list of available keys for nodes by inspecting the
+~org-roam-node~ struct. At the time of writing, it is:
+
+#+begin_src emacs-lisp
+  (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
+                               (:copier nil))
+    "A heading or top level file with an assigned ID property."
+    file file-hash file-atime file-mtime
+    id level point todo priority scheduled deadline title properties olp
+    tags aliases refs)
+#+end_src
+
+This makes ~${file}~, ~${file-hash}~ etc. all valid substitutions.
+
+* Extensions
+** org-roam-protocol
 
 Org-roam provides extensions for capturing content from external applications
 such as the browser, via ~org-protocol~. Org-roam extends ~org-protocol~ with 2
 protocols: the ~roam-node~ and ~roam-ref~ protocols.
 
-** Installation
+*** Installation
 
 To enable Org-roam's protocol extensions, simply add the following to your init
 file:
@@ -723,9 +917,18 @@ file:
 #+END_SRC
 
 We also need to set up ~org-protocol~: the instructions for setting up
-~org-protocol~ are reproduced below.
+~org-protocol~ are reproduced here.
 
-*** Linux
+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.
+
+**** Linux
 For Linux users, create a desktop application in
 ~~/.local/share/applications/org-protocol.desktop~:
 
@@ -766,7 +969,7 @@ make the new policy take effect.
 See [[https://www.chromium.org/administrators/linux-quick-start][here]] for more info on the ~/etc/opt/chrome/policies/managed~ directory and
 [[https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox][here]] for information on the ~ExternalProtocolDialogShowAlwaysOpenCheckbox~ policy.
 
-*** Mac OS
+**** Mac OS
 For Mac OS, we need to create our own application.
 
 1. Launch Script Editor
@@ -776,7 +979,7 @@ For Mac OS, we need to create our own application.
   on open location this_URL
       set EC to "/usr/local/bin/emacsclient --no-wait "
       set filePath to quoted form of this_URL
-      do shell script EC & filePath
+      do shell script EC & filePath & " &> /dev/null &"
       tell application "Emacs" to activate
   end open location
 #+end_src
@@ -821,7 +1024,45 @@ defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandle
 
 Then restart your computer.
 
-*** Windows
+If you're using the [[https://formulae.brew.sh/formula/emacs][Emacs Homebrew formula]], you may need one of the following additional configurations:
+
+a) Add option `-c` to `emacsclient` in the script, and start emacs from command line with `emacs --daemon`
+
+#+begin_src emacs-lisp
+  on open location this_URL
+      set EC to "/usr/local/bin/emacsclient -c --no-wait "
+      set filePath to quoted form of this_URL
+      do shell script EC & filePath & " &> /dev/null &"
+      tell application "Emacs" to activate
+  end open location
+#+end_src
+
+b) Add `(server-start)` in .emacs (in this case you do not need option `-c` for `emacsclient` in the script, and you do not need to start emacs with `emacs --daemon`
+
+***** Testing org-protocol
+
+To test that you have the handler setup and registered properly from the command
+line you can run:
+
+#+begin_src bash
+  open org-protocol://roam-ref\?template=r\&ref=test\&title=this
+#+end_src
+
+If you get an error similar too this or the wrong handler is run:
+
+#+begin_quote
+No application knows how to open URL org-protocol://roam-ref?template=r&ref=test&title=this (Error Domain=NSOSStatusErrorDomain Code=-10814 "kLSApplicationNotFoundErr: E.g. no application claims the file" UserInfo={_LSLine=1489, _LSFunction=runEvaluator}).
+
+#+end_quote
+
+You may need to manually register your handler, like this:
+
+#+begin_src bash
+/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -R  -f /Applications/OrgProtocolClient.app
+#+end_src
+
+Here is a link to the lsregister command that is really useful: https://eclecticlight.co/2019/03/25/lsregister-a-valuable-undocumented-command-for-launchservices/
+**** Windows
 For Windows, create a temporary ~org-protocol.reg~ file:
 
 #+BEGIN_SRC text
@@ -846,13 +1087,13 @@ Windows, replace the last line with:
 After executing the .reg file, the protocol is registered and you can delete the
 file.
 
-** The roam-node protocol
+*** The roam-node protocol
 
 The roam-node protocol opens the node with ID specified by the ~node~ key (e.g.
 ~org-protocol://roam-node?node=node-id~). ~org-roam-graph~ uses this to make the
 graph navigable.
 
-** The roam-ref protocol
+*** The roam-ref protocol
 
 This protocol finds or creates a new note with a given ~ROAM_REFS~:
 
@@ -880,89 +1121,11 @@ or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
 where ~template~ is the template key for a template in
 ~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]).
 
-* The Templating System
+** org-roam-graph
-
-Org-roam extends the ~org-capture~ system, providing a smoother note-taking
-experience. However, these extensions mean Org-roam capture templates are
-incompatible with ~org-capture~ templates.
-
-Org-roam's templates are specified by ~org-roam-capture-templates~. Just like
-~org-capture-templates~, ~org-roam-capture-templates~ can contain multiple
-templates. If ~org-roam-capture-templates~ only contains one template, there
-will be no prompt for template selection.
-
-** Template Walkthrough
-
-To demonstrate the additions made to org-capture templates. Here, we explain
-the default template, reproduced below. You will find some most of the elements
-of the template are similar to ~org-capture~ templates.
-
-#+BEGIN_SRC emacs-lisp
-(("d" "default" plain "%?"
-  :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
-                     "#+title: ${title}\n")
-  :unnarrowed t))
-#+END_SRC
-
-1. The template has short key ~"d"~. If you have only one template, org-roam
-   automatically chooses this template for you.
-2. The template is given a description of ~"default"~.
-3. ~plain~ text is inserted. Other options include Org headings via
-   ~entry~.
-4. Notice that the ~target~ that's usually in Org-capture templates is missing
-   here.
-5. ~"%?"~ is the template inserted on each call to ~org-roam-capture-~.
-   This template means don't insert any content, but place the cursor here.
-6. ~:if-new~ is a compulsory specification in the Org-roam capture template.
-   This indicates the location for the new node.
-7. ~:unnarrowed t~ tells org-capture to show the contents for the whole file,
-   rather than narrowing to just the entry. This is part of the Org-capture
-   templates.
-
-See the ~org-roam-capture-templates~ documentation for more details and
-customization options.
-
-** Org-roam Template Expansion
-
-Org-roam's template definitions also extend org-capture's template syntax, to
-allow prefilling of strings. We have seen a glimpse of this in [[*Template Walkthrough][Template
-Walkthrough]].
-
-Org-roam provides the ~${foo}~ syntax for substituting variables with known
-strings. ~${foo}~'s substitution is performed as follows:
-
-1. If ~foo~ is a function, ~foo~ is called with the current node as its
-   argument.
-2. Else if ~org-roam-node-foo~ is a function, ~foo~ is called with the current node
-   as its argument. The ~org-roam-node-~ prefix defines many of Org-roam's node
-   accessors such as ~org-roam-node-title~ and ~org-roam-node-level~.
-3. Else look up ~org-roam-capture--info~ for ~foo~. This is an internal variable
-   that is set before the capture process begins.
-4. If none of the above applies, read a string using ~completing-read~.
-   a. Org-roam also provides the ~${foo=default_val}~ syntax, where if a default
-      value is provided, will be the initial value for the ~foo~ key during
-      minibuffer completion.
-
-One can check the list of available keys for nodes by inspecting the
-~org-roam-node~ struct. At the time of writing, it is:
-
-#+begin_src emacs-lisp
-  (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
-                               (:copier nil))
-    "A heading or top level file with an assigned ID property."
-    file file-hash file-atime file-mtime
-    id level point todo priority scheduled deadline title properties olp
-    tags aliases refs)
-#+end_src
-
-This makes ~${file}~, ~${file-hash}~ etc. all valid substitutions.
-
-* Graphing
 
 Org-roam provides basic graphing capabilities to explore interconnections
 between notes, in ~org-roam-graph~. This is done by performing SQL queries and
-generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Org-roam Protocol][Roam
+generating images using [[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*org-roam-protocol][org-roam-protocol]].
-Protocol]].
 
 The entry point to graph creation is ~org-roam-graph~.
 
@@ -1003,7 +1166,7 @@ ARG may be any of the following values:
           (org-roam-graph--open (concat "file://///wsl$/Ubuntu" file)))))
   #+END_SRC
 
-** Graph Options
+*** Graph Options
 
 Graphviz provides many options for customizing the graph output, and Org-roam
 supports some of them. See https://graphviz.gitlab.io/_pages/doc/info/attrs.html
@@ -1029,12 +1192,12 @@ for customizable options.
   Extra options for edges in the graphviz output (The "E" attributes).
   Example: ~'(("dir" . "back"))~
 
-* Org-roam Dailies
+** org-roam-dailies
 
 Org-roam provides journaling capabilities akin to
 Org-journal with ~org-roam-dailies~.
 
-** Configuration
+*** Configuration
 
 For ~org-roam-dailies~ to work, you need to define two variables:
 
@@ -1054,13 +1217,13 @@ Here is a sane default configuration:
 (setq org-roam-dailies-capture-templates
       '(("d" "default" entry
          "* %?"
-         :if-new (file+head "%<%Y-%m-%d>.org"
+         :target (file+head "%<%Y-%m-%d>.org"
                             "#+title: %<%Y-%m-%d>\n"))))
 #+end_src
 
 See [[*The Templating System][The Templating System]] for creating new templates.
 
-** Usage
+*** Usage
 
 ~org-roam-dailies~ provides these interactive functions:
 
@@ -1078,7 +1241,7 @@ There are variants of those commands for ~-yesterday~ and ~-tomorrow~:
 
 - Function: ~org-roam-dailies-capture-yesterday~ n &optional goto
 
-  Create an entry in the daily note for yesteday.
+  Create an entry in the daily note for yesterday.
 
   With numeric argument ~n~, use the daily note ~n~ days in the past.
 
@@ -1114,6 +1277,18 @@ There are also commands which allow you to use Emacs’s ~calendar~ to find the
 - Function: ~org-roam-dailies-goto-next-note~
 
   When in an daily-note, find the next one.
+** org-roam-export
+
+Because Org-roam files are plain org files, they can be exported easily using
+~org-export~ to a variety of formats, including ~html~ and ~pdf~. However,
+Org-roam relies heavily on ID links, which Org's html export has poor support
+of. To fix this, Org-roam provides a bunch of overrides to better support
+export. To use them, simply run:
+
+#+begin_src emacs-lisp
+  (require 'org-roam-export)
+#+end_src
+
 * Performance Optimization
 ** Garbage Collection
 
@@ -1187,7 +1362,7 @@ The Deft interface can slow down quickly when the number of files get huge.
 
 [[https://github.com/bastibe/org-journal][Org-journal]] provides journaling capabilities to Org-mode. A lot of its
 functionalities have been incorporated into Org-roam under the name
-[[*Org-roam Dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
+[[*org-roam-dailies][~org-roam-dailies~]]. It remains a good tool if you want to isolate your verbose
 journal entries from the ideas you would write on a scratchpad.
 
 #+BEGIN_SRC emacs-lisp
@@ -1240,6 +1415,9 @@ 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~.
 
@@ -1267,20 +1445,27 @@ variable using directory-local variables. This is what ~.dir-locals.el~ may
 contain:
 
 #+BEGIN_SRC emacs-lisp
-  ((nil . ((org-roam-directory . (expand-file-name "."))
+  ((nil . ((org-roam-directory . "/path/to/alt/org-roam-dir")
-           (org-roam-db-location . (expand-file-name "./org-roam.db")))))
+           (org-roam-db-location . "/path/to/alt/org-roam-dir/org-roam.db"))))
+#+END_SRC
+
+Note ~org-roam-directory~ and ~org-roam-db-location~ should be an absolute path, not relative.
+
+Alternatively, use ~eval~ if you wish to call functions:
+
+#+BEGIN_SRC emacs-lisp
+  ((nil . ((eval . (setq-local
+                    org-roam-directory (expand-file-name (locate-dominating-file
+                                                          default-directory ".dir-locals.el"))))
+           (eval . (setq-local
+                    org-roam-db-location (expand-file-name "org-roam.db"
+                                                           org-roam-directory))))))
 #+END_SRC
 
 All files within that directory will be treated as their own separate set of
 Org-roam files. Remember to run ~org-roam-db-sync~ from a file within
 that directory, at least once.
 
-** How do I migrate from Roam Research?
-
-Fabio has produced a command-line tool that converts markdown files exported
-from Roam Research into Org-roam compatible markdown. More instructions are
-provided [[https://github.com/fabioberger/roam-migration][in the repository]].
-
 ** How do I create a note whose title already matches one of the candidates?
 
 This situation arises when, for example, one would like to create a note titled
@@ -1301,28 +1486,110 @@ you don't want them to be (e.g. when tangling an Org file), check the value you
 have set for ~org-id-link-to-org-use-id~: setting it to ~'create-if-interactive~
 is a popular option.
 
-* Migrating from Org-roam v1
+** How do I migrate from Roam Research?
+
+Fabio has produced a command-line tool that converts markdown files exported
+from Roam Research into Org-roam compatible markdown. More instructions are
+provided [[https://github.com/fabioberger/roam-migration][in the repository]].
+
+** How to migrate from Org-roam v1?
 
 Those coming from Org-roam v1 will do well treating v2 as entirely new software.
 V2 has a smaller core and fewer moving parts, while retaining the bulk of its
 functionality. It is recommended to read the documentation above about nodes.
 
-It is still desirable to migrate notes collected in v1 to v2. To migrate your v1
+It is still desirable to migrate notes collected in v1 to v2.
-notes to v2, you may use the migration script provided in [[https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4][this gist]], or [[https://gist.github.com/jethrokuan/02f41028fb4a6f81787dc420fb99b6e4#gistcomment-3737019][this
+To migrate your v1 notes to v2, use =M-x org-roam-migrate-wizard=.
-gist]], the latter being better tested. [[https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html][This blog post]] provides a good overview of
+[[https://d12frosted.io/posts/2021-06-11-path-to-org-roam-v2.html][This blog post]]
-what's new in v2 and how to migrate.
+provides a good overview of what's new in v2 and how to migrate.
 
-Simply put, to migrate notes from v1 to v2, one must:
+Essentially, to migrate notes from v1 to v2, one must:
 
-1. Add IDs to all existing notes. These are located in top-level property
+1. Add IDs to all existing notes.
-   drawers (Although note that in v2, not all files need to have IDs)
+   These are located in top-level property drawers
+   (Although note that in v2, not all files need to have IDs).
 2. Update the Org-roam database to conform to the new schema.
 3. Replace ~#+ROAM_KEY~ into the ~ROAM_REFS~ property
 4. Replace ~#+ROAM_ALIAS~ into the ~ROAM_ALIASES~ property
-5. Move ~#+ROAM_TAGS~ into the ~#+FILETAGS~ property for file-level nodes, and
+5. Move ~#+ROAM_TAGS~ into the ~#+FILETAGS~ property for file-level nodes,
-   the ~ROAM_TAGS~ property for headline nodes
+   and the ~ROAM_TAGS~ property for headline nodes
 6. Replace existing file links with ID links.
 
+** How do I publish my notes with an Internet-friendly graph?
+
+The default graph builder creates a graph with an [[https://orgmode.org/worg/org-contrib/org-protocol.html][org-protocol]]
+handler which is convenient when you're working locally but
+inconvenient when you want to publish your notes for remote access.
+Likewise, it defaults to displaying the graph in Emacs which has the
+exact same caveats.  This problem is solvable in the following way
+using org-mode's native [[https://orgmode.org/manual/Publishing.html][publishing]] capability:
+
+1. configure org-mode to publish your org-roam notes as a project.
+2. create a function that overrides the default org-protocol link
+   creation function(=org-roam-default-link-builder=).
+3. create a hook that's called at the end of graph creation to copy
+   the generated graph to the appropriate place.
+
+The example code below is used to publish to a local directory where a
+separate shell script copies the files to the remote site.
+
+*** Configure org-mode for publishing
+This has two steps:
+1. Setting of a /roam/ project that publishes your notes.
+2. Configuring the /sitemap.html/ generation.
+3. Setting up =org-publish= to generate the graph.
+  
+This will require code like the following:
+#+begin_src emacs-lisp
+  (defun roam-sitemap (title list)
+    (concat "#+OPTIONS: ^:nil author:nil html-postamble:nil\n"
+            "#+SETUPFILE: ./simple_inline.theme\n"
+            "#+TITLE: " title "\n\n"
+            (org-list-to-org list) "\nfile:sitemap.svg"))
+
+  (setq my-publish-time 0)   ; see the next section for context
+  (defun roam-publication-wrapper (plist filename pubdir)
+    (org-roam-graph)
+    (org-html-publish-to-html plist filename pubdir)
+    (setq my-publish-time (cadr (current-time))))
+
+  (setq org-publish-project-alist
+    '(("roam"
+       :base-directory "~/roam"
+       :auto-sitemap t
+       :sitemap-function roam-sitemap
+       :sitemap-title "Roam notes"
+       :publishing-function roam-publication-wrapper
+       :publishing-directory "~/roam-export"
+       :section-number nil
+       :table-of-contents nil
+       :style "<link rel=\"stylesheet\" href=\"../other/mystyle.cs\" type=\"text/css\">")))
+#+end_src
+
+*** Overriding the default link creation function
+The code below will generate a link to the generated html file instead
+of the default org-protocol link.
+#+begin_src emacs-lisp
+  (defun org-roam-custom-link-builder (node)
+    (let ((file (org-roam-node-file node)))
+      (concat (file-name-base file) ".html")))
+
+  (setq org-roam-graph-link-builder 'org-roam-custom-link-builder)
+#+end_src
+
+*** Copying the generated file to the export directory
+The default behavior of =org-roam-graph= is to generate the graph and
+display it in Emacs.  There is an =org-roam-graph-generation-hook=
+available that provides access to the file names so they can be copied
+to the publishing directory.  Example code follows:
+
+#+begin_src emacs-lisp
+  (add-hook 'org-roam-graph-generation-hook
+            (lambda (dot svg) (if (< (- (cadr (current-time)) my-publish-time) 5)
+                                  (progn (copy-file svg "~/roam-export/sitemap.svg" 't)
+                                         (kill-buffer (file-name-nondirectory svg))
+                                         (setq my-publish-time 0)))))
+#+end_src
 * Developer's Guide to Org-roam
 ** Org-roam's Design Principle
 
@@ -1361,7 +1628,7 @@ queries on their Org files.
 ** Building Extensions and Advanced Customization of Org-roam
 
 Because Org-roam's core functionality is small, it is possible and sometimes
-desirable to build extensions on top of it. These extensions may one or more of
+desirable to build extensions on top of it. These extensions may use one or more of
 the following functionalities:
 
 - Access to Org-roam's database
@@ -1468,7 +1735,7 @@ When GOTO is non-nil, go the note without creating an entry."
 :END:
 
