update title to not truncate

Addresses #1488

.dir-locals.el

@@ -4,11 +4,7 @@
   (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)

.github/FUNDING.yml

@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: [jethrokuan]
+github: [jethrokuan, zaeph]
 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

@@ -39,3 +39,5 @@ 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:
-      - main
+      - master
 
 jobs:
   build:

.github/workflows/test.yml

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

.github/workflows/tidy-issues.yml

@@ -1,93 +0,0 @@
-name: 'Manage stale/dormant issues and PRs'
-
-on:
-  schedule:
-    - cron: '0 1 * * *'  # Daily at 1 AM UTC
-  workflow_dispatch:  # Allow this to be run manually
-    inputs:
-      dry_run:
-        description: 'Dry run: Show what would happen without making changes'
-        required: false
-        default: 'false'
-        type: boolean
-
-jobs:
-  stale:
-    runs-on: ubuntu-latest
-    steps:
-      # Handle stale issues/PRs
-      - name: Mark/close stale issues and PRs
-        uses: actions/stale@v9
-        with:
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-
-          # Dry run setting
-          debug-only: ${{ github.event.inputs.dry_run == 'true' }}
-
-          # Messages
-          stale-issue-message: |
-            📅 **Stale Issue Notice**
-
-            This issue has been automatically marked as stale because it has not had recent activity for **6 months**.
-
-            **⏰ This issue will be closed in 2 weeks** if no further activity occurs.
-
-            **To keep this issue open:**
-            - Comment on this issue
-            - Reference it in a commit or PR
-            - Add new information or updates
-
-            Thank you for your contributions to org-roam! 🙏
-
-          close-issue-message: |
-            🔒 **Issue Automatically Closed**
-
-            This issue was automatically closed due to **6 months of inactivity** followed by 2 weeks notice.
-
-            **To reopen:**
-            - If still relevant, comment below and we'll reopen
-            - Or create a new issue with updated information
-
-            If this issue is not reopened in 2 weeks, it will be locked.
-            
-            This helps keep our issue tracker focused and manageable.
-
-          stale-pr-message: |
-            📅 **Stale Pull Request Notice**
-
-            This pull request has been automatically marked as stale because it has not had recent activity for **6 months**.
-
-            **⏰ This PR will be closed in 2 weeks** if no further activity occurs.
-
-            **To keep this PR open:**
-            - Push new commits
-            - Comment with updates
-            - Rebase on latest main branch
-
-            Thank you for your contributions to org-roam! 🙏
-
-          close-pr-message: |
-            🔒 **Pull Request Automatically Closed**
-
-            This pull request was automatically closed due to **6 months of inactivity** followed by 2 weeks notice.
-
-          # Timing (6 months + 2 weeks)
-          days-before-stale: 182  # ~6 months
-          days-before-close: 14   # 2 weeks notice
-
-          # Performance
-          operations-per-run: 1000
-
-      # Show dry run summary
-      - name: Dry run summary
-        if: github.event.inputs.dry_run == 'true'
-        run: |
-          echo "🧪 DRY RUN COMPLETED"
-          echo "This was a dry run - no actual changes were made."
-          echo "Check the action logs above to see what would have happened."
-          echo ""
-          echo "To run for real:"
-          echo "1. Go to Actions tab"
-          echo "2. Click 'Run workflow'"
-          echo "3. Leave 'Dry run mode' unchecked"
-          echo "4. Click 'Run workflow'"

CHANGELOG.md

@@ -1,213 +1,9 @@
 # Changelog
 
-## 2.3.1 (2025-06-26)
+## 1.2.4 (TBD)
-
-* (fix): Use correct type specifications to suppress warnings by @okomestudio in https://github.com/org-roam/org-roam/pull/2522
-* perf: suppress extra org features in the temp buffer by @dustinfarris in https://github.com/org-roam/org-roam/pull/2524
-
-## 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`
-- [#1758](https://github.com/org-roam/org-roam/pull/1758) added `org-roam-db-autosync-mode`, replacing `org-roam-setup` and `org-roam-teardown`
-
-### Removed
-- [#1716](https://github.com/org-roam/org-roam/pull/1716) helper function `org-roam-get-keyword` is now obsolete: prefer `org-collect-keywords`
-
-### Changed
-- [#1595](https://github.com/org-roam/org-roam/pull/1595), [#1724](https://github.com/org-roam/org-roam/pull/1724) Major refactoring and restructuring of the codebase
-- [#1655](https://github.com/org-roam/org-roam/pull/1655) improved org-roam contents preview
-- [#1741](https://github.com/org-roam/org-roam/pull/1741) expose `org-roam-capture-` keys in interactive commands
-- [#1786](https://github.com/org-roam/org-roam/pull/1786) org-roam-version now outputs commit hash if found
-- [#1788](https://github.com/org-roam/org-roam/pull/1788) the point is not moved if the node is already visited
-
-### Fixed
-- [#1608](https://github.com/org-roam/org-roam/pull/1608) migration: empty ROAM_REFS are now removed
-- [#1609](https://github.com/org-roam/org-roam/pull/1609) migration: fixed file-link replacement
-- [#1653](https://github.com/org-roam/org-roam/pull/1653) migration: fixed tags migration
-- [#1694](https://github.com/org-roam/org-roam/pull/1694) core: nodes with no title are now skipped
-- [#1637](https://github.com/org-roam/org-roam/pull/1637) core: fix org-ref multi-cite links not being split
-- [#1651](https://github.com/org-roam/org-roam/pull/1651) core: fix org-roam-file-p crashing when there is no corresponding file
-- [#1705](https://github.com/org-roam/org-roam/pull/1705) core: fix for add/remove of file-level tags
-- [#1769](https://github.com/org-roam/org-roam/pull/1769) core: gracefully handle absence of `org-id-locations-file`
-- [#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 (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`.
 - [#1353](https://github.com/org-roam/org-roam/pull/1353) support file-level property drawers
@@ -215,8 +11,6 @@ A few symbols have been marked as obsolete. Have a look at the content of [org-r
 ### Changed
 
 - [#1352](https://github.com/org-roam/org-roam/pull/1352) prefer lower-case for roam_tag and roam_alias in interactive commands
-- [#1513](https://github.com/org-roam/org-roam/pull/1513) replaced hardcoded "svg" with defcustom org-roam-graph-filetype
-- [#1540](https://github.com/org-roam/org-roam/pull/1540) allow `roam_tag` and `roam_alias` to be specified on multiple lines
 
 ### Fixed
 
@@ -231,9 +25,8 @@ A few symbols have been marked as obsolete. Have a look at the content of [org-r
 - [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file
 - [#1403](https://github.com/org-roam/org-roam/issues/1403) fixed inconsistency between how we write and read props like alias and tags
 - [#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 (2020-11-13)
+## 1.2.3 (13-11-2020)
 
 Primarily a stabilization and bug-fix release.
 
@@ -264,7 +57,7 @@ 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 (2020-10-06)
+## 1.2.2 (06-10-2020)
 
 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`.
 
@@ -302,7 +95,7 @@ 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 (2020-07-27)
+## 1.2.1 (27-07-2020)
 
 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.
 
@@ -335,7 +128,7 @@ 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 (2020-06-12)
+## 1.2.0 (12-06-2020)
 
 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.
 
@@ -363,7 +156,7 @@ 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 (2020-05-18)
+## 1.1.1 (18-05-2020)
 
 In this release, we added two new features:
 
@@ -403,7 +196,7 @@ 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 (2020-04-21)
+## 1.1.0 (21-04-2020)
 
 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:
 
@@ -441,7 +234,7 @@ 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 (2020-03-23)
+## 1.0.0 (23-03-2020)
 
 Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
 been stable for the most part.
@@ -460,7 +253,7 @@ 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 (2020-03-06)
+## 1.0.0-rc1 (06-03-2020)
 
 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

@@ -33,180 +33,32 @@ solution for anyone already using Org-mode for their personal wiki.
 
 ## Installation
 
-Down below you will find basic installation instructions for how to quickly
+You can install `org-roam` using `package.el`:
-install `org-roam` using various environments for various purposes. For more
-detailed information, please read the [manual][docs].
-
-### Using `package.el`
-<details>
-<summary>Toggle instructions</summary>
-
-You can install `org-roam` from [MELPA](https://melpa.org/) or [MELPA
-Stable](https://stable.melpa.org/) using `package.el`:
 
 ```
 M-x package-install RET org-roam RET
 ```
-</details>
 
-### Using `straight.el`
+Here's a sample configuration with `use-package`:
-<details>
-<summary>Toggle instructions</summary>
-
-Installation from MELPA or MELPA Stable using `straight.el`:
-
-```emacs-lisp
-(straight-use-package 'org-roam)
-```
-
-Or with `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
-  :straight t
+      :ensure t
-  ...)
+      :hook
+      (after-init . org-roam-mode)
+      :custom
+      (org-roam-directory "/path/to/org-files/")
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n g" . org-roam-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
 ```
 
-If you need to install the package directly from the source repository, instead
+Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
-of from MELPA, the next sample shows how to do so:
+graph-related functionality. It is recommended to install PCRE-enabled ripgrep
-
+for better performance and extended functionality.
-```emacs-lisp
-(use-package org-roam
-  :straight (:host github :repo "org-roam/org-roam"
-             :files (:defaults "extensions/*"))
-  ...)
-```
-
-If you plan to use your own local fork for the development and contribution, the
-next sample will get you there:
-
-```emacs-lisp
-(use-package org-roam
-  :straight (:local-repo "/path/to/org-roam-fork"
-             :files (:defaults "extensions/*")
-             :build (:not compile))
-  ...)
-```
-</details>
-
-### Using Doom Emacs
-<details>
-<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
-`$DOOMDIR/init.el` (e.g. `(org +roam2)`), save the file and run `doom sync -u`
-in your shell.
-
-To provide better stability, Doom pins the package to a specific commit. If you
-need to unpin it *(not recommended doing that, request Doom to bump the package
-instead)* use the next in your `packages.el`:
-
-```emacs-lisp
-(unpin! org-roam)
-```
-
-If for some reasons you want to use a different recipe for `org-roam`, you can
-use the next form in your `packages.el` to install the package from a recipe
-repository (e.g. MELPA):
-
-```emacs-lisp
-(package! org-roam)
-```
-
-You can pass `:pin "commit hash"` to pin the package to a specific commit.
-
-With the next sample you can install the package directly from the source
-repository:
-
-```emacs-lisp
-(package! org-roam
-  :recipe (:host github :repo "org-roam/org-roam"
-           :files (:defaults "extensions/*")))
-```
-
-And if you plan to use your own local fork for the development or contribution,
-the next sample will get you there:
-
-```emacs-lisp
-(package! org-roam
-  :recipe (:local-repo "/path/to/org-roam-fork"
-           :files (:defaults "extensions/*")
-           :build (:not compile)))
-```
-</details>
-
-### Without a package manager
-<details>
-<summary>Toggle instructions</summary>
-
-To install the package without using a package manager you have the next two
-options:
-
-1. Install the package by cloning it with `git` from the source repository.
-2. Or install the package by downloading the latest [release
-   version](https://github.com/org-roam/org-roam/releases).
-   
-In both of the cases you will need to ensure that you have all the required
-dependencies. These include:
-
-- dash
-- f
-- s
-- org (9.6 is the minimum required version!)
-- emacsql
-- magit-section
-- filenotify-recursive
-
-After installing the package, you will need to properly setup `load-path` to the
-package:
-
-``` emacs-lisp
-(add-to-list 'load-path "/path/to/org-roam/")
-(add-to-list 'load-path "/path/to-org-roam/extensions/")
-```
-
-After which you should be able to resolve `(require 'org-roam)` call without any
-problems.
-
-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
-Crafters](https://www.youtube.com/c/SystemCrafters) has produced an introductory
-video that covers the basic commands:
-
-[![Getting Started with Org Roam - Build a Second Brain in Emacs](https://img.youtube.com/vi/AyhPmypHDEw/0.jpg)](https://www.youtube.com/watch?v=AyhPmypHDEw)
 
 ## Getting Help
 
@@ -227,9 +79,7 @@ it has not already been addressed on [GitHub][issues] or on
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-- [Alexey Shmalko](https://www.alexeyshmalko.com/)
+- [Alexey Shmalko](https://braindump.rasen.dev/)
-- [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
-- [Martin Edström](https://edstrom.dev/)
 
 ## Contributing
 
@@ -252,6 +102,6 @@ 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-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ
+[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
 [issues]: https://github.com/org-roam/org-roam/issues
 [faq]: https://www.orgroam.com/manual.html#FAQ

default.mk

@@ -44,17 +44,16 @@ HTMLDIRS  = $(PACKAGES)
 PDFFILES  = $(addsuffix .pdf,$(PACKAGES))
 EPUBFILES = $(addsuffix .epub,$(PACKAGES))
 
-ELS = org-roam.el
+ELS = org-roam-buffer.el
 ELS += org-roam-capture.el
 ELS += org-roam-compat.el
+ELS += org-roam-completion.el
+ELS += org-roam-dailies.el
 ELS += org-roam-db.el
-ELS += org-roam-mode.el
+ELS += org-roam.el
-ELS += org-roam-node.el
+ELS += org-roam-graph.el
-ELS += org-roam-utils.el
+ELS += org-roam-macs.el
-ELS += extensions/org-roam-dailies.el
+ELS += org-roam-protocol.el
-ELS += extensions/org-roam-graph.el
-ELS += extensions/org-roam-overlay.el
-ELS += extensions/org-roam-protocol.el
 ELCS = $(ELS:.el=.elc)
 ELMS = org-roam.el $(filter-out $(addsuffix .el,$(PACKAGES)),$(ELS))
 ELGS = org-roam-autoloads.el org-roam-version.el

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-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ">Slack</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>
           </ul>
       </div>
     </section>
@@ -116,8 +116,8 @@
         <div class="row">
           <a
             class="content footer-links"
-            href="https://github.com/org-roam/org-roam-ui"
+            href="https://github.com/org-roam/org-roam-server"
-            >org-roam-ui</a
+            >org-roam-server</a
           >
         </div>
       </div>
@@ -151,7 +151,7 @@
         <div class="row">
           <a
             class="content footer-links"
-            href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
             >Slack</a
           >
         </div>

extensions/org-roam-export.el

@@ -1,75 +0,0 @@
-;;; 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: 2.3.1
-;; 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

@@ -1,302 +0,0 @@
-;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- 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: 2.3.1
-;; 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 extension implements capability to build and generate graphs in Org-roam
-;; with the help of Graphviz.
-;;
-;;; Code:
-(require 'xml) ;xml-escape-string
-(require 'org-roam)
-
-;;; Options
-(defcustom org-roam-graph-viewer (executable-find "firefox")
-  "Method to view the org-roam graph.
-It may be one of the following:
-  - a string representing the path to the executable for viewing the graph.
-  - a function accepting a single argument: the graph file path.
-  - nil uses `view-file' to view the graph."
-  :type '(choice
-          (string   :tag "Path to executable")
-          (function :tag "Function to display graph" eww-open-file)
-          (const    :tag "view-file"))
-  :group 'org-roam)
-
-(defcustom org-roam-graph-executable "dot"
-  "Path to graphing executable, or its name."
-  :type 'string
-  :group 'org-roam)
-
-(defcustom org-roam-graph-filetype "svg"
-  "File type to generate when producing graphs."
-  :type 'string
-  :group 'org-roam)
-
-
-(defcustom org-roam-graph-extra-config nil
-  "Extra options passed to graphviz.
-Example:
- '((\"rankdir\" . \"LR\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-edge-extra-config nil
-  "Extra edge options passed to graphviz.
-Example:
- '((\"dir\" . \"back\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-node-extra-config
-  '(("id" . (("style"      . "bold,rounded,filled")
-             ("fillcolor"  . "#EEEEEE")
-             ("color"      . "#C9C9C9")
-             ("fontcolor"  . "#111111")))
-    ("http" . (("style"      . "rounded,filled")
-               ("fillcolor"  . "#EEEEEE")
-               ("color"      . "#C9C9C9")
-               ("fontcolor"  . "#0A97A6")))
-    ("https" . (("style"      . "rounded,filled")
-                ("fillcolor"  . "#EEEEEE")
-                ("color"      . "#C9C9C9")
-                ("fontcolor"  . "#0A97A6"))))
-  "Extra options for graphviz nodes."
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-link-hidden-types
-  '("file")
-  "What sort of links to hide from the Org-roam graph."
-  :type '(repeat string)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-max-title-length 100
-  "Maximum length of titles in graph nodes."
-  :type 'number
-  :group 'org-roam)
-
-(defcustom org-roam-graph-shorten-titles 'truncate
-  "Determines how long titles appear in graph nodes.
-Recognized values are the symbols `truncate' and `wrap', in which
-cases the title will be truncated or wrapped, respectively, if it
-is longer than `org-roam-graph-max-title-length'.
-
-All other values including nil will have no effect."
-  :type '(choice
-          (const :tag "truncate" truncate)
-          (const :tag "wrap" wrap)
-          (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)
-  "Build and possibly display a graph for NODE.
-ARG may be any of the following values:
-  - nil       show the graph.
-  - `\\[universal-argument]'     show the graph for NODE.
-  - `\\[universal-argument]' N   show the graph for NODE limiting nodes to N steps."
-  (interactive
-   (list current-prefix-arg
-         (and current-prefix-arg
-              (org-roam-node-at-point 'assert))))
-  (let ((graph (cl-typecase arg
-                 (null (org-roam-graph--dot nil 'all-nodes))
-                 (cons (org-roam-graph--dot (org-roam-graph--connected-component
-                                             (org-roam-node-id node) 0)))
-                 (integer (org-roam-graph--dot (org-roam-graph--connected-component
-                                                (org-roam-node-id node) (abs arg)))))))
-    (org-roam-graph--build graph #'org-roam-graph--open)))
-
-;;; Generation and Build process
-(defun org-roam-graph--build (graph &optional callback)
-  "Generate the GRAPH, and execute CALLBACK when process exits successfully.
-CALLBACK is passed the graph file as its sole argument."
-  (unless (stringp org-roam-graph-executable)
-    (user-error "`org-roam-graph-executable' is not a string"))
-  (unless (executable-find org-roam-graph-executable)
-    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
-                        "Please adjust `org-roam-graph-executable'")
-                org-roam-graph-executable))
-  (let* ((temp-dot   (make-temp-file "graph." nil ".dot" graph))
-         (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
-    (org-roam-message "building graph")
-    (make-process
-     :name "*org-roam-graph*"
-     :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))
-                     (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.
-If ALL-NODES, include also nodes without edges."
-  (let ((org-roam-directory-temp org-roam-directory)
-        (nodes-table (make-hash-table :test #'equal))
-        (seen-nodes (list))
-        (edges (or edges (org-roam-db-query [:select :distinct [source dest type] :from links]))))
-    (pcase-dolist (`(,id ,file ,title)
-                   (org-roam-db-query [:select [id file title] :from nodes]))
-      (puthash id (org-roam-node-create :file file :id id :title title) nodes-table))
-    (with-temp-buffer
-      (setq-local org-roam-directory org-roam-directory-temp)
-      (insert "digraph \"org-roam\" {\n")
-      (dolist (option org-roam-graph-extra-config)
-        (insert (org-roam-graph--dot-option option) ";\n"))
-      (insert (format " edge [%s];\n"
-                      (mapconcat (lambda (var)
-                                   (org-roam-graph--dot-option var nil "\""))
-                                 org-roam-graph-edge-extra-config
-                                 ",")))
-      (pcase-dolist (`(,source ,dest ,type) edges)
-        (unless (member type org-roam-graph-link-hidden-types)
-          (pcase-dolist (`(,node ,node-type) `((,source "id")
-                                               (,dest ,type)))
-            (unless (member node seen-nodes)
-              (insert (org-roam-graph--format-node
-                       (or (gethash node nodes-table) node) node-type))
-              (push node seen-nodes)))
-          (insert (format "  \"%s\" -> \"%s\";\n"
-                          (xml-escape-string source)
-                          (xml-escape-string dest)))))
-      (when all-nodes
-        (maphash (lambda (id node)
-                   (unless (member id seen-nodes)
-                     (insert (org-roam-graph--format-node node "id"))))
-                 nodes-table))
-      (insert "}")
-      (buffer-string))))
-
-(defun org-roam-graph--connected-component (id distance)
-  "Return the edges for all nodes reachable from/connected to ID.
-DISTANCE is the maximum distance away from the root node."
-  (let* ((query
-          (if (= distance 0)
-              "
-WITH RECURSIVE
-  links_of(source, dest) AS
-  (SELECT source, dest FROM links UNION
-   SELECT dest, source FROM links),
-   connected_component(source) AS
-  (SELECT dest FROM links_of WHERE source = $s1 UNION
-   SELECT dest FROM links_of JOIN connected_component USING(source))
-SELECT DISTINCT source, dest, type FROM links
-WHERE source IN connected_component OR dest IN connected_component;"
-            "
-WITH RECURSIVE
-  links_of(source, dest) AS
-  (SELECT source, dest FROM links UNION
-   SELECT dest, source FROM links),
-  connected_component(source, trace) AS
-  (VALUES ($s1 , json_array($s1)) UNION
-   SELECT lo.dest, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.dest) FROM
-   connected_component AS cc JOIN links_of AS lo USING(source)
-   WHERE (
-    -- Avoid cycles by only visiting each node once.
-    (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.dest) == 0
-    -- Note: BFS is cut off early here.
-    AND json_array_length(cc.trace) < $s2)),
-  nodes(source) as (SELECT DISTINCT source
-   FROM connected_component GROUP BY source ORDER BY min(json_array_length(trace)))
-SELECT DISTINCT source, dest, type FROM links WHERE source IN nodes OR dest IN nodes;")))
-    (org-roam-db-query query id distance)))
-
-(defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
-  "Return dot string of form KEY=VAL for OPTION cons.
-If WRAP-KEY is non-nil it wraps the KEY.
-If WRAP-VAL is non-nil it wraps the VAL."
-  (concat wrap-key (car option) wrap-key
-          "="
-          wrap-val (cdr option) wrap-val))
-
-(defun org-roam-graph--format-node (node type)
-  "Return a graphviz NODE with TYPE.
-Handles both Org-roam nodes, and string nodes (e.g. urls)."
-  (let (node-id node-properties)
-    (if (org-roam-node-p node)
-        (let* ((title (org-roam-quote-string (org-roam-node-title node)))
-               (shortened-title
-                (org-roam-quote-string
-                 (pcase org-roam-graph-shorten-titles
-                   (`truncate (truncate-string-to-width title org-roam-graph-max-title-length nil nil "..."))
-                   (`wrap (org-roam-word-wrap org-roam-graph-max-title-length title))
-                   (_ title)))))
-          (setq node-id (org-roam-node-id node)
-                node-properties `(("label"   . ,shortened-title)
-                                  ("URL"     . ,(funcall org-roam-graph-link-builder node))
-                                  ("tooltip" . ,(xml-escape-string title)))))
-      (setq node-id node
-            node-properties (append `(("label" . ,(concat type ":" node)))
-                                    (when (member type (list "http" "https"))
-                                      `(("URL" . ,(xml-escape-string (concat type ":" node))))))))
-    (format "\"%s\" [%s];\n"
-            node-id
-            (mapconcat (lambda (n)
-                         (org-roam-graph--dot-option n nil "\""))
-                       (append (cdr (assoc type org-roam-graph-node-extra-config))
-                               node-properties) ","))))
-
-(defun org-roam-graph--open (file)
-  "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
-  (pcase org-roam-graph-viewer
-    ((pred stringp)
-     (if (executable-find org-roam-graph-viewer)
-         (condition-case err
-             (call-process org-roam-graph-viewer nil 0 nil file)
-           (error (user-error "Failed to open org-roam graph: %s" err)))
-       (user-error "Executable not found: \"%s\"" org-roam-graph-viewer)))
-    ((pred functionp) (funcall org-roam-graph-viewer file))
-    ('nil (view-file file))
-    (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
-
-
-(provide 'org-roam-graph)
-
-;;; org-roam-graph.el ends here

extensions/org-roam-overlay.el

@@ -1,96 +0,0 @@
-;;; org-roam-overlay.el --- Link overlay for [id:] links to Org-roam nodes -*- 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: 2.3.1
-;; 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 extension allows to render [[id:]] links that don't have an associated
-;; descriptor with an overlay that displays the node's current title.
-;;
-;;; Code:
-(require 'org-roam)
-
-(defface org-roam-overlay
-  '((((class color) (background light))
-     :background "grey90" :box (:line-width -1 :color "black"))
-    (((class color) (background dark))
-     :background "grey10" :box (:line-width -1 :color "white")))
-  "Face for the Org-roam overlay."
-  :group 'org-roam-faces)
-
-(defun org-roam-overlay--make (l r &rest props)
-  "Make an overlay from L to R with PROPS."
-  (let ((o (make-overlay l (or r l))))
-    (overlay-put o 'category 'org-roam)
-    (while props (overlay-put o (pop props) (pop props)))
-    o))
-
-(defun org-roam-overlay-make-link-overlay (link)
-  "Create overlay for LINK."
-  (save-excursion
-    (save-match-data
-      (let* ((type (org-element-property :type link))
-             (id (org-element-property :path link))
-             (pos (org-element-property :end link))
-             (desc-p (org-element-property :contents-begin link))
-             node)
-        (when (and (string-equal type "id")
-                   (setq node (org-roam-node-from-id id))
-                   (not desc-p))
-          (org-roam-overlay--make
-           pos pos
-           'after-string (format "%s "
-                                 (propertize (org-roam-node-title node)
-                                             'face 'org-roam-overlay))))))))
-
-(defun org-roam-overlay-enable ()
-  "Enable Org-roam overlays."
-  (org-roam-db-map-links
-   (list #'org-roam-overlay-make-link-overlay)))
-
-(defun org-roam-overlay-disable ()
-  "Disable Org-roam overlays."
-  (remove-overlays nil nil 'category 'org-roam))
-
-(defun org-roam-overlay-redisplay ()
-  "Redisplay Org-roam overlays."
-  (org-roam-overlay-disable)
-  (org-roam-overlay-enable))
-
-(define-minor-mode org-roam-overlay-mode
-  "Overlays for Org-roam ID links.
-Org-roam overlay mode is a minor mode.  When enabled,
-overlay displaying the node's title is displayed."
-  :lighter " org-roam-overlay"
-  (if org-roam-overlay-mode
-      (progn
-        (org-roam-overlay-enable)
-        (add-hook 'after-save-hook #'org-roam-overlay-redisplay nil t))
-    (org-roam-overlay-disable)
-    (remove-hook 'after-save-hook #'org-roam-overlay-redisplay t)))
-
-(provide 'org-roam-overlay)
-;;; org-roam-overlay.el ends here

extensions/org-roam-protocol.el

@@ -1,174 +0,0 @@
-;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- 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: 2.3.1
-;; 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 extension extends `org-protocol', adding custom Org-roam handlers to it
-;; to provide the next new protocols:
-;;
-;; 1. "roam-node": This protocol simply opens the node given by the node ID
-;; 2. "roam-ref": This protocol creates or opens the node with the given REF
-;;
-;; You can find detailed instructions on how to setup the protocol in the
-;; documentation for Org-roam.
-;;
-;;; Code:
-(require 'org-protocol)
-(require 'ol) ;; for org-link-decode
-(require 'org-roam)
-
-;;; Options
-(defcustom org-roam-protocol-store-links nil
-  "Whether to store links when capturing websites with `org-roam-protocol'."
-  :type 'boolean
-  :group 'org-roam)
-
-(defcustom org-roam-capture-ref-templates
-  '(("r" "ref" plain "%?"
-     :target (file+head "${slug}.org"
-                        "#+title: ${title}")
-     :unnarrowed t))
-  "The Org-roam templates used during a capture from the roam-ref protocol.
-See `org-roam-capture-templates' for the template documentation."
-  :group 'org-roam
-  :type '(repeat
-          (choice (list :tag "Multikey description"
-                        (string :tag "Keys       ")
-                        (string :tag "Description"))
-                  (list :tag "Template entry"
-                        (string :tag "Keys           ")
-                        (string :tag "Description    ")
-                        (choice :tag "Capture Type   " :value entry
-                                (const :tag "Org entry" entry)
-                                (const :tag "Plain list item" item)
-                                (const :tag "Checkbox item" checkitem)
-                                (const :tag "Plain text" plain)
-                                (const :tag "Table line" table-line))
-                        (choice :tag "Template       "
-                                (string)
-                                (list :tag "File"
-                                      (const :format "" file)
-                                      (file :tag "Template file"))
-                                (list :tag "Function"
-                                      (const :format "" function)
-                                      (function :tag "Template function")))
-                        (plist :inline t
-                               ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :target)
-                                          (choice :tag "Node location"
-                                                  (list :tag "File"
-                                                        (const :format "" file)
-                                                        (string :tag "  File"))
-                                                  (list :tag "File & Head Content"
-                                                        (const :format "" file+head)
-                                                        (string :tag "  File")
-                                                        (string :tag "  Head Content"))
-                                                  (list :tag "File & Outline path"
-                                                        (const :format "" file+olp)
-                                                        (string :tag "  File")
-                                                        (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))
-                                                  (list :tag "File & Head Content & Outline path"
-                                                        (const :format "" file+head+olp)
-                                                        (string :tag "  File")
-                                                        (string :tag "  Head Content")
-                                                        (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))))
-                                         ((const :format "%v " :prepend) (const t))
-                                         ((const :format "%v " :immediate-finish) (const t))
-                                         ((const :format "%v " :jump-to-captured) (const t))
-                                         ((const :format "%v " :empty-lines) (const 1))
-                                         ((const :format "%v " :empty-lines-before) (const 1))
-                                         ((const :format "%v " :empty-lines-after) (const 1))
-                                         ((const :format "%v " :clock-in) (const t))
-                                         ((const :format "%v " :clock-keep) (const t))
-                                         ((const :format "%v " :clock-resume) (const t))
-                                         ((const :format "%v " :time-prompt) (const t))
-                                         ((const :format "%v " :tree-type) (const week))
-                                         ((const :format "%v " :unnarrowed) (const t))
-                                         ((const :format "%v " :table-line-pos) (string))
-                                         ((const :format "%v " :kill-buffer) (const t))))))))
-
-;;; Handlers
-(defun org-roam-protocol-open-ref (info)
-  "Process an org-protocol://roam-ref?ref= style url with INFO.
-
-It opens or creates a note with the given ref.
-
-  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
-        encodeURIComponent(location.href) + \\='&title=\\=' + \\
-        encodeURIComponent(document.title) + \\='&body=\\=' + \\
-        encodeURIComponent(window.getSelection())"
-  (unless (plist-get info :ref)
-    (user-error "No ref key provided"))
-  (org-roam-plist-map! (lambda (k v)
-                         (org-link-decode
-                          (if (equal k :ref)
-                              (org-protocol-sanitize-uri v)
-                            v))) info)
-  (when org-roam-protocol-store-links
-    (push (list (plist-get info :ref)
-                (plist-get info :title)) org-stored-links))
-  (org-link-store-props :type (and (string-match org-link-plain-re
-                                                 (plist-get info :ref))
-                                   (match-string 1 (plist-get info :ref)))