 #+BEGIN_QUOTE
-Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+Copyright (C) 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 
 You can redistribute this document and/or modify it under the terms
 of the GNU General Public License as published by the Free Software

extensions/org-roam-dailies.el

@@ -1,14 +1,14 @@
 ;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org-roam "2.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,10 +34,9 @@
 ;; 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 and whatever else you can came up with.
+;; scratch notes or whatever else you can think of.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)
 (require 'org-roam)
 
@@ -62,7 +61,7 @@ This path is relative to `org-roam-directory'."
 (defcustom org-roam-dailies-capture-templates
   `(("d" "default" entry
      "* %?"
-     :if-new (file+head "%<%Y-%m-%d>.org"
+     :target (file+head "%<%Y-%m-%d>.org"
                         "#+title: %<%Y-%m-%d>\n")))
   "Capture templates for daily-notes in Org-roam.
 Note that for daily files to show up in the calendar, they have to be of format
@@ -92,7 +91,7 @@ See `org-roam-capture-templates' for the template documentation."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
+                               :options (((const :format "%v " :target)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -130,79 +129,103 @@ See `org-roam-capture-templates' for the template documentation."
 ;;; Commands
 ;;;; Today
 ;;;###autoload
-(defun org-roam-dailies-capture-today (&optional goto)
+(defun org-roam-dailies-capture-today (&optional goto keys)
   "Create an entry in the daily-note for today.
-When GOTO is non-nil, go the note without creating an entry."
+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."
   (interactive "P")
-  (org-roam-dailies--capture (current-time) goto))
+  (org-roam-dailies--capture (current-time) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-today ()
+(defun org-roam-dailies-goto-today (&optional keys)
-  "Find the daily-note for today, creating it if necessary."
+  "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."
   (interactive)
-  (org-roam-dailies-capture-today t))
+  (org-roam-dailies-capture-today t keys))
 
 ;;;; Tomorrow
 ;;;###autoload
-(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
   "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."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-tomorrow (n)
+(defun org-roam-dailies-goto-tomorrow (n &optional keys)
   "Find the daily-note for tomorrow, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow n t))
+  (org-roam-dailies-capture-tomorrow n t keys))
 
 ;;;; Yesterday
 ;;;###autoload
-(defun org-roam-dailies-capture-yesterday (n &optional goto)
+(defun org-roam-dailies-capture-yesterday (n &optional goto keys)
   "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."
+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."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) goto))
+  (org-roam-dailies-capture-tomorrow (- n) goto keys))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-yesterday (n)
+(defun org-roam-dailies-goto-yesterday (n &optional keys)
   "Find the daily-note for yesterday, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
-future."
+future.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "p")
-  (org-roam-dailies-capture-tomorrow (- n) t))
+  (org-roam-dailies-capture-tomorrow (- n) t keys))
 
 ;;;; Date
 ;;;###autoload
-(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
   "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."
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
   (interactive "P")
   (let ((time (let ((org-read-date-prefer-future prefer-future))
-                (org-read-date t t nil (if goto
+                (org-read-date nil t nil (if goto
                                              "Find daily-note: "
                                            "Capture to daily-note: ")))))
-    (org-roam-dailies--capture time goto)))
+    (org-roam-dailies--capture time goto keys)))
 
 ;;;###autoload
-(defun org-roam-dailies-goto-date (&optional prefer-future)
+(defun org-roam-dailies-goto-date (&optional prefer-future keys)
   "Find the daily-note for a date using the calendar, creating it if necessary.
-Prefer past dates, unless PREFER-FUTURE is non-nil."
+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."
   (interactive)
-  (org-roam-dailies-capture-date t prefer-future))
+  (org-roam-dailies-capture-date t prefer-future keys))
 
 ;;;; Navigation
 (defun org-roam-dailies-goto-next-note (&optional n)
@@ -266,7 +289,7 @@ If FILE is not specified, use the current buffer's file-path."
     (save-match-data
       (and
        (org-roam-file-p path)
-       (f-descendant-of-p path directory)))))
+       (org-roam-descendant-of-p path directory)))))
 
 ;;;###autoload
 (defun org-roam-dailies-find-directory ()
@@ -300,11 +323,16 @@ 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)
+(defun org-roam-dailies--capture (time &optional goto keys)
   "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."
+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)))
+
+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 "./"))
     (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-export.el

@@ -0,0 +1,75 @@
+;;; org-roam-export.el --- Org-roam org-export tweaks -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2025 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: 2.3.0
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
+
+;; 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 package provides the necessary changes required to make org-export work out-of-the-box.
+;;
+;; To enable it, run:
+;;
+;;    (require 'org-roam-export)
+;;
+;; The key issue Org's export-to-html functionality has is that it does not respect the ID property, which
+;; Org-roam relies heavily on. This patches the necessary function in ox-html to export ID links correctly,
+;; pointing to the correct place.
+;;
+;;; Code:
+(require 'ox-html)
+
+(defun org-roam-export--org-html--reference (datum info &optional named-only)
+  "Org-roam's patch for `org-html--reference' to support ID link export.
+See `org-html--reference' for DATUM, INFO and NAMED-ONLY."
+  (let* ((type (org-element-type datum))
+         (user-label
+          (org-element-property
+           (pcase type
+             ((or `headline `inlinetask) :CUSTOM_ID)
+             ((or `radio-target `target) :value)
+             (_ :name))
+           datum))
+         (user-label
+          (or user-label
+              (when-let ((path (org-element-property :ID datum)))
+                ;; see `org-html-link' for why we use "ID-"
+                ;; (search for "ID-" in ox-html.el)
+                (concat "ID-" path)))))
+    (cond
+     ((and user-label
+           (or (plist-get info :html-prefer-user-labels)
+               (memq type '(headline inlinetask))))
+      user-label)
+     ((and named-only
+           (not (memq type '(headline inlinetask radio-target target)))
+           (not user-label))
+      nil)
+     (t
+      (org-export-get-reference datum info)))))
+
+(advice-add 'org-html--reference :override #'org-roam-export--org-html--reference)
+
+(provide 'org-roam-export)
+;;; org-roam-export.el ends here

extensions/org-roam-graph.el

@@ -1,12 +1,12 @@
 ;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -81,7 +81,7 @@ Example:
                ("fillcolor"  . "#EEEEEE")
                ("color"      . "#C9C9C9")
                ("fontcolor"  . "#0A97A6")))
-    ("https" . (("shape"      . "rounded,filled")
+    ("https" . (("style"      . "rounded,filled")
                 ("fillcolor"  . "#EEEEEE")
                 ("color"      . "#C9C9C9")
                 ("fontcolor"  . "#0A97A6"))))
@@ -113,6 +113,25 @@ All other values including nil will have no effect."
           (const :tag "no" nil))
   :group 'org-roam)
 
+(defcustom org-roam-graph-link-builder 'org-roam-org-protocol-link-builder
+  "Function used to build the Org-roam graph links.
+Given a node name, return a string to be used for the link fed to
+the graph generation utility."
+  :type 'function
+  :group 'org-roam)
+
+(defcustom org-roam-graph-generation-hook nil
+  "Functions to run after the graph has been generated.
+Each function is called with two arguments: the filename
+containing the graph generation tool, and the generated graph."
+  :type 'hook
+  :group 'org-roam)
+
+(defun org-roam-org-protocol-link-builder (node)
+  "Default org-roam link builder.  Generate an org-protocol link using NODE."
+  (concat "org-protocol://roam-node?node="
+          (url-hexify-string (org-roam-node-id node))))
+
 ;;; Interactive command
 ;;;###autoload
 (defun org-roam-graph (&optional arg node)
@@ -147,13 +166,14 @@ CALLBACK is passed the graph file as its sole argument."
          (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
     (org-roam-message "building graph")
     (make-process
-     :name "*org-roam-graph--build-process*"
+     :name "*org-roam-graph*"
-     :buffer "*org-roam-graph--build-process*"
+     :buffer " *org-roam-graph*"
      :command `(,org-roam-graph-executable ,temp-dot "-T" ,org-roam-graph-filetype "-o" ,temp-graph)
      :sentinel (when callback
                  (lambda (process _event)
                    (when (= 0 (process-exit-status process))
-                     (funcall callback temp-graph)))))))
+                     (progn (funcall callback temp-graph)
+                            (run-hook-with-args 'org-roam-graph-generation-hook temp-dot temp-graph))))))))
 
 (defun org-roam-graph--dot (&optional edges all-nodes)
   "Build the graphviz given the EDGES of the graph.
@@ -246,12 +266,11 @@ 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 (s-word-wrap org-roam-graph-max-title-length title))
+                   (`wrap (org-roam-word-wrap org-roam-graph-max-title-length title))
                    (_ title)))))
           (setq node-id (org-roam-node-id node)
                 node-properties `(("label"   . ,shortened-title)
-                                  ("URL"     . ,(concat "org-protocol://roam-node?node="
+                                  ("URL"     . ,(funcall org-roam-graph-link-builder node))
-                                                        (url-hexify-string (org-roam-node-id node))))
                                   ("tooltip" . ,(xml-escape-string title)))))
       (setq node-id node
             node-properties (append `(("label" . ,(concat type ":" node)))

extensions/org-roam-overlay.el

@@ -1,12 +1,12 @@
 ;;; org-roam-overlay.el --- Link overlay for [id:] links to Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,8 +27,8 @@
 
 ;;; Commentary:
 ;;
-;; This extension provides allows to render [[id:]] links that don't have an
+;; This extension allows to render [[id:]] links that don't have an associated
-;; asscoiated descriptor with an overlay that displays the node's current title.
+;; descriptor with an overlay that displays the node's current title.
 ;;
 ;;; Code:
 (require 'org-roam)

extensions/org-roam-protocol.el

@@ -1,11 +1,11 @@
 ;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (org "9.4") (org-roam "2.1"))
+;; Package-Requires: ((emacs "26.1") (org "9.6") (org-roam "2.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -48,7 +48,7 @@
 
 (defcustom org-roam-capture-ref-templates
   '(("r" "ref" plain "%?"
-     :if-new (file+head "${slug}.org"
+     :target (file+head "${slug}.org"
                         "#+title: ${title}")
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
@@ -77,7 +77,7 @@ See `org-roam-capture-templates' for the template documentation."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
+                               :options (((const :format "%v " :target)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -141,12 +141,13 @@ It opens or creates a note with the given ref.
                                                               (plist-get info :ref)))
                         :initial (or (plist-get info :body) ""))
   (raise-frame)
+  (let ((org-capture-link-is-already-stored t))
     (org-roam-capture-
      :keys (plist-get info :template)
      :node (org-roam-node-create :title (plist-get info :title))
      :info (list :ref (plist-get info :ref)
                  :body (plist-get info :body))
-   :templates org-roam-capture-ref-templates)
+     :templates org-roam-capture-ref-templates))
   nil)
 
 (defun org-roam-protocol-open-node (info)
@@ -168,25 +169,6 @@ 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

@@ -0,0 +1,11 @@
+#! /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

@@ -1,12 +1,12 @@
 ;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; 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 "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -40,7 +40,7 @@
 ;;; Options
 (defcustom org-roam-capture-templates
   '(("d" "default" plain "%?"
-     :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+     :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                         "#+title: ${title}\n")
      :unnarrowed t))
   "Templates for the creation of new entries within Org-roam.
@@ -92,30 +92,41 @@ template     The template for creating the capture item.
              in order to get a template from a file, or dynamically
              from a function.
 
-The template contains a compulsory :if-new property. This determines the
+The template contains a compulsory :target property. The :target property
-location of the new node. The :if-new property contains a list, supporting
+contains a list, where:
-the following options:
+  - The first element indicates the type of the target.
+  - The second element indicates the location of the captured node.
+  - And the rest of the list indicate the prefilled template, that will be
+    inserted and the position of the point will be adjusted for.
+    This behavior varies from type to type.
+
+The following options are supported for the :target property:
 
    (file \"path/to/file\")
        The file will be created, and prescribed an ID.
 
    (file+head \"path/to/file\" \"head content\")
        The file will be created, prescribed an ID, and head content will be
-       inserted into the file.
+       inserted if the node is a newly captured one.
 
    (file+olp \"path/to/file\" (\"h1\" \"h2\"))
-       The file will be created, prescribed an ID. The OLP (h1, h2) will be
+       The file will be created, prescribed an ID. If the file doesn't contain
-       created, and the point placed after.
+       the outline path (h1, h2), it will be automatically created. The point
+       will be adjusted to the last element in the OLP.
 
    (file+head+olp \"path/to/file\" \"head content\" (\"h1\" \"h2\"))
        The file will be created, prescribed an ID. Head content will be
-       inserted at the start of the file. The OLP (h1, h2) will be created,
+       inserted at the start of the file if the node is a newly captured one.
-       and the point placed after.
+       If the file doesn't contain the outline path (h1, h2), it will be
+       automatically created. The point will be adjusted to the last element in
+       the OLP.
 
-   (file+datetree \"path/to/file\" day)
+   (file+datetree \"path/to/file\" tree-type)
-       The file will be created, prescribed an ID. Head content will be
+       The file will be created, prescribed an ID. A date based outline path
-       inserted at the start of the file. The datetree will be created,
+       will be created for today's date. The tree-type can be one of the
-       available options are day, week, month.
+       following symbols: day, week or month. The point will adjusted to the
+       last element in the tree. To prompt for date instead of using today's,
+       use the :time-prompt property.
 
    (node \"title or alias or ID of an existing node\")
        The point will be placed for an existing node, based on either, its
@@ -194,7 +205,8 @@ be replaced with content and expanded:
               introduced with %[pathname] are expanded this way.  Since this
               happens after expanding non-interactive %-escapes, those can
               be used to fill the expression.
-  %<...>      The result of `format-time-string' on the ... format specification.
+  %<...>      The result of `format-time-string' on the ... format
+              specification.
   %t          Time stamp, date only.  The time stamp is the current time,
               except when called from agendas with `\\[org-agenda-capture]' or
               with `org-capture-use-agenda-date' set.
@@ -289,7 +301,7 @@ streamlined user experience in Org-roam."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :if-new)
+                               :options (((const :format "%v " :target)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -377,7 +389,7 @@ during the Org-roam capture process.")
 This variable is populated dynamically, and is only non-nil
 during the Org-roam capture process.")
 
-(defconst org-roam-capture--template-keywords (list :if-new :id :link-description :call-location
+(defconst org-roam-capture--template-keywords (list :target :id :link-description :call-location
                                                     :region)
   "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
 
@@ -395,6 +407,8 @@ 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)
@@ -433,36 +447,33 @@ the capture)."
   "Get the value for KEYWORD from the `org-roam-capture-template'."
   (plist-get (plist-get org-capture-plist :org-roam) keyword))
 
-(defun org-roam-capture--put (&rest stuff)
+(defun org-roam-capture--put (prop value)
-  "Put properties from STUFF into the `org-roam-capture-template'."
+  "Set property PROP to VALUE in the `org-roam-capture-template'."
   (let ((p (plist-get org-capture-plist :org-roam)))
-    (while stuff
-      (setq p (plist-put p (pop stuff) (pop stuff))))
     (setq org-capture-plist
-          (plist-put org-capture-plist :org-roam p))))
+          (plist-put org-capture-plist
+                     :org-roam
+                     (plist-put p prop value)))))
 
 ;;;; Capture target
 (defun org-roam-capture--prepare-buffer ()
   "Prepare the capture buffer for the current Org-roam based capture template.
 This function will initialize and setup the capture buffer,
-create the target node (`:if-new') if it doesn't exist, and place
+position the point to the current :target (and if necessary,
-the point for further processing by `org-capture'.
+create it if it doesn't exist), and place the point for further
+processing by `org-capture'.
 
 Note: During the capture process this function is run by
 `org-capture-set-target-location', as a (function ...) based
 capture target."
   (let ((id (cond ((run-hook-with-args-until-success 'org-roam-capture-preface-hook))
-                  ((and (org-roam-node-file org-roam-capture--node)
+                  (t (org-roam-capture--setup-target-location)))))
-                        (org-roam-node-point org-roam-capture--node))
-                   (set-buffer (org-capture-target-buffer (org-roam-node-file org-roam-capture--node)))
-                   (goto-char (org-roam-node-point org-roam-capture--node))
-                   (widen)
-                   (org-roam-node-id org-roam-capture--node))
-                  (t
-                   (org-roam-capture--setup-target-location)))))
     (org-roam-capture--adjust-point-for-capture-type)
-    (org-capture-put :template
+    (let ((template (org-capture-get :template)))
-                     (org-roam-capture--fill-template (org-capture-get :template)))
+      (when (stringp template)
+        (org-capture-put
+         :template
+         (org-roam-capture--fill-template template))))
     (org-roam-capture--put :id id)
     (org-roam-capture--put :finalize (or (org-capture-get :finalize)
                                          (org-roam-capture--get :finalize)))))
@@ -471,22 +482,17 @@ capture target."
   "Initialize the buffer, and goto the location of the new capture.
 Return the ID of the location."
   (let (p new-file-p)
-    (pcase (or (org-roam-capture--get :if-new)
+    (pcase (org-roam-capture--get-target)
-               (user-error "Template needs to specify `:if-new'"))
       (`(file ,path)
-       (setq path (expand-file-name
+       (setq path (org-roam-capture--target-truepath path)
-                   (string-trim (org-roam-capture--fill-template path t))
+             new-file-p (org-roam-capture--new-file-p path))
-                   org-roam-directory))
-       (setq new-file-p (org-roam-capture--new-file-p path))
        (when new-file-p (org-roam-capture--put :new-file path))
        (set-buffer (org-capture-target-buffer path))
        (widen)
        (setq p (goto-char (point-min))))
       (`(file+olp ,path ,olp)
-       (setq path (expand-file-name
+       (setq path (org-roam-capture--target-truepath path)
-                   (string-trim (org-roam-capture--fill-template path t))
+             new-file-p (org-roam-capture--new-file-p path))
-                   org-roam-directory))
-       (setq new-file-p (org-roam-capture--new-file-p path))
        (when new-file-p (org-roam-capture--put :new-file path))
        (set-buffer (org-capture-target-buffer path))
        (setq p (point-min))
@@ -494,33 +500,27 @@ Return the ID of the location."
          (goto-char m))
        (widen))
       (`(file+head ,path ,head)
-       (setq path (expand-file-name
+       (setq path (org-roam-capture--target-truepath path)
-                   (string-trim (org-roam-capture--fill-template path t))
+             new-file-p (org-roam-capture--new-file-p path))
-                   org-roam-directory))
-       (setq new-file-p (org-roam-capture--new-file-p path))
        (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 t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
        (widen)
        (setq p (goto-char (point-min))))
       (`(file+head+olp ,path ,head ,olp)
-       (setq path (expand-file-name
+       (setq path (org-roam-capture--target-truepath path)
-                   (string-trim (org-roam-capture--fill-template path t))
+             new-file-p (org-roam-capture--new-file-p path))
-                   org-roam-directory))
-       (setq new-file-p (org-roam-capture--new-file-p path))
        (set-buffer (org-capture-target-buffer path))
        (widen)
        (when new-file-p
          (org-roam-capture--put :new-file path)
-         (insert (org-roam-capture--fill-template head t)))
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m)))
       (`(file+datetree ,path ,tree-type)
-       (setq path (expand-file-name
+       (setq path (org-roam-capture--target-truepath path))
-                   (string-trim (org-roam-capture--fill-template path t))
-                   org-roam-directory))
        (require 'org-datetree)
        (widen)
        (set-buffer (org-capture-target-buffer path))
@@ -574,13 +574,29 @@ Return the ID of the location."
     ;; caller.
     (save-excursion
       (goto-char p)
-      (when-let* ((node org-roam-capture--node)
+      (if-let ((id (org-entry-get p "ID")))
-                  (id (org-roam-node-id node)))
+          (setf (org-roam-node-id org-roam-capture--node) id)
-        (org-entry-put p "ID" id))
+        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
       (prog1
-          (org-id-get-create)
+          (org-id-get)
         (run-hooks 'org-roam-capture-new-node-hook)))))
 
+(defun org-roam-capture--get-target ()
+  "Get the current capture :target for the capture template in use."
+  (or (org-roam-capture--get :target)
+      (user-error "Template needs to specify `:target'")))
+
+(defun org-roam-capture--target-truepath (path)
+  "From PATH get the correct path to the current capture target and return it.
+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)
+        (string-trim)
+        (expand-file-name org-roam-directory))))
+
 (defun org-roam-capture--new-file-p (path)
   "Return t if PATH is for a new file with no visiting buffer."
   (not (or (file-exists-p path)
@@ -602,6 +618,7 @@ 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))
        (let ((re (format org-complex-heading-regexp-format
                          (regexp-quote heading)))
              (cnt 0))
@@ -663,6 +680,24 @@ 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 ()
@@ -672,14 +707,15 @@ the current value of `point'."
 