-                        :link (plist-get info :ref)
-                        :annotation (org-link-make-string (plist-get info :ref)
-                                                          (or (plist-get info :title)
-                                                              (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))
-  nil)
-
-(defun org-roam-protocol-open-node (info)
-  "This handler simply opens the file with emacsclient.
-
-INFO is a plist containing additional information passed by the protocol URL.
-It should contain the FILE key, pointing to the path of the file to open.
-
-  Example protocol string:
-
-org-protocol://roam-node?node=uuid"
-  (when-let ((node (plist-get info :node)))
-    (raise-frame)
-    (org-roam-node-visit (org-roam-populate (org-roam-node-create :id node)) nil 'force))
-  nil)
-
-(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
-      org-protocol-protocol-alist)
-(push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
-      org-protocol-protocol-alist)
-
-(provide 'org-roam-protocol)
-
-;;; org-roam-protocol.el ends here

github-eldev

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

org-roam-capture.el

@@ -1,12 +1,12 @@
 ;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,20 +27,38 @@
 
 ;;; Commentary:
 ;;
-;; This module provides `org-capture' functionality for Org-roam. With this
+;; This library provides capture functionality for org-roam
-;; module the user can capture new nodes or capture new content to existing
-;; nodes.
-;;
 ;;; Code:
-(require 'org-roam)
+;;;
+;;;; Library Requires
+(require 'org-capture)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'org-roam-db)
+(require 'dash)
+(require 'cl-lib)
 
-;;;; Declarations
+;; Declarations
-(defvar org-end-time-was-given)
+(declare-function org-roam-ref-add "org-roam" (ref))
+
+(defvar org-roam-directory)
+
+(defvar org-roam-capture--node nil
+  "The node passed during an Org-roam capture.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defvar org-roam-capture--info nil
+  "A property-list of additional information passed to the Org-roam template.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defconst org-roam-capture--template-keywords '(:if-new :id :link-description :call-location)
+  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
 
-;;; Options
 (defcustom org-roam-capture-templates
   '(("d" "default" plain "%?"
-     :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+     :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
                         "#+title: ${title}\n")
      :unnarrowed t))
   "Templates for the creation of new entries within Org-roam.
@@ -92,45 +110,25 @@ 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 :target property. The :target property
+The template contains a compulsory :if-new property. This determines the
-contains a list, where:
+location of the new node. The :if-new property contains a list, supporting
-  - The first element indicates the type of the target.
+the following options:
-  - 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 if the node is a newly captured one.
+       inserted into the file.
 
-   (file+olp \"path/to/file\" (\"h1\" \"h2\"))
+   (file+olp \"path/to/file\" '(\"h1\" \"h2\"))
-       The file will be created, prescribed an ID. If the file doesn't contain
+       The file will be created, prescribed an ID. The OLP (h1, h2) will be
-       the outline path (h1, h2), it will be automatically created. The point
+       created, and the point placed after.
-       will be adjusted to the last element in the OLP.
 
-   (file+head+olp \"path/to/file\" \"head content\" (\"h1\" \"h2\"))
+   (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 if the node is a newly captured one.
+       inserted at the start of the file. The OLP (h1, h2) will be created,
-       If the file doesn't contain the outline path (h1, h2), it will be
+       and the point placed after.
-       automatically created. The point will be adjusted to the last element in
-       the OLP.
-
-   (file+datetree \"path/to/file\" tree-type)
-       The file will be created, prescribed an ID. A date based outline path
-       will be created for today's date. The tree-type can be one of the
-       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
-       title, alias or ID.
 
 The rest of the entry is a property list of additional options.  Recognized
 properties are:
@@ -205,8 +203,7 @@ 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
+  %<...>      The result of `format-time-string' on the ... format specification.
-              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.
@@ -301,7 +298,7 @@ streamlined user experience in Org-roam."
                                       (function :tag "Template function")))
                         (plist :inline t
                                ;; Give the most common options as checkboxes
-                               :options (((const :format "%v " :target)
+                               :options (((const :format "%v " :if-new)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -314,13 +311,13 @@ streamlined user experience in Org-roam."
                                                         (const :format "" file+olp)
                                                         (string :tag "  File")
                                                         (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))
+                                                              (repeat string :tag "Headline")))
                                                   (list :tag "File & Head Content & Outline path"
                                                         (const :format "" file+head+olp)
                                                         (string :tag "  File")
                                                         (string :tag "  Head Content")
                                                         (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))))
+                                                              (repeat string :tag "Headline")))))
                                          ((const :format "%v " :prepend) (const t))
                                          ((const :format "%v " :immediate-finish) (const t))
                                          ((const :format "%v " :jump-to-captured) (const t))
@@ -336,106 +333,77 @@ streamlined user experience in Org-roam."
                                          ((const :format "%v " :table-line-pos) (string))
                                          ((const :format "%v " :kill-buffer) (const t))))))))
 
-(defcustom org-roam-capture-new-node-hook nil
+(defvar org-roam-capture-new-node-hook (list #'org-roam-capture--insert-ref)
   "Normal-mode hooks run when a new Org-roam node is created.
 The current point is the point of the new node.
-The hooks must not move the point."
+The hooks must not move the point.")
+
+(defcustom org-roam-capture-ref-templates
+  '(("r" "ref" plain "%?"
+     :if-new (file+head "${slug}.org"
+                        "#+title: ${title}")
+     :unnarrowed t))
+  "The Org-roam templates used during a capture from the roam-ref protocol.
+See `org-roam-capture-templates' for the template documentation."
   :group 'org-roam
-  :type 'hook)
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
 
-(defvar org-roam-capture-preface-hook nil
-  "Hook run when Org-roam tries to determine capture location of the node.
-If any hook returns a value (which should be an ID), all hooks
-after it are ignored.
-
-With this hook you can hijack controls over the location of the
-node for which the capture process is currently running for, or
-use to just perform an arbitrary side effect, e.g. modify the
-state related to the capture process. See `org-roam-protocol' and
-`org-roam-dailies' as examples for what and how this hook is used
-for.
-
-If you're trying to perform the hijack, it's mandatory for you to:
-  1. Set the currently active buffer for editing operations using
-     `org-capture-target-buffer'.
-  2. Place the point in this buffer from where the location starts
-     from (e.g. if it's a file based node it should be the BOB,
-     otherwise it should be the position from where the heading
-     based node starts from).
-  3. Return the ID (as a string) of the capturing node.
-
-If you use this hook for any other purpose, but not the hijack,
-it's mandatory that you should return nil as the return value; so
-the capture process would be able to setup the capture buffer.
-
-If you need to do something when you capture new nodes, use
-`org-roam-capture-new-node-hook' instead of this hook.
-
-WARNING: This hook is primarily designed for the usage by the
-extensions and packages, and requires understanding of the
-internal capture process. If you don't understand it, you should
-learn these internals before using this or use it at your own
-risk breaking things.")
-
-;;; Variables
-
-(defvar org-roam-capture--node nil
-  "The node passed during an Org-roam capture.
-This variable is populated dynamically, and is only non-nil
-during the Org-roam capture process.")
-
-(defvar org-roam-capture--info nil
-  "A property-list of additional information passed to the Org-roam template.
-This variable is populated dynamically, and is only non-nil
-during the Org-roam capture process.")
-
-(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.")
-
-;;; Main entry point
-;;;###autoload
-(cl-defun org-roam-capture- (&key goto keys node info props templates)
-  "Main entry point of `org-roam-capture' module.
-GOTO and KEYS correspond to `org-capture' arguments.
-INFO is a plist for filling up Org-roam's capture templates.
-NODE is an `org-roam-node' construct containing information about the node.
-PROPS is a plist containing additional Org-roam properties for each template.
-TEMPLATES is a list of org-roam templates."
-  (let* ((props (plist-put props :call-location (point-marker)))
-         (org-capture-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)
-               (= (length org-capture-templates) 1))
-      (setq keys (caar org-capture-templates)))
-    (org-capture goto keys)))
-
-;;;###autoload
-(cl-defun org-roam-capture (&optional goto keys &key filter-fn templates info)
-  "Launches an `org-capture' process for a new or existing node.
-This uses the templates defined at `org-roam-capture-templates'.
-Arguments GOTO and KEYS see `org-capture'.
-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.
-The TEMPLATES, if provided, override the list of capture templates (see
-`org-roam-capture-'.)
-The INFO, if provided, is passed along to the underlying `org-roam-capture-'."
-  (interactive "P")
-  (let ((node (org-roam-node-read nil filter-fn)))
-    (org-roam-capture- :goto goto
-                       :info info
-                       :keys keys
-                       :templates templates
-                       :node node
-                       :props '(:immediate-finish nil))))
-
-;;; Capture process
 (defun org-roam-capture-p ()
   "Return t if the current capture process is an Org-roam capture.
 This function is to only be called when `org-capture-plist' is
@@ -447,160 +415,153 @@ 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 (prop value)
+(defun org-roam-capture--put (&rest stuff)
-  "Set property PROP to VALUE in the `org-roam-capture-template'."
+  "Put properties from STUFF into 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
+          (plist-put org-capture-plist :org-roam p))))
-                     :org-roam
-                     (plist-put p prop value)))))
 
-;;;; Capture target
+;; FIXME: Pending upstream patch
-(defun org-roam-capture--prepare-buffer ()
+;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
-  "Prepare the capture buffer for the current Org-roam based capture template.
+;;
-This function will initialize and setup the capture buffer,
+;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
-position the point to the current :target (and if necessary,
+;; during the initialization of the Org-capture buffer. The value of
-create it if it doesn't exist), and place the point for further
+;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
-processing by `org-capture'.
+;; However, the value for that particular capture is no longer accessible for
+;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
+;; cleaned up.
+;;
+;; This advice restores the global `org-capture-plist' during finalization, so
+;; the plist is valid during both initialization and finalization of the
+;; capture.
+(defun org-roam-capture--update-plist (&optional _)
+  "Update global plist from local var."
+  (setq org-capture-plist org-capture-current-plist))
 
-Note: During the capture process this function is run by
+(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
-`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))
-                  (t (org-roam-capture--setup-target-location)))))
-    (org-roam-capture--adjust-point-for-capture-type)
-    (let ((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)))))
 
-(defun org-roam-capture--setup-target-location ()
+(defun org-roam-capture--finalize-find-file ()
+  "Visit the buffer after Org-capture is done.
+This function is to be called in the Org-capture finalization process.
+ID is unused."
+  (switch-to-buffer (org-capture-get :buffer)))
+
+(defun org-roam-capture--finalize-insert-link ()
+  "Insert a link to ID into the buffer where Org-capture was called.
+ID is the Org id of the newly captured content.
+This function is to be called in the Org-capture finalization process."
+  (when-let* ((mkr (org-roam-capture--get :call-location))
+              (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))
+      (org-with-point-at mkr
+        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
+                                      (org-roam-capture--get :link-description)))))))
+
+(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)))
+  (unless org-note-abort
+    (when-let ((finalize (org-roam-capture--get :finalize)))
+      (funcall (intern (concat "org-roam-capture--finalize-"
+                               (symbol-name (org-roam-capture--get :finalize)))))))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
+
+(defun org-roam-capture--install-finalize ()
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
+  (when (org-roam-capture-p)
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
+
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
+
+(defun org-roam-capture--fill-template (template &optional org-capture-p)
+  "Expand TEMPLATE and return it.
+It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+also run Org-capture's template expansion."
+  (funcall (if org-capture-p #'org-capture-fill-template #'identity)
+           (org-roam-format
+            template
+            (lambda (key)
+              (let ((fn (intern (concat "org-roam-node-" key)))
+                    (ksym (intern (concat ":" key))))
+                (cond
+                 ((fboundp fn)
+                  (funcall 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)))
+                      (plist-put org-roam-capture--info ksym r)
+                      r))))))))
+
+(defun org-roam-capture--insert-ref ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
+(defun org-roam-capture--goto-location ()
   "Initialize the buffer, and goto the location of the new capture.
 Return the ID of the location."
-  (let (p new-file-p)
+  (let (p)
-    (pcase (org-roam-capture--get-target)
+    (pcase (or (org-roam-capture--get :if-new)
+               (user-error "Template needs to specify `:if-new'"))
       (`(file ,path)
-       (setq path (org-roam-capture--target-truepath path)
+       (setq path (expand-file-name
-             new-file-p (org-roam-capture--new-file-p path))
+                   (string-trim (org-roam-capture--fill-template path t))
-       (when new-file-p (org-roam-capture--put :new-file path))
+                   org-roam-directory))
        (set-buffer (org-capture-target-buffer path))
        (widen)
-       (setq p (goto-char (point-min))))
+       (setq p (point)))
       (`(file+olp ,path ,olp)
-       (setq path (org-roam-capture--target-truepath path)
+       (setq path (expand-file-name
-             new-file-p (org-roam-capture--new-file-p path))
+                   (string-trim (org-roam-capture--fill-template path t))
-       (when new-file-p (org-roam-capture--put :new-file path))
+                   org-roam-directory))
        (set-buffer (org-capture-target-buffer path))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m))
        (widen))
       (`(file+head ,path ,head)
-       (setq path (org-roam-capture--target-truepath path)
+       (setq path (expand-file-name
-             new-file-p (org-roam-capture--new-file-p path))
+                   (string-trim (org-roam-capture--fill-template path t))
-       (set-buffer (org-capture-target-buffer path))
+                   org-roam-directory))
-       (when new-file-p
+       (let ((exists-p (file-exists-p path)))
-         (org-roam-capture--put :new-file path)
+         (set-buffer (org-capture-target-buffer path))
-         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+         (unless exists-p
+           (insert (org-roam-capture--fill-template head t))))
        (widen)
-       (setq p (goto-char (point-min))))
+       (setq p (point-min)))
       (`(file+head+olp ,path ,head ,olp)
-       (setq path (org-roam-capture--target-truepath path)
+       (setq path (expand-file-name
-             new-file-p (org-roam-capture--new-file-p path))
+                   (string-trim (org-roam-capture--fill-template path t))
-       (set-buffer (org-capture-target-buffer path))
+                   org-roam-directory))
        (widen)
-       (when new-file-p
+       (let ((exists-p (file-exists-p path)))
-         (org-roam-capture--put :new-file path)
+         (set-buffer (org-capture-target-buffer path))
-         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+         (unless exists-p
+           (insert (org-roam-capture--fill-template head t))))
        (setq p (point-min))
        (let ((m (org-roam-capture-find-or-create-olp olp)))
          (goto-char m)))
-      (`(file+datetree ,path ,tree-type)
-       (setq path (org-roam-capture--target-truepath path))
-       (require 'org-datetree)
-       (widen)
-       (set-buffer (org-capture-target-buffer path))
-       (unless (file-exists-p path)
-         (org-roam-capture--put :new-file path))
-       (funcall
-        (pcase tree-type
-          (`week #'org-datetree-find-iso-week-create)
-          (`month #'org-datetree-find-month-create)
-          (_ #'org-datetree-find-date-create))
-        (calendar-gregorian-from-absolute
-         (cond
-          (org-overriding-default-time
-           ;; Use the overriding default time.
-           (time-to-days org-overriding-default-time))
-          ((org-capture-get :default-time)
-           (time-to-days (org-capture-get :default-time)))
-          ((org-capture-get :time-prompt)
-           ;; Prompt for date.  Bind `org-end-time-was-given' so
-           ;; that `org-read-date-analyze' handles the time range
-           ;; case and returns `prompt-time' with the start value.
-           (let* ((org-time-was-given nil)
-                  (org-end-time-was-given nil)
-                  (prompt-time (org-read-date
-                                nil t nil "Date for tree entry:")))
-             (org-capture-put
-              :default-time
-              (if (or org-time-was-given
-                      (= (time-to-days prompt-time) (org-today)))
-                  prompt-time
-                ;; Use 00:00 when no time is given for another
-                ;; date than today?
-                (apply #'encode-time 0 0
-                       org-extend-today-until
-                       (cl-cdddr (decode-time prompt-time)))))
-             (time-to-days prompt-time)))
-          (t
-           ;; Current date, possibly corrected for late night
-           ;; workers.
-           (org-today)))))
-       (setq p (point)))
       (`(node ,title-or-id)
        ;; first try to get ID, then try to get title/alias
        (let ((node (or (org-roam-node-from-id title-or-id)
                        (org-roam-node-from-title-or-alias title-or-id)
-                       (user-error "No node with title or id \"%s\"" title-or-id))))
+                       (user-error "No node with title or id \"%s\" title-or-id"))))
          (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
          (goto-char (org-roam-node-point node))
-         (setq p (org-roam-node-point node)))))
+         (setq p (org-roam-node-point node))
-    ;; Setup `org-id' for the current capture target and return it back to the
+         (org-end-of-subtree t t))))
-    ;; caller.
     (save-excursion
       (goto-char p)
-      (if-let ((id (org-entry-get p "ID")))
+      (run-hooks 'org-roam-capture-new-node-hook)
-          (setf (org-roam-node-id org-roam-capture--node) id)
+      (org-id-get-create))))
-        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
-      (prog1
-          (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)
-           (org-find-base-buffer-visiting path))))
 
 (defun org-roam-capture-find-or-create-olp (olp)
   "Return a marker pointing to the entry at OLP in the current buffer.
@@ -618,7 +579,6 @@ 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))
@@ -632,10 +592,8 @@ you can catch it with `condition-case'."
            ;; Create heading if it doesn't exist
            (goto-char end)
            (unless (bolp) (newline))
-           (let (org-insert-heading-respect-content)
+           (org-insert-heading nil nil t)
-             (org-insert-heading nil nil t))
+           (unless (= lmax 1) (org-do-demote))
-           (unless (= lmax 1)
-             (dotimes (_ level) (org-do-demote)))
            (insert heading)
            (setq end (point))
            (goto-char start)
@@ -647,161 +605,61 @@ you can catch it with `condition-case'."
        (setq lmin (1+ flevel) lmax (+ lmin (if org-odd-levels-only 1 0)))
        (setq start found
              end (save-excursion (org-end-of-subtree t t))))
-     (point-marker))))
+     (copy-marker end))))
 
-(defun org-roam-capture--adjust-point-for-capture-type (&optional pos)
+(defun org-roam-capture--get-node-from-ref (ref)
-  "Reposition the point for template insertion dependently on the capture type.
+  "Return the node from reference REF."
-Return the newly adjusted position of `point'.
+  (save-match-data
+    (when (string-match org-link-plain-re ref)
+      (let ((type (match-string 1 ref))
+            (path (match-string 2 ref)))
+        (when-let ((id (caar (org-roam-db-query
+                              [:select [nodes:id]
+                               :from refs
+                               :left-join nodes
+                               :on (= refs:node-id nodes:id)
+                               :where (= refs:type $s1)
+                               :and (= refs:ref $s2)
+                               :limit 1]
+                              type path))))
+          (org-roam-populate (org-roam-node-create :id id)))))))
 
-POS is the current position of point (an integer) inside the
+(defun org-roam-capture--get-point ()
-currently active capture buffer, where the adjustment should
+  "Return exact point to file for org-capture-template.
-start to begin from. If it's nil, then it will default to
+This function is used solely in Org-roam's capture templates: see
-the current value of `point'."
+`org-roam-capture-templates'."
-  (or pos (setq pos (point)))
+  (let ((id (cond ((plist-get org-roam-capture--info :ref)
-  (goto-char pos)
+                   (if-let ((node (org-roam-capture--get-node-from-ref
-  (let ((location-type (if (= pos 1) 'beginning-of-file 'heading-at-point)))
+                                   (plist-get org-roam-capture--info :ref))))
-    (and (eq location-type 'heading-at-point)
+                       (progn
-         (cl-assert (org-at-heading-p)))
+                         (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-    (pcase (org-capture-get :type)
+                         (goto-char (org-roam-node-point node))
-      (`plain
+                         (widen)
-       (cl-case location-type
+                         (org-end-of-subtree t t))
-         (beginning-of-file
+                     (org-roam-capture--goto-location)))
-          (if (org-capture-get :prepend)
+                  ((and (org-roam-node-file org-roam-capture--node)
-              (let ((el (org-element-at-point)))
+                        (org-roam-node-point org-roam-capture--node))
-                (while (and (not (eobp))
+                   (set-buffer (org-capture-target-buffer (org-roam-node-file org-roam-capture--node)))
-                            (memq (org-element-type el)
+                   (goto-char (org-roam-node-point org-roam-capture--node))
-                                  '(drawer property-drawer keyword comment comment-block horizontal-rule)))
+                   (widen)
-                  (goto-char (org-element-property :end el))
+                   (org-end-of-subtree t t)
-                  (setq el (org-element-at-point))))
+                   (org-roam-node-id org-roam-capture--node))
-            (goto-char (org-entry-end-position))))
+                  (t
-         (heading-at-point
+                   (org-roam-capture--goto-location)))))
-          (if (org-capture-get :prepend)
+    (org-capture-put :template
-              (org-end-of-meta-data t)
+                     (org-roam-capture--fill-template (org-capture-get :template)))
-            (goto-char (org-entry-end-position))))))))
+    (org-roam-capture--put :id id)
-  (point))
+    (org-roam-capture--put :finalize (or (org-capture-get :finalize)
-
+                                         (org-roam-capture--get :finalize)))))
-;;; 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 ()
-  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
-  (when (org-roam-capture-p)
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
-
-(defun org-roam-capture--finalize ()
-  "Finalize the `org-roam-capture' process."
-  (if org-note-abort
-      (when-let ((new-file (org-roam-capture--get :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)))))
-      (if (functionp org-roam-finalize-fn)
-          (funcall org-roam-finalize-fn)
-        (funcall finalize))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
-
-(defun org-roam-capture--finalize-find-file ()
-  "Visit the buffer after Org-capture is done.
-This function is to be called in the Org-capture finalization process.
-ID is unused."
-  (switch-to-buffer (org-capture-get :buffer)))
-
-(defun org-roam-capture--finalize-insert-link ()
-  "Insert a link to ID into the buffer where Org-capture was called.
-ID is the Org id of the newly captured content.
-This function is to be called in the Org-capture finalization process."
-  (when-let* ((mkr (org-roam-capture--get :call-location))
-              (buf (marker-buffer mkr)))
-    (with-current-buffer buf
-      (when-let ((region (org-roam-capture--get :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 link)))
-        (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 ensure-newline)
-  "Expand TEMPLATE and return it.
-It expands ${var} occurrences in TEMPLATE, and then runs
-org-capture's template expansion.
-When ENSURE-NEWLINE, always ensure there's a newline behind."
-  (let* ((template (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)
-             (let ((fn (intern key))
-                   (node-fn (intern (concat "org-roam-node-" key)))
-                   (ksym (intern (concat ":" key))))
-               (cond
-                ((fboundp fn)
-                 (funcall fn org-roam-capture--node))
-                ((fboundp node-fn)
-                 (funcall node-fn org-roam-capture--node))
-                ((plist-get org-roam-capture--info ksym)
-                 (plist-get org-roam-capture--info ksym))
-                (t (let ((r (read-from-minibuffer (format "%s: " key) default-val)))
-                     (plist-put org-roam-capture--info ksym r)
-                     r)))))))
-    ;; WARNING:
-    ;; `org-capture-fill-template' fills the template, but post-processes whitespace such that the resultant
-    ;; template does not start with any whitespace, and only ends with a single newline
-    ;;
-    ;; Instead, we restore the whitespace in the original template.
-    (setq template (replace-regexp-in-string "[\n]*\\'" "" (org-capture-fill-template template)))
-    (when (and ensure-newline
-               (string-equal template-whitespace-content ""))
-      (setq template-whitespace-content "\n"))
-    (setq template (concat template template-whitespace-content))
-    template))
 
 (defun org-roam-capture--convert-template (template &optional props)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.
 PROPS is a plist containing additional Org-roam specific
 properties to be added to the template."
   (pcase template
-    (`(,_key ,_desc)
+    (`(,key ,desc)
      template)
-    ((or `(,key ,desc ,type ignore ,body . ,rest)
+    (`(,key ,desc ,type ,body . ,rest)
-         `(,key ,desc ,type (function ignore) ,body . ,rest)
-         `(,key ,desc ,type ,body . ,rest))
      (setq rest (append rest props))
      (let (org-roam-plist options)
        (while rest
@@ -814,12 +672,43 @@ properties to be added to the template."
            (if custom
                (setq org-roam-plist (plist-put org-roam-plist key val))
              (setq options (plist-put options key val)))))
-       (append `(,key ,desc ,type #'org-roam-capture--prepare-buffer ,body)
+       (append `(,key ,desc ,type #'org-roam-capture--get-point ,body)
                options
                (list :org-roam org-roam-plist))))
     (_
      (signal 'invalid-template template))))
 
+;;;###autoload
+(cl-defun org-roam-capture- (&key goto keys node info props templates)
+  "Main entry point.
+GOTO and KEYS correspond to `org-capture' arguments.
+INFO is an alist for filling up Org-roam's capture templates.
+NODE is an `org-roam-node' construct containing information about the node.
+PROPS is a plist containing additional Org-roam properties for each template.
+TEMPLATES is a list of org-roam templates."
+  (let* ((props (plist-put props :call-location (point-marker)))
+         (org-capture-templates
+          (mapcar (lambda (template)
+                    (org-roam-capture--convert-template template props))
+                  (or templates org-roam-capture-templates)))
+         (org-roam-capture--node node)
+         (org-roam-capture--info info))
+    (when (and (not keys)
+               (= (length org-capture-templates) 1))
+      (setq keys (caar org-capture-templates)))
+    (org-capture goto keys)))
+
+;;;###autoload
+(defun org-roam-capture (&optional goto keys)
+  "Launches an `org-capture' process for a new or existing note.
+This uses the templates defined at `org-roam-capture-templates'.
+Arguments GOTO and KEYS see `org-capture'."
+  (interactive "P")
+  (let ((node (org-roam-node-read)))
+    (org-roam-capture- :goto goto
+                       :keys keys
+                       :node node
+                       :props '(:immediate-finish nil))))
 
 (provide 'org-roam-capture)
 

org-roam-compat.el

@@ -1,12 +1,12 @@
-;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,214 +27,14 @@
 
 ;;; Commentary:
 ;;
-;; This file is dedicated to maintain backward compatibility with older older
+;; This file contains code needed for backward compatibility with older Emacsen
-;; Emacsen and Org-roam versions.
+;; and previous versions of org-roam.
 ;;
 ;;; Code:
-(require 'org-roam)
+;;;; Library Requires
-
-;;; 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
-;; parameter from Emacs 27.
-(defun org-roam--directory-files-recursively (dir regexp
-                                                  &optional include-directories predicate
-                                                  follow-symlinks)
-  "Return list of all files under directory DIR whose names match REGEXP.
-This function works recursively.  Files are returned in \"depth
-first\" order, and files from each directory are sorted in
-alphabetical order.  Each file name appears in the returned list
-in its absolute form.
-
-By default, the returned list excludes directories, but if
-optional argument INCLUDE-DIRECTORIES is non-nil, they are
-included.
-
-PREDICATE can be either nil (which means that all subdirectories
-of DIR are descended into), t (which means that subdirectories that
-can't be read are ignored), or a function (which is called with
-the name of each subdirectory, and should return non-nil if the
-subdirectory is to be descended into).
-
-If FOLLOW-SYMLINKS is non-nil, symbolic links that point to
-directories are followed.  Note that this can lead to infinite
-recursion."
-  (let* ((result nil)
-         (files nil)
-         (dir (directory-file-name dir))
-         ;; When DIR is "/", remote file names like "/method:" could
-         ;; also be offered.  We shall suppress them.
-         (tramp-mode (and tramp-mode (file-remote-p (expand-file-name dir)))))
-    (dolist (file (sort (file-name-all-completions "" dir)
-                        'string<))
-      (unless (member file '("./" "../"))
-        (if (directory-name-p file)
-            (let* ((leaf (substring file 0 (1- (length file))))
-                   (full-file (concat dir "/" leaf)))
-              ;; Don't follow symlinks to other directories.
-              (when (and (or (not (file-symlink-p full-file))
-                             (and (file-symlink-p full-file)
-                                  follow-symlinks))
-                         ;; Allow filtering subdirectories.
-                         (or (eq predicate nil)
-                             (eq predicate t)
-                             (funcall predicate full-file)))
-                (let ((sub-files
-                       (if (eq predicate t)
-                           (condition-case nil
-                               (org-roam--directory-files-recursively
-                                full-file regexp include-directories
-                                predicate follow-symlinks)
-                             (file-error nil))
-                         (org-roam--directory-files-recursively
-                          full-file regexp include-directories
-                          predicate follow-symlinks))))
-                  (setq result (nconc result sub-files))))
-              (when (and include-directories
-                         (string-match regexp leaf))
-                (setq result (nconc result (list full-file)))))
-          (when (string-match regexp file)
-            (push (concat dir "/" file) files)))))
-    (nconc result (nreverse files))))
-
-;;; Compatibility hacks and patches
-(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-add-location' that comes from advice and ARGS are
-passed to it."
-  (condition-case err
-      (apply fn args)
-    ;; `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, the
-    ;; users *do* change the path to this file and `with-temp-file' unable to create the file, if the path to
-    ;; it consists of directories that don't exist. We'll have to handle this ourselves.
-    (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
-           (progn (org-roam-message (concat "`org-id-locations-file' (%s) doesn't exist. "
-                                            "Trying to regenerate it (this may take a while)...")
-                                    org-id-locations-file)
-                  (make-directory (file-name-directory (file-truename org-id-locations-file)))
-                  (org-roam-update-org-id-locations)
-                  (apply fn args))
-         ;; In case of failure (lack of permissions), we'll patch it to at least handle the current session
-         ;; without errors.
-         (file-error (org-roam-message "Failed to regenerate `org-id-locations-file'")
-                     (lwarn 'org-roam :error "
---------
-WARNING: `org-id-locations-file' (%s) doesn't exist!
-         Org-roam is unable to create it for you.
---------
-
-This happens when Emacs doesn't have permissions to create the
-path to your `org-id-locations-file'. Org-roam will now fallback
-storing the file in your current `org-roam-directory', but the
-warning will keep popup with each new session.
-
-To stop this warning from popping up, set `org-id-locations-file'
-to the location you want and ensure that the path exists on your
-filesystem, then run M-x `org-roam-update-org-id-locations'.
-
-Note: While Org-roam doesn't depend on `org-id-locations-file' to
-lookup IDs for the nodes that are stored in the database, it
-still tries to keep it updated so IDs work across other files in
-Org-mode, so the IDs used in your `org-roam-directory' would be
-able to cross-reference outside of `org-roam-directory'. It also
-allows to keep linking with \"id:\" links within the current
-`org-roam-directory' to headings and files that are excluded from
-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)))))
 
 ;;; Obsolete aliases (remove after next major release)
-(define-obsolete-function-alias
-  'org-roam-setup
-  'org-roam-db-autosync-enable "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-teardown
-  'org-roam-db-autosync-disable "org-roam 2.0")
-
-(define-obsolete-variable-alias
-  'org-roam-current-node
-  'org-roam-buffer-current-node "org-roam 2.0")
-(define-obsolete-variable-alias
-  'org-roam-current-directory
-  'org-roam-buffer-current-directory "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-buffer-render
-  'org-roam-buffer-render-contents "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-buffer
-  'org-roam-buffer-display-dedicated "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-visit-thing
-  'org-roam-buffer-visit-thing "org-roam 2.0")
-
-(define-obsolete-function-alias
-  'org-roam-dailies-find-today
-  'org-roam-dailies-goto-today "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-dailies-find-yesterday
-  'org-roam-dailies-goto-yesterday "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-dailies-find-tomorrow
-  'org-roam-dailies-goto-tomorrow "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-dailies-find-next-note
-  'org-roam-dailies-goto-next-note "org-roam 2.0")
-(define-obsolete-function-alias
-  'org-roam-dailies-find-previous-note
-  'org-roam-dailies-goto-previous-note "org-roam 2.0")
-(define-obsolete-function-alias
-  '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")
 
 (provide 'org-roam-compat)
 

org-roam-completion.el

@@ -0,0 +1,133 @@
+;;; org-roam-completion.el --- Completion features -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 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: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+;; 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 library provides completion-at-point functions for Org-roam.
+;;
+;; The two main functions provided to capf are:
+;;
+;;    `org-roam-complete-link-at-point' provides completions to nodes
+;;    within link brackets
+;;
+;;    `org-roam-complete-everywhere' provides completions for nodes everywhere,
+;;    matching the symbol at point
+;;
+;;; Code:
+(require 'cl-lib)
+(require 'org-element)
+
+(declare-function org-roam--get-titles "org-roam")
+
+(defcustom org-roam-completion-ignore-case t
+  "Whether to ignore case in Org-roam `completion-at-point' completions."
+  :group 'org-roam
+  :type 'boolean)
+
+(defcustom org-roam-completion-everywhere nil
+  "When non-nil, provide link completion matching outside of Org links."
+  :group 'org-roam
+  :type 'boolean)
+
+(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
+                                            #'org-roam-complete-everywhere)
+  "List of functions to be used with `completion-at-point' for Org-roam.")
+
+(defun org-roam-complete-everywhere ()
+  "Provides completions for links for any word at point.
+This is a `completion-at-point' function, and is active when
+`org-roam-completion-everywhere' is non-nil."
+  (let ((end (point))
+        (start (point))
+        (exit-fn (lambda (&rest _) nil))
+        collection)
+    (when (and org-roam-completion-everywhere
+               (thing-at-point 'word)
+               (not (save-match-data (org-in-regexp org-link-any-re))))
+      (let ((bounds (bounds-of-thing-at-point 'word)))
+        (setq start (car bounds)
+              end (cdr bounds)
+              collection #'org-roam--get-titles
+              exit-fn (lambda (str _status)
+                        (delete-char (- (length str)))
+                        (insert "[[roam:" str "]]")))))
+    (when collection
+      (let ((prefix (buffer-substring-no-properties start end)))
+        (list start end
+              (if (functionp collection)
+                  (completion-table-case-fold
+                   (completion-table-dynamic
+                    (lambda (_)
+                      (cl-remove-if (apply-partially #'string= prefix)
+                                    (funcall collection))))
+                   (not org-roam-completion-ignore-case))
+                collection)
+              :exit-function exit-fn)))))
+
+(defun org-roam-complete-link-at-point ()
+  "Do appropriate completion for the link at point."
+  (let ((end (point))
+        (start (point))
+        collection link-type)
+    (when (org-in-regexp org-link-bracket-re 1)
+      (setq start (match-beginning 1)
+            end (match-end 1))
+      (let ((context (org-element-context)))
+        (pcase (org-element-lineage context '(link) t)
+          (`nil nil)
+          (link
+           (setq link-type (org-element-property :type link))
+           (when (member link-type '("roam" "fuzzy"))
+             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
+             (setq collection #'org-roam--get-titles))))))
+    (when collection
+      (let ((prefix (buffer-substring-no-properties start end)))
+        (list start end
+              (if (functionp collection)
+                  (completion-table-case-fold
+                   (completion-table-dynamic
+                    (lambda (_)
+                      (cl-remove-if (apply-partially #'string= prefix)
+                                    (funcall collection))))
+                   (not org-roam-completion-ignore-case))
+                collection)
+              :exit-function
+              (lambda (str &rest _)
+                (delete-char (- 0 (length str)))
+                (insert (concat (unless (string= link-type "roam") "roam:")
+                                str))
+                (forward-char 2)))))))
+
+(defun org-roam--register-completion-functions ()
+  "."
+  (dolist (fn org-roam-completion-functions)
+    (add-hook 'completion-at-point-functions fn nil t)))
+
+(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)
+
+(provide 'org-roam-completion)
+
+;;; org-roam-completion.el ends here

org-roam-dailies.el

@@ -1,14 +1,14 @@
 ;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
-;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org-roam "2.1"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -29,27 +29,29 @@
 
 ;;; Commentary:
 ;;
-;; This extension provides functionality for creating daily-notes, or shortly
+;; This library provides functionality for creating daily-notes. This is a
-;; "dailies". Dailies implemented here as a unique node per unique file, where
+;; concept borrowed from Roam Research.
-;; each file named after certain date and stored in `org-roam-dailies-directory'.
-;;
-;; One can use dailies for various purposes, e.g. journaling, fleeting notes,
-;; scratch notes or whatever else you can think of.
 ;;
 ;;; Code:
-(require 'dash)
+;;; Library Requires
-(require 'org-roam)
+(require 'org-capture)
+(require 'org-roam-capture)
+(require 'f)
 
-;;; Faces
+;;;; Declarations
+(defvar org-roam-directory)
+(defvar org-roam-file-extensions)
+(declare-function org-roam--org-file-p        "org-roam")
+
+;;;; Faces
 (defface org-roam-dailies-calendar-note
   '((t :inherit (org-link) :underline nil))
   "Face for dates with a daily-note in the calendar."
   :group 'org-roam-faces)
 
-;;; Options
+;;;; Customizable variables
 (defcustom org-roam-dailies-directory "daily/"
-  "Path to daily-notes.
+  "Path to daily-notes."
-This path is relative to `org-roam-directory'."
   :group 'org-roam
   :type 'string)
 
@@ -59,13 +61,11 @@ This path is relative to `org-roam-directory'."
   :type 'hook)
 
 (defcustom org-roam-dailies-capture-templates
-  `(("d" "default" entry
+  '(("d" "default" entry
      "* %?"
-     :target (file+head "%<%Y-%m-%d>.org"
+     :if-new `(file+head ,(concat org-roam-dailies-directory "%<%Y-%m-%d>.org")
-                        "#+title: %<%Y-%m-%d>\n")))
+                         "#+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
-\"org-time-string.org\".
 See `org-roam-capture-templates' for the template documentation."
   :group 'org-roam
   :type '(repeat
@@ -91,7 +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 " :target)
+                               :options (((const :format "%v " :if-new)
                                           (choice :tag "Node location"
                                                   (list :tag "File"
                                                         (const :format "" file)
@@ -104,13 +104,13 @@ See `org-roam-capture-templates' for the template documentation."
                                                         (const :format "" file+olp)
                                                         (string :tag "  File")
                                                         (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))
+                                                              (repeat string :tag "Headline")))
                                                   (list :tag "File & Head Content & Outline path"
                                                         (const :format "" file+head+olp)
                                                         (string :tag "  File")
                                                         (string :tag "  Head Content")
                                                         (list :tag "Outline path"
-                                                              (repeat (string :tag "Headline"))))))
+                                                              (repeat string :tag "Headline")))))
                                          ((const :format "%v " :prepend) (const t))
                                          ((const :format "%v " :immediate-finish) (const t))
                                          ((const :format "%v " :jump-to-captured) (const t))
@@ -126,109 +126,170 @@ See `org-roam-capture-templates' for the template documentation."
                                          ((const :format "%v " :table-line-pos) (string))
                                          ((const :format "%v " :kill-buffer) (const t))))))))
 
-;;; Commands
+;;;; Utilities
-;;;; Today
+(defun org-roam-dailies-directory--get-absolute-path ()
-;;;###autoload
+  "Get absolute path to `org-roam-dailies-directory'."
-(defun org-roam-dailies-capture-today (&optional goto keys)
+  (expand-file-name org-roam-dailies-directory org-roam-directory))
-  "Create an entry in the daily-note for today.
-When GOTO is non-nil, go the note without creating an entry.
 
-ELisp programs can set KEYS to a string associated with a template.
+(defun org-roam-dailies-find-directory ()
-In this case, interactive selection will be bypassed."
+  "Find and open `org-roam-dailies-directory'."
-  (interactive "P")
-  (org-roam-dailies--capture (current-time) goto keys))
-
-;;;###autoload
-(defun org-roam-dailies-goto-today (&optional keys)
-  "Find the daily-note for today, creating it if necessary.
-
-ELisp programs can set KEYS to a string associated with a template.
-In this case, interactive selection will be bypassed."
   (interactive)
-  (org-roam-dailies-capture-today t keys))
+  (find-file (org-roam-dailies-directory--get-absolute-path)))
 
-;;;; Tomorrow
+(defun org-roam-dailies--daily-note-p (&optional file)
-;;;###autoload
+  "Return t if FILE is an Org-roam daily-note, nil otherwise.
-(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
+
+If FILE is not specified, use the current buffer's file-path."
+  (when-let ((path (or file
+                       (buffer-base-buffer (buffer-file-name))))
+             (directory (org-roam-dailies-directory--get-absolute-path)))
+    (setq path (expand-file-name path))
+    (save-match-data
+      (and
+       (org-roam--org-file-p path)
+       (f-descendant-of-p path directory)))))
+
+(defun org-roam-dailies--capture (time &optional goto)
+  "Capture an entry in a daily-note for TIME, creating it if necessary.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (org-roam-capture- :goto (when goto '(4))
+                     :node (org-roam-node-create)
+                     :templates org-roam-dailies-capture-templates
+                     :props (list :default-time time)))
+
+;;;; Commands
+;;; Today
+(defun org-roam-dailies-capture-today (&optional goto)
+  "Create an entry in the daily-note for today.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto)
+  (when goto
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-find-today ()
+  "Find the daily-note for today, creating it if necessary."
+  (interactive)
+  (org-roam-dailies-capture-today t))
+
+;;; Tomorrow
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
   "Create an entry in the daily-note for tomorrow.
 
 With numeric argument N, use the daily-note N days in the future.
 
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry.
+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 keys))
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
 
-;;;###autoload
+(defun org-roam-dailies-find-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 keys))
+  (org-roam-dailies-capture-tomorrow n t))
 
-;;;; Yesterday
+;;; 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 keys))
+  (org-roam-dailies-capture-tomorrow (- n) goto))
 
-;;;###autoload
+(defun org-roam-dailies-find-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 keys))
+  (org-roam-dailies-capture-tomorrow (- n) t))
 
-;;;; Date
+;;; Calendar
-;;;###autoload
+(defvar org-roam-dailies-calendar-hook (list 'org-roam-dailies-calendar-mark-entries)
-(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
+  "Hooks to run when showing the `org-roam-dailies-calendar'.")
+
+(defun org-roam-dailies-calendar--install-hook ()
+  "Install Org-roam-dailies hooks to calendar."
+  (add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
+  (add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
+
+(defun org-roam-dailies-calendar--run-hook ()
+  "Run Org-roam-dailies hooks to calendar."
+  (run-hooks 'org-roam-dailies-calendar-hook)
+  (remove-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
+  (remove-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
+
+(defun org-roam-dailies-calendar--file-to-date (&optional file)
+  "Convert FILE to date.
+
+Return (MONTH DAY YEAR)."
+  (let ((file (or file
+                  (buffer-base-buffer (buffer-file-name)))))
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (org-parse-time-string
+         (file-name-sans-extension
+          (file-name-nondirectory file)))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar--date-to-time (date)
+  "Convert DATE as returned from the calendar (MONTH DAY YEAR) to a time."