 (defun org-roam-capture--finalize ()
   "Finalize the `org-roam-capture' process."
-  (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)))
+      (when-let ((new-file (org-roam-capture--get :new-file))
-        (org-roam-message "Deleting file for aborted capture %s" new-file)
+                 (_ (yes-or-no-p "Delete file for aborted capture?")))
         (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)))))
@@ -702,20 +738,32 @@ This function is to be called in the Org-capture finalization process."
               (buf (marker-buffer mkr)))
     (with-current-buffer buf
       (when-let ((region (org-roam-capture--get :region)))
-        (org-roam-unshield-region (car region) (cdr region))
         (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 (org-link-make-string (concat "id:" (org-roam-capture--get :id))
+            (insert link)))
-                                      (org-roam-capture--get :link-description)))))))
+        (run-hook-with-args 'org-roam-post-node-insert-hook
+                            id
+                            description)))))
 
 ;;;; Processing of the capture templates
-(defun org-roam-capture--fill-template (template &optional org-capture-p)
+(defun org-roam-capture--fill-template (template &optional ensure-newline)
   "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+It expands ${var} occurrences in TEMPLATE, and then runs
-also run Org-capture's template expansion."
+org-capture's template expansion.
-  (funcall (if org-capture-p #'org-capture-fill-template #'identity)
+When ENSURE-NEWLINE, always ensure there's a newline behind."
+  (let* ((template (if (functionp template)
+                       (funcall template)
+                     template))
+         (template-whitespace-content (org-roam-whitespace-content template)))
+    (setq template
           (org-roam-format-template
            template
            (lambda (key default-val)
@@ -729,9 +777,20 @@ also run Org-capture's template expansion."
                  (funcall node-fn org-roam-capture--node))
                 ((plist-get org-roam-capture--info ksym)
                  (plist-get org-roam-capture--info ksym))
-                 (t (let ((r (completing-read (format "%s: " key) nil nil nil default-val)))
+                (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
                      (plist-put org-roam-capture--info ksym r)
-                      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))
 
 (defun org-roam-capture--convert-template (template &optional props)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.

org-roam-compat.el

@@ -1,11 +1,11 @@
 ;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
 ;; Package-Requires: ((emacs "26.1"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -31,6 +31,8 @@
 ;; Emacsen and Org-roam versions.
 ;;
 ;;; Code:
+(require 'org-roam)
+
 ;;; Backports
 ;; REVIEW Remove when 26.x support is dropped. This is exact the same as
 ;; `directory-files-recursively' from Emacs 26, but with FOLLOW-SYMLINKS
@@ -99,22 +101,20 @@ recursion."
 (advice-add #'org-id-add-location :around #'org-roam--handle-absent-org-id-locations-file-a)
 (defun org-roam--handle-absent-org-id-locations-file-a (fn &rest args)
   "Gracefully handle errors related to absence of `org-id-locations-file'.
-FN is `org-id-locations-file' that comes from advice and ARGS are
+FN is `org-id-add-location' that comes from advice and ARGS are
 passed to it."
-  (let (result)
+  (condition-case err
-    ;; Use `unwind-protect' over `condition-case' because `org-id' can produce various other errors, but all
+      (apply fn args)
-    ;; of its errors are generic ones, so trapping all of them isn't a good idea and preserving the correct
-    ;; backtrace is valuable.
-    (unwind-protect (setq result (apply fn args))
-      (unless result
-        (unless org-id-locations
-          ;; Pre-allocate the hash table to avoid weird access related errors during the regeneration.
-          (setq org-id-locations (make-hash-table :type 'equal)))
     ;; `org-id' makes the assumption that `org-id-locations-file' will be stored in `user-emacs-directory'
-        ;; which always exist if you have Emacs, so it uses `with-temp-file' to write to the file. However,
+    ;; which always exist if you have Emacs, so it uses `with-temp-file' to write to the file. However, the
-        ;; the users *do* change the path to this file and `with-temp-file' unable to create the file, if the
+    ;; users *do* change the path to this file and `with-temp-file' unable to create the file, if the path to
-        ;; path to it consists of directories that don't exist. We'll have to handle this ourselves.
+    ;; it consists of directories that don't exist. We'll have to handle this ourselves.
-        (unless (file-exists-p (file-truename org-id-locations-file))
+    (error
+     (advice-remove 'org-id-add-location #'org-roam--handle-absent-org-id-locations-file-a)
+     (if (file-exists-p (file-truename org-id-locations-file))
+         (signal (car err) (cdr err))
+       ;; Pre-allocate the hash table to avoid weird access related errors during the regeneration.
+       (or org-id-locations (setq org-id-locations (make-hash-table :test 'equal)))
        ;; If permissions allow that, try to create the user specified directory path to
        ;; `org-id-locations-file' ourselves.
        (condition-case _err
@@ -153,8 +153,30 @@ identification (e.g. with \"ROAM_EXCLUDE\" property) as Org-roam
 nodes." org-id-locations-file)
                      (setq org-id-locations-file
                            (expand-file-name ".orgids" (file-truename org-roam-directory)))
+                     (apply fn args)))))))
+
+;;;; Deprecated :if-new capture template keyword
+(with-eval-after-load 'org-roam-capture
+  (add-to-list 'org-roam-capture--template-keywords :if-new)
+
+  (let ((inhibit-warning-p t)) ; REVIEW Set this to nil close to next major release
+    (advice-add 'org-roam-capture--get-target :around #'org-roam-capture--get-if-new-target-a)
+    (defun org-roam-capture--get-if-new-target-a (fn &rest args)
+      "Get the current capture target using deprecated :if-new property."
+      (if-let ((target (org-roam-capture--get :if-new)))
+          (prog1 target
+            (unless inhibit-warning-p
+              (lwarn 'org-roam-capture :warning
+                     (mapconcat
+                      #'identity
+                      ["`:if-new' property is deprecated in favor of `:target'."
+                       "This warning will popup once per each session. In order to get"
+                       "rid of it, rename all the references to the `:if-new' property"
+                       "in your capture templates to `:target'."]
+                      "\n"))
+              ;; Don't irritate the user too much. Displaying the warning once per session should be enough.
+              (setq inhibit-warning-p t)))
         (apply fn args)))))
-      result)))
 
 ;;; Obsolete aliases (remove after next major release)
 (define-obsolete-function-alias
@@ -199,6 +221,18 @@ nodes." org-id-locations-file)
   'org-roam-dailies-find-date
   'org-roam-dailies-goto-date "org-roam 2.0")
 
+(define-obsolete-function-alias
+  'org-roam-add-property
+  'org-roam-property-add "org-roam 2.1")
+
+(define-obsolete-function-alias
+  '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

@@ -1,12 +1,12 @@
 ;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; 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 "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,10 +31,12 @@
 ;;
 ;;; Code:
 (require 'org-roam)
+(require 'url-parse)
+(require 'ol)
 (defvar org-outline-path-cache)
 
 ;;; Options
-(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
+(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
   "The path to file where the Org-roam database is stored.
 
 It is the user's responsibility to set this correctly, especially
@@ -78,14 +80,35 @@ slow."
   :type 'boolean
   :group 'org-roam)
 
-;;; Variables
+(defcustom org-roam-db-extra-links-elements '(node-property keyword)
-(defconst org-roam-db-version 16)
+  "The list of Org element types to include for parsing by Org-roam.
 
-;; TODO Rename this
+By default, when parsing Org's AST, links within keywords and
-(defconst org-roam--sqlite-available-p
+property drawers are not parsed as links. Sometimes however, it
-  (with-demoted-errors "Org-roam initialization: %S"
+is desirable to parse and cache these links (e.g. hiding links in
-    (emacsql-sqlite-ensure-binary)
+a property drawer)."
-    t))
+  :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 20)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
@@ -93,7 +116,7 @@ slow."
 ;;; Core Functions
 (defun org-roam-db--get-connection ()
   "Return the database connection, if any."
-  (gethash (expand-file-name org-roam-directory)
+  (gethash (expand-file-name (file-name-as-directory org-roam-directory))
            org-roam-db--connection))
 
 (defun org-roam-db ()
@@ -104,9 +127,8 @@ Performs a database upgrade when required."
                (emacsql-live-p (org-roam-db--get-connection)))
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (emacsql-sqlite org-roam-db-location)))
+      (let ((conn (emacsql-sqlite-open org-roam-db-location)))
-        (set-process-query-on-exit-flag (emacsql-process conn) nil)
+        (puthash (expand-file-name (file-name-as-directory org-roam-directory))
-        (puthash (expand-file-name org-roam-directory)
                  conn
                  org-roam-db--connection)
         (when init-db
@@ -117,7 +139,7 @@ Performs a database upgrade when required."
            ((> version org-roam-db-version)
             (emacsql-close conn)
             (user-error
-             "The Org-roam database was created with a newer Org-roam version.  "
+             "The Org-roam database was created with a newer Org-roam version.  %s"
              "You need to update the Org-roam package"))
            ((< version org-roam-db-version)
             (emacsql-close conn)
@@ -145,6 +167,7 @@ The query is expected to be able to fail, in this situation, run HANDLER."
 (defconst org-roam-db--table-schemata
   '((files
      [(file :unique :primary-key)
+      title
       (hash :not-null)
       (atime :not-null)
       (mtime :not-null)])
@@ -168,6 +191,13 @@ The query is expected to be able to fail, in this situation, run HANDLER."
        alias]
       (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
+    (citations
+     ([(node-id :not-null)
+       (cite-key :not-null)
+       (pos :not-null)
+       properties]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
     (refs
      ([(node-id :not-null)
        (ref :not-null)
@@ -195,7 +225,6 @@ 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-with-transaction db
-    (emacsql db "PRAGMA foreign_keys = ON")
     (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
       (emacsql db [:create-table $i1 $S2] table schema))
     (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
@@ -246,51 +275,93 @@ If FILE is nil, clear the current buffer."
                      file))
 
 ;;;; Updating tables
-(defun org-roam-db-insert-file ()
+
+(defun org-roam-db--file-title ()
+  "In current Org buffer, get the title.
+If there is no title, return the file name relative to
+`org-roam-directory'."
+  (org-link-display-format
+   (or (string-join (cdr (assoc "TITLE" (org-collect-keywords '("title")))) " ")
+       (file-name-sans-extension (file-relative-name
+                                  (buffer-file-name (buffer-base-buffer))
+                                  org-roam-directory)))))
+
+(defun org-roam-db-insert-file (&optional hash)
   "Update the files table for the current buffer.
-If UPDATE-P is non-nil, first remove the file in the database."
+If UPDATE-P is non-nil, first remove the file in the database.
+If HASH is non-nil, use that as the file's hash without recalculating it."
   (let* ((file (buffer-file-name))
+         (file-title (org-roam-db--file-title))
          (attr (file-attributes file))
          (atime (file-attribute-access-time attr))
          (mtime (file-attribute-modification-time attr))
-         (hash (org-roam-db--file-hash)))
+         (hash (or hash (org-roam-db--file-hash file))))
     (org-roam-db-query
      [:insert :into files
       :values $v1]
-     (list (vector file hash atime mtime)))))
+     (list (vector file file-title hash atime mtime)))))
 
 (defun org-roam-db-get-scheduled-time ()
   "Return the scheduled time at point in ISO8601 format."
   (when-let ((time (org-get-scheduled-time (point))))
-    (org-format-time-string "%FT%T%z" time)))
+    (format-time-string "%FT%T" time)))
 
 (defun org-roam-db-get-deadline-time ()
   "Return the deadline time at point in ISO8601 format."
   (when-let ((time (org-get-deadline-time (point))))
-    (org-format-time-string "%FT%T%z" time)))
+    (format-time-string "%FT%T" time)))
 
 (defun org-roam-db-node-p ()
   "Return t if headline at point is an Org-roam node, else return nil."
   (and (org-id-get)
-       (not (cdr (assoc "ROAM_EXCLUDE" (org-entry-properties))))
+       (not (org-entry-get (point) "ROAM_EXCLUDE"))
        (funcall org-roam-db-node-include-function)))
 
 (defun org-roam-db-map-nodes (fns)
   "Run FNS over all nodes in the current buffer."
-  (org-with-point-at 1
+  (org-with-wide-buffer
-    (org-map-entries
+   (org-map-region
     (lambda ()
       (when (org-roam-db-node-p)
         (dolist (fn fns)
-           (funcall fn)))))))
+          (funcall fn))))
+    (point-min) (point-max))))
 
 (defun org-roam-db-map-links (fns)
   "Run FNS over all links in the current buffer."
   (org-with-point-at 1
-    (org-element-map (org-element-parse-buffer) 'link
+    (while (re-search-forward org-link-any-re nil :no-error)
-      (lambda (link)
+      ;; `re-search-forward' let the cursor one character after the link, we need to go backward one char to
+      ;; make the point be on the link.
+      (backward-char)
+      (let* ((begin (match-beginning 0))
+             (element (org-element-context))
+             (type (org-element-type element))
+             link)
+        (cond
+         ;; Links correctly recognized by Org Mode
+         ((eq type 'link)
+          (setq link element))
+         ;; 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))))
+               (setq link (save-excursion
+                            (goto-char begin)
+                            (save-match-data (org-element-link-parser)))))))
+        (when link
           (dolist (fn fns)
-          (funcall fn link))))))
+            (funcall fn link)))))))
+
+(defun org-roam-db-map-citations (info fns)
+  "Run FNS over all citations in the current buffer.
+INFO is the org-element parsed buffer."
+  (org-element-map info 'citation-reference
+    (lambda (cite)
+      (dolist (fn fns)
+        (funcall fn cite)))))
 
 (defun org-roam-db-insert-file-node ()
   "Insert the file-level node into the Org-roam cache."
@@ -299,19 +370,14 @@ If UPDATE-P is non-nil, first remove the file in the database."
                (org-roam-db-node-p))
       (when-let ((id (org-id-get)))
         (let* ((file (buffer-file-name (buffer-base-buffer)))
-               (title (org-link-display-format
+               (title (org-roam-db--file-title))
-                       (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
-                                        #'string-equal))
-                           (file-relative-name file org-roam-directory))))
                (pos (point))
                (todo nil)
                (priority nil)
                (scheduled nil)
                (deadline nil)
                (level 0)
-               (aliases (org-entry-get (point) "ROAM_ALIASES"))
                (tags org-file-tags)
-               (refs (org-entry-get (point) "ROAM_REFS"))
                (properties (org-entry-properties))
                (olp nil))
           (org-roam-db-query!
@@ -330,29 +396,8 @@ If UPDATE-P is non-nil, first remove the file in the database."
              (mapcar (lambda (tag)
                        (vector id (substring-no-properties tag)))
                      tags)))
-          (when aliases
+          (org-roam-db-insert-aliases)
-            (org-roam-db-query
+          (org-roam-db-insert-refs))))))
-             [:insert :into aliases
-              :values $v1]
-             (mapcar (lambda (alias)
-                       (vector id alias))
-                     (split-string-and-unquote aliases))))
-          (when refs
-            (setq refs (split-string-and-unquote refs))
-            (let (rows)
-              (dolist (ref refs)
-                (if (string-match org-link-plain-re ref)
-                    (progn
-                      (push (vector id (match-string 2 ref)
-                                    (match-string 1 ref)) rows))
-                  (lwarn '(org-roam) :warning
-                         "%s:%s\tInvalid ref %s, skipping..."
-                         (buffer-file-name) (point) ref)))
-              (when rows
-                (org-roam-db-query
-                 [:insert :into refs
-                  :values $v1]
-                 rows)))))))))
 
 (cl-defun org-roam-db-insert-node-data ()
   "Insert node data for headline at point into the Org-roam cache."
@@ -386,13 +431,14 @@ If UPDATE-P is non-nil, first remove the file in the database."
 