+  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (org-roam-dailies-directory--get-absolute-path))
+    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
+                          (org-roam-dailies--list-files)))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
+;;; Date
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
   "Create an entry in the daily-note for a date using the calendar.
+
 Prefer past dates, unless PREFER-FUTURE is non-nil.
+
 With a `C-u' prefix or when GOTO is non-nil, go the note without
-creating an entry.
+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-roam-dailies-calendar--install-hook)
-                (org-read-date nil t nil (if goto
+  (let* ((time-str (let ((org-read-date-prefer-future prefer-future))
-                                             "Find daily-note: "
+                     (org-read-date nil nil nil (if goto
-                                           "Capture to daily-note: ")))))
+                                                    "Find daily-note: "
-    (org-roam-dailies--capture time goto keys)))
+                                                  "Capture to daily-note: "))))
+         (time (org-read-date nil t time-str)))
+    (org-roam-dailies--capture time goto)
+    (when goto
+      (run-hooks 'org-roam-dailies-find-file-hook))))
 
-;;;###autoload
+(defun org-roam-dailies-find-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 keys))
+  (org-roam-dailies-capture-date t prefer-future))
 
-;;;; Navigation
+;;; Navigation
-(defun org-roam-dailies-goto-next-note (&optional n)
+(defun org-roam-dailies--list-files (&rest extra-files)
+  "List all files in `org-roam-dailies-directory'.
+EXTRA-FILES can be used to append extra files to the list."
+  (let ((dir (org-roam-dailies-directory--get-absolute-path))
+        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+    (append (--remove (let ((file (file-name-nondirectory it)))
+                        (when (or (auto-save-file-name-p file)
+                                  (backup-file-name-p file)
+                                  (string-match "^\\." file))
+                          it))
+                      (directory-files-recursively dir regexp))
+            extra-files)))
+
+(defun org-roam-dailies-find-next-note (&optional n)
   "Find next daily-note.
 
 With numeric argument N, find note N days in the future. If N is
@@ -256,108 +317,28 @@ negative, find note N days in the past."
     (find-file note)
     (run-hooks 'org-roam-dailies-find-file-hook)))
 
-(defun org-roam-dailies-goto-previous-note (&optional n)
+(defun org-roam-dailies-find-previous-note (&optional n)
   "Find previous daily-note.
 
 With numeric argument N, find note N days in the past. If N is
 negative, find note N days in the future."
   (interactive "p")
   (let ((n (if n (- n) -1)))
-    (org-roam-dailies-goto-next-note n)))
+    (org-roam-dailies-find-next-note n)))
 
-(defun org-roam-dailies--list-files (&rest extra-files)
+;;;; Bindings
-  "List all files in `org-roam-dailies-directory'.
-EXTRA-FILES can be used to append extra files to the list."
-  (let ((dir (expand-file-name org-roam-dailies-directory org-roam-directory))
-        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
-    (append (--remove (let ((file (file-name-nondirectory it)))
-                        (when (or (auto-save-file-name-p file)
-                                  (backup-file-name-p file)
-                                  (string-match "^\\." file))
-                          it))
-                      (directory-files-recursively dir regexp))
-            extra-files)))
-
-(defun org-roam-dailies--daily-note-p (&optional file)
-  "Return t if FILE is an Org-roam daily-note, nil otherwise.
-If FILE is not specified, use the current buffer's file-path."
-  (when-let ((path (expand-file-name
-                    (or file
-                        (buffer-file-name (buffer-base-buffer)))))
-             (directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
-    (setq path (expand-file-name path))
-    (save-match-data
-      (and
-       (org-roam-file-p path)
-       (org-roam-descendant-of-p path directory)))))
-
-;;;###autoload
-(defun org-roam-dailies-find-directory ()
-  "Find and open `org-roam-dailies-directory'."
-  (interactive)
-  (find-file (expand-file-name org-roam-dailies-directory org-roam-directory)))
-
-;;; Calendar integration
-(defun org-roam-dailies-calendar--file-to-date (file)
-  "Convert FILE to date.
-Return (MONTH DAY YEAR) or nil if not an Org time-string."
-  (ignore-errors
-    (cl-destructuring-bind (_ _ _ d m y _ _ _)
-        (org-parse-time-string
-         (file-name-sans-extension
-          (file-name-nondirectory file)))
-      (list m d y))))
-
-(defun org-roam-dailies-calendar-mark-entries ()
-  "Mark days in the calendar for which a daily-note is present."
-  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
-    (dolist (date (remove nil
-                          (mapcar #'org-roam-dailies-calendar--file-to-date
-                                  (org-roam-dailies--list-files))))
-      (when (calendar-date-is-visible-p date)
-        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
-
-(add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar-mark-entries)
-(add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar-mark-entries)
-
-;;; Capture implementation
-(add-to-list 'org-roam-capture--template-keywords :override-default-time)
-
-(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.
-
-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)))
-  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))
-
-(add-hook 'org-roam-capture-preface-hook #'org-roam-dailies--override-capture-time-h)
-(defun org-roam-dailies--override-capture-time-h ()
-  "Override the `:default-time' with the time from `:override-default-time'."
-  (prog1 nil
-    (when (org-roam-capture--get :override-default-time)
-      (org-capture-put :default-time (org-roam-capture--get :override-default-time)))))
-
-;;; Bindings
 (defvar org-roam-dailies-map (make-sparse-keymap)
   "Keymap for `org-roam-dailies'.")
 
 (define-prefix-command 'org-roam-dailies-map)
 
-(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-goto-today)
+(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-find-today)
-(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-goto-yesterday)
+(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-find-yesterday)
-(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-goto-tomorrow)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-find-tomorrow)
 (define-key org-roam-dailies-map (kbd "n") #'org-roam-dailies-capture-today)
-(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-goto-next-note)
+(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-find-next-note)
-(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-goto-previous-note)
+(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-find-previous-note)
-(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-goto-date)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-find-date)
 (define-key org-roam-dailies-map (kbd "v") #'org-roam-dailies-capture-date)
 (define-key org-roam-dailies-map (kbd ".") #'org-roam-dailies-find-directory)
 

org-roam-db.el

@@ -1,12 +1,12 @@
 ;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,17 +27,37 @@
 
 ;;; Commentary:
 ;;
-;; This module provides the underlying database API to Org-roam.
+;; This library provides the underlying database api to org-roam.
 ;;
 ;;; Code:
-(require 'org-roam)
+;;;; Library Requires
-(require 'url-parse)
+(eval-when-compile (require 'subr-x))
-(require 'ol)
+(require 'emacsql)
-(defvar org-outline-path-cache)
+(require 'emacsql-sqlite3)
+(require 'seq)
 
-;;; Options
+(eval-and-compile
-(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
+  (require 'org-roam-macs)
-  "The path to file where the Org-roam database is stored.
+  ;; For `org-with-wide-buffer'
+  (require 'org-macs))
+(require 'org)
+(require 'ol)
+(require 'org-roam-utils)
+
+(defvar org-roam-find-file-hook)
+(defvar org-roam-directory)
+(defvar org-roam-verbose)
+(defvar org-agenda-files)
+
+(declare-function org-roam-id-at-point "org-roam")
+(declare-function org-roam--org-roam-file-p "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam-node-at-point "org-roam")
+
+;;;; Options
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
+  "The full path to file where the Org-roam database is stored.
+If this is non-nil, the Org-roam sqlite database is saved here.
 
 It is the user's responsibility to set this correctly, especially
 when used with multiple Org-roam instances."
@@ -46,77 +66,29 @@ when used with multiple Org-roam instances."
 
 (defcustom org-roam-db-gc-threshold gc-cons-threshold
   "The value to temporarily set the `gc-cons-threshold' threshold to.
-During `org-roam-db-sync', Emacs can pause multiple times to
+During large, heavy operations like `org-roam-db-sync',
-perform garbage collection because of the large number of
+many GC operations happen because of the large number of
-temporary structures generated (e.g. parsed ASTs).
+temporary structures generated (e.g. parsed ASTs). Temporarily
+increasing `gc-cons-threshold' will help reduce the number of GC
+operations, at the cost of temporary memory usage.
 
-`gc-cons-threshold' is temporarily set to
+This defaults to the original value of `gc-cons-threshold', but
-`org-roam-db-gc-threshold' during this operation, and increasing
+tweaking this number may lead to better overall performance. For
-`gc-cons-threshold' will help reduce the number of GC operations,
+example, to reduce the number of GCs, one may set it to a large
-at the cost of memory usage. Tweaking this value may lead to
+value like `most-positive-fixnum'."
-better overall performance.
-
-For example, to reduce the number of GCs to the minimum, on
-machines with large memory one may set it to
-`most-positive-fixnum'."
   :type 'int
   :group 'org-roam)
 
-(defcustom org-roam-db-node-include-function (lambda () t)
+(defconst org-roam-db--version 12)
-  "A custom function to check if the point contains a valid node.
-This function is called each time a node (both file and headline)
-is about to be saved into the Org-roam database.
-
-If the function returns nil, Org-roam will skip the node. This
-function is useful for excluding certain nodes from the Org-roam
-database."
-  :type 'function
-  :group 'org-roam)
-
-(defcustom org-roam-db-update-on-save t
-  "If t, update the Org-roam database upon saving the file.
-Disable this if your files are large and updating the database is
-slow."
-  :type 'boolean
-  :group 'org-roam)
-
-(defcustom org-roam-db-extra-links-elements '(node-property keyword)
-  "The list of Org element types to include for parsing by Org-roam.
-
-By default, when parsing Org's AST, links within keywords and
-property drawers are not parsed as links. Sometimes however, it
-is desirable to parse and cache these links (e.g. hiding links in
-a property drawer)."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
-  :type '(set
-          (const :tag "keywords" keyword)
-          (const :tag "property drawers" node-property)))
-
-(defcustom org-roam-db-extra-links-exclude-keys '((node-property . ("ROAM_REFS"))
-                                                  (keyword . ("transclude")))
-  "Keys to ignore when mapping over links.
-
-The car of the association list is the Org element type (e.g.
-keyword). The cdr is a list of case-insensitive strings to
-exclude from being treated as links.
-
-For example, we use this to prevent self-referential links in
-ROAM_REFS."
-  :package-version '(org-roam . "2.2.0")
-  :group 'org-roam
-  :type '(alist))
-
-;;; Variables
-(defconst org-roam-db-version 20)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
-;;; Core Functions
+;;;; Core Functions
+
 (defun org-roam-db--get-connection ()
   "Return the database connection, if any."
-  (gethash (expand-file-name (file-name-as-directory org-roam-directory))
+  (gethash (expand-file-name org-roam-directory)
            org-roam-db--connection))
 
 (defun org-roam-db ()
@@ -127,8 +99,9 @@ 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-open org-roam-db-location)))
+      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
-        (puthash (expand-file-name (file-name-as-directory org-roam-directory))
+        (set-process-query-on-exit-flag (emacsql-process conn) nil)
+        (puthash (expand-file-name org-roam-directory)
                  conn
                  org-roam-db--connection)
         (when init-db
@@ -136,109 +109,88 @@ Performs a database upgrade when required."
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
                (version (org-roam-db--upgrade-maybe conn version)))
           (cond
-           ((> version org-roam-db-version)
+           ((> version org-roam-db--version)
             (emacsql-close conn)
             (user-error
-             "The Org-roam database was created with a newer Org-roam version.  %s"
+             "The Org-roam database was created with a newer Org-roam version.  "
              "You need to update the Org-roam package"))
-           ((< version org-roam-db-version)
+           ((< version org-roam-db--version)
             (emacsql-close conn)
             (error "BUG: The Org-roam database scheme changed %s"
                    "and there is no upgrade path")))))))
   (org-roam-db--get-connection))
 
-;;; Entrypoint: (org-roam-db-query)
+;;;; Entrypoint: (org-roam-db-query)
-(define-error 'emacsql-constraint "SQL constraint violation")
 (defun org-roam-db-query (sql &rest args)
   "Run SQL query on Org-roam database with ARGS.
 SQL can be either the emacsql vector representation, or a string."
-  (apply #'emacsql (org-roam-db) sql args))
+  (if  (stringp sql)
+      (emacsql (org-roam-db) (apply #'format sql args))
+    (apply #'emacsql (org-roam-db) sql args)))
 
-(defun org-roam-db-query! (handler sql &rest args)
+;;;; Schemata
-  "Run SQL query on Org-roam database with ARGS.
+;; NOTE: Foreign key somehow doesn't work! Adding a file column to every table as a workaround.
-SQL can be either the emacsql vector representation, or a string.
-The query is expected to be able to fail, in this situation, run HANDLER."
-  (condition-case err
-      (org-roam-db-query sql args)
-    (emacsql-constraint
-     (funcall handler err))))
-
-;;; Schemata
 (defconst org-roam-db--table-schemata
   '((files
      [(file :unique :primary-key)
-      title
+      (hash :not-null)])
-      (hash :not-null)
-      (atime :not-null)
-      (mtime :not-null)])
 
     (nodes
-     ([(id :not-null :primary-key)
+     [(id :primary-key :not-null)
-       (file :not-null)
+      (file :not-null)
-       (level :not-null)
+      (level :not-null)
-       (pos :not-null)
+      (pos :not-null)
-       todo
+      todo
-       priority
+      priority
-       (scheduled text)
+      (scheduled text)
-       (deadline text)
+      (deadline text)
-       title
+      title]
-       properties
+     (:foreign-key [file] :references files [file] :on-delete :cascade))
-       olp]
-      (:foreign-key [file] :references files [file] :on-delete :cascade)))
 
     (aliases
-     ([(node-id :not-null)
+     [(file :not-null)
-       alias]
+      (node-id :not-null)
-      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+      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)
+     ([(file :not-null)
+       (node-id :not-null)
        (ref :not-null)
        (type :not-null)]
       (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
 
     (tags
-     ([(node-id :not-null)
+     [(file :not-null)
-       tag]
+      (node-id :not-null)
-      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+      tag]
+     (:foreign-key [node-id] :references nodes [id] :on-delete :cascade))
 
     (links
-     ([(pos :not-null)
+     [(file :not-null)
-       (source :not-null)
+      (pos :not-null)
-       (dest :not-null)
+      (source :not-null)
-       (type :not-null)
+      (dest :not-null)
-       (properties :not-null)]
+      (type :not-null)
-      (:foreign-key [source] :references nodes [id] :on-delete :cascade)))))
+      (properties :not-null)]
-
+     (:foreign-key [file] :references files [file] :on-delete :cascade))))
-(defconst org-roam-db--table-indices
-  '((alias-node-id aliases [node-id])
-    (refs-node-id refs [node-id])
-    (tags-node-id tags [node-id])))
 
 (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)
+    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
-      (emacsql db [:create-index $i1 :on $i2 $S3] index-name table columns))
-    (emacsql db (format "PRAGMA user_version = %s" org-roam-db-version))))
 
 (defun org-roam-db--upgrade-maybe (db version)
   "Upgrades the database schema for DB, if VERSION is old."
   (emacsql-with-transaction db
     'ignore
-    (if (< version org-roam-db-version)
+    (if (< version org-roam-db--version)
         (progn
           (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
-                                    version org-roam-db-version))
+                                    version org-roam-db--version))
           (org-roam-db-sync t))))
   version)
 
@@ -256,8 +208,8 @@ the current `org-roam-directory'."
   (dolist (conn (hash-table-values org-roam-db--connection))
     (org-roam-db--close conn)))
 
-;;; Database API
+;;;; Database API
-;;;; Clearing
+;;;;; Clearing
 (defun org-roam-db-clear-all ()
   "Clears all entries in the Org-roam cache."
   (interactive)
@@ -270,136 +222,107 @@ the current `org-roam-directory'."
 This is equivalent to removing the node from the graph.
 If FILE is nil, clear the current buffer."
   (setq file (or file (buffer-file-name (buffer-base-buffer))))
-  (org-roam-db-query [:delete :from files
+  (dolist (table (mapcar #'car org-roam-db--table-schemata))
-                      :where (= file $s1)]
+    (org-roam-db-query `[:delete :from ,table
-                     file))
+                         :where (= file $s1)]
+                       file)))
 
-;;;; Updating tables
+;;;;; 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))
+         (hash (org-roam-db--file-hash)))
-         (attr (file-attributes file))
-         (atime (file-attribute-access-time attr))
-         (mtime (file-attribute-modification-time attr))
-         (hash (or hash (org-roam-db--file-hash file))))
     (org-roam-db-query
      [:insert :into files
       :values $v1]
-     (list (vector file file-title hash atime mtime)))))
+     (list (vector file hash)))))
 
 (defun org-roam-db-get-scheduled-time ()
   "Return the scheduled time at point in ISO8601 format."
   (when-let ((time (org-get-scheduled-time (point))))
-    (format-time-string "%FT%T" time)))
+    (org-format-time-string "%FT%T%z" 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))))
-    (format-time-string "%FT%T" time)))
+    (org-format-time-string "%FT%T%z" time)))
 
-(defun org-roam-db-node-p ()
+(defun org-roam-db-map-headlines (fns)
-  "Return t if headline at point is an Org-roam node, else return nil."
+  "Run FNS over all headlines in the current buffer."
-  (and (org-id-get)
+  (org-with-point-at 1
-       (not (org-entry-get (point) "ROAM_EXCLUDE"))
+    (org-map-entries
-       (funcall org-roam-db-node-include-function)))
+     (lambda ()
-
+       (dolist (fn fns)
-(defun org-roam-db-map-nodes (fns)
+         (funcall fn))))))
-  "Run FNS over all nodes in the current buffer."
-  (org-with-wide-buffer
-   (org-map-region
-    (lambda ()
-      (when (org-roam-db-node-p)
-        (dolist (fn fns)
-          (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
-    (while (re-search-forward org-link-any-re nil :no-error)
+    (org-element-map (org-element-parse-buffer) 'link
-      ;; `re-search-forward' let the cursor one character after the link, we need to go backward one char to
+      (lambda (link)
-      ;; make the point be on the link.
+        (dolist (fn fns)
-      (backward-char)
+          (funcall fn link))))))
-      (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)))))))
-
-(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."
   (org-with-point-at 1
-    (when (and (= (org-outline-level) 0)
+    (when (= (org-outline-level) 0)
-               (org-roam-db-node-p))
       (when-let ((id (org-id-get)))
         (let* ((file (buffer-file-name (buffer-base-buffer)))
-               (title (org-roam-db--file-title))
+               (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)
-               (properties (org-entry-properties))
+               (refs (org-entry-get (point) "ROAM_REFS")))
-               (olp nil))
+          (condition-case nil
-          (org-roam-db-query!
+              (progn
-           (lambda (err)
+                (org-roam-db-query
-             (lwarn 'org-roam :warning "%s for %s (%s) in %s"
+                 [:insert :into nodes
-                    (error-message-string err)
+                  :values $v1]
-                    title id file))
+                 (vector id file level pos todo priority
-           [:insert :into nodes
+                         scheduled deadline title))
-            :values $v1]
+                (when tags
-           (vector id file level pos todo priority
+                  (org-roam-db-query
-                   scheduled deadline title properties olp))
+                   [:insert :into tags
-          (when tags
+                    :values $v1]
-            (org-roam-db-query
+                   (mapcar (lambda (tag)
-             [:insert :into tags
+                             (vector file id (substring-no-properties tag)))
-              :values $v1]
+                           tags)))
-             (mapcar (lambda (tag)
+                (when aliases
-                       (vector id (substring-no-properties tag)))
+                  (org-roam-db-query
-                     tags)))
+                   [:insert :into aliases
-          (org-roam-db-insert-aliases)
+                    :values $v1]
-          (org-roam-db-insert-refs))))))
+                   (mapcar (lambda (alias)
+                             (vector file 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 file 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)))))
+            (t
+             (lwarn '(org-roam) :error "Duplicate ID %s, skipping..." id))))))))
 
-(cl-defun org-roam-db-insert-node-data ()
+(defun org-roam-db-insert-node-data ()
   "Insert node data for headline at point into the Org-roam cache."
   (when-let ((id (org-id-get)))
     (let* ((file (buffer-file-name (buffer-base-buffer)))
@@ -410,139 +333,72 @@ INFO is the org-element parsed buffer."
            (level (nth 1 heading-components))
            (scheduled (org-roam-db-get-scheduled-time))
            (deadline (org-roam-db-get-deadline-time))
-           (title (or (nth 4 heading-components)
+           (title (nth 4 heading-components)))
-                      (progn (lwarn 'org-roam :warning "Node in %s:%s:%s has no title, skipping..."
+      (condition-case nil
-                                    file
+          (org-roam-db-query
-                                    (line-number-at-pos)
+           [:insert :into nodes
-                                    (1+ (- (point) (line-beginning-position))))
+            :values $v1]
-                             (cl-return-from org-roam-db-insert-node-data))))
+           (vector id file level pos todo priority
-           (properties (org-entry-properties))
+                   scheduled deadline title))
-           (olp (org-get-outline-path nil 'use-cache))
+        (t
-           (title (org-link-display-format title)))
+         (lwarn '(org-roam) :error
-      (org-roam-db-query!
+                "Duplicate ID %s, skipping..." id))))))
-       (lambda (err)
-         (lwarn 'org-roam :warning "%s for %s (%s) in %s"
-                (error-message-string err)
-                title id file))
-       [:insert :into nodes
-        :values $v1]
-       (vector id file level pos todo priority
-               scheduled deadline title properties olp)))))
 
 (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 ((file (buffer-file-name (buffer-base-buffer)))
-              (aliases (org-entry-get (point) "ROAM_ALIASES"))
+             (node-id (org-id-get))
-              (aliases (split-string-and-unquote aliases)))
+             (aliases (org-entry-get (point) "ROAM_ALIASES")))
     (org-roam-db-query [:insert :into aliases
                         :values $v1]
                        (mapcar (lambda (alias)
-                                 (vector node-id alias))
+                                 (vector file node-id alias))
-                               aliases))))
+                               (split-string-and-unquote aliases)))))
 
 (defun org-roam-db-insert-tags ()
   "Insert tags for node at point into Org-roam cache."
-  (when-let ((node-id (org-id-get))
+  (when-let ((file (buffer-file-name (buffer-base-buffer)))
+             (node-id (org-id-get))
              (tags (org-get-tags)))
     (org-roam-db-query [:insert :into tags
                         :values $v1]
                        (mapcar (lambda (tag)
-                                 (vector node-id (substring-no-properties tag))) tags))))
+                                 (vector file node-id tag)) tags))))
 
 (defun org-roam-db-insert-refs ()
   "Insert refs for node at point into Org-roam cache."
-  (when-let* ((node-id (org-id-get))
+  (when-let* ((file (buffer-file-name (buffer-base-buffer)))
+              (node-id (org-id-get))
               (refs (org-entry-get (point) "ROAM_REFS"))
               (refs (split-string-and-unquote refs)))
     (let (rows)
       (dolist (ref refs)
         (save-match-data
-          (cond (;; @citeKey
+          (if (string-match org-link-plain-re ref)