 (defun org-roam-db-insert-aliases ()
   "Insert aliases for node at point into Org-roam cache."
-  (when-let ((node-id (org-id-get))
+  (when-let* ((node-id (org-id-get))
-             (aliases (org-entry-get (point) "ROAM_ALIASES")))
+              (aliases (org-entry-get (point) "ROAM_ALIASES"))
+              (aliases (split-string-and-unquote aliases)))
     (org-roam-db-query [:insert :into aliases
                         :values $v1]
                        (mapcar (lambda (alias)
                                  (vector node-id alias))
-                               (split-string-and-unquote aliases)))))
+                               aliases))))
 
 (defun org-roam-db-insert-tags ()
   "Insert tags for node at point into Org-roam cache."
@@ -411,39 +457,90 @@ If UPDATE-P is non-nil, first remove the file in the database."
     (let (rows)
       (dolist (ref refs)
         (save-match-data
-          (if (string-match org-link-plain-re ref)
+          (cond (;; @citeKey
-              (progn
+                 (string-prefix-p "@" ref)
-                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
+                 (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 ref %s, skipping..." (buffer-file-name) (point) ref))))
+                           "%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-any-re (org-link-encode ref '(#x20)))
+                 (setq ref (org-link-encode ref '(#x20)))
+                 (let ((ref-url (url-generic-parse-url (or (match-string 2 ref) (match-string 0 ref))))
+                       (link-type ()) ;; clear url-type for backward compatible.
+                       (path ()))
+                   (setq link-type (url-type ref-url))
+                   (setf (url-type ref-url) nil)
+                   (setq path (org-link-decode (url-recreate-url ref-url)))
+                   (if (and (boundp 'org-ref-cite-types)
+                            (or (assoc link-type org-ref-cite-types)
+                                (member link-type org-ref-cite-types)))
+                       (dolist (key (org-roam-org-ref-path-to-keys path))
+                         (push (vector node-id key link-type) rows))
+                     (push (vector node-id path link-type) rows))))
+                (t
+                 (lwarn '(org-roam) :warning
+                        "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref)))))
+      (when rows
         (org-roam-db-query [:insert :into refs
                             :values $v1]
-                         rows))))
+                           rows)))))
 
 (defun org-roam-db-insert-link (link)
   "Insert link data for LINK at current point into the Org-roam cache."
   (save-excursion
     (goto-char (org-element-property :begin link))
-    (let ((type (org-element-property :type link))
+    (let* ((type (org-element-property :type link))
            (path (org-element-property :path link))
+           (option (and (string-match "::\\(.*\\)\\'" path)
+                        (match-string 1 path)))
+           (path (if (not option) path
+                   (substring path 0 (match-beginning 0))))
+           (source (org-roam-id-at-point))
            (properties (list :outline (ignore-errors
                                         ;; This can error if link is not under any headline
                                         (org-get-outline-path 'with-self 'use-cache))))
-          (source (org-roam-id-at-point)))
+           (properties (if option (plist-put properties :search-option option)
+                         properties)))
       ;; For Org-ref links, we need to split the path into the cite keys
-      (when (and (boundp 'org-ref-cite-types)
-                 (fboundp 'org-ref-split-and-strip-string)
-                 (member type org-ref-cite-types))
-        (setq path (org-ref-split-and-strip-string path)))
-      (unless (listp path)
-        (setq path (list path)))
       (when (and source path)
+        (if (and (boundp 'org-ref-cite-types)
+                 (or (assoc type org-ref-cite-types)
+                     (member type org-ref-cite-types)))
+            (org-roam-db-query
+             [:insert :into citations
+              :values $v1]
+             (mapcar (lambda (k) (vector source k (point) properties))
+                     (org-roam-org-ref-path-to-keys path)))
           (org-roam-db-query
            [:insert :into links
             :values $v1]
-         (mapcar (lambda (p)
+           (vector (point) source path type properties)))))))
-                   (vector (point) source p type properties))
+
-                 path))))))
+(defun org-roam-db-insert-citation (citation)
+  "Insert data for CITATION at current point into the Org-roam cache."
+  (save-excursion
+    (goto-char (org-element-property :begin citation))
+    (let ((key (org-element-property :key citation))
+          (source (org-roam-id-at-point))
+          (properties (list :outline (ignore-errors
+                                       ;; This can error if link is not under any headline
+                                       (org-get-outline-path 'with-self 'use-cache)))))
+      (when (and source key)
+        (org-roam-db-query
+         [:insert :into citations
+          :values $v1]
+         (vector source key (point) properties))))))
 
 ;;;; Fetching
 (defun org-roam-db--get-current-files ()
@@ -454,35 +551,40 @@ If UPDATE-P is non-nil, first remove the file in the database."
       (puthash (car row) (cadr row) ht))
     ht))
 
-(defun org-roam-db--file-hash (&optional file-path)
+(defun org-roam-db--file-hash (file-path)
-  "Compute the hash of FILE-PATH, a file or current buffer."
+  "Compute the hash of FILE-PATH."
-  ;; If it is a GPG encrypted file, we always want to compute the hash
-  ;; for the GPG encrypted file (undecrypted)
-  (when (and (not file-path) (equal "gpg" (file-name-extension (buffer-file-name))))
-    (setq file-path (buffer-file-name)))
-  (if file-path
   (with-temp-buffer
     (set-buffer-multibyte nil)
     (insert-file-contents-literally file-path)
-        (secure-hash 'sha1 (current-buffer)))
+    (secure-hash 'sha1 (current-buffer))))
-    (org-with-wide-buffer
-     (secure-hash 'sha1 (current-buffer)))))
 
 ;;;; Synchronization
-(defun org-roam-db-update-file (&optional file-path)
+(defun org-roam-db-update-file (&optional file-path no-require)
   "Update Org-roam cache for FILE-PATH.
+
 If the file does not exist anymore, remove it from the cache.
-If the file exists, update the cache with information."
+
+If the file exists, update the cache with information.
+
+If NO-REQUIRE, don't require optional libraries. Set NO-REQUIRE
+when the libraries are already required at some toplevel, e.g.
+in `org-roam-db-sync'."
   (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
   (let ((content-hash (org-roam-db--file-hash file-path))
         (db-hash (caar (org-roam-db-query [:select hash :from files
-                                           :where (= file $s1)] file-path))))
+                                           :where (= file $s1)] file-path)))
+        info)
     (unless (string= content-hash db-hash)
+      (unless no-require
+        (org-roam-require '(org-ref oc)))
       (org-roam-with-file file-path nil
-        (save-excursion
+        (emacsql-with-transaction (org-roam-db)
+          (org-with-wide-buffer
            (org-set-regexps-and-options 'tags-only)
+           ;; Org doesn't use this anymore, so we probably should stop too.
+           ;; (org-refresh-category-properties)
            (org-roam-db-clear-file)
-          (org-roam-db-insert-file)
+           (org-roam-db-insert-file content-hash)
            (org-roam-db-insert-file-node)
            (setq org-outline-path-cache nil)
            (org-roam-db-map-nodes
@@ -491,8 +593,14 @@ If the file exists, update the cache with information."
                   #'org-roam-db-insert-tags
                   #'org-roam-db-insert-refs))
            (setq org-outline-path-cache nil)
+           (setq info (org-element-parse-buffer))
            (org-roam-db-map-links
-           (list #'org-roam-db-insert-link)))))))
+            (list #'org-roam-db-insert-link))
+           (when (fboundp 'org-cite-insert)
+             (require 'oc)             ;ensure feature is loaded
+             (org-roam-db-map-citations
+              info
+              (list #'org-roam-db-insert-citation)))))))))
 
 ;;;###autoload
 (defun org-roam-db-sync (&optional force)
@@ -502,6 +610,7 @@ If FORCE, force a rebuild of the cache from scratch."
   (org-roam-db--close) ;; Force a reconnect
   (when force (delete-file org-roam-db-location))
   (org-roam-db) ;; To initialize the database, no-op if already initialized
+  (org-roam-require '(org-ref oc))
   (let* ((gc-cons-threshold org-roam-db-gc-threshold)
          (org-agenda-files nil)
          (org-roam-files (org-roam-list-files))
@@ -514,18 +623,17 @@ If FORCE, force a rebuild of the cache from scratch."
           (push file modified-files)))
       (remhash file current-files))
     (emacsql-with-transaction (org-roam-db)
-      (if (fboundp 'dolist-with-progress-reporter)
+      (org-roam-dolist-with-progress (file (hash-table-keys current-files))
-          (dolist-with-progress-reporter (file (hash-table-keys current-files))
           "Clearing removed files..."
         (org-roam-db-clear-file file))
-        (dolist (file (hash-table-keys current-files))
+      (org-roam-dolist-with-progress (file modified-files)
-          (org-roam-db-clear-file file)))
-      (if (fboundp 'dolist-with-progress-reporter)
-          (dolist-with-progress-reporter (file modified-files)
           "Processing modified files..."
-            (org-roam-db-update-file file))
+        (condition-case err
-        (dolist (file modified-files)
+            (org-roam-db-update-file file 'no-require)
-          (org-roam-db-update-file file))))))
+          (error
+           (org-roam-db-clear-file file)
+           (lwarn 'org-roam :error "Failed to process %s with error %s, skipping..."
+                  file (error-message-string err))))))))
 
 ;;;###autoload
 (define-minor-mode org-roam-db-autosync-mode

org-roam-id.el

@@ -0,0 +1,94 @@
+;;; org-roam-id.el --- ID-related utilities for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright © 2020-2025 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: 2.3.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (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
+          (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))))))
+
+(defalias 'org-roam-id-open 'org-id-open
+  "Obsolete alias - use `org-id-open' directly.")
+
+(advice-add 'org-id-find :before-until #'org-roam-id-find)
+
+;;;###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-log.el

@@ -0,0 +1,53 @@
+;;; org-roam-log.el --- Integrations with Org-log -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2022-2025 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: 2.3.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (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 integrations with Org-log.
+;;
+;;; Code:
+(require 'org-roam)
+
+(defcustom org-roam-log-setup-hook nil
+  "Hook run when a log for an Org-roam file is setup."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam-log-p ()
+  "Return t if the log buffer is for an Org-roam file, nil otherwise."
+  (and org-log-note-marker
+       (org-roam-file-p (buffer-file-name (marker-buffer org-log-note-marker)))))
+
+(defun org-roam-log--setup ()
+  "Run hooks in `org-roam-log-setup-hook'."
+  (run-hooks 'org-roam-log-setup-hook))
+
+(add-hook 'org-roam-log-setup-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-log-buffer-setup-hook #'org-roam-log--setup)
+
+(provide 'org-roam-log)
+;;; org-roam-log.el ends here

org-roam-migrate.el

@@ -1,12 +1,12 @@
 ;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; 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 "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,48 +34,6 @@
 ;;; Code:
 (require 'org-roam)
 
-;;; v1 breaking warning
-(defvar org-roam-v2-ack nil
-  "When set to t, won't display the annoying warning message about the upgrade.
-Need to be set before the package is loaded, otherwise won't take
-any affect.")
-
-(unless org-roam-v2-ack
-  (lwarn 'org-roam :error "
-------------------------------------
-WARNING: You're now on Org-roam v2!
-------------------------------------
-
-You may have arrived here from a package upgrade. Please read the
-wiki entry at
-%s
-for an overview of the major changes.
-
-Notes taken in v1 are incompatible with v2, but you can upgrade
-them to the v2 format via a simple command. To migrate your
-notes, first make sure you're on at least Org 9.4 (check with
-C-h v org-version) and set your org-roam-directory to your notes:
-
-(setq org-roam-directory \"path/to/org/files\")
-
-then, run:
-
-  M-x org-roam-migrate-wizard
-
-If you wish to stay on v1, v1 is unfortunately not distributed on
-MELPA. See org-roam/org-roam-v1 on GitHub on how to install v1.
-
-If you've gone through the migration steps (if necessary), and
-know what you're doing set `org-roam-v2-ack' to `t' to disable
-this warning. You can do so by adding:
-
-(setq org-roam-v2-ack t)
-
-To your init file.
-
-"
-         "https://github.com/org-roam/org-roam/wiki/Hitchhiker's-Rough-Guide-to-Org-roam-V2"))
-
 ;;; Migration wizard (v1 -> v2)
 ;;;###autoload
 (defun org-roam-migrate-wizard ()

org-roam-mode.el

@@ -1,12 +1,12 @@
 ;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; 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 "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -39,12 +39,50 @@
 (defvar org-ref-buffer-hacked)
 
 ;;; Options
-(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
                                         #'org-roam-reflinks-section)
-  "Functions that insert sections in the `org-roam-mode' based buffers.
+  "A list of sections for the `org-roam-mode' based buffers.
-Each function is called with one argument, which is an
+Each section is a function that is passed the `org-roam-node'
-`org-roam-node' for which the buffer will be constructed for.
+for which the section will be constructed as the first
-Normally this node is `org-roam-buffer-current-node'."
+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."
+  :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"))))))
+
+(defcustom org-roam-buffer-postrender-functions (list)
+  "Functions to run after the Org-roam buffer is rendered.
+Each function accepts no arguments, and is run with the Org-roam
+buffer as the current buffer."
+  :group 'org-roam
+  :type 'hook)
+
+(defcustom org-roam-preview-function #'org-roam-preview-default-function
+  "The preview function to use to populate the Org-roam buffer.
+
+The function takes no arguments, but the point is temporarily set
+to the exact location of the backlink."
+  :group 'org-roam
+  :type 'function)
+
+(defcustom org-roam-preview-postprocess-functions (list #'org-roam-strip-comments)
+  "A list of functions to postprocess the preview content.
+
+Each function takes a single argument, the string for the preview
+content, and returns the post-processed string. The functions are
+applied in order of appearance in the list."
   :group 'org-roam
   :type 'hook)
 
@@ -144,7 +182,7 @@ 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-section-functions'), with which the user can
+`org-roam-mode-sections'), with which the user can
 interact with."
   :group 'org-roam
   (face-remap-add-relative 'header-line 'org-roam-header-line))
@@ -160,7 +198,8 @@ value shows the current node in the persistent `org-roam-buffer'.")
 
 (defvar org-roam-buffer-current-directory nil
   "The `org-roam-directory' value of `org-roam-buffer-current-node'.
-Set both, locally and globally in the same way as `org-roam-buffer-current-node'.")
+Set both, locally and globally in the same way as
+`org-roam-buffer-current-node'.")
 
 (put 'org-roam-buffer-current-directory 'permanent-local t)
 
@@ -203,7 +242,15 @@ buffer."
      (org-roam-node-title org-roam-buffer-current-node))
     (magit-insert-section (org-roam)
       (magit-insert-heading)
-      (run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node))
+      (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-hooks 'org-roam-buffer-postrender-functions)
     (goto-char 0)))
 
 (defun org-roam-buffer-set-header-line-format (string)
@@ -263,7 +310,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
   (pcase (org-roam-buffer--visibility)
     ('visible
      (progn
-       (delete-window (get-buffer-window org-roam-buffer))
+       (quit-window nil (get-buffer-window org-roam-buffer))
        (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
     ((or 'exists 'none)
      (progn
@@ -272,7 +319,7 @@ To toggle its display use `org-roam-buffer-toggle' command.")
 
 (define-inline org-roam-buffer--visibility ()
   "Return the current visibility state of the persistent `org-roam-buffer'.
-Valid states are 'visible, 'exists and 'none."
+Valid states are `visible', `exists' and `none'."
   (declare (side-effect-free t))
   (inline-quote
    (cond
@@ -292,7 +339,7 @@ Has no effect when there's no `org-roam-node-at-point'."
         (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))
 
 (defun org-roam-buffer--persistent-cleanup-h ()
-  "Clean-up global state thats dedicated for the persistent `org-roam-buffer'."
+  "Clean-up global state that's dedicated for the persistent `org-roam-buffer'."
   (setq-default org-roam-buffer-current-node nil
                 org-roam-buffer-current-directory nil))
 
@@ -394,90 +441,32 @@ In interactive calls OTHER-WINDOW is set with
     (with-current-buffer buf
       (widen)
       (goto-char point))
-    (when (org-invisible-p) (org-show-context))
+    (when (org-invisible-p) (org-fold-show-context))
     buf))
 
-(defun org-roam-preview-get-contents (file point)
+(defun org-roam-preview-default-function ()
-  "Get preview content for FILE at POINT."
+  "Return the preview content at point.
+
+This function returns the all contents under the current
+headline, up to the next headline."
+  (let ((beg (save-excursion
+               (org-roam-end-of-meta-data t)
+               (point)))
+        (end (save-excursion
+               (org-next-visible-heading 1)
+               (point))))
+    (string-trim (buffer-substring-no-properties beg end))))
+
+(defun org-roam-preview-get-contents (file pt)
+  "Get preview content for FILE at PT."
   (save-excursion
     (org-roam-with-temp-buffer file
-      (goto-char point)
-      (let ((elem (org-element-at-point)))
-        ;; We want the parent element always
-        (while (org-element-property :parent elem)
-          (setq elem (org-element-property :parent elem)))
-        (pcase (car elem)
-          ('headline                    ; show subtree
-           (org-roam-preview-get-entry-text (point-marker) most-positive-fixnum))
-          (_
-           (let ((begin (org-element-property :begin elem))
-                 (end (org-element-property :end elem)))
-             (or (string-trim (buffer-substring-no-properties begin end))
-                 (org-element-property :raw-value elem)))))))))
-
-(defun org-roam-preview-get-entry-text (marker n-lines &optional indent)
-  "Extract entry text from MARKER, at most N-LINES lines.
-This will ignore drawers etc, just get the text.
-If INDENT is given, prefix every line with this string."
-  (let (txt ind)
-    (save-excursion
-      (with-current-buffer (marker-buffer marker)
-        (if (not (derived-mode-p 'org-mode))
-            (setq txt "")
       (org-with-wide-buffer
-           (goto-char marker)
+       (goto-char pt)
-           (end-of-line 1)
+       (let ((s (funcall org-roam-preview-function)))
-           (setq txt (buffer-substring
+         (dolist (fn org-roam-preview-postprocess-functions)
-                      (min (1+ (point)) (point-max))
+           (setq s (funcall fn s)))
-                      (progn (outline-next-heading) (point))))
+         s)))))
-           (with-temp-buffer
-             (insert txt)
-             (goto-char (point-min))
-             (while (org-activate-links (point-max))
-               (goto-char (match-end 0)))
-             (goto-char (point-min))
-             (while (re-search-forward org-link-bracket-re (point-max) t)
-               (set-text-properties (match-beginning 0) (match-end 0)
-                                    nil))
-             (goto-char (point-min))
-             (while (re-search-forward org-drawer-regexp nil t)
-               (delete-region
-                (match-beginning 0)
-                (progn (re-search-forward
-                        "^[ \t]*:END:.*\n?" nil 'move)
-                       (point))))
-             (goto-char (point-min))
-             (goto-char (point-max))
-             (skip-chars-backward " \t\n")
-             (when (looking-at "[ \t\n]+\\'") (replace-match ""))
-
-             ;; find and remove min common indentation
-             (goto-char (point-min))
-             (untabify (point-min) (point-max))
-             (setq ind (current-indentation))
-             (while (not (eobp))
-               (unless (looking-at "[ \t]*$")
-                 (setq ind (min ind (current-indentation))))
-               (beginning-of-line 2))
-             (goto-char (point-min))
-             (while (not (eobp))
-               (unless (looking-at "[ \t]*$")
-                 (move-to-column ind)
-                 (delete-region (point-at-bol) (point)))
-               (beginning-of-line 2))
-             (goto-char (point-min))
-             (when indent
-               (while (and (not (eobp)) (re-search-forward "^" nil t))
-                 (replace-match indent t t)))
-             (goto-char (point-min))
-             (while (looking-at "[ \t]*\n") (replace-match ""))
-             (goto-char (point-max))
-             (when (> (org-current-line)
-                      n-lines)
-               (org-goto-line (1+ n-lines))
-               (backward-char 1))
-             (setq txt (buffer-substring (point-min) (point))))))))
-    txt))
 
 ;;;; Backlinks
 (cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
@@ -493,14 +482,23 @@ If INDENT is given, prefix every line with this string."
         (org-roam-populate (org-roam-backlink-target-node backlink)))
   backlink)
 
-(defun org-roam-backlinks-get (node)
+(cl-defun org-roam-backlinks-get (node &key unique)
-  "Return the backlinks for NODE."
+  "Return the backlinks for NODE.
-  (let ((backlinks (org-roam-db-query
+
+ 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")]
+                 :and (= type "id")]))
-                    (org-roam-node-id node))))
+         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
     (cl-loop for backlink in backlinks
              collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                        (org-roam-populate
@@ -516,16 +514,28 @@ Sorts by title."
   (string< (org-roam-node-title (org-roam-backlink-source-node a))
            (org-roam-node-title (org-roam-backlink-source-node b))))
 
-(defun org-roam-backlinks-section (node)
+(cl-defun org-roam-backlinks-section (node &key (unique nil) (show-backlink-p nil)
-  "The backlinks section for NODE."
+                                           (section-heading "Backlinks:"))
-  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+  "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 SHOW-BACKLINK-P is not null, only show backlinks for which
+this predicate is not nil.
+
+SECTION-HEADING is the string used as a heading for the backlink section."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
     (magit-insert-section (org-roam-backlinks)
-      (magit-insert-heading "Backlinks:")
+      (magit-insert-heading section-heading)
       (dolist (backlink backlinks)
+        (when (or (null show-backlink-p)
+                  (and (not (null show-backlink-p))
+                       (funcall show-backlink-p backlink)))
           (org-roam-node-insert-section
            :source-node (org-roam-backlink-source-node backlink)
            :point (org-roam-backlink-point backlink)
-         :properties (org-roam-backlink-properties backlink)))
+           :properties (org-roam-backlink-properties backlink))))
       (insert ?\n))))
 
 ;;;; Reflinks
@@ -542,22 +552,27 @@ Sorts by title."
 