-                 (string-prefix-p "@" ref)
+              (progn
-                 (push (vector node-id (substring ref 1) "cite") rows))
+                (push (vector file node-id (match-string 2 ref) (match-string 1 ref)) rows))
-                (;; [cite:@citeKey]
+            (lwarn '(org-roam) :warning
-                 (string-prefix-p "[cite:" ref)
+                   "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
-                 (condition-case nil
+      (org-roam-db-query [:insert :into refs
-                     (let ((cite-obj (org-cite-parse-objects ref)))
+                          :values $v1]
-                       (org-element-map cite-obj 'citation-reference
+                         rows))))
-                         (lambda (cite)
-                           (let ((key (org-element-property :key cite)))
-                             (push (vector node-id key "cite") rows)))))
-                   (error
-                    (lwarn '(org-roam) :warning
-                           "%s:%s\tInvalid cite %s, skipping..." (buffer-file-name) (point) ref))))
-                (;; https://google.com, cite:citeKey
-                 ;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
-                 ;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
-                 (string-match org-link-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)))))
 
 (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 ((file (buffer-file-name (buffer-base-buffer)))
-           (path (org-element-property :path link))
+          (type (org-element-property :type link))
-           (option (and (string-match "::\\(.*\\)\\'" path)
+          (dest (org-element-property :path link))
-                        (match-string 1 path)))
+          (properties (list :outline (org-get-outline-path)))
-           (path (if (not option) path
+          (source (org-roam-id-at-point)))
-                   (substring path 0 (match-beginning 0))))
+      (when source
-           (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))))
-           (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 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]
-           (vector (point) source path type properties)))))))
-
-(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
+         [:insert :into links
           :values $v1]
-         (vector source key (point) properties))))))
+         (vector file (point) source dest type properties))))))
 
-;;;; Fetching
+;;;;; Fetching
 (defun org-roam-db--get-current-files ()
   "Return a hash-table of file to the hash of its file contents."
   (let ((current-files (org-roam-db-query [:select [file hash] :from files]))
@@ -551,69 +407,27 @@ INFO is the org-element parsed buffer."
       (puthash (car row) (cadr row) ht))
     ht))
 
-(defun org-roam-db--file-hash (file-path)
+(defun org-roam-db--file-hash (&optional file-path)
-  "Compute the hash of FILE-PATH."
+  "Compute the hash of FILE-PATH, a file or current buffer."
-  (with-temp-buffer
+  (if file-path
-    (set-buffer-multibyte nil)
+      (with-temp-buffer
-    (insert-file-contents-literally file-path)
+        (set-buffer-multibyte nil)
-    (secure-hash 'sha1 (current-buffer))))
+        (insert-file-contents-literally file-path)
+        (secure-hash 'sha1 (current-buffer)))
+    (org-with-wide-buffer
+     (secure-hash 'sha1 (current-buffer)))))
 
-;;;; Synchronization
+;;;;; Updating
-(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 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)))
-        info)
-    (unless (string= content-hash db-hash)
-      (unless no-require
-        (org-roam-require '(org-ref oc)))
-      (org-roam-with-file file-path nil
-        (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 content-hash)
-           (org-roam-db-insert-file-node)
-           (setq org-outline-path-cache nil)
-           (org-roam-db-map-nodes
-            (list #'org-roam-db-insert-node-data
-                  #'org-roam-db-insert-aliases
-                  #'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))
-           (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)
   "Synchronize the cache state with the current Org files on-disk.
 If FORCE, force a rebuild of the cache from scratch."
   (interactive "P")
-  (org-roam-db--close) ;; Force a reconnect
   (when force (delete-file org-roam-db-location))
+  (org-roam-db--close) ;; Force a reconnect
   (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))
+         (org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
          (modified-files nil))
     (dolist (file org-roam-files)
@@ -622,116 +436,49 @@ If FORCE, force a rebuild of the cache from scratch."
                          contents-hash)
           (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..."
+            "Clearing removed files..."
-        (org-roam-db-clear-file file))
+          (org-roam-db-clear-file file))
-      (org-roam-dolist-with-progress (file modified-files)
+      (dolist (file (hash-table-keys current-files))
-          "Processing modified files..."
+        (org-roam-db-clear-file file)))
-        (condition-case err
+    (if (fboundp 'dolist-with-progress-reporter)
-            (org-roam-db-update-file file 'no-require)
+        (dolist-with-progress-reporter (file modified-files)
-          (error
+            "Processing modified files..."
-           (org-roam-db-clear-file file)
+          (org-roam-db-update-file file))
-           (lwarn 'org-roam :error "Failed to process %s with error %s, skipping..."
+      (dolist (file modified-files)
-                  file (error-message-string err))))))))
+        (org-roam-db-update-file file)))))
 
-;;;###autoload
+(defun org-roam-db-update-file (&optional file-path)
-(define-minor-mode org-roam-db-autosync-mode
+  "Update Org-roam cache for FILE-PATH.
-  "Global minor mode to keep your Org-roam session automatically synchronized.
+If the file does not exist anymore, remove it from the cache.
-Through the session this will continue to setup your
+If the file exists, update the cache with information."
-buffers (that are Org-roam file visiting), keep track of the
+  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
-related changes, maintain cache consistency and incrementally
+  (let ((content-hash (org-roam-db--file-hash file-path))
-update the currently active database.
+        (db-hash (caar (org-roam-db-query [:select hash :from files
+                                           :where (= file $s1)] file-path))))
+    (unless (string= content-hash db-hash)
+      (org-roam-with-file file-path nil
+        (save-excursion
+          (org-set-regexps-and-options 'tags-only)
+          (org-roam-db-clear-file)
+          (org-roam-db-insert-file)
+          (org-roam-db-insert-file-node)
+          (org-roam-db-map-headlines
+           (list #'org-roam-db-insert-node-data
+                 #'org-roam-db-insert-aliases
+                 #'org-roam-db-insert-tags
+                 #'org-roam-db-insert-refs))
+          (org-roam-db-map-links
+           (list #'org-roam-db-insert-link)))))))
 
-If you need to manually trigger resync of the currently active
+(defun org-roam-db--update-on-save-h ()
-database, see `org-roam-db-sync' command."
+  "."
-  :group 'org-roam
+  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
-  :global t
-  :init-value nil
-  (let ((enabled org-roam-db-autosync-mode))
-    (cond
-     (enabled
-      (add-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
-      (add-hook 'kill-emacs-hook #'org-roam-db--close-all)
-      (advice-add #'rename-file :after  #'org-roam-db-autosync--rename-file-a)
-      (advice-add #'delete-file :before #'org-roam-db-autosync--delete-file-a)
-      (advice-add #'vc-delete-file :around #'org-roam-db-autosync--vc-delete-file-a)
-      (org-roam-db-sync))
-     (t
-      (remove-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
-      (remove-hook 'kill-emacs-hook #'org-roam-db--close-all)
-      (advice-remove #'rename-file #'org-roam-db-autosync--rename-file-a)
-      (advice-remove #'delete-file #'org-roam-db-autosync--delete-file-a)
-      (advice-remove #'vc-delete-file #'org-roam-db-autosync--vc-delete-file-a)
-      (org-roam-db--close-all)
-      ;; Disable local hooks for all org-roam buffers
-      (dolist (buf (org-roam-buffer-list))
-        (with-current-buffer buf
-          (remove-hook 'after-save-hook #'org-roam-db-autosync--try-update-on-save-h t)))))))
 
-;;;###autoload
+(add-to-list 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
-(defun org-roam-db-autosync-enable ()
-  "Activate `org-roam-db-autosync-mode'."
-  (org-roam-db-autosync-mode +1))
 
-(defun org-roam-db-autosync-disable ()
+;; Diagnostic Interactives
-  "Deactivate `org-roam-db-autosync-mode'."
-  (org-roam-db-autosync-mode -1))
-
-(defun org-roam-db-autosync-toggle ()
-  "Toggle `org-roam-db-autosync-mode' enabled/disabled."
-  (org-roam-db-autosync-mode 'toggle))
-
-(defun org-roam-db-autosync--delete-file-a (file &optional _trash)
-  "Maintain cache consistency when file deletes.
-FILE is removed from the database."
-  (when (and (not (auto-save-file-name-p file))
-             (not (backup-file-name-p file))
-             (org-roam-file-p file))
-    (org-roam-db-clear-file (expand-file-name file))))
-
-(defun org-roam-db-autosync--vc-delete-file-a (fun file)
-  "Maintain cache consistency on file deletion by FUN.
-FILE is removed from the database."
-  (let ((org-roam-file-p (and (not (auto-save-file-name-p file))
-                              (not (backup-file-name-p file))
-                              (org-roam-file-p file))))
-    (apply fun `(,file))
-    (when (and org-roam-file-p
-               (not (file-exists-p file)))
-      (org-roam-db-clear-file (expand-file-name file)))))
-
-(defun org-roam-db-autosync--rename-file-a (old-file new-file-or-dir &rest _args)
-  "Maintain cache consistency of file rename.
-OLD-FILE is cleared from the database, and NEW-FILE-OR-DIR is added."
-  (let ((new-file (if (directory-name-p new-file-or-dir)
-                      (expand-file-name (file-name-nondirectory old-file) new-file-or-dir)
-                    new-file-or-dir)))
-    (setq new-file (expand-file-name new-file))
-    (setq old-file (expand-file-name old-file))
-    (when (and (not (auto-save-file-name-p old-file))
-               (not (auto-save-file-name-p new-file))
-               (not (backup-file-name-p old-file))
-               (not (backup-file-name-p new-file))
-               (org-roam-file-p old-file))
-      (org-roam-db-clear-file old-file))
-    (when (org-roam-file-p new-file)
-      (org-roam-db-update-file new-file))))
-
-(defun org-roam-db-autosync--setup-file-h ()
-  "Setup the current buffer if it visits an Org-roam file."
-  (when (org-roam-file-p) (run-hooks 'org-roam-find-file-hook)))
-
-(add-hook 'org-roam-find-file-hook #'org-roam-db-autosync--setup-update-on-save-h)
-(defun org-roam-db-autosync--setup-update-on-save-h ()
-  "Setup the current buffer to update the DB after saving the current file."
-  (add-hook 'after-save-hook #'org-roam-db-autosync--try-update-on-save-h nil t))
-
-(defun org-roam-db-autosync--try-update-on-save-h ()
-  "If appropriate, update the database for the current file after saving buffer."
-  (when org-roam-db-update-on-save (org-roam-db-update-file)))
-
-;;; Diagnostics
 (defun org-roam-db-diagnose-node ()
   "Print information about node at point."
   (interactive)

org-roam-doctor.el

@@ -0,0 +1,221 @@
+;;; org-roam-doctor.el --- Linter for Org-roam files -*- coding: utf-8; lexical-binding: t; -*-
+;;
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; 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 library provides `org-roam-doctor', a utility for diagnosing and fixing
+;; Org-roam files. Running `org-roam-doctor' launches a list of checks defined
+;; by `org-roam-doctor--checkers'. Every checker is an instance of
+;; `org-roam-doctor-checker'.
+;;
+;; Each checker is given the Org parse tree (AST), and is expected to return a
+;; list of errors. The checker can also provide "actions" for auto-fixing errors
+;; (see `org-roam-doctor--remove-link' for an example).
+;;
+;; The UX experience is inspired by both org-lint and checkdoc, and their code
+;; is heavily referenced.
+;;
+;;; Code:
+;; Library Requires
+(require 'cl-lib)
+(require 'org)
+(require 'org-element)
+(require 'dash)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'org-roam)
+
+(defvar org-roam-mode-map)
+
+(declare-function org-roam--get-roam-buffers "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam--org-roam-file-p "org-roam")
+
+(defvar org-roam-verbose)
+
+(defcustom org-roam-doctor-inhibit-startup t
+  "Inhibit `org-mode' startup when processing files with `org-doctor'.
+When non-nil, images and LaTeX preview will not be generated,
+tables will not be aligned, and headlines will not respect
+startup visability. This significantly improves performance when
+processing multiple files"
+  :type 'boolean
+  :group 'org-roam)
+
+(cl-defstruct (org-roam-doctor-checker (:copier nil))
+  (name 'missing-checker-name)
+  (description "")
+  (actions nil))
+
+(defconst org-roam-doctor--checkers
+  (list
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-broken-links
+    :description "Fix broken links."
+    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
+               ("r" . ("Replace link" . org-roam-doctor--replace-link))))))
+
+(defun org-roam-doctor-broken-links (ast)
+  "Checker for detecting broken links.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'link
+      (lambda (l)
+        (when (equal "id" (org-element-property :type l))
+          (let ((id (org-element-property :path l)))
+            (unless (org-id-find id)
+              (push `(,(org-element-property :begin l)
+                      ,(format "Broken id link \"%s\"" id))
+                    reports))))))
+    reports))
+
+(defun org-roam-doctor--check (buffer checkers)
+  "Check BUFFER for errors.
+CHECKERS is the list of checkers used."
+  (with-current-buffer buffer
+    (save-excursion
+      (goto-char (point-min))
+      (let* ((ast (org-element-parse-buffer))
+             (errors (sort (cl-mapcan
+                            (lambda (c)
+                              (mapcar
+                               (lambda (report)
+                                 (list (set-marker (make-marker) (car report))
+                                       (nth 1 report) c))
+                               (save-excursion
+                                 (funcall
+                                  (org-roam-doctor-checker-name c)
+                                  ast))))
+                            checkers)
+                           #'car-less-than-car)))
+        (dolist (e errors)
+          (pcase-let ((`(,m ,msg ,checker) e))
+            (switch-to-buffer buffer)
+            (goto-char m)
+            (org-reveal)
+            (undo-boundary)
+            (org-roam-doctor--resolve msg checker)
+            (set-marker m nil)))
+        errors))))
+
+;;; Actions
+(defun org-roam-doctor--recursive-edit ()
+  "Launch into a recursive edit."
+  (message "When you're done editing press C-M-c to continue.")
+  (recursive-edit))
+
+(defun org-roam-doctor--skip ()
+  "Skip the current error."
+  (org-roam-message "Skipping..."))
+
+(defun org-roam-doctor--replace-link ()
+  "Replace the current link with a new link."
+  (save-match-data
+    (unless (org-in-regexp org-link-bracket-re 1)
+      (user-error "No link at point"))
+    (let ((orig (buffer-string))
+          (p (point)))
+      (condition-case nil
+          (save-excursion
+            (replace-match "")
+            (org-roam-node-insert))
+        (quit (progn
+                (replace-buffer-contents orig)
+                (goto-char p)))))))
+
+(defun org-roam-doctor--remove-link ()
+  "Unlink the text at point."
+  (unless (org-in-regexp org-link-bracket-re 1)
+    (user-error "No link at point"))
+  (save-excursion
+    (let ((label (if (match-end 2)
+                     (match-string-no-properties 2)
+                   (org-link-unescape (match-string-no-properties 1)))))
+      (delete-region (match-beginning 0) (match-end 0))
+      (insert label))))
+
+(defun org-roam-doctor--resolve (msg checker)
+  "Resolve an error.
+MSG is the error that was found, which is displayed in a help buffer.
+CHECKER is a `org-roam-doctor' checker instance."
+  (let ((actions (org-roam-doctor-checker-actions checker))
+        c)
+    (push '("e" . ("Edit" . org-roam-doctor--recursive-edit)) actions)
+    (push '("s" . ("Skip" . org-roam-doctor--skip)) actions)
+    (with-output-to-temp-buffer "*Org-roam-doctor Help*"
+      (mapc #'princ
+            (list "Error message:\n   " msg "\n\n"))
+      (dolist (action actions)
+        (princ (format "[%s]: %s\n"
+                       (car action)
+                       (cadr action))))
+      (princ "\n\n"))
+    (shrink-window-if-larger-than-buffer
+     (get-buffer-window "*Org-roam-doctor Help*"))
+    (message "Press key for command:")
+    (unwind-protect
+        (progn
+          (cl-loop
+           do (setq c (char-to-string (read-char-exclusive)))
+           until (assoc c actions)
+           do (message "Please enter a valid key for command:"))
+          (funcall (cddr (assoc c actions)))
+          (redisplay))
+      (when (get-buffer-window "*Org-roam-doctor Help*")
+        (delete-window (get-buffer-window "*Org-roam-doctor Help*"))
+        (kill-buffer "*Org-roam-doctor Help*")))))
+
+;;;###autoload
+(defun org-roam-doctor (&optional checkall)
+  "Perform a check on the current buffer to ensure cleanliness.
+If CHECKALL, run the check for all Org-roam files."
+  (interactive "P")
+  (let ((files (if checkall
+                   (org-roam--list-all-files)
+                 (unless (org-roam--org-roam-file-p)
+                   (user-error "Not in an org-roam file"))
+                 `(,(buffer-file-name)))))
+    (org-roam-doctor-start files org-roam-doctor--checkers)))
+
+(defun org-roam-doctor-start (files checkers)
+  "Lint FILES using CHECKERS."
+  (save-window-excursion
+    (let ((existing-buffers (org-roam--get-roam-buffers))
+          (org-inhibit-startup org-roam-doctor-inhibit-startup))
+      (org-id-update-id-locations)
+      (dolist (f files)
+        (let ((buf (find-file-noselect f)))
+          (org-roam-doctor--check buf checkers)
+          (unless (memq buf existing-buffers)
+            (save-buffer buf)
+            (kill-buffer buf))))))
+  (org-roam-message "Linting completed."))
+
+(provide 'org-roam-doctor)
+
+;;; org-roam-doctor.el ends here

org-roam-id.el

@@ -1,94 +0,0 @@
-;;; 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: 2.3.1
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (magit-section "3.0.0"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; 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

@@ -1,53 +0,0 @@
-;;; 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: 2.3.1
-;; 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.
-
-;; 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-macs.el

@@ -0,0 +1,86 @@
+;;; org-roam-macs.el --- Macros/utility functions -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 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: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; 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 library implements macros used throughout org-roam.
+;;
+;;; Code:
+(defmacro org-roam-plist-map! (fn plist)
+  "Map FN over PLIST, modifying it in-place."
+  (declare (indent 1))
+  (let ((plist-var (make-symbol "plist"))
+        (k (make-symbol "k"))
+        (v (make-symbol "v")))
+    `(let ((,plist-var (copy-sequence ,plist)))
+       (while ,plist-var
+         (setq ,k (pop ,plist-var))
+         (setq ,v (pop ,plist-var))
+         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
+
+(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.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (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
+                   (progn
+                     (setq new-buf t)
+                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
+          res)
+     (with-current-buffer buf
+       (unless (equal major-mode 'org-mode)
+         (delay-mode-hooks (org-mode)))
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+       (when (find-buffer-visiting ,file)
+         (kill-buffer (find-buffer-visiting ,file))))
+     res))
+
+(defmacro org-roam-with-temp-buffer (file &rest body)
+  "Execute BODY within a temp buffer.
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `default-directory' to FILE's directory and insert its contents."
+  (declare (indent 1) (debug t))
+  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
+    `(let ((,current-org-roam-directory org-roam-directory))
+       (with-temp-buffer
+         (let ((org-roam-directory ,current-org-roam-directory))
+           (delay-mode-hooks (org-mode))
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local default-directory (file-name-directory ,file)))
+           ,@body)))))
+
+(provide 'org-roam-macs)
+
+;;; org-roam-macs.el ends here

org-roam-migrate.el

@@ -1,168 +0,0 @@
-;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- 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: 2.3.1
-;; 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.
-
-;; 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 is a special library provided for the v1 users of this package. It's
-;; purpose is to ease the transition from v1 to v2, by providing migration
-;; utilities to convert from v1 notes to v2 nodes.
-;;
-;;; Code:
-(require 'org-roam)
-
-;;; Migration wizard (v1 -> v2)
-;;;###autoload
-(defun org-roam-migrate-wizard ()
-  "Migrate all notes from to be compatible with Org-roam v2.
-1. Convert all notes from v1 format to v2.
-2. Rebuild the cache.
-3. Replace all file links with ID links."
-  (interactive)
-  (when (yes-or-no-p "Org-roam will now convert all your notes from v1 to v2.
-This will take a while. Are you sure you want to do this?")
-    ;; Back up notes
-    (let ((backup-dir (expand-file-name "org-roam.bak"
-                                        (file-name-directory (directory-file-name org-roam-directory)))))
-      (message "Backing up files to %s" backup-dir)
-      (copy-directory org-roam-directory backup-dir))
-
-    ;; Upgrade database to v2
-    (org-roam-db-sync 'force)
-
-    ;; Convert v1 to v2
-    (dolist (f (org-roam-list-files))
-      (org-roam-with-file f nil
-        (org-roam-migrate-v1-to-v2)))
-
-    ;; Rebuild cache
-    (org-roam-db-sync 'force)
-
-    ;;Replace all file links with ID links
-    (dolist (f (org-roam-list-files))
-      (org-roam-with-file f nil
-        (org-roam-migrate-replace-file-links-with-id)
-        (save-buffer)))))
-
-(defun org-roam-migrate-v1-to-v2 ()
-  "Convert the current buffer to v2 format."
-  ;; Create file level ID
-  (org-with-point-at 1
-    (org-id-get-create))
-  ;; Replace roam_key into properties drawer roam_ref
-  (when-let* ((refs (mapcan #'split-string-and-unquote
-                            (cdar (org-collect-keywords '("roam_key"))))))
-    (let ((case-fold-search t))
-      (org-with-point-at 1
-        (dolist (ref refs)
-          (org-roam-ref-add ref))
-        (while (re-search-forward "^#\\+roam_key:" (point-max) t)
-          (beginning-of-line)
-          (kill-line 1)))))
-
-  ;; Replace roam_alias into properties drawer roam_aliases
-  (when-let* ((aliases (mapcan #'split-string-and-unquote
-                               (cdar (org-collect-keywords '("roam_alias"))))))
-    (dolist (alias aliases)
-      (org-roam-alias-add alias)))
-  (let ((case-fold-search t))
-    (org-with-point-at 1
-      (while (re-search-forward "^#\\+roam_alias:" (point-max) t)
-        (beginning-of-line)
-        (kill-line 1))))
-
-  ;; Replace #+roam_tags into #+filetags
-  (org-with-point-at 1
-    (let* ((roam-tags (org-roam-migrate-get-prop-list "ROAM_TAGS"))
-           (file-tags (cl-mapcan (lambda (value)
-                                   (cl-mapcan
-                                    (lambda (k) (org-split-string k ":"))
-                                    (split-string value)))
-                                 (org-roam-migrate-get-prop-list "FILETAGS")))
-           (tags (append roam-tags file-tags))
-           (tags (seq-map (lambda (tag)
-                            (replace-regexp-in-string
-                             "[^[:alnum:]_@#%]"
-                             "_"
-                             tag)) tags))
-           (tags (seq-uniq tags)))
-      (when tags
-        (org-roam-migrate-prop-set "filetags" (org-make-tag-string tags))))
-    (let ((case-fold-search t))
-      (org-with-point-at 1
-        (while (re-search-forward "^#\\+roam_tags:" (point-max) t)
-          (beginning-of-line)
-          (kill-line 1)))))
-  (save-buffer))
-
-(defun org-roam-migrate-get-prop-list (keyword)
-  "Return prop list for KEYWORD."
-  (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase keyword)))
-        lst)
-    (goto-char (point-min))
-    (while (re-search-forward re 2048 t)
-      (setq lst (append lst (split-string-and-unquote
-                             (buffer-substring-no-properties
-                              (match-beginning 1) (match-end 1))))))
-    lst))
-
-(defun org-roam-migrate-prop-set (name value)
-  "Set a file property called NAME to VALUE in buffer file.
-If the property is already set, replace its value."
-  (setq name (downcase name))
-  (org-with-point-at 1
-    (let ((case-fold-search t))
-      (if (re-search-forward (concat "^#\\+" name ":\\(.*\\)")
-                             (point-max) t)
-          (replace-match (concat "#+" name ": " value) 'fixedcase)
-        (while (and (not (eobp))
-                    (looking-at "^[#:]"))
-          (if (save-excursion (end-of-line) (eobp))
-              (progn
-                (end-of-line)
-                (insert "\n"))
-            (forward-line)
-            (beginning-of-line)))
-        (insert "#+" name ": " value "\n")))))
-
-(defun org-roam-migrate-replace-file-links-with-id ()
-  "Replace all file: links with ID links in current buffer."
-  (org-with-point-at 1
-    (while (re-search-forward org-link-bracket-re nil t)
-      (let* ((mdata (match-data))
-             (path (match-string 1))
-             (desc (match-string 2)))
-        (when (string-prefix-p "file:" path)
-          (setq path (expand-file-name (substring path 5)))
-          (when-let ((node-id (caar (org-roam-db-query [:select [id] :from nodes
-                                                        :where (= file $s1)
-                                                        :and (= level 0)] path))))
-            (set-match-data mdata)
-            (replace-match (org-link-make-string (concat "id:" node-id)
-                                                 desc) nil t)))))))
-
-(provide 'org-roam-migrate)
-;;; org-roam-migrate.el ends here

org-roam-mode.el

@@ -1,12 +1,11 @@
-;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
+;;; org-roam-mode.el --- create and refresh Org-roam buffers -*- lexical-binding: t -*-
-
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6") (emacsql "4.1.0") (magit-section "3.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,64 +26,19 @@
 
 ;;; Commentary:
 ;;
-;; This module implements `org-roam-mode', which is a major mode that used by
+;; This library implements the abstract major-mode `org-roam-mode', from which
-;; special Org-roam buffers to display various content in a section-like manner
+;; almost all other Org-roam major-modes derive.
-;; about the nodes and relevant to them information (e.g. backlinks) with which
-;; the user can interact with.
 ;;
 ;;; Code:
-(require 'org-roam)
+(require 'magit-section)
 
-;;;; Declarations
+(require 'org-roam-utils)
-(defvar org-ref-buffer-hacked)
 
-;;; Options
+(defvar org-roam-directory)
-(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+(defvar org-roam-find-file-hook)
-                                        #'org-roam-reflinks-section)
-  "A list of sections for the `org-roam-mode' based buffers.
-Each section is a function that is passed the `org-roam-node'
-for which the section will be constructed as the first
-argument. Normally this node is `org-roam-buffer-current-node'.
-The function may also accept other optional arguments. Each item
-in the list is either:
 
-1. A function, which is called only with the `org-roam-node' as the argument
+(declare-function org-roam--org-file-p "org-roam")
-2. A list, containing the function and the optional arguments.
+(declare-function org-roam-node-at-point "org-roam")
-
-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)
 
 ;;; Faces
 (defface org-roam-header-line
@@ -166,160 +120,84 @@ and `:slant'."
   "Face for the dimmer part of the widgets."
   :group 'org-roam-faces)
 
-;;; Major mode
+;;; Variables
+(defvar org-roam-current-node nil
+  "The current node at point.")
+
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+                                        #'org-roam-reflinks-section)
+  "List of functions that insert sections for Org-roam."
+  :group 'org-roam
+  :type '(repeat function))
+
+;;; The mode
 (defvar org-roam-mode-map
   (let ((map (make-sparse-keymap)))
     (set-keymap-parent map magit-section-mode-map)
-    (define-key map [C-return]  'org-roam-buffer-visit-thing)
+    (define-key map [C-return]  'org-roam-visit-thing)
-    (define-key map (kbd "C-m") 'org-roam-buffer-visit-thing)
+    (define-key map (kbd "C-m") 'org-roam-visit-thing)
-    (define-key map [remap revert-buffer] 'org-roam-buffer-refresh)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-render)
     map)
   "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")
 
 (define-derived-mode org-roam-mode magit-section-mode "Org-roam"
-  "Major mode for displaying relevant information about Org-roam nodes.
+  "Major mode for Org-roam's buffer."
-This mode is used by special Org-roam buffers, such as persistent
-`org-roam-buffer' and dedicated Org-roam buffers
-\(`org-roam-buffer-display-dedicated'), which render the
-information in a section-like manner (see
-`org-roam-mode-sections'), with which the user can
-interact with."
   :group 'org-roam
   (face-remap-add-relative 'header-line 'org-roam-header-line))
 
-;;; Buffers
+;;; Key functions
-(defvar org-roam-buffer-current-node nil
+(defun org-roam-visit-thing ()
-  "The node for which an `org-roam-mode' based buffer displays its contents.
-This set both, locally and globally. Normally the local value is
-only set in the `org-roam-mode' based buffers, while the global
-value shows the current node in the persistent `org-roam-buffer'.")
-
-(put 'org-roam-buffer-current-node 'permanent-local t)
-
-(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'.")
-
-(put 'org-roam-buffer-current-directory 'permanent-local t)
-
-;;;; Library
-(defun org-roam-buffer-visit-thing ()
   "This is a placeholder command.
 Where applicable, section-specific keymaps bind another command
 which visits the thing at point."
   (interactive)
   (user-error "There is no thing at point that could be visited"))
 
-(defun org-roam-buffer-file-at-point (&optional assert)
+(defun org-roam-buffer-render ()
-  "Return the file at point in the current `org-roam-mode' based buffer.
+  "Render the current node at point."
-If ASSERT, throw an error."
-  (if-let ((file (magit-section-case
-                   (org-roam-node-section (org-roam-node-file (oref it node)))
-                   (org-roam-grep-section (oref it file))
-                   (org-roam-preview-section (oref it file))
-                   (t (cl-assert (derived-mode-p 'org-roam-mode))))))
-      file
-    (when assert
-      (user-error "No file at point"))))
-
-(defun org-roam-buffer-refresh ()
-  "Refresh the contents of the currently selected Org-roam buffer."
   (interactive)
-  (cl-assert (derived-mode-p 'org-roam-mode))
+  (when (derived-mode-p 'org-roam-mode)
-  (save-excursion (org-roam-buffer-render-contents)))
+    (let ((inhibit-read-only t))
+      (erase-buffer)
+      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+      (magit-insert-section (org-roam)
+        (magit-insert-heading)
+        (dolist (fn org-roam-mode-sections)
+          (funcall fn org-roam-current-node))))))
 
-(defun org-roam-buffer-render-contents ()
+(defun org-roam-buffer ()
-  "Recompute and render the contents of an Org-roam buffer.
+  "Launch an Org-roam buffer for the current node at point."
-Assumes that the current buffer is an `org-roam-mode' based
+  (interactive)
-buffer."
+  (if-let ((node (org-roam-node-at-point)))
-  (let ((inhibit-read-only t))
+      (progn
-    (erase-buffer)
+        (let ((buffer (get-buffer-create
-    (org-roam-mode)
+                       (concat "org-roam: "
-    (setq-local default-directory org-roam-buffer-current-directory)
+                               (file-relative-name (buffer-file-name) org-roam-directory)))))
-    (setq-local org-roam-directory org-roam-buffer-current-directory)
+          (with-current-buffer buffer
-    (org-roam-buffer-set-header-line-format
+            (org-roam-mode)
-     (org-roam-node-title org-roam-buffer-current-node))
+            (setq-local org-roam-current-node node)
-    (magit-insert-section (org-roam)
+            (org-roam-buffer-render))
-      (magit-insert-heading)
+          (switch-to-buffer-other-window buffer)))
-      (dolist (section org-roam-mode-sections)
+    (user-error "No node at point")))
-        (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)
+;;; Persistent buffer
-  "Set the header-line using STRING.
-If the `face' property of any part of STRING is already set, then
-that takes precedence. Also pad the left side of STRING so that
-it aligns with the text area."
-  (setq-local header-line-format
-              (concat (propertize " " 'display '(space :align-to 0))
-                      string)))
-
-;;;; Dedicated buffer
-;;;###autoload
-(defun org-roam-buffer-display-dedicated (node)
-  "Launch NODE dedicated Org-roam buffer.
-Unlike the persistent `org-roam-buffer', the contents of this
-buffer won't be automatically changed and will be held in place.
-
-In interactive calls prompt to select NODE, unless called with
-`universal-argument', in which case NODE will be set to
-`org-roam-node-at-point'."
-  (interactive
-   (list (if current-prefix-arg
-             (org-roam-node-at-point 'assert)
-           (org-roam-node-read nil nil nil 'require-match))))
-  (let ((buffer (get-buffer-create (org-roam-buffer--dedicated-name node))))
-    (with-current-buffer buffer
-      (setq-local org-roam-buffer-current-node node)
-      (setq-local org-roam-buffer-current-directory org-roam-directory)
-      (org-roam-buffer-render-contents))
-    (display-buffer buffer)))
-
-(defun org-roam-buffer--dedicated-name (node)
-  "Construct buffer name for NODE dedicated Org-roam buffer."
-  (let ((title (org-roam-node-title node))
-        (filename (file-relative-name (org-roam-node-file node) org-roam-directory)))
-    (format "*org-roam: %s<%s>*" title filename)))
-
-(defun org-roam-buffer-dedicated-p (&optional buffer)
-  "Return t if an Org-roam BUFFER is a node dedicated one.
-See `org-roam-buffer-display-dedicated' for more details.
-If BUFFER is nil, default it to `current-buffer'."
-  (or buffer (setq buffer (current-buffer)))
-  (string-match-p (concat "^" (regexp-quote "*org-roam: "))
-                  (buffer-name buffer)))
-
-;;;; Persistent buffer
 (defvar org-roam-buffer "*org-roam*"
-  "The persistent Org-roam buffer name. Must be surround with \"*\".
+  "The persistent Org-roam buffer name.")
-The content inside of this buffer will be automatically updated
-to the nearest node at point that comes from the current buffer.
-To toggle its display use `org-roam-buffer-toggle' command.")
 
-(defun org-roam-buffer-toggle ()
+(defun org-roam-buffer--post-command-h ()
-  "Toggle display of the persistent `org-roam-buffer'."
+  "Reconstructs the Org-roam buffer.
-  (interactive)
+This needs to be quick or infrequent, because this is run at
-  (pcase (org-roam-buffer--visibility)
+`post-command-hook'.  If REDISPLAY, force an update of
-    ('visible
+the Org-roam buffer."
-     (progn
+  (when (get-buffer-window org-roam-buffer)
-       (quit-window nil (get-buffer-window org-roam-buffer))
+    (when-let ((node (org-roam-node-at-point)))
-       (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
+      (unless (equal node org-roam-current-node)
-    ((or 'exists 'none)
+        (setq org-roam-current-node node)
-     (progn
+        (org-roam-buffer-persistent-redisplay)))))
-       (display-buffer (get-buffer-create org-roam-buffer))
-       (org-roam-buffer-persistent-redisplay)))))
 
 (define-inline org-roam-buffer--visibility ()
-  "Return the current visibility state of the persistent `org-roam-buffer'.
+  "Return whether the current visibility state of the 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
@@ -327,147 +205,41 @@ Valid states are `visible', `exists' and `none'."
     ((get-buffer org-roam-buffer) 'exists)
     (t 'none))))
 
+(defun org-roam-buffer-toggle ()
+  "Toggle display of the Org-roam buffer."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (delete-window (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--post-command-h)))
+    ((or 'exists 'none)
+     (progn
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (setq org-roam-current-node (org-roam-node-at-point))
+       (org-roam-buffer-persistent-redisplay)))))
+
 (defun org-roam-buffer-persistent-redisplay ()
-  "Recompute contents of the persistent `org-roam-buffer'.
+  "Recompute contents of the persistent Org-roam buffer.
-Has no effect when there's no `org-roam-node-at-point'."
+Has no effect when `org-roam-current-node' is nil."
-  (when-let ((node (org-roam-node-at-point)))
+  (when org-roam-current-node
-    (unless (equal node org-roam-buffer-current-node)
+    (with-current-buffer (get-buffer-create org-roam-buffer)
-      (setq org-roam-buffer-current-node node
+      (let ((inhibit-read-only t))
-            org-roam-buffer-current-directory org-roam-directory)
+        (erase-buffer)
-      (with-current-buffer (get-buffer-create org-roam-buffer)
+        (org-roam-mode)
-        (org-roam-buffer-render-contents)
+        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
-        (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))
+        (magit-insert-section (org-roam)
+          (magit-insert-heading)
+          (dolist (fn org-roam-mode-sections)
+            (funcall fn org-roam-current-node)))))))
 
-(defun org-roam-buffer--persistent-cleanup-h ()
+(defun org-roam-buffer--redisplay ()
-  "Clean-up global state that's dedicated for the persistent `org-roam-buffer'."
+  "."
-  (setq-default org-roam-buffer-current-node nil
+  (add-hook 'post-command-hook #'org-roam-buffer--post-command-h nil t))
-                org-roam-buffer-current-directory nil))
 
-(add-hook 'org-roam-find-file-hook #'org-roam-buffer--setup-redisplay-h)
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--redisplay)
-(defun org-roam-buffer--setup-redisplay-h ()
-  "Setup automatic redisplay of the persistent `org-roam-buffer'."
-  (add-hook 'post-command-hook #'org-roam-buffer--redisplay-h nil t))
-
-(defun org-roam-buffer--redisplay-h ()
-  "Reconstruct the persistent `org-roam-buffer'.
-This needs to be quick or infrequent, because this designed to
-run at `post-command-hook'."
-  (and (get-buffer-window org-roam-buffer)
-       (org-roam-buffer-persistent-redisplay)))
 
 ;;; Sections
-;;;; Node
-(defvar org-roam-node-map
-  (let ((map (make-sparse-keymap)))
-    (set-keymap-parent map org-roam-mode-map)
-    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-node-visit)
-    map)
-  "Keymap for `org-roam-node-section's.")
-
-(defclass org-roam-node-section (magit-section)
-  ((keymap :initform 'org-roam-node-map)
-   (node :initform nil))
-  "A `magit-section' used by `org-roam-mode' to outline NODE in its own heading.")
-
-(cl-defun org-roam-node-insert-section (&key source-node point properties)
-  "Insert section for a link from SOURCE-NODE to some other node.
-The other node is normally `org-roam-buffer-current-node'.
-
-SOURCE-NODE is an `org-roam-node' that links or references with
-the other node.
-
-POINT is a character position where the link is located in
-SOURCE-NODE's file.
-
-PROPERTIES (a plist) contains additional information about the
-link.
-
-Despite the name, this function actually inserts 2 sections at
-the same time:
-
-1. `org-roam-node-section' for a heading that describes
-   SOURCE-NODE. Acts as a parent section of the following one.
-
-2. `org-roam-preview-section' for a preview content that comes
-   from SOURCE-NODE's file for the link (that references the
-   other node) at POINT. Acts a child section of the previous
-   one."
-  (magit-insert-section section (org-roam-node-section)
-    (let ((outline (if-let ((outline (plist-get properties :outline)))
-                       (mapconcat #'org-link-display-format outline " > ")
-                     "Top")))
-      (insert (concat (propertize (org-roam-node-title source-node)
-                                  'font-lock-face 'org-roam-title)
-                      (format " (%s)"
-                              (propertize outline 'font-lock-face 'org-roam-olp)))))
-    (magit-insert-heading)
-    (oset section node source-node)
-    (magit-insert-section section (org-roam-preview-section)
-      (insert (org-roam-fontify-like-in-org-mode
-               (org-roam-preview-get-contents (org-roam-node-file source-node) point))
-              "\n")
-      (oset section file (org-roam-node-file source-node))
-      (oset section point point)
-      (insert ?\n))))
-
-;;;; Preview
-(defvar org-roam-preview-map
-  (let ((map (make-sparse-keymap)))
-    (set-keymap-parent map org-roam-mode-map)
-    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-preview-visit)
-    map)
-  "Keymap for `org-roam-preview-section's.")
-
-(defclass org-roam-preview-section (magit-section)
-  ((keymap :initform 'org-roam-preview-map)
-   (file :initform nil)
-   (point :initform nil))
-  "A `magit-section' used by `org-roam-mode' to contain preview content.
-The preview content comes from FILE, and the link as at POINT.")
-
-(defun org-roam-preview-visit (file point &optional other-window)
-  "Visit FILE at POINT and return the visited buffer.
-With OTHER-WINDOW non-nil do so in another window.
-In interactive calls OTHER-WINDOW is set with
-`universal-argument'."
-  (interactive (list (org-roam-buffer-file-at-point 'assert)
-                     (oref (magit-current-section) point)
-                     current-prefix-arg))
-  (let ((buf (find-file-noselect file))
-        (display-buffer-fn (if other-window
-                               #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)))
-    (funcall display-buffer-fn buf)
-    (with-current-buffer buf
-      (widen)
-      (goto-char point))
-    (when (org-invisible-p) (org-fold-show-context))
-    buf))
-
-(defun org-roam-preview-default-function ()
-  "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
-      (org-with-wide-buffer
-       (goto-char pt)
-       (let ((s (funcall org-roam-preview-function)))
-         (dolist (fn org-roam-preview-postprocess-functions)
-           (setq s (funcall fn s)))
-         s)))))
-
 ;;;; Backlinks
 (cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
                                  (:copier nil))
@@ -482,23 +254,14 @@ headline, up to the next headline."
         (org-roam-populate (org-roam-backlink-target-node backlink)))
   backlink)
 
-(cl-defun org-roam-backlinks-get (node &key unique)
+(defun org-roam-backlinks-get (node)
-  "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.
+                    [:select [source dest pos properties]
- When UNIQUE is t, limit to unique sources."
+                     :from links
-  (let* ((sql (if unique
+                     :where (= dest $s1)
-                  [:select :distinct [source dest pos properties]
+                     :and (= type "id")]
-                   :from links
+                    (org-roam-node-id node))))
-                   :where (= dest $s1)
-                   :and (= type "id")
-                   :group :by source
-                   :having (funcall min pos)]
-                [:select [source dest pos properties]
-                 :from links
-                 :where (= dest $s1)
-                 :and (= type "id")]))
-         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
     (cl-loop for backlink in backlinks
              collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
                        (org-roam-populate
@@ -514,28 +277,16 @@ Sorts by title."
   (string< (org-roam-node-title (org-roam-backlink-source-node a))
            (org-roam-node-title (org-roam-backlink-source-node b))))
 
-(cl-defun org-roam-backlinks-section (node &key (unique nil) (show-backlink-p nil)
+(defun org-roam-backlinks-section (node)
-                                           (section-heading "Backlinks:"))
+  "The backlinks section for NODE."
-  "The backlinks section for NODE.
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get 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 section-heading)
+      (magit-insert-heading "Backlinks:")
       (dolist (backlink backlinks)
-        (when (or (null show-backlink-p)
+        (org-roam-node-insert-section
-                  (and (not (null show-backlink-p))
+         :source-node (org-roam-backlink-source-node backlink)
-                       (funcall show-backlink-p backlink)))
+         :point (org-roam-backlink-point backlink)
-          (org-roam-node-insert-section
+         :properties (org-roam-backlink-properties backlink)))
-           :source-node (org-roam-backlink-source-node backlink)
-           :point (org-roam-backlink-point backlink)
-           :properties (org-roam-backlink-properties backlink))))
       (insert ?\n))))
 
 ;;;; Reflinks
@@ -552,27 +303,22 @@ SECTION-HEADING is the string used as a heading for the backlink section."
 
 (defun org-roam-reflinks-get (node)
   "Return the reflinks for NODE."
-  (let ((refs (org-roam-db-query [:select :distinct [refs:ref links:source links:pos links:properties]
+  (let ((refs (org-roam-db-query [:select [ref] :from refs
-                                  :from refs
+                                  :where (= node-id $s1)]
-                                  :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 ,source-id ,pos ,properties) refs)
+    (pcase-dolist (`(,ref) refs)
-      (push (org-roam-populate
+      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
-             (org-roam-reflink-create
+                                                     [:select [source pos properties]
-              :source-node (org-roam-node-create :id source-id)
+                                                      :from links
-              :ref ref
+                                                      :where (= dest $s1)]
-              :point pos
+                                                     ref))
-              :properties properties)) links))
+        (push (org-roam-populate
+               (org-roam-reflink-create
+                :source-node (org-roam-node-create :id source-id)
+                :ref ref
+                :point pos
+                :properties properties)) links)))
     links))
 
 (defun org-roam-reflinks-sort (a b)
@@ -583,46 +329,52 @@ Sorts by title."
 
 (defun org-roam-reflinks-section (node)
   "The reflinks section for NODE."
-  (when-let ((refs (org-roam-node-refs node))
+  (when (org-roam-node-refs node)
-             (reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+    (let* ((reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
-    (magit-insert-section (org-roam-reflinks)
+      (magit-insert-section (org-roam-reflinks)
-      (magit-insert-heading "Reflinks:")
+        (magit-insert-heading "Reflinks:")
-      (dolist (reflink reflinks)
+        (dolist (reflink reflinks)
-        (org-roam-node-insert-section
+          (org-roam-node-insert-section
-         :source-node (org-roam-reflink-source-node reflink)
+           :source-node (org-roam-reflink-source-node reflink)
-         :point (org-roam-reflink-point reflink)
+           :point (org-roam-reflink-point reflink)
-         :properties (org-roam-reflink-properties reflink)))
+           :properties (org-roam-reflink-properties reflink)))
-      (insert ?\n))))
+        (insert ?\n)))))
 
-;;;; Grep
+;;;; Unlinked references
 (defvar org-roam-grep-map
   (let ((map (make-sparse-keymap)))
     (set-keymap-parent map org-roam-mode-map)
-    (define-key map [remap org-roam-buffer-visit-thing] 'org-roam-grep-visit)
+    (define-key map [remap org-roam-visit-thing] 'org-roam-file-visit)
     map)
   "Keymap for Org-roam grep result sections.")
 
 (defclass org-roam-grep-section (magit-section)
-  ((keymap :initform 'org-roam-grep-map)
+  ((keymap :initform org-roam-grep-map)
    (file :initform nil)
    (row :initform nil)
-   (col :initform nil))
+   (col :initform nil)))
-  "A `magit-section' used by `org-roam-mode' to contain grep output.")
 
-(defun org-roam-grep-visit (file &optional other-window row col)
+(defun org-roam-file-at-point (&optional assert)
-  "Visit FILE at row ROW (if any) and column COL (if any). Return the buffer.
+  "Return the file at point.
-With OTHER-WINDOW non-nil (in interactive calls set with
+If ASSERT, throw an error."
-`universal-argument') display the buffer in another window
+  (if-let ((file (magit-section-case
-instead."
+                   (org-roam-node-section (org-roam-node-file (oref it node)))
-  (interactive (list (org-roam-buffer-file-at-point t)
+                   (org-roam-grep-section (oref it file))
+                   (org-roam-preview-section (oref it file)))))
+      file
+    (when assert
+      (user-error "No file at point"))))
+
+(defun org-roam-file-visit (file &optional other-window row col)
+  "Visits FILE.
+With a prefix argument OTHER-WINDOW, display the buffer in
+another window instead.
+If ROW, move to the row, and if COL move to the COL."
+  (interactive (list (org-roam-file-at-point t)
                      current-prefix-arg
                      (oref (magit-current-section) row)
                      (oref (magit-current-section) col)))
-  (let ((buf (find-file-noselect file))
+  (let ((buf (find-file-noselect file)))
-        (display-buffer-fn (if other-window
-                               #'switch-to-buffer-other-window
-                             #'pop-to-buffer-same-window)))
-    (funcall display-buffer-fn buf)
     (with-current-buffer buf
       (widen)
       (goto-char (point-min))
@@ -630,10 +382,10 @@ instead."
         (forward-line (1- row)))
       (when col
         (forward-char (1- col))))
-    (when (org-invisible-p) (org-fold-show-context))
+    (funcall (if other-window
-    buf))
+                 #'switch-to-buffer-other-window
+               #'pop-to-buffer-same-window) buf)))
 
-;;;; Unlinked references
 (defvar org-roam-unlinked-references-result-re
   (rx (group (one-or-more anything))
       ":"
@@ -648,7 +400,7 @@ instead."
   "Return the preview line from FILE.
 This is the ROW within FILE."
   (with-temp-buffer
-    (insert-file-contents file)
+    (insert-file-contents-literally file)
     (forward-line (1- row))
     (buffer-substring-no-properties
      (save-excursion
@@ -658,69 +410,49 @@ This is the ROW within FILE."
        (end-of-line)
        (point)))))
 