 (defun org-roam-reflinks-get (node)
   "Return the reflinks for NODE."
-  (let ((refs (org-roam-db-query [:select [ref] :from refs
+  (let ((refs (org-roam-db-query [:select :distinct [refs:ref links:source links:pos links:properties]
-                                  :where (= node-id $s1)]
+                                  :from refs
+                                  :left-join links
+                                  :where (= refs:node-id $s1)
+                                  :and (= links:dest refs:ref)
+                                  :union
+                                  :select :distinct [refs:ref citations:node-id
+                                                     citations:pos citations:properties]
+                                  :from refs
+                                  :left-join citations
+                                  :where (= refs:node-id $s1)
+                                  :and (= citations:cite-key refs:ref)]
                                  (org-roam-node-id node)))
         links)
-    (pcase-dolist (`(,ref) refs)
+    (pcase-dolist (`(,ref ,source-id ,pos ,properties) refs)
-      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
-                                                     [:select [source pos properties]
-                                                      :from links
-                                                      :where (= dest $s1)]
-                                                     ref))
       (push (org-roam-populate
              (org-roam-reflink-create
               :source-node (org-roam-node-create :id source-id)
               :ref ref
               :point pos
-                :properties properties)) links)))
+              :properties properties)) links))
     links))
 
 (defun org-roam-reflinks-sort (a b)
@@ -568,8 +583,8 @@ Sorts by title."
 
 (defun org-roam-reflinks-section (node)
   "The reflinks section for NODE."
-  (when (org-roam-node-refs node)
+  (when-let ((refs (org-roam-node-refs node))
-    (let* ((reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+             (reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
     (magit-insert-section (org-roam-reflinks)
       (magit-insert-heading "Reflinks:")
       (dolist (reflink reflinks)
@@ -577,7 +592,7 @@ Sorts by title."
          :source-node (org-roam-reflink-source-node reflink)
          :point (org-roam-reflink-point reflink)
          :properties (org-roam-reflink-properties reflink)))
-        (insert ?\n)))))
+      (insert ?\n))))
 
 ;;;; Grep
 (defvar org-roam-grep-map
@@ -615,7 +630,7 @@ instead."
         (forward-line (1- row)))
       (when col
         (forward-char (1- col))))
-    (when (org-invisible-p) (org-show-context))
+    (when (org-invisible-p) (org-fold-show-context))
     buf))
 
 ;;;; Unlinked references
@@ -643,23 +658,28 @@ This is the ROW within FILE."
        (end-of-line)
        (point)))))
 
-(defun org-roam-unlinked-references-section (node)
+(defun org-roam-unlinked-references--rg-command (titles)
-  "The unlinked references section for NODE.
+  "Return the ripgrep command searching for TITLES."
-References from FILE are excluded."
+  (concat "rg --follow --only-matching --vimgrep --pcre2 --ignore-case "
-  (when (and (executable-find "rg")
+          (mapconcat (lambda (glob) (concat "--glob " glob))
-             (not (string-match "PCRE2 is not available"
-                                (shell-command-to-string "rg --pcre2-version"))))
-    (let* ((titles (cons (org-roam-node-title node)
-                         (org-roam-node-aliases node)))
-           (rg-command (concat "rg -o --vimgrep -P -i "
-                               (mapconcat (lambda (glob) (concat "-g " glob))
                      (org-roam--list-files-search-globs org-roam-file-extensions)
                      " ")
           (format " '\\[([^[]]++|(?R))*\\]%s' "
                   (mapconcat (lambda (title)
                                (format "|(\\b%s\\b)" (shell-quote-argument title)))
                              titles ""))
-                               org-roam-directory))
+          (shell-quote-argument org-roam-directory)))
+
+(defun org-roam-unlinked-references-section (node)
+  "The unlinked references section for NODE.
+References from FILE are excluded."
+  (when (and (executable-find "rg")
+             (org-roam-node-title node)
+             (not (string-match "PCRE2 is not available"
+                                (shell-command-to-string "rg --pcre2-version"))))
+    (let* ((titles (cons (org-roam-node-title node)
+                         (org-roam-node-aliases node)))
+           (rg-command (org-roam-unlinked-references--rg-command titles))
            (results (split-string (shell-command-to-string rg-command) "\n"))
            f row col match)
       (magit-insert-section (unlinked-references)
@@ -672,14 +692,14 @@ References from FILE are excluded."
                     col (string-to-number (match-string 3 line))
                     match (match-string 4 line))
               (when (and match
-                         (not (f-equal-p (org-roam-node-file node) f))
+                         (not (file-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)
                   (oset section row row)
                   (oset section col col)
                   (insert (propertize (format "%s:%s:%s"
-                                              (truncate-string-to-width (file-name-base f) 15 nil nil "...")
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil t)
                                               row col) 'font-lock-face 'org-roam-dim)
                           " "
                           (org-roam-fontify-like-in-org-mode

org-roam-node.el

@@ -1,12 +1,12 @@
 ;;; org-roam-node.el --- Interfacing and interacting with nodes -*- lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -32,12 +32,12 @@
 ;; interactively.
 ;;
 ;;; Code:
+(require 'crm)
 (require 'org-roam)
 
 ;;; Options
 ;;;; Completing-read
-(defcustom org-roam-node-display-template
+(defcustom org-roam-node-display-template "${title}"
-  "${title:*} ${tags:10}"
   "Configures display formatting for Org-roam node.
 Patterns of form \"${field-name:length}\" are interpolated based
 on the current node.
@@ -60,9 +60,13 @@ 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."
+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."
   :group 'org-roam
-  :type  'string)
+  :type  '(string function))
 
 (defcustom org-roam-node-annotation-function #'org-roam-node-read--annotation
   "This function used to attach annotations for `org-roam-node-read'.
@@ -72,10 +76,22 @@ It takes a single argument NODE, which is an `org-roam-node' construct."
 
 (defcustom org-roam-node-default-sort 'file-mtime
   "Default sort order for Org-roam node completions."
-  :type '(choice (const :tag "file-mtime" file-mtime)
+  :type '(choice
+          (const :tag "none" nil)
+          (const :tag "file-mtime" file-mtime)
           (const :tag "file-atime" file-atime))
   :group 'org-roam)
 
+(defcustom org-roam-node-formatter nil
+  "The link description for node insertion.
+If a function is provided, the function should take a single
+argument, an `org-roam-node', and return a string.
+
+If a string is provided, it is a template string expanded by
+`org-roam-node--format-entry'."
+  :group 'org-roam
+  :type '(string function))
+
 (defcustom org-roam-node-template-prefixes
   '(("tags" . "#")
     ("todo" . "t:"))
@@ -93,7 +109,15 @@ has the entry (\"tags\" . \"#\"), these will appear as
 
 (defcustom org-roam-ref-annotation-function #'org-roam-ref-read--annotation
   "This function used to attach annotations for `org-roam-ref-read'.
-It takes a single argument REF, which is a propertized string.")
+It takes a single argument REF, which is a propertized string."
+  :group 'org-roam
+  :type  '(function))
+
+(defcustom org-roam-ref-prompt-function nil
+  "Function to prompt for ref strings in `org-roam-ref-add'.
+Should take no arguments, prompt the user, and return a string."
+  :group 'org-roam
+  :type 'function)
 
 ;;;; Completion-at-point
 (defcustom org-roam-completion-everywhere nil
@@ -114,18 +138,36 @@ 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 to use when a node is extracted to its own file."
+  "The file path template to use when a node is extracted to its own file.
+This path is relative to `org-roam-directory'."
   :group 'org-roam
   :type 'string)
 
+(defvar org-roam-node-history nil
+  "Minibuffer history of nodes.")
+
+(defvar org-roam-ref-history nil
+  "Minibuffer history of refs.")
+
 ;;; Definition
 (cl-defstruct (org-roam-node (:constructor org-roam-node-create)
                              (:copier nil))
   "A heading or top level file with an assigned ID property."
-  file file-hash file-atime file-mtime
+  file file-title file-hash file-atime file-mtime
   id level point todo priority scheduled deadline title properties olp
   tags aliases refs)
 
+;; Shim `string-glyph-compose' and `string-glyph-decompose' for Emacs versions that do not have it.
+;; The functions were introduced in emacs commit 3f096eb3405b2fce7c35366eb2dcf025dda55783 and the
+;; (original) functions behind them aren't autoloaded anymore.
+(dolist (sym.replace
+         '((string-glyph-compose . ucs-normalize-NFC-string)
+           (string-glyph-decompose . ucs-normalize-NFD-string)))
+  (let ((emacs-29-symbol (car sym.replace))
+        (previous-implementation (cdr sym.replace)))
+    (unless (fboundp emacs-29-symbol)
+      (defalias emacs-29-symbol previous-implementation))))
+
 (cl-defmethod org-roam-node-slug ((node org-roam-node))
   "Return the slug of NODE."
   (let ((title (org-roam-node-title node))
@@ -140,6 +182,7 @@ It takes a single argument REF, which is a propertized string.")
                            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
@@ -151,14 +194,12 @@ It takes a single argument REF, which is a propertized string.")
                            816 ; U+0330 COMBINING TILDE BELOW
                            817 ; U+0331 COMBINING MACRON BELOW
                            )))
-    (cl-flet* ((nonspacing-mark-p (char)
+    (cl-flet* ((nonspacing-mark-p (char) (memq char slug-trim-chars))
-                                  (memq char slug-trim-chars))
+               (strip-nonspacing-marks (s) (string-glyph-compose
-               (strip-nonspacing-marks (s)
+                                            (apply #'string
-                                       (ucs-normalize-NFC-string
+                                                   (seq-remove #'nonspacing-mark-p
-                                        (apply #'string (seq-remove #'nonspacing-mark-p
+                                                               (string-glyph-decompose s)))))
-                                                                    (ucs-normalize-NFD-string s)))))
+               (cl-replace (title pair) (replace-regexp-in-string (car pair) (cdr pair) title)))
-               (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
@@ -166,6 +207,20 @@ It takes a single argument REF, which is a propertized string.")
              (slug (-reduce-from #'cl-replace (strip-nonspacing-marks title) pairs)))
         (downcase slug)))))
 
+(cl-defmethod org-roam-node-formatted ((node org-roam-node))
+  "Return a formatted string for NODE."
+  (pcase org-roam-node-formatter
+    ((pred functionp)
+     (funcall org-roam-node-formatter node))
+    ((pred stringp)
+     (org-roam-node--format-entry (org-roam-node--process-display-format org-roam-node-formatter) node))
+    (_
+     (org-roam-node-title node))))
+
+(cl-defmethod org-roam-node-category ((node org-roam-node))
+  "Return the category for NODE."
+  (cdr (assoc-string "CATEGORY" (org-roam-node-properties node))))
+
 ;;; Nodes
 ;;;; Getters
 (defun org-roam-node-at-point (&optional assert)
@@ -180,9 +235,12 @@ populated."
                                     (magit-section-up)
                                     (org-roam-node-at-point)))
         (t (org-with-wide-buffer
-            (org-back-to-heading-or-point-min)
+            (while (not (or (org-roam-db-node-p)
-            (while (and (not (org-roam-db-node-p))
+                            (bobp)
-                        (not (bobp)))
+                            (eq (funcall outline-level)
+                                (save-excursion
+                                  (org-roam-up-heading-or-point-min)
+                                  (funcall outline-level)))))
               (org-roam-up-heading-or-point-min))
             (when-let ((id (org-id-get)))
               (org-roam-populate
@@ -199,17 +257,21 @@ Return nil if a node with ID does not exist."
                                     id)) 0)
     (org-roam-populate (org-roam-node-create :id id))))
 
-(defun org-roam-node-from-title-or-alias (s)
+(defun org-roam-node-from-title-or-alias (s &optional nocase)
   "Return an `org-roam-node' for the node with title or alias S.
 Return nil if the node does not exist.
-Throw an error if multiple choices exist."
+Throw an error if multiple choices exist.
+
+If NOCASE is non-nil, the query is case insensitive.  It is case sensitive otherwise."
   (let ((matches (seq-uniq
                   (append
-                   (org-roam-db-query [:select [id] :from nodes
+                   (org-roam-db-query (vconcat [:select [id] :from nodes
                                                 :where (= title $s1)]
+                                               (if nocase [ :collate NOCASE ]))
                                       s)
-                   (org-roam-db-query [:select [node-id] :from aliases
+                   (org-roam-db-query (vconcat [:select [node-id] :from aliases
                                                 :where (= alias $s1)]
+                                               (if nocase [ :collate NOCASE ]))
                                       s)))))
     (cond
      ((seq-empty-p matches)
@@ -223,9 +285,15 @@ Throw an error if multiple choices exist."
   "Return an `org-roam-node' from REF reference.
 Return nil if there's no node with such REF."
   (save-match-data
-    (when (string-match org-link-plain-re ref)
+    (let (type path)
-      (let ((type (match-string 1 ref))
+      (cond
-            (path (match-string 2 ref)))
+       ((string-match org-link-plain-re ref)
+        (setq type (match-string 1 ref)
+              path (match-string 2 ref)))
+       ((string-prefix-p "@" ref)
+        (setq type "cite"
+              path (substring ref 1))))
+      (when (and type path)
         (when-let ((id (caar (org-roam-db-query
                               [:select [nodes:id]
                                :from refs
@@ -242,14 +310,15 @@ Return nil if there's no node with such REF."
 Uses the ID, and fetches remaining details from the database.
 This can be quite costly: avoid, unless dealing with very few
 nodes."
-  (when-let ((node-info (car (org-roam-db-query [:select [file level pos todo priority
+  (when-let ((node-info (car (org-roam-db-query [:select [
+                                                          file level pos todo priority
                                                           scheduled deadline title properties olp]
                                                  :from nodes
                                                  :where (= id $s1)
                                                  :limit 1]
                                                 (org-roam-node-id node)))))
     (pcase-let* ((`(,file ,level ,pos ,todo ,priority ,scheduled ,deadline ,title ,properties ,olp) node-info)
-                 (`(,atime ,mtime) (car (org-roam-db-query [:select [atime mtime]
+                 (`(,atime ,mtime ,file-title) (car (org-roam-db-query [:select [atime mtime title]
                                                                         :from files
                                                                         :where (= file $s1)]
                                                                        file)))
@@ -263,6 +332,7 @@ nodes."
                                                               :where (= node-id $s1)]
                                                              (org-roam-node-id node)))))
       (setf (org-roam-node-file node) file
+            (org-roam-node-file-title node) file-title
             (org-roam-node-file-atime node) atime
             (org-roam-node-file-mtime node) mtime
             (org-roam-node-level node) level
@@ -285,6 +355,7 @@ nodes."
                "SELECT
   id,
   file,
+  filetitle,
   \"level\",
   todo,
   pos,
@@ -304,6 +375,7 @@ FROM
   SELECT
     id,
     file,
+    filetitle,
     \"level\",
     todo,
     pos,
@@ -334,6 +406,7 @@ FROM
       nodes.olp as olp,
       files.atime as atime,
       files.mtime as mtime,
+      files.title as filetitle,
       tags.tag as tags,
       aliases.alias as aliases,
       '(' || group_concat(RTRIM (refs.\"type\", '\"') || ':' || LTRIM(refs.ref, '\"'), ' ') || ')' as refs
@@ -346,13 +419,15 @@ FROM
   GROUP BY id, tags )
 GROUP BY id")))
     (cl-loop for row in rows
-             append (pcase-let* ((`(,id ,file ,level ,todo ,pos ,priority ,scheduled ,deadline
+             append (pcase-let* ((`(
+                                    ,id ,file ,file-title ,level ,todo ,pos ,priority ,scheduled ,deadline
                                     ,title ,properties ,olp ,atime ,mtime ,tags ,aliases ,refs)
                                   row)
                                  (all-titles (cons title aliases)))
                       (mapcar (lambda (temp-title)
                                 (org-roam-node-create :id id
                                                       :file file
+                                                      :file-title file-title
                                                       :file-atime atime
                                                       :file-mtime mtime
                                                       :level level
@@ -362,6 +437,7 @@ GROUP BY id")))
                                                       :scheduled scheduled
                                                       :deadline deadline
                                                       :title temp-title
+                                                      :aliases aliases
                                                       :properties properties
                                                       :olp olp
                                                       :tags tags
@@ -369,19 +445,40 @@ GROUP BY id")))
                               all-titles)))))
 
 ;;;; Finders
-(defun org-roam-node-find-noselect (node &optional force)
+(defun org-roam-node-marker (node)
-  "Navigate to the point for NODE, and return the buffer.
+  "Get the marker for NODE."
-If NODE is already visited, this won't automatically move the
+  (let* ((file (org-roam-node-file node))
-point to the beginning of the NODE, unless FORCE is non-nil."
+         (buffer (or (find-buffer-visiting file)
-  (unless (org-roam-node-file node)
+                     (find-file-noselect file))))
-    (user-error "Node does not have corresponding file"))
+    (with-current-buffer buffer
-  (let ((buf (find-file-noselect (org-roam-node-file node))))
+      (move-marker (make-marker) (org-roam-node-point node) buffer))))
-    (with-current-buffer buf
+
+(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 (org-roam-node-point node))))
+      (goto-char m))
-    buf))
+    (move-marker m nil))
+  (org-fold-show-context))
 