-(defun org-roam-unlinked-references--rg-command (titles temp-file)
-  "Return the ripgrep command searching for TITLES using TEMP-FILE for pattern.
-This avoids shell escaping issues by writing the pattern to a file instead
-of passing it directly through the shell command line."
-  ;; Write pattern to temp file to avoid shell escaping issues with quotes,
-  ;; spaces, and other special characters in titles
-  (with-temp-file temp-file
-    (insert "\\[([^[]]++|(?R))*\\]"
-            (mapconcat (lambda (title)
-                         ;; Use regexp-quote instead of shell-quote-argument
-                         ;; since we're writing a regex pattern, not a shell argument
-                         (format "|(\\b%s\\b)" (regexp-quote title)))
-                       titles "")))
-
-  (concat "rg --follow --only-matching --vimgrep --pcre2 --ignore-case "
-          (mapconcat (lambda (glob) (concat "--glob " glob))
-                     (org-roam--list-files-search-globs org-roam-file-extensions)
-                     " ")
-          " --file " (shell-quote-argument temp-file) " "
-          (shell-quote-argument (expand-file-name 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)))
-           ;; Create temp file for the regex pattern
+           (rg-command (concat "rg -o --vimgrep -P -i "
-           (temp-file (make-temp-file "org-roam-rg-pattern-"))
+                               (string-join (mapcar (lambda (glob) (concat "-g " glob))
-           (rg-command (org-roam-unlinked-references--rg-command titles temp-file)))
+                                                    (org-roam--list-files-search-globs
-      ;; Use unwind-protect to ensure temp file cleanup even if errors occur
+                                                     org-roam-file-extensions)) " ")
-      (unwind-protect
+                               (format " '\\[([^[]]++|(?R))*\\]%s' "
-          (let* ((results (split-string (shell-command-to-string rg-command) "\n"))
+                                       (mapconcat (lambda (title)
-                 f row col match)
+                                                    (format "|(\\b%s\\b)" (shell-quote-argument title)))
-            (magit-insert-section (unlinked-references)
+                                                  titles ""))
-              (magit-insert-heading "Unlinked References:")
+                               org-roam-directory))
-              (dolist (line results)
+           (results (split-string (shell-command-to-string rg-command) "\n"))
-                (save-match-data
+           f row col match)
-                  (when (string-match org-roam-unlinked-references-result-re line)
+      (magit-insert-section (unlinked-references)
-                    (setq f (match-string 1 line)
+        (magit-insert-heading "Unlinked References:")
-                          row (string-to-number (match-string 2 line))
+        (dolist (line results)
-                          col (string-to-number (match-string 3 line))
+          (save-match-data
-                          match (match-string 4 line))
+            (when (string-match org-roam-unlinked-references-result-re line)
-                    (when (and match
+              (setq f (match-string 1 line)
-                               (not (file-equal-p (org-roam-node-file node) f))
+                    row (string-to-number (match-string 2 line))
-                               (member (downcase match) (mapcar #'downcase titles)))
+                    col (string-to-number (match-string 3 line))
-                      (magit-insert-section section (org-roam-grep-section)
+                    match (match-string 4 line))
-                        (oset section file f)
+              (when (and match
-                        (oset section row row)
+                         (not (f-equal-p (org-roam-node-file node) f))
-                        (oset section col col)
+                         (member (downcase match) (mapcar #'downcase titles)))
-                        (insert (propertize (format "%s:%s:%s"
+                (magit-insert-section section (org-roam-grep-section)
-                                                    (truncate-string-to-width (file-name-base f) 15 nil nil t)
+                  (oset section file f)
-                                                    row col) 'font-lock-face 'org-roam-dim)
+                  (oset section row row)
-                                " "
+                  (oset section col col)
-                                (org-roam-fontify-like-in-org-mode
+                  (insert (propertize (format "%s:%s:%s"
-                                 (org-roam-unlinked-references-preview-line f row))
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil "...")
-                                "\n"))))))
+                                              row col) 'font-lock-face 'org-roam-dim)
-              (insert ?\n)))
+                          " "
-        ;; Clean up temp file - this runs even if an error occurs above
+                          (org-roam-fontify-like-in-org-mode
-        (delete-file temp-file)))))
+                           (org-roam-unlinked-references-preview-line f row))
+                          "\n"))))))
+        (insert ?\n)))))
 
 (provide 'org-roam-mode)
 ;;; org-roam-mode.el ends here

org-roam-protocol.el

@@ -0,0 +1,107 @@
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 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: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; 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:
+;;
+;; We extend org-protocol, adding custom Org-roam handlers. The setup
+;; instructions for `org-protocol' can be found in org-protocol.el.
+;;
+;; We define 2 protocols:
+;;
+;; 1. "roam-file": This protocol simply opens the file given by the FILE key
+;; 2. "roam-ref": This protocol creates or opens a note with the given REF
+;;
+;;; Code:
+(require 'org-protocol)
+(require 'org-roam)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'ol) ;; for org-link-decode
+
+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
+
+;;;; Functions
+(defun org-roam-protocol-open-ref (info)
+  "Process an org-protocol://roam-ref?ref= style url with INFO.
+
+It opens or creates a note with the given ref.
+
+  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
+        encodeURIComponent(location.href) + \\='&title=\\=' + \\
+        encodeURIComponent(document.title) + \\='&body=\\=' + \\
+        encodeURIComponent(window.getSelection())"
+  (unless (plist-get info :ref)
+    (user-error "No ref key provided"))
+  (org-roam-plist-map! (lambda (k v)
+                         (org-link-decode
+                          (if (equal k :ref)
+                              (org-protocol-sanitize-uri v)
+                            v))) info)
+  (when org-roam-protocol-store-links
+    (push (list (plist-get info :ref)
+                (plist-get info :title)) org-stored-links))
+  (org-link-store-props :type (and (string-match org-link-plain-re
+                                                 (plist-get info :ref))
+                                   (match-string 1 (plist-get info :ref)))
+                        :link (plist-get info :ref)
+                        :annotation (org-link-make-string (plist-get info :ref)
+                                                          (or (plist-get info :title)
+                                                              (plist-get info :ref)))
+                        :initial (or (plist-get info :body) ""))
+  (raise-frame)
+  (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)
+  nil)
+
+(defun org-roam-protocol-open-file (info)
+  "This handler simply opens the file with emacsclient.
+
+INFO is an alist containing additional information passed by the protocol URL.
+It should contain the FILE key, pointing to the path of the file to open.
+
+  Example protocol string:
+
+org-protocol://roam-file?file=/path/to/file.org"
+  (when-let ((file (plist-get info :file)))
+    (raise-frame)
+    (find-file file))
+  nil)
+
+(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
+      org-protocol-protocol-alist)
+(push '("org-roam-file"  :protocol "roam-file"   :function org-roam-protocol-open-file)
+      org-protocol-protocol-alist)
+
+(provide 'org-roam-protocol)
+
+;;; org-roam-protocol.el ends here

org-roam-refile.el

@@ -0,0 +1,77 @@
+;;; org-roam-refile.el --- Refile Org-roam Notes             -*- lexical-binding: t; -*-
+
+;; Copyright © 2020 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: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; 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:
+;;
+;; Org-roam refile allows you to refile notes to your nodes.
+;;
+;;; Code:
+(defvar org-auto-align-tags)
+(defvar org-loop-over-headlines-in-active-region)
+
+(defun org-roam-refile ()
+  "Refile to node."
+  (interactive)
+  (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 'require-match))
+         (file (org-roam-node-file node))
+         (nbuf (or (find-buffer-visiting file)
+                   (find-file-noselect file)))
+         level reversed)
+    (if regionp
+        (progn
+          (org-kill-new (buffer-substring region-start region-end))
+          (org-save-markers-in-region region-start region-end))
+      (org-copy-subtree 1 nil t))
+    (with-current-buffer nbuf
+      (org-with-wide-buffer
+       (goto-char (org-roam-node-point node))
+       (setq level (org-get-valid-level (funcall outline-level) 1)
+             reversed (org-notes-order-reversed-p))
+       (goto-char
+        (if reversed
+            (or (outline-next-heading) (point-max))
+          (or (save-excursion (org-get-next-sibling))
+              (org-end-of-subtree t t)
+              (point-max))))
+       (unless (bolp) (newline))
+       (org-paste-subtree level nil nil t)
+       (and org-auto-align-tags
+            (let ((org-loop-over-headlines-in-active-region nil))
+              (org-align-tags)))
+       (when (fboundp 'deactivate-mark) (deactivate-mark))))
+    (if regionp
+        (delete-region (point) (+ (point) (- region-end region-start)))
+      (org-preserve-local-variables
+       (delete-region
+        (and (org-back-to-heading t) (point))
+        (min (1+ (buffer-size)) (org-end-of-subtree t t) (point)))))))
+
+(provide 'org-roam-refile)
+;;; org-roam-refile.el ends here

org-roam-utils.el

@@ -1,12 +1,12 @@
-;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
+;;; org-roam-utils.el --- Utilities for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020-2025 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 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: 2.3.1
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.6"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,184 +27,47 @@
 
 ;;; Commentary:
 ;;
-;; This library provides definitions for utilities that used throughout the
+;; This library implements utility functions used throughout
-;; whole package.
+;; Org-roam.
+;;
 ;;
 ;;; Code:
+;;;; Library Requires
+(require 'dash)
+(require 's)
 
-(require 'org-roam)
+(defvar org-roam-verbose)
 
-(defun org-roam-require (libs)
+;; This is necessary to ensure all dependents on this module see
-  "Require LIBS."
+;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
-  (dolist (lib libs)
+;; regardless of whether Org is loaded before their compilation.
-    (require lib nil 'noerror)))
+(require 'org)
 
-;;; String utilities
+;;;; Utility Functions
-;; TODO Refactor this.
+(defun org-roam--list-interleave (lst separator)
-(defun org-roam-replace-string (old new s)
+  "Interleaves elements in LST with SEPARATOR."
-  "Replace OLD with NEW in S."
+  (when lst
-  (declare (pure t) (side-effect-free t))
+    (let ((new-lst (list (pop lst))))
-  (replace-regexp-in-string (regexp-quote old) new s t t))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
 
-(defun org-roam-quote-string (s)
+(defun org-roam-up-heading-or-point-min ()
-  "Quotes string S."
+  "Fixed version of Org's `org-up-heading-or-point-min'."
-  (->> s
+  (ignore-errors (org-back-to-heading t))
-       (org-roam-replace-string "\\" "\\\\")
+  (let ((p (point)))
-       (org-roam-replace-string "\"" "\\\"")))
+    (if (< 1 (funcall outline-level))
+        (progn
+          (org-up-heading-safe)
+          (when (= (point) p)
+            (goto-char (point-min))))
+      (unless (bobp) (goto-char (point-min))))))
 
-(defun org-roam-word-wrap (len s)
+(defun org-roam-message (format-string &rest args)
-  "If S is longer than LEN, wrap the words with newlines."
+  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
-  (declare (side-effect-free t))
+  (when org-roam-verbose
-  (save-match-data
+    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
-    (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
-(defun org-roam-plist-map! (fn plist)
-  "Map FN over PLIST, modifying it in-place and returning it.
-FN must take two arguments: the key and the value."
-  (let ((plist-index plist))
-    (while plist-index
-      (let ((key (pop plist-index)))
-        (setf (car plist-index) (funcall fn key (car plist-index))
-              plist-index (cdr plist-index)))))
-  plist)
-
-(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.
-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
-                   (progn
-                     (setq new-buf t)
-                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
-          res)
-     (with-current-buffer buf
-       (unless (derived-mode-p 'org-mode)
-         (delay-mode-hooks
-           (let ((org-inhibit-startup t)
-                 (org-agenda-files nil))
-             (org-mode)
-             (hack-local-variables))))
-       (setq res (progn ,@body))
-       (unless (and new-buf (not ,keep-buf-p))
-         (save-buffer)))
-     (if (and new-buf (not ,keep-buf-p))
-         (when (find-buffer-visiting ,file)
-           (kill-buffer (find-buffer-visiting ,file))))
-     res))
-
-;;; Buffer utilities
-(defmacro org-roam-with-temp-buffer (file &rest body)
-  "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'.
-If FILE, set `default-directory' to FILE's directory and insert its contents."
-  (declare (indent 1) (debug t))
-  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
-    `(let ((,current-org-roam-directory org-roam-directory))
-       (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory)
-               (org-inhibit-startup t))
-           (delay-mode-hooks (org-mode))
-           (when ,file
-             (insert-file-contents ,file)
-             (setq-local default-directory (file-name-directory ,file)))
-           ,@body)))))
-
-;;; Formatting
-(defun org-roam-format-template (template replacer)
-  "Format TEMPLATE with the function REPLACER.
-The templates are of form ${foo} for variable foo, and
-${foo=default} for variable foo with default value \"default\".
-REPLACER takes an argument of the format variable and the default
-value (possibly nil). Adapted from `s-format'."
-  (let ((saved-match-data (match-data)))
-    (unwind-protect
-        (replace-regexp-in-string
-         "\\${\\([^}]+\\)}"
-         (lambda (md)
-           (let ((var (match-string 1 md))
-                 (replacer-match-data (match-data))
-                 default-val)
-             (when (string-match "\\(.+\\)=\\(.+\\)" var)
-               (setq default-val (match-string 2 var)
-                     var (match-string 1 var)))
-             (unwind-protect
-                 (let ((v (progn
-                            (set-match-data saved-match-data)
-                            (funcall replacer var default-val))))
-                   (if v
-                       (format (apply #'propertize "%s" (text-properties-at 0 var)) v)
-                     (signal 'org-roam-format-resolve md)))
-               (set-match-data replacer-match-data))))
-         (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)
@@ -230,211 +93,102 @@ Like `org-fontify-like-in-org-mode', but supports `org-ref'."
     (insert s)
     (let ((org-ref-buffer-hacked t))
       (org-mode)
-      (setq-local org-fold-core-style 'overlays)
+      (org-font-lock-ensure)
-      (font-lock-ensure)
       (buffer-string))))
 
-;;; Org-mode utilities
+(defun org-roam-set-header-line-format (string)
-;;;; Motions
+  "Set the header-line using STRING.
-(defun org-roam-up-heading-or-point-min ()
+If the `face' property of any part of STRING is already set, then
-  "Fixed version of Org's `org-up-heading-or-point-min'."
+that takes precedence. Also pad the left side of STRING so that
-  (ignore-errors (org-back-to-heading t))
+it aligns with the text area."
-  (let ((p (point)))
+  (setq-local header-line-format
-    (if (< 1 (funcall outline-level))
+              (concat (propertize " " 'display '(space :align-to 0))
-        (progn
+                      string)))
-          (org-up-heading-safe)
-          (when (= (point) p)
-            (goto-char (point-min))))
-      (unless (bobp) (goto-char (point-min))))))
 
-;;;; Keywords
+;;; Shielding regions
-(defun org-roam-get-keyword (name &optional file bound)
+(defface org-roam-shielded
-  "Return keyword property NAME from an org FILE.
+  '((t :inherit (warning)))
-FILE defaults to current file.
+  "Face for regions that are shielded (marked as read-only).
-Only scans up to BOUND bytes of the document."
+This face is used on the region target by org-roam-insertion
-  (unless bound
+during an `org-roam-capture'."
-    (setq bound 1024))
+  :group 'org-roam-faces)
-  (if file
-      (with-temp-buffer
-        (insert-file-contents file nil 0 bound)
-        (org-roam--get-keyword name))
-    (org-roam--get-keyword name bound)))
 
-(defun org-roam--get-keyword (name &optional bound)
+(defun org-roam-shield-region (beg end)
-  "Return keyword property NAME in current buffer.
+  "Shield region against modifications.
-If BOUND, scan up to BOUND bytes of the buffer."
+BEG and END are markers for the beginning and end regions.
-  (save-excursion
+REGION must be a cons-cell containing the marker to the region
-    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
+beginning and maximum values."
-      (goto-char (point-min))
+  (add-text-properties beg end
-      (when (re-search-forward re bound t)
+                       '(font-lock-face org-roam-shielded
-        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
+                                        read-only t)
+                       (marker-buffer beg)))
 
-(defun org-roam-end-of-meta-data (&optional full)
+(defun org-roam-unshield-region (beg end)
-  "Like `org-end-of-meta-data', but supports file-level metadata.
+  "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))))
 
-When FULL is non-nil but not t, skip planning information,
+;;; Formatting
-properties, clocking lines and logbook drawers.
+(defun org-roam-format (template replacer)
+  "Format TEMPLATE with the function REPLACER.
+REPLACER takes an argument of the format variable and optionally
+an extra argument which is the EXTRA value from the call to
+`org-roam-format'.
+Adapted from `s-format'."
+  (let ((saved-match-data (match-data)))
+    (unwind-protect
+        (replace-regexp-in-string
+         "\\${\\([^}]+\\)}"
+         (lambda (md)
+           (let ((var (match-string 1 md))
+                 (replacer-match-data (match-data)))
+             (unwind-protect
+                 (let ((v (progn
+                            (set-match-data saved-match-data)
+                            (funcall replacer var))))
+                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
+               (set-match-data replacer-match-data)))) template
+         ;; Need literal to make sure it works
+         t t)
+      (set-match-data saved-match-data))))
 
-When optional argument FULL is t, skip everything above, and also
+(defun org-roam--process-display-format (format)
-skip keywords."
+  "Pre-calculate minimal widths needed by the FORMAT string."
-  (org-back-to-heading-or-point-min t)
+  (let* ((fields-width 0)
-  (when (org-at-heading-p) (forward-line))
+         (string-width
-  ;; Skip planning information.
+          (string-width
-  (when (looking-at-p org-planning-line-re) (forward-line))
+           (org-roam-format
-  ;; Skip property drawer.
+            format
-  (when (looking-at org-property-drawer-re)
+            (lambda (field)
-    (goto-char (match-end 0))
+              (setq fields-width
-    (forward-line))
+                    (+ fields-width
-  ;; When FULL is not nil, skip more.
+                       (string-to-number
-  (when (and full (not (org-at-heading-p)))
+                        (or (cadr (split-string field ":"))
-    (catch 'exit
+                            "")))))))))
-      (let ((end (save-excursion (outline-next-heading) (point)))
+    (cons format (+ fields-width string-width))))
-            (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."
-  (org-with-point-at 1
-    (let ((case-fold-search t))
-      (if (re-search-forward (concat "^#\\+" key ":\\(.*\\)") (point-max) t)
-          (if (string-blank-p value)
-              (kill-whole-line)
-            (replace-match (concat " " value) 'fixedcase nil nil 1))
-        (org-roam-end-of-meta-data 'drawers)
-        (if (save-excursion (end-of-line) (eobp))
-            (progn
-              (end-of-line)
-              (insert "\n"))
-          (forward-line)
-          (beginning-of-line))
-        (insert "#+" key ": " value "\n")))))
-
-(defun org-roam-erase-keyword (keyword)
-  "Erase the line where the KEYWORD is, setting line from the top of the file."
-  (let ((case-fold-search t))
-    (org-with-point-at 1
-      (when (re-search-forward (concat "^#\\+" keyword ":") nil t)
-        (beginning-of-line)
-        (delete-region (point) (line-end-position))
-        (delete-char 1)))))
-
-;;;; 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)))
-         (lst (if (memq val lst) lst (cons val lst)))
-         (lst (seq-uniq lst)))
-    (org-set-property prop (combine-and-quote-strings lst))
-    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.
-
-If VAL is not specified, user is prompted to select a value."
-  (let* ((p (org-entry-get (point) prop))
-         (lst (when p (split-string-and-unquote p)))
-         (prop-to-remove (or val (completing-read "Remove: " lst)))
-         (lst (delete prop-to-remove lst)))
-    (if lst
-        (org-set-property prop (combine-and-quote-strings lst))
-      (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)
-  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
-  (when org-roam-verbose
-    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
 
 ;;; Diagnostics
-;; TODO Update this to also get commit hash
 ;;;###autoload
 (defun org-roam-version (&optional message)
   "Return `org-roam' version.
 Interactively, or when MESSAGE is non-nil, show in the echo area."
   (interactive)
-  (let* ((toplib (or load-file-name buffer-file-name))
+  (let* ((version
-         gitdir topdir version)
+          (with-temp-buffer
-    (unless (and toplib (equal (file-name-nondirectory toplib) "org-roam-utils.el"))
+            (insert-file-contents-literally (locate-library "org-roam.el"))
-      (setq toplib (locate-library "org-roam-utils.el")))
+            (goto-char (point-min))
-    (setq toplib (and toplib (org-roam--straight-chase-links toplib)))
+            (save-match-data
-    (when toplib
+              (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
-      (setq topdir (file-name-directory toplib)
+                  (substring-no-properties (match-string 1))
-            gitdir (expand-file-name ".git" topdir)))
+                "N/A")))))
-    (when (file-exists-p gitdir)
-      (setq version
-            (let ((default-directory topdir))
-              (shell-command-to-string "git describe --tags --dirty --always"))))
-    (unless version
-      (setq version (with-temp-buffer
-                      (insert-file-contents-literally (locate-library "org-roam.el"))
-                      (goto-char (point-min))
-                      (save-match-data
-                        (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
-                            (substring-no-properties (match-string 1))
-                          "N/A")))))
     (if (or message (called-interactively-p 'interactive))
         (message "%s" version)
       version)))
 
-(defun org-roam--straight-chase-links (filename)
-  "Chase links in FILENAME until a name that is not a link.
-
-This is the same as `file-chase-links', except that it also
-handles fake symlinks that are created by the package manager
-straight.el on Windows.
-
-See <https://github.com/raxod502/straight.el/issues/520>."
-  (when (and (bound-and-true-p straight-symlink-emulation-mode)
-             (fboundp 'straight-chase-emulated-symlink))
-    (when-let ((target (straight-chase-emulated-symlink filename)))
-      (unless (eq target 'broken)
-        (setq filename target))))
-  (file-chase-links filename))
-
 ;;;###autoload
 (defun org-roam-diagnostics ()
   "Collect and print info for `org-roam' issues."
@@ -449,11 +203,7 @@ 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

tests/roam-files/demoteable.org

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

tests/roam-files/family.org

@@ -1,19 +0,0 @@
-: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

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

tests/roam-files/ref_with_space.org

@@ -1,7 +0,0 @@
-: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/roam-exclude.org

@@ -1,7 +0,0 @@
-:PROPERTIES:
-:ID:       53fadc75-f48e-461e-be06-44a1e88b2abe
-:ROAM_EXCLUDE: t
-:END:
-#+TITLE: Excluded by Org-roam
-
-This node is excluded by declaring ~ROAM_EXCLUDE: t~.

tests/roam-files/with-alias.org

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

tests/roam-files/with-times.org

@@ -