 (defun org-roam-node-visit (node &optional other-window force)
   "From the current buffer, visit NODE. Return the visited buffer.
@@ -393,16 +490,13 @@ 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))
-  (let ((buf (org-roam-node-find-noselect node 'force))
+  (org-roam-node-open node (if other-window
-        (display-buffer-fn (if other-window
                                #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)))
+                             #'pop-to-buffer-same-window)
-    (funcall display-buffer-fn buf)
+                      force))
-    (when (org-invisible-p) (org-show-context))
-    buf))
 
 ;;;###autoload
-(cl-defun org-roam-node-find (&optional other-window initial-input filter-fn &key templates)
+(cl-defun org-roam-node-find (&optional other-window initial-input filter-fn pred &key templates)
   "Find and open an Org-roam node by its title or alias.
 INITIAL-INPUT is the initial input for the prompt.
 FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
@@ -411,7 +505,7 @@ If OTHER-WINDOW, visit the NODE in another window.
 The TEMPLATES, if provided, override the list of capture templates (see
 `org-roam-capture-'.)"
   (interactive current-prefix-arg)
-  (let ((node (org-roam-node-read initial-input filter-fn)))
+  (let ((node (org-roam-node-read initial-input filter-fn pred)))
     (if (org-roam-node-file node)
         (org-roam-node-visit node other-window)
       (org-roam-capture-
@@ -420,70 +514,89 @@ The TEMPLATES, if provided, override the list of capture templates (see
        :props '(:finalize find-file)))))
 
 ;;;###autoload
-(defun org-roam-node-random (&optional other-window)
+(defun org-roam-node-random (&optional other-window filter-fn)
   "Find and open a random Org-roam node.
 With prefix argument OTHER-WINDOW, visit the node in another
-window instead."
+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."
   (interactive current-prefix-arg)
-  (let ((random-row (seq-random-elt (org-roam-db-query [:select [id file pos] :from nodes]))))
+  (org-roam-node-visit
-    (org-roam-node-visit (org-roam-node-create :id (nth 0 random-row)
+   (cdr (seq-random-elt (org-roam-node-read--completions filter-fn)))
-                                               :file (nth 1 random-row)
+   other-window))
-                                               :point (nth 2 random-row))
-                         other-window)))
 
 ;;;; Completing-read interface
-(defun org-roam-node-read (&optional initial-input filter-fn sort-fn require-match)
+(defun org-roam-node-read (&optional initial-input filter-fn sort-fn require-match prompt)
   "Read and return an `org-roam-node'.
 INITIAL-INPUT is the initial minibuffer prompt value.
 FILTER-FN is a function to filter out nodes: it takes an `org-roam-node',
 and when nil is returned the node will be filtered out.
 SORT-FN is a function to sort nodes. See `org-roam-node-read-sort-by-file-mtime'
 for an example sort function.
-If REQUIRE-MATCH, the minibuffer prompt will require a match."
+If REQUIRE-MATCH, the minibuffer prompt will require a match.
-  (let* ((nodes (org-roam-node-read--completions))
+PROMPT is a string to show at the beginning of the mini-buffer, defaulting to \"Node: \""
-         (nodes (cl-remove-if-not (lambda (n)
+  (let* ((nodes (org-roam-node-read--completions filter-fn sort-fn))
-                                    (if filter-fn (funcall filter-fn (cdr n)) t)) nodes))
+         (prompt (or prompt "Node: "))
-         (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))))
          (node (completing-read
-                "Node: "
+                prompt
                 (lambda (string pred action)
                   (if (eq action 'metadata)
-                      '(metadata
+                      `(metadata
-                        (annotation-function . (lambda (title)
+                        ;; Preserve sorting in the completion UI if a sort-fn is used
+                        ,@(when sort-fn
+                            '((display-sort-function . identity)
+                              (cycle-sort-function . identity)))
+                        (annotation-function
+                         . ,(lambda (title)
                               (funcall org-roam-node-annotation-function
                                        (get-text-property 0 'node title))))
                         (category . org-roam-node))
                     (complete-with-action action nodes string pred)))
-                nil require-match initial-input)))
+                nil require-match initial-input 'org-roam-node-history)))
     (or (cdr (assoc node nodes))
         (org-roam-node-create :title node))))
 
-(defvar org-roam-node-read--cached-display-format nil)
+(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'."
-  (setq org-roam-node-read--cached-display-format nil)
+  (let* ((template (org-roam-node--process-display-format org-roam-node-display-template))
-  (let ((nodes (org-roam-node-list)))
+         (nodes (org-roam-node-list))
-    (mapcar #'org-roam-node-read--to-candidate nodes)))
+         (nodes (if filter-fn
+                    (cl-remove-if-not
+                     (lambda (n) (funcall filter-fn n))
+                     nodes)
+                  nodes))
+         (nodes (mapcar (lambda (node)
+                          (org-roam-node-read--to-candidate node template)) 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))
 
-(defun org-roam-node-read--to-candidate (node)
+(defun org-roam-node-read--to-candidate (node template)
-  "Return a minibuffer completion candidate given NODE."
+  "Return a minibuffer completion candidate given NODE.
-  (let ((candidate-main (org-roam-node-read--format-entry node (1- (frame-width)))))
+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))))))
     (cons (propertize candidate-main 'node node) node)))
 
-(defun org-roam-node-read--format-entry (node width)
+(defun org-roam-node--format-entry (template node &optional width)
   "Formats NODE for display in the results list.
 WIDTH is the width of the results list.
-Uses `org-roam-node-display-template' to format the entry."
+TEMPLATE is the processed template used to format the entry."
-  (pcase-let ((`(,tmpl . ,tmpl-width)
+  (pcase-let ((`(,tmpl . ,tmpl-width) template))
-               (org-roam-node-read--process-display-format org-roam-node-display-template)))
     (org-roam-format-template
      tmpl
      (lambda (field _default-val)
@@ -508,26 +621,28 @@ Uses `org-roam-node-display-template' to format the entry."
                             ((not field-width)
                              field-width)
                             ((string-equal field-width "*")
-                             (- width tmpl-width))
+                             (if width
+                                 (- width tmpl-width)
+                               tmpl-width))
                             ((>= (string-to-number field-width) 0)
                              (string-to-number field-width))))
-         ;; Setting the display (which would be padded out to the field length) for an
+         (when field-width
-         ;; empty string results in an empty string and misalignment for candidates that
+           (let* ((truncated (truncate-string-to-width field-value field-width 0 ?\s))
-         ;; don't have some field. This uses the actual display string, made of spaces
+                  (tlen (length truncated))
-         ;; when the field-value is "" so that we actually take up space.
+                  (len (length field-value)))
-         (let ((display-string (if field-width
+             (if (< tlen len)
-                                   (truncate-string-to-width field-value field-width 0 ?\s)
+                 ;; Make the truncated part of the string invisible. If strings
-                                 field-value)))
+                 ;; are pre-propertized with display or invisible properties, the
-           (if (equal field-value "")
+                 ;; formatting may get messed up. Ideally, truncated strings are
-               display-string
+                 ;; not preformatted with these properties. Face properties are
-             ;; Remove properties from the full candidate string, otherwise the display
+                 ;; allowed without restriction.
-             ;; formatting with pre-prioritized field-values gets messed up.
+                 (put-text-property tlen len 'invisible t field-value)
-             (propertize (substring-no-properties field-value) 'display display-string))))))))
+               ;; If the string wasn't truncated, but padded, use this string instead.
+               (setq field-value truncated))))
+         field-value)))))
 
-(defun org-roam-node-read--process-display-format (format)
+(defun org-roam-node--process-display-format (format)
   "Pre-calculate minimal widths needed by the FORMAT string."
-  (or org-roam-node-read--cached-display-format
-      (setq org-roam-node-read--cached-display-format
   (let* ((fields-width 0)
          (string-width
           (string-width
@@ -539,11 +654,12 @@ Uses `org-roam-node-display-template' to format the entry."
                        (string-to-number
                         (or (cadr (split-string field ":"))
                             "")))))))))
-              (cons format (+ fields-width string-width))))))
+    (cons format (+ fields-width string-width))))
 
 (defun org-roam-node-read-sort-by-file-mtime (completion-a completion-b)
   "Sort files such that files modified more recently are shown first.
-COMPLETION-A and COMPLETION-B are items in the form of (node-title org-roam-node-struct)"
+COMPLETION-A and COMPLETION-B are items in the form of
+\(node-title org-roam-node-struct)"
   (let ((node-a (cdr completion-a))
         (node-b (cdr completion-b)))
     (time-less-p (org-roam-node-file-mtime node-b)
@@ -551,7 +667,8 @@ COMPLETION-A and COMPLETION-B are items in the form of (node-title org-roam-node
 
 (defun org-roam-node-read-sort-by-file-atime (completion-a completion-b)
   "Sort files such that files accessed more recently are shown first.
-COMPLETION-A and COMPLETION-B are items in the form of (node-title org-roam-node-struct)"
+COMPLETION-A and COMPLETION-B are items in the form of
+\(node-title org-roam-node-struct)"
   (let ((node-a (cdr completion-a))
         (node-b (cdr completion-b)))
     (time-less-p (org-roam-node-file-atime node-b)
@@ -583,15 +700,19 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
                     (setq region-text (org-link-display-format (buffer-substring-no-properties beg end)))))
                (node (org-roam-node-read region-text filter-fn))
                (description (or region-text
-                                (org-roam-node-title node))))
+                                (org-roam-node-formatted node))))
           (if (org-roam-node-id node)
               (progn
                 (when region-text
                   (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:" (org-roam-node-id node))
+                           (concat "id:" id)
+                           description))
+                  (run-hook-with-args 'org-roam-post-node-insert-hook
+                                      id
                                       description)))
             (org-roam-capture-
              :node node
@@ -600,31 +721,10 @@ The INFO, if provided, is passed to the underlying `org-roam-capture-'."
              :props (append
                      (when (and beg end)
                        (list :region (cons beg end)))
-                     (list :insert-at (point-marker)
+                     (list :link-description description
-                           :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 ()
-  "Try to navigate \"id:\" link to find and visit node with an assigned ID.
-Assumes that the cursor was put where the link is."
-  (let* ((context (org-element-context))
-         (type (org-element-property :type context))
-         (id (org-element-property :path context)))
-    (when (string= type "id")
-      (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)
@@ -676,7 +776,7 @@ Assumes that the cursor was put where the link is."
 
 ;;;;;; Completion-at-point interface
 (defconst org-roam-bracket-completion-re
-  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*\\)]]"
+  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*?\\)]]"
   "Regex for completion within link brackets.
 We use this as a substitute for `org-link-bracket-re', because
 `org-link-bracket-re' requires content within the brackets for a match.")
@@ -685,13 +785,12 @@ We use this as a substitute for `org-link-bracket-re', because
   "Complete \"roam:\" link at point to an existing Org-roam node."
   (let (roam-p start end)
     (when (org-in-regexp org-roam-bracket-completion-re 1)
-      (setq roam-p (not (string-blank-p (match-string 1)))
+      (setq roam-p (not (or (org-in-src-block-p)
+                            (string-blank-p (match-string 1))))
             start (match-beginning 2)
             end (match-end 2))
       (list start end
-            (completion-table-dynamic
+            (org-roam--get-titles)
-             (lambda (_)
-               (funcall #'org-roam--get-titles)))
             :exit-function
             (lambda (str &rest _)
               (delete-char (- 0 (length str)))
@@ -709,25 +808,27 @@ outside of the bracket syntax for links (i.e. \"[[roam:|]]\"),
 hence \"everywhere\"."
   (when (and org-roam-completion-everywhere
              (thing-at-point 'word)
+             (not (org-in-src-block-p))
              (not (save-match-data (org-in-regexp org-link-any-re))))
     (let ((bounds (bounds-of-thing-at-point 'word)))
       (list (car bounds) (cdr bounds)
-            (completion-table-dynamic
+            (org-roam--get-titles)
-             (lambda (_)
-               (funcall #'org-roam--get-titles)))
             :exit-function
             (lambda (str _status)
               (delete-char (- (length str)))
-              (insert "[[roam:" str "]]"))))))
+              (insert "[[roam:" str "]]"))
-
+            ;; Proceed with the next completion function if the returned titles
-(defun org-roam-complete-at-point ()
+            ;; do not match. This allows the default Org capfs or custom capfs
-  "Try get completion candidates at point using `org-roam-completion-functions'."
+            ;; of lower priority to run.
-  (run-hook-with-args-until-success 'org-roam-completion-functions))
+            :exclusive 'no))))
 
 (add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-roam-indirect-buffer-hook #'org-roam--register-completion-functions-h)
+
 (defun org-roam--register-completion-functions-h ()
   "Setup `org-roam-completion-functions' for `completion-at-point'."
-  (add-hook 'completion-at-point-functions #'org-roam-complete-at-point nil t))
+  (dolist (f org-roam-completion-functions)
+    (add-hook 'completion-at-point-functions f nil t)))
 
 ;;;; Editing
 (defun org-roam-demote-entire-buffer ()
@@ -741,7 +842,8 @@ 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-entries 'org-do-demote)
+    (org-map-region #'org-do-demote
+                    (point-min) (point-max))
     (insert "* "
             (org-roam--get-keyword "title")
             "\n")
@@ -750,35 +852,58 @@ Any top level properties drawers are incorporated into the new heading."
     (org-roam-erase-keyword "title")
     (org-roam-erase-keyword "filetags")))
 
+(defun org-roam--h1-count ()
+  "Count level-1 headings in the current file."
+  (let ((h1-count 0))
+    (org-with-wide-buffer
+     (org-map-region (lambda ()
+                       (if (= (org-current-level) 1)
+                           (cl-incf h1-count)))
+                     (point-min) (point-max))
+     h1-count)))
+
+(defun org-roam--buffer-promoteable-p ()
+  "Verify that this buffer is promoteable:
+There is a single level-1 heading
+and no extra content before the first heading."
+  (and
+   (= (org-roam--h1-count) 1)
+   (org-with-point-at 1 (org-at-heading-p))))
+
 (defun org-roam-promote-entire-buffer ()
   "Promote the current buffer.
-Converts a file containing a headline node at the top to a file
+Converts a file containing a single level-1 headline node to a file
 node."
   (interactive)
+  (unless (org-roam--buffer-promoteable-p)
+    (user-error "Cannot promote: multiple root headings or there is extra file-level text"))
   (org-with-point-at 1
-    (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))))
+          (tags (org-get-tags)))
-      (beginning-of-line)
+      (org-fold-show-all)
-      (kill-line 1)
+      (kill-whole-line)
-      (org-roam-set-keyword "title" title)
+      (org-roam-end-of-meta-data t)
-      (when tags (org-roam-set-keyword "filetags" tags)))))
+      (insert "#+title: " title "\n")
+      (when tags (org-roam-tag-add tags))
+      (org-map-region #'org-promote (point-min) (point-max))
+      (org-roam-db-update-file))))
 
 ;;;###autoload
-(defun org-roam-refile ()
+(defun org-roam-refile (node)
-  "Refile node at point to an Org-roam node.
+  "Refile node at point to an org-roam NODE.
+
 If region is active, then use it instead of the node at point."
-  (interactive)
+  (interactive
+   (list (org-roam-node-read nil nil nil 'require-match)))
   (let* ((regionp (org-region-active-p))
          (region-start (and regionp (region-beginning)))
          (region-end (and regionp (region-end)))
-         (node (org-roam-node-read nil nil nil 'require-match))
          (file (org-roam-node-file node))
          (nbuf (or (find-buffer-visiting file)
                    (find-file-noselect file)))
          level reversed)
+    (if (equal (org-roam-node-at-point) node)
+        (user-error "Target is the same as current node")
       (if regionp
           (progn
             (org-kill-new (buffer-substring region-start region-end))
@@ -816,18 +941,18 @@ If region is active, then use it instead of the node at point."
         (if (buffer-file-name)
             (delete-file (buffer-file-name)))
         (set-buffer-modified-p nil)
-      ;; In this was done during capture, abort the capture process.
+        ;; If this was done during capture, abort the capture process.
         (when (and org-capture-mode
                    (buffer-base-buffer (current-buffer)))
           (org-capture-kill))
-      (kill-buffer (current-buffer)))))
+        (kill-buffer (current-buffer))))))
 
 ;;;###autoload
 (defun org-roam-extract-subtree ()
   "Convert current subtree at point to a node, and extract it into a new file."
   (interactive)
   (save-excursion
-    (org-back-to-heading-or-point-min)
+    (org-back-to-heading-or-point-min t)
     (when (bobp) (user-error "Already a top-level node"))
     (org-id-get-create)
     (save-buffer)
@@ -845,55 +970,25 @@ If region is active, then use it instead of the node at point."
                             (funcall fn node))
                            ((fboundp node-fn)
                             (funcall node-fn node))
-                           (t (let ((r (completing-read (format "%s: " key) nil nil nil default-val)))
+                           (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
                                 (plist-put template-info ksym r)
                                 r)))))))
-           (file-path (read-file-name "Extract node to: " org-roam-directory template nil template)))
+           (file-path
+            (expand-file-name
+             (read-file-name "Extract node to: "
+                             (file-name-as-directory org-roam-directory) template nil template)
+             org-roam-directory)))
       (when (file-exists-p file-path)
         (user-error "%s exists. Aborting" file-path))
       (org-cut-subtree)
       (save-buffer)
       (with-current-buffer (find-file-noselect file-path)
         (org-paste-subtree)
+        (while (> (org-current-level) 1) (org-promote-subtree))
+        (save-buffer)
         (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)
-   (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 with files 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)
@@ -908,13 +1003,12 @@ filtered out."
          (ref (completing-read "Ref: "
                                (lambda (string pred action)
                                  (if (eq action 'metadata)
-                                     '(metadata
+                                     `(metadata
-                                       (annotation-function . (lambda (ref)
+                                       (annotation-function
-                                                                (funcall org-roam-ref-annotation-function
+                                        . ,org-roam-ref-annotation-function)
-                                                                         ref)))
                                        (category . org-roam-ref))
                                    (complete-with-action action refs string pred)))
-                               nil t initial-input)))
+                               nil t initial-input 'org-roam-ref-history)))
     (cdr (assoc ref refs))))
 
 (defun org-roam-ref-read--completions ()
@@ -931,7 +1025,9 @@ The car is the ref, and the cdr is the corresponding node for the ref."
                                                               :file file
                                                               :point pos
                                                               :title title)))
-                       (cons (propertize ref 'node node 'type type)
+                       (cons
+                        (concat (propertize ref 'node node 'type type)
+                                (propertize id 'invisible t))
                         node)))))
 
 (defun org-roam-ref-read--annotation (ref)
@@ -955,11 +1051,15 @@ and when nil is returned the node will be filtered out."
 ;;;; Editing
 (defun org-roam-ref-add (ref)
   "Add REF to the node at point."
-  (interactive "sRef: ")
+  (interactive `(,(if org-roam-ref-prompt-function
+                      (funcall org-roam-ref-prompt-function)
+                    (read-string "Ref: "))))
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
-      (org-roam-add-property ref "ROAM_REFS"))))
+      (org-roam-property-add "ROAM_REFS" (if (member " " (string-to-list ref))
+                                             (concat "\"" ref "\"")
+                                           ref)))))
 
 (defun org-roam-ref-remove (&optional ref)
   "Remove a REF from the node at point."
@@ -967,7 +1067,7 @@ and when nil is returned the node will be filtered out."
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
-      (org-roam-remove-property "ROAM_REFS" ref))))
+      (org-roam-property-remove "ROAM_REFS" ref))))
 
 ;;; Tags
 ;;;; Getters
@@ -987,7 +1087,8 @@ and when nil is returned the node will be filtered out."
 (defun org-roam-tag-add (tags)
   "Add TAGS to the node at point."
   (interactive
-   (list (completing-read-multiple "Tag: " (org-roam-tag-completions))))
+   (list (let ((crm-separator "[ 	]*:[ 	]*"))
+           (completing-read-multiple "Tag: " (org-roam-tag-completions)))))
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
@@ -1016,7 +1117,7 @@ and when nil is returned the node will be filtered out."
                                   (org-make-tag-string (seq-difference current-tags tags #'string-equal))))
         (let* ((current-tags (or (org-get-tags)
                                  (user-error "No tag to remove")))
-               (tags (completing-read-multiple "Tag: " current-tags)))
+               (tags (or tags (completing-read-multiple "Tag: " current-tags))))
           (org-set-tags (seq-difference current-tags tags #'string-equal))))
       tags)))
 
@@ -1034,7 +1135,7 @@ and when nil is returned the node will be filtered out."
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
-      (org-roam-add-property alias "ROAM_ALIASES"))))
+      (org-roam-property-add "ROAM_ALIASES" alias))))
 
 (defun org-roam-alias-remove (&optional alias)
   "Remove an ALIAS from the node at point."
@@ -1042,7 +1143,7 @@ and when nil is returned the node will be filtered out."
   (let ((node (org-roam-node-at-point 'assert)))
     (save-excursion
       (goto-char (org-roam-node-point node))
-      (org-roam-remove-property "ROAM_ALIASES" alias))))
+      (org-roam-property-remove "ROAM_ALIASES" alias))))
 
 
 (provide 'org-roam-node)

org-roam-utils.el

@@ -1,12 +1,12 @@
 ;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -32,6 +32,13 @@
 ;;
 ;;; Code:
 
+(require 'org-roam)
+
+(defun org-roam-require (libs)
+  "Require LIBS."
+  (dolist (lib libs)
+    (require lib nil 'noerror)))
+
 ;;; String utilities
 ;; TODO Refactor this.
 (defun org-roam-replace-string (old new s)
@@ -45,20 +52,78 @@
        (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."
+  (and (= (length s1) (length s2))
+       (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
+    (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
+    (insert s)
+    (goto-char (point-min))
+    (while (not (eobp))
+      (if (org-at-comment-p)
+          (delete-region (line-beginning-position)
+                         (progn (forward-line) (point)))
+        (forward-line)))
+    (buffer-string)))
+
 ;;; List utilities
-(defmacro org-roam-plist-map! (fn plist)
+(defun org-roam-plist-map! (fn plist)
-  "Map FN over PLIST, modifying it in-place."
+  "Map FN over PLIST, modifying it in-place and returning it.
-  (declare (indent 1))
+FN must take two arguments: the key and the value."
-  (let ((plist-var (make-symbol "plist"))
+  (let ((plist-index plist))
-        (k (make-symbol "k"))
+    (while plist-index
-        (v (make-symbol "v")))
+      (let ((key (pop plist-index)))
-    `(let ((,plist-var (copy-sequence ,plist)))
+        (setf (car plist-index) (funcall fn key (car plist-index))
-       (while ,plist-var
+              plist-index (cdr plist-index)))))
-         (setq ,k (pop ,plist-var))
+  plist)
-         (setq ,v (pop ,plist-var))
+
-         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
+(defmacro org-roam-dolist-with-progress (spec msg &rest body)
+  "Loop over a list and report progress in the echo area.
+Like `dolist-with-progress-reporter', but falls back to `dolist'
+if the function does not yet exist.
+
+Evaluate BODY with VAR bound to each car from LIST, in turn.
+Then evaluate RESULT to get return value, default nil.
+
+MSG is a progress reporter object or a string.  In the latter
+case, use this string to create a progress reporter.
+
+SPEC is a list, as per `dolist'."
+  (declare (indent 2))
+  (if (fboundp 'dolist-with-progress-reporter)
+      `(dolist-with-progress-reporter ,spec ,msg ,@body)
+    `(dolist ,spec ,@body)))
 
 ;;; File utilities
+(defun org-roam-descendant-of-p (a b)
+  "Return t if A is descendant of B."
+  (unless (and a b (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.
@@ -66,6 +131,7 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
   (declare (indent 2) (debug t))
   `(let* (new-buf
           (auto-mode-alist nil)
+          (find-file-hook nil)
           (buf (or (and (not ,file)
                         (current-buffer)) ;If FILE is nil, use current buffer
                    (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
@@ -74,11 +140,12 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
                      (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
           res)
      (with-current-buffer buf
-       (unless (equal major-mode 'org-mode)
+       (unless (derived-mode-p 'org-mode)
          (delay-mode-hooks
            (let ((org-inhibit-startup t)
                  (org-agenda-files nil))
-             (org-mode))))
+             (org-mode)
+             (hack-local-variables))))
        (setq res (progn ,@body))
        (unless (and new-buf (not ,keep-buf-p))
          (save-buffer)))
@@ -125,14 +192,20 @@ value (possibly nil). Adapted from `s-format'."
                  (let ((v (progn
                             (set-match-data saved-match-data)
                             (funcall replacer var default-val))))
-                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
+                   (if v
+                       (format (apply #'propertize "%s" (text-properties-at 0 var)) v)
+                     (signal 'org-roam-format-resolve md)))
                (set-match-data replacer-match-data))))
-         template
+         (if (functionp template)
+             (funcall template)
+           template)
          ;; Need literal to make sure it works
          t t)
       (set-match-data saved-match-data))))
 
 ;;; Fontification
+(defvar org-ref-buffer-hacked)
+
 (defun org-roam-fontify-like-in-org-mode (s)
   "Fontify string S like in Org mode.
 Like `org-fontify-like-in-org-mode', but supports `org-ref'."
@@ -156,36 +229,10 @@ Like `org-fontify-like-in-org-mode', but supports `org-ref'."
     (insert s)
     (let ((org-ref-buffer-hacked t))
       (org-mode)
-      (org-font-lock-ensure)
+      (setq-local org-fold-core-style 'overlays)
+      (font-lock-ensure)
       (buffer-string))))
 
-;;;; Shielding regions
-(defface org-roam-shielded
-  '((t :inherit (warning)))
-  "Face for regions that are shielded (marked as read-only).
-This face is used on the region target by org-roam-insertion
-during an `org-roam-capture'."
-  :group 'org-roam-faces)
-
-(defun org-roam-shield-region (beg end)
-  "Shield region against modifications.
-BEG and END are markers for the beginning and end regions.
-REGION must be a cons-cell containing the marker to the region
-beginning and maximum values."
-  (add-text-properties beg end
-                       '(font-lock-face org-roam-shielded
-                                        read-only t)
-                       (marker-buffer beg)))
-
-(defun org-roam-unshield-region (beg end)
-  "Unshield the shielded REGION.
-BEG and END are markers for the beginning and end regions."
-  (let ((inhibit-read-only t))
-    (remove-text-properties beg end
-                            '(font-lock-face org-roam-shielded
-                                             read-only t)
-                            (marker-buffer beg))))
-
 ;;; Org-mode utilities
 ;;;; Motions
 (defun org-roam-up-heading-or-point-min ()
@@ -221,6 +268,45 @@ If BOUND, scan up to BOUND bytes of the buffer."
       (when (re-search-forward re bound t)
         (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
 
+(defun org-roam-end-of-meta-data (&optional full)
+  "Like `org-end-of-meta-data', but supports file-level metadata.
+
+When FULL is non-nil but not t, skip planning information,
+properties, clocking lines and logbook drawers.
+
+When optional argument FULL is t, skip everything above, and also
+skip keywords."
+  (org-back-to-heading-or-point-min t)
+  (when (org-at-heading-p) (forward-line))
+  ;; Skip planning information.
+  (when (looking-at-p org-planning-line-re) (forward-line))
+  ;; Skip property drawer.
+  (when (looking-at org-property-drawer-re)
+    (goto-char (match-end 0))
+    (forward-line))
+  ;; When FULL is not nil, skip more.
+  (when (and full (not (org-at-heading-p)))
+    (catch 'exit
+      (let ((end (save-excursion (outline-next-heading) (point)))
+            (re (concat "[ \t]*$" "\\|" org-clock-line-re)))
+        (while (not (eobp))
+          (cond ;; Skip clock lines.
+           ((looking-at-p re) (forward-line))
+           ;; Skip logbook drawer.
+           ((looking-at-p org-logbook-drawer-re)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ((looking-at-p org-drawer-regexp)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ;; When FULL is t, skip keywords too.
+           ((and (eq full t)
+                 (looking-at-p org-keyword-regexp))
+            (forward-line))
+           (t (throw 'exit t))))))))
+
 (defun org-roam-set-keyword (key value)
   "Set keyword KEY to VALUE.
 If the property is already set, it's value is replaced."
@@ -230,14 +316,13 @@ If the property is already set, it's value is replaced."
           (if (string-blank-p value)
               (kill-whole-line)
             (replace-match (concat " " value) 'fixedcase nil nil 1))
-        (while (and (not (eobp))
+        (org-roam-end-of-meta-data 'drawers)
-                    (looking-at "^[#:]"))
         (if (save-excursion (end-of-line) (eobp))
             (progn
               (end-of-line)
               (insert "\n"))
           (forward-line)
-            (beginning-of-line)))
+          (beginning-of-line))
         (insert "#+" key ": " value "\n")))))
 
 (defun org-roam-erase-keyword (keyword)
@@ -252,6 +337,18 @@ If the property is already set, it's value is replaced."
 ;;;; Properties
 (defun org-roam-add-property (val prop)
   "Add VAL value to PROP property for the node at point.
+Both, VAL and PROP are strings."
+  (org-roam-property-add prop val))
+
+(defun org-roam-remove-property (prop &optional val)
+  "Remove VAL value from PROP property for the node at point.
+Both VAL and PROP are strings.
+
+If VAL is not specified, user is prompted to select a value."
+  (org-roam-property-remove prop val))
+
+(defun org-roam-property-add (prop val)
+  "Add VAL value to PROP property for the node at point.
 Both, VAL and PROP are strings."
   (let* ((p (org-entry-get (point) prop))
          (lst (when p (split-string-and-unquote p)))
@@ -260,7 +357,7 @@ Both, VAL and PROP are strings."
     (org-set-property prop (combine-and-quote-strings lst))
     val))
 
-(defun org-roam-remove-property (prop &optional val)
+(defun org-roam-property-remove (prop &optional val)
   "Remove VAL value from PROP property for the node at point.
 Both VAL and PROP are strings.
 
@@ -274,6 +371,16 @@ If VAL is not specified, user is prompted to select a value."
       (org-delete-property prop))
     prop-to-remove))
 
+;;; Refs
+(defun org-roam-org-ref-path-to-keys (path)
+  "Return a list of keys given an org-ref cite: PATH.
+Accounts for both v2 and v3."
+  (cond ((fboundp 'org-ref-parse-cite-path)
+         (mapcar (lambda (cite) (plist-get cite :key))
+                 (plist-get (org-ref-parse-cite-path path) :references)))
+        ((fboundp 'org-ref-split-and-strip-string)
+         (org-ref-split-and-strip-string path))))
+
 ;;; Logs
 (defvar org-roam-verbose)
 (defun org-roam-message (format-string &rest args)
@@ -341,8 +448,11 @@ See <https://github.com/raxod502/straight.el/issues/520>."
                                          '("Doom" "Spacemacs" "N/A" "I don't know"))
                       (quit "N/A"))))
     (insert (format "- Org: %s\n" (org-version nil 'full)))
-    (insert (format "- Org-roam: %s" (org-roam-version)))))
+    (insert (format "- Org-roam: %s" (org-roam-version)))
-
+    (insert (format "- sqlite-connector: %s"
+                    (if-let ((conn (org-roam-db--get-connection)))
+                        (eieio-object-class conn)
+                      "not connected")))))
 
 (provide 'org-roam-utils)
 ;;; org-roam-utils.el ends here

org-roam.el

@@ -1,12 +1,12 @@
 ;;; org-roam.el --- A database abstraction layer for Org-mode -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2025 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: 2.1.0
+;; Version: 2.3.0
-;; 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 "2.90.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -71,7 +71,6 @@
 ;; majority of them can be found at https://github.com/org-roam and MELPA.
 ;;
 ;;; Code:
-(require 'f)
 (require 'dash)
 
 (require 'rx)
@@ -81,9 +80,13 @@
 (require 'magit-section)
 
 (require 'emacsql)
+;; REVIEW: is this require needed?
+;; emacsql-sqlite provides a common interface to an emacsql SQLite backend (e.g. emacs-sqlite-builtin)
+;; not to be confused with a backend itself named emacsql-sqlite that existed in emacsql < 4.0.
 (require 'emacsql-sqlite)
 
 (require 'org)
+(require 'org-attach)                   ; To set `org-attach-id-dir'
 (require 'org-id)
 (require 'ol)
 (require 'org-element)
@@ -94,9 +97,6 @@
 (eval-when-compile
   (require 'subr-x))
 
-(require 'org-roam-utils)
-(require 'org-roam-compat)
-
 ;;; Options
 (defgroup org-roam nil
   "A database abstraction layer for Org-mode."
@@ -126,6 +126,12 @@ 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
@@ -134,9 +140,11 @@ responsibility to ensure that."
   :type '(repeat string)
   :group 'org-roam)
 
-(defcustom org-roam-file-exclude-regexp nil
+(defcustom org-roam-file-exclude-regexp (list org-attach-id-dir)
-  "Files matching this regular expression are excluded from the Org-roam."
+  "Files matching this regular expression or list of regular expressions are excluded from the Org-roam."
   :type '(choice
+          (repeat
+           (string :tag "Regular expression matching files to ignore"))
           (string :tag "Regular expression matching files to ignore")
           (const :tag "Include everything" nil))
   :group 'org-roam)
@@ -147,32 +155,42 @@ responsibility to ensure that."
     '(find fd fdfind rg))
   "Commands that will be used to find Org-roam files.
 
-It should be a list of symbols or cons cells representing any of the following
+It should be a list of symbols or cons cells representing any of
-supported file search methods.
+the following supported file search methods.
 
-The commands will be tried in order until an executable for a command is found.
+The commands will be tried in order until an executable for a
-The Elisp implementation is used if no command in the list is found.
+command is found. The Elisp implementation is used if no command
+in the list is found.
 
   `find'
+
     Use find as the file search method.
     Example command:
-    find /path/to/dir -type f \( -name \"*.org\" -o -name \"*.org.gpg\" \)
+      find /path/to/dir -type f \
+        \( -name \"*.org\" -o -name \"*.org.gpg\" -name \"*.org.age\" \)
 
   `fd'
+
     Use fd as the file search method.
-    Example command: fd /path/to/dir/ --type file -e \".org\" -e \".org.gpg\"
+    Example command:
+      fd /path/to/dir/ --type file -e \".org\" -e \".org.gpg\" -e \".org.age\"
 
   `fdfind'
+
     Same as `fd'. It's an alias that used in some OSes (e.g. Debian, Ubuntu)
 
   `rg'
-    Use ripgrep as the file search method.
-    Example command: rg /path/to/dir/ --files -g \"*.org\" -g \"*.org.gpg\"
 
-By default, `executable-find' will be used to look up the path to the
+    Use ripgrep as the file search method.
-executable. If a custom path is required, it can be specified together with the
+    Example command:
-method symbol as a cons cell. For example: '(find (rg . \"/path/to/rg\"))."
+       rg /path/to/dir/ --files -g \"*.org\" -g \"*.org.gpg\" -g \"*.org.age\"
-  :type '(set (const :tag "find" find)
+
+By default, `executable-find' will be used to look up the path to
+the executable. If a custom path is required, it can be specified
+together with the method symbol as a cons cell. For example:
+\\='(find (rg . \"/path/to/rg\"))."
+  :type '(set
+          (const :tag "find" find)
           (const :tag "fd" fd)
           (const :tag "fdfind" fdfind)
           (const :tag "rg" rg)
@@ -187,19 +205,34 @@ FILE is an Org-roam file if:
 - It's located somewhere under `org-roam-directory'
 - It has a matching file extension (`org-roam-file-extensions')
 - It doesn't match excluded regexp (`org-roam-file-exclude-regexp')"
+  (when (or file (buffer-file-name (buffer-base-buffer)))
     (let* ((path (or file (buffer-file-name (buffer-base-buffer))))
-         (ext (when path (org-roam--file-name-extension path)))
+           (relative-path (file-relative-name path org-roam-directory))
-         (ext (if (string= ext "gpg")
+           (ext (org-roam--file-name-extension path))
+           (ext (if (or (string= ext "gpg")
+                        (string= ext "age"))
                     (org-roam--file-name-extension (file-name-sans-extension path))
-                ext)))
+                  ext))
+           (org-roam-dir-p (org-roam-descendant-of-p path org-roam-directory))
+           (valid-file-ext-p (member ext org-roam-file-extensions))
+           (match-exclude-regexp-p
+            (cond
+             ((not org-roam-file-exclude-regexp) nil)
+             ((stringp org-roam-file-exclude-regexp)
+              (string-match-p org-roam-file-exclude-regexp relative-path))
+             ((listp org-roam-file-exclude-regexp)
+              (let (is-match)
+                (dolist (exclude-re org-roam-file-exclude-regexp)
+                  (setq is-match (or is-match (string-match-p exclude-re relative-path))))
+                is-match)))))
       (save-match-data
         (and
          path
-       (member ext org-roam-file-extensions)
+         org-roam-dir-p
-       (not (and org-roam-file-exclude-regexp
+         valid-file-ext-p
-                 (string-match-p org-roam-file-exclude-regexp path)))
+         (not match-exclude-regexp-p))))))
-       (f-descendant-of-p path (expand-file-name org-roam-directory))))))
 
+;;;###autoload
 (defun org-roam-list-files ()
   "Return a list of all Org-roam files under `org-roam-directory'.
 See `org-roam-file-p' for how each file is determined to be as
@@ -263,27 +296,29 @@ 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 #'s-present? it)))
+       (seq-filter (lambda (s)
+                     (not (or (null s) (string= "" s)))) it)))
 
 (defun org-roam--list-files-search-globs (exts)
   "Given EXTS, return a list of search globs.
 E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
   (cl-loop for e in exts
            append (list (format "\"*.%s\"" e)
-                        (format "\"*.%s.gpg\"" e))))
+                        (format "\"*.%s.gpg\"" e)
+                        (format "\"*.%s.age\"" e))))
 
 (defun org-roam--list-files-find (executable dir)
   "Return all Org-roam files under DIR, using \"find\", provided as EXECUTABLE."
   (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
-         (names (s-join " -o " (mapcar (lambda (glob) (concat "-name " glob)) globs)))
+         (names (string-join (mapcar (lambda (glob) (concat "-name " glob)) globs) " -o "))
-         (command (s-join " " `(,executable "-L" ,dir "-type f \\(" ,names "\\)"))))
+         (command (string-join `(,executable "-L" ,dir "-type f \\(" ,names "\\)") " ")))
     (org-roam--shell-command-files command)))
 
 (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 (s-join " -e " (mapcar (lambda (glob) (substring glob 2 -1)) globs)))
+         (extensions (string-join (mapcar (lambda (glob) (concat "-e " (substring glob 2 -1))) globs) " "))
-         (command (s-join " " `(,executable "-L" ,dir "--type file" ,extensions))))
+         (command (string-join `(,executable "-L" "--type file" ,extensions "." ,dir) " ")))
     (org-roam--shell-command-files command)))
 
 (defalias 'org-roam--list-files-fdfind #'org-roam--list-files-fd)
@@ -291,15 +326,18 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
 (defun org-roam--list-files-rg (executable dir)
   "Return all Org-roam files under DIR, using \"rg\", provided as EXECUTABLE."
   (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
-         (command (s-join " " `(,executable "-L" ,dir "--files"
+         (command (string-join `(
-                                            ,@(mapcar (lambda (glob) (concat "-g " glob)) globs)))))
+                                 ,executable "-L" ,dir "--files"
+                                 ,@(mapcar (lambda (glob) (concat "-g " glob)) globs)) " ")))
     (org-roam--shell-command-files command)))
 
+(declare-function org-roam--directory-files-recursively "org-roam-compat")
+
 (defun org-roam--list-files-elisp (dir)
   "Return all Org-roam files under DIR, using Elisp based implementation."
   (let ((regex (concat "\\.\\(?:"(mapconcat
                                   #'regexp-quote org-roam-file-extensions
-                                  "\\|" )"\\)\\(?:\\.gpg\\)?\\'"))
+                                  "\\|" )"\\)\\(?:\\.gpg\\|\\.age\\)?\\'"))
         result)
     (dolist (file (org-roam--directory-files-recursively dir regex nil nil t) result)
       (when (and (file-readable-p file)
@@ -310,10 +348,14 @@ E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
 (provide 'org-roam)
 
 (cl-eval-when (load eval)
+  (require 'org-roam-compat)
+  (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-log)
   (require 'org-roam-migrate))
 
 ;;; org-roam.el ends here

tests/roam-files/demoteable.org

@@ -0,0 +1,8 @@
+:PROPERTIES:
+:ID: 97bf31cf-dfee-45d8-87a5-2ae0dabc4734
+:END:
+#+title: Demoteable
+
+* Demoteable h1
+
+** Demoteable child

tests/roam-files/family.org

@@ -0,0 +1,19 @@
+:PROPERTIES:
+:ID: 998b2341-b7fe-434d-848c-5282c0727870
+:END:
+#+title: Family
+
+* Grand-Parent
+:PROPERTIES:
+:ID: 77a90980-1994-464e-901f-7e3d3df07fd3
+:END:
+
+** Parent
+:PROPERTIES:
+:ID: 0fa5bb3e-3d8c-4966-8bc9-78d32e505d69
+:END:
+
+*** Child
+:PROPERTIES:
+:ID: 5fb4fdc5-b6d2-4f75-8d54-e60053e467ec
+:END:

tests/roam-files/promoteable.org

@@ -0,0 +1,3 @@
+* Promoteable h1
+
+** Promoteable child

tests/roam-files/ref_with_space.org

@@ -0,0 +1,7 @@
+:PROPERTIES:
+:ROAM_REFS: "http://site.net/docs/01. introduction - hello world.html"
+:ID: 5b9a7400-f59c-4ef9-acbb-045b69af98f1
+:END:
+#+title: ref with space
+* Note
+hello

tests/roam-files/with-alias.org

@@ -0,0 +1,5 @@
+:PROPERTIES:
+:ID: 57ff3ce7-5bda-4825-8fca-c09f523e87ba
+:ROAM_ALIASES: Batman
+:END:
+#+title: Bruce Wayne

tests/roam-files/with-times.org

@@ -0,0 +1,16 @@
+:PROPERTIES:
+:ID: 9a20ca6c-5555-41c9-a039-ac38bf59c7a9
+:END:
+#+title: With Times
+
+* Scheduled heading
+SCHEDULED: <2024-07-16 Tue>
+:PROPERTIES:
+:ID: a523c198-4cb4-44d2-909c-a0e3258089cd
+:END:
+
+* Deadline heading
+DEADLINE: <2024-07-17 Tue>
+:PROPERTIES:
+:ID: 3ab84701-d1c1-463f-b5c6-715e6ff5a0bf
+:END:

tests/test-org-roam-capture.el

@@ -0,0 +1,63 @@
+;;; 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"))
+
+  (it "fills template without deleting newlines in its body"
+    (expect
+     (org-roam-capture--fill-template "foo\n\n\nbar\n\n")
+     :to-equal "foo\n\n\nbar\n\n"))
+
+  (it "expands templates when it's a function"
+    (expect
+     (org-roam-capture--fill-template (lambda () "foo"))
+     :to-equal "foo")))
+
+(provide 'test-org-roam-capture)
+
+;;; test-org-roam-capture.el ends here

tests/test-org-roam-db.el

@@ -0,0 +1,120 @@
+;;; test-org-roam-db.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)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-db-get-scheduled-time"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "should get scheduled time for current heading node"
+    (org-roam-id-open "a523c198-4cb4-44d2-909c-a0e3258089cd" nil)
+    (expect (org-roam-db-get-scheduled-time) :to-equal "2024-07-16T00:00:00")))
+
+(describe "org-roam-db-get-deadline-time"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "should get deadline time for current heading node"
+    (org-roam-id-open "3ab84701-d1c1-463f-b5c6-715e6ff5a0bf" nil)
+    (expect (org-roam-db-get-deadline-time) :to-equal "2024-07-17T00:00:00")))
+
+(describe "org-roam-db--file-hash"
+  (it "computes the SHA1 of file"
+    (expect (org-roam-db--file-hash "tests/roam-files/family.org")
+            :to-equal
+            "c4ebf8918c1533df72e4d182cbf1bbd90f776b3b")))
+
+(describe "org-roam-db-sync"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "has the correct number of files"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
+            :to-equal
+            9))
+
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
+            :to-equal
+            12))
+
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
+            :to-equal
+            1))
+
+  (it "respects ROAM_EXCLUDE"
+    ;; The excluded node has ID "53fadc75-f48e-461e-be06-44a1e88b2abe"
+    (expect (mapcar #'car (org-roam-db-query [:select id :from nodes]))
+            :to-have-same-items-as
+            '("884b2341-b7fe-434d-848c-5282c0727861"
+              "440795d0-70c1-4165-993d-aebd5eef7a24"
+              "5b9a7400-f59c-4ef9-acbb-045b69af98f1"
+              "0fa5bb3e-3d8c-4966-8bc9-78d32e505d69"
+              "5fb4fdc5-b6d2-4f75-8d54-e60053e467ec"
+              "77a90980-1994-464e-901f-7e3d3df07fd3"
+              "57ff3ce7-5bda-4825-8fca-c09f523e87ba"
+              "998b2341-b7fe-434d-848c-5282c0727870"
+              "a523c198-4cb4-44d2-909c-a0e3258089cd"
+              "3ab84701-d1c1-463f-b5c6-715e6ff5a0bf"
+              "9a20ca6c-5555-41c9-a039-ac38bf59c7a9"
+              "97bf31cf-dfee-45d8-87a5-2ae0dabc4734")))
+
+  (it "reads ref in quotes correctly"
+    (expect (mapcar #'car (org-roam-db-query [:select [ref] :from refs]))
+            :to-have-same-items-as
+            '("//site.net/docs/01. introduction - hello world.html"))))
+
+(provide 'test-org-roam-db)
+
+;;; test-org-roam-db.el ends here

tests/test-org-roam-id.el

@@ -0,0 +1,79 @@
+;;; test-org-roam-id.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)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-id-at-point"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "returns the correct node ids"
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam-id-at-point) :to-equal "998b2341-b7fe-434d-848c-5282c0727870")
+
+    (search-forward "Grand")
+    (expect (org-roam-id-at-point) :to-equal "77a90980-1994-464e-901f-7e3d3df07fd3")
+
+    (search-forward "Child")
+    (expect (org-roam-id-at-point) :to-equal "5fb4fdc5-b6d2-4f75-8d54-e60053e467ec")))
+
+(describe "org-roam-id-find"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "finds nothing for non-existing node"
+    (expect (org-roam-id-find "non-existing") :to-equal nil))
+
+  (it "finds the correct file node"
+    (let ((location (org-roam-id-find "884b2341-b7fe-434d-848c-5282c0727861")))
+      (expect (car location) :to-match ".*/tests/roam-files/foo.org")
+      (expect (cdr location) :to-equal 1)))
+
+  (it "finds the correct heading node"
+    (let ((location (org-roam-id-find "0fa5bb3e-3d8c-4966-8bc9-78d32e505d69")))
+      (expect (car location) :to-match ".*/tests/roam-files/family.org")
+      (expect (cdr location) :to-equal 156))))
+
+(provide 'test-org-roam-id)
+
+;;; test-org-roam-id.el ends here

tests/test-org-roam-mode.el

@@ -0,0 +1,39 @@
+;;; test-org-roam-mode.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-unlinked-references--rg-command"
+  (before-each
+    ;; the space in the directory is on purpose
+    (setq org-roam-directory "/tmp/org roam"))
+
+  (it "returns the correct rg command for unlinked references"
+    (expect (org-roam-unlinked-references--rg-command '("foo" "bar"))
+            :to-equal
+            "rg --follow --only-matching --vimgrep --pcre2 --ignore-case --glob \"*.org\" --glob \"*.org.gpg\" --glob \"*.org.age\" '\\[([^[]]++|(?R))*\\]|(\\bfoo\\b)|(\\bbar\\b)' /tmp/org\\ roam")))
+
+(provide 'test-org-roam-mode)
+
+;;; test-org-roam-mode.el ends here

tests/test-org-roam-node.el

@@ -0,0 +1,164 @@
+;;; test-org-roam-node.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)
+
+(defvar root-directory default-directory)
+
+(describe "org-roam-node-from-id"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns nil for unknown id"
+    (expect (org-roam-node-from-id "non-existing") :to-equal nil))
+
+  (it "returns correct node from id"
+    (let ((node (org-roam-node-from-id "884b2341-b7fe-434d-848c-5282c0727861")))
+      (expect (org-roam-node-title node) :to-equal "Foo"))))
+
+(describe "org-roam-node-from-title-or-alias"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns nil for unknown title"
+    (expect (org-roam-node-from-title-or-alias "non-existing") :to-equal nil))
+
+  (it "returns correct node from title"
+    (let ((node (org-roam-node-from-title-or-alias "Foo")))
+      (expect (org-roam-node-title node) :to-equal "Foo")))
+
+  (it "returns correct node from alias"
+    (let ((node (org-roam-node-from-title-or-alias "Batman")))
+      (expect (org-roam-node-title node) :to-equal "Bruce Wayne")))
+
+  (it "returns correct node from alias with nocase"
+    (let ((node (org-roam-node-from-title-or-alias "batman" t)))
+      (expect (org-roam-node-title node) :to-equal "Bruce Wayne"))))
+
+(describe "org-roam-demote-entire-buffer"
+  (after-each
+    (cd root-directory))
+
+  (it "demotes an entire org buffer"
+    (find-file "tests/roam-files/demoteable.org" nil)
+    (org-roam-demote-entire-buffer)
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal "* Demoteable\n:PROPERTIES:\n:ID: 97bf31cf-dfee-45d8-87a5-2ae0dabc4734\n:END:\n\n** Demoteable h1\n\n*** Demoteable child\n")))
+
+(describe "org-roam--h1-count"
+  (after-each
+    (cd root-directory))
+
+  (it "returns the correct number of level-1 headings"
+    (find-file "tests/roam-files/foo.org" nil)
+    (expect (org-roam--h1-count) :to-equal 0)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam--h1-count) :to-equal 1)))
+
+(describe "org-roam--buffer-promoteable-p"
+  (after-each
+    (cd root-directory))
+
+  (it "should check if buffer is promoteable"
+    (find-file "tests/roam-files/foo.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal nil)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal nil)
+
+    (cd root-directory)
+
+    (find-file "tests/roam-files/promoteable.org" nil)
+    (expect (org-roam--buffer-promoteable-p) :to-equal t)))
+
+(describe "org-roam--get-titles"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
+  (it "returns the list of titles and aliases"
+    (expect (org-roam--get-titles)
+            :to-have-same-items-as
+            `("Bar" "Batman" "Bruce Wayne" "Child" "Deadline heading" "Demoteable" "Family"
+              "Foo" "Grand-Parent" "Parent" "ref with space" "Scheduled heading" "With Times"))))
+
+
+(describe "org-roam-alias"
+  (before-all
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+          org-roam-file-extensions '("org")
+          org-roam-file-exclude-regexp nil)
+    (org-roam-db-sync))
+
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location)
+    (cd root-directory))
+
+  (it "adds an alias to a node"
+    (cd root-directory)
+    (find-file "tests/roam-files/foo.org" nil)
+    (org-roam-alias-add "qux")
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal ":PROPERTIES:\n:ID:       884b2341-b7fe-434d-848c-5282c0727861\n:ROAM_ALIASES: qux\n:END:\n#+title: Foo\n"))
+
+  (it "removes an alias from a node"
+    (cd root-directory)
+    (find-file "tests/roam-files/with-alias.org" nil)
+    (org-roam-alias-remove "Batman")
+    (expect (buffer-substring-no-properties (point) (point-max))
+            :to-equal ":PROPERTIES:\n:ID: 57ff3ce7-5bda-4825-8fca-c09f523e87ba\n:END:\n#+title: Bruce Wayne\n")))
+
+(provide 'test-org-roam-node)
+
+;;; test-org-roam-node.el ends here

tests/test-org-roam-utils.el

@@ -0,0 +1,64 @@
+;;; 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")))
+
+(describe "org-roam-db--file-title"
+  (it "supports normal titles"
+    (expect
+     (with-temp-buffer
+       (insert "#+title:normal title")
+       (org-roam-db--file-title))
+     :to-equal "normal title"))
+  (it "supports multi-line titles"
+    (expect
+     (with-temp-buffer
+       (insert "#+title: title:\n#+title: separated by newline")
+       (org-roam-db--file-title))
+     :to-equal "title: separated by newline"))
+  (it "supports file-name based titles"
+    (progn
+      (setq org-roam-directory temporary-file-directory
+            org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
+            org-roam-file-extensions '("org"))
+      (with-temp-buffer
+        (write-file (expand-file-name "test file.org" org-roam-directory))
+        (org-roam-db--file-title)))
+    :to-equal "test file"))
+
+(provide 'test-org-roam-utils)
+
+;;; test-org-roam-utils.el ends here

tests/test-org-roam.el

@@ -24,6 +24,28 @@
 (require 'buttercup)
 (require 'org-roam)
 
+(defvar root-directory default-directory)
+
+(describe "org-roam-file-p"
+  (it "checks if given file respects criteria"
+    (setq org-roam-directory "/non-existent")
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal nil)
+
+    (setq org-roam-directory (expand-file-name "tests/roam-files"))
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal t)
+    (expect (org-roam-file-p "tests/roam-files/markdown.md") :to-equal nil)
+
+    (setq org-roam-file-exclude-regexp (regexp-quote "family.org"))
+    (expect (org-roam-file-p "tests/roam-files/family.org") :to-equal nil)))
+
+(describe "org-roam-buffer-p"
+  (it "checks if current buffer respects criteria"
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-file-exclude-regexp nil)
+    (find-file "tests/roam-files/family.org" nil)
+    (expect (org-roam-buffer-p) :to-equal t)
+    (cd root-directory)))
+
 (describe "org-roam-list-files"
   (before-each
     (setq org-roam-directory (expand-file-name "tests/roam-files")
@@ -31,52 +53,29 @@
           org-roam-file-extensions '("org")
           org-roam-file-exclude-regexp nil))
 
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
+
   (it "gets files correctly"
-    (expect (length (org-roam-list-files))
+    (expect (length (org-roam-list-files)) :to-equal 9))
-            :to-equal 3))
 
   (it "respects org-roam-file-extensions"
     (setq org-roam-file-extensions '("md"))
     (expect (length (org-roam-list-files)) :to-equal 1)
     (setq org-roam-file-extensions '("org" "md"))
-    (expect (length (org-roam-list-files)) :to-equal 4))
+    (expect (length (org-roam-list-files)) :to-equal 10))
 
   (it "respects org-roam-file-exclude-regexp"
     (setq org-roam-file-exclude-regexp (regexp-quote "foo.org"))
-    (expect (length (org-roam-list-files)) :to-equal 2)))
+    (expect (length (org-roam-list-files)) :to-equal 8)))
 
-(describe "org-roam-db-sync"
+(describe "org-roam--list-files-search-globs"
-  (before-all
-    (setq org-roam-directory (expand-file-name "tests/roam-files")
-          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
-          org-roam-file-extensions '("org")
-          org-roam-file-exclude-regexp nil)
-    (org-roam-db-sync))
 
-  (after-all
+  (it "returns the correct list of globs"
-    (org-roam-db--close)
+    (expect (org-roam--list-files-search-globs org-roam-file-extensions)
-    (delete-file org-roam-db-location))
-
-  (it "has the correct number of files"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
-            :to-equal
-            3))
-
-  (it "has the correct number of nodes"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
-            :to-equal
-            2))
-
-  (it "has the correct number of links"
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
-            :to-equal
-            1))
-
-  (it "respects ROAM_EXCLUDE"
-    ;; The excluded node has ID "53fadc75-f48e-461e-be06-44a1e88b2abe"
-    (expect (mapcar #'car (org-roam-db-query [:select id :from nodes]))
             :to-have-same-items-as
-            '("884b2341-b7fe-434d-848c-5282c0727861" "440795d0-70c1-4165-993d-aebd5eef7a24"))))
+            '("\"*.org\"" "\"*.org.gpg\"" "\"*.org.age\""))))
 
 (provide 'test-org-roam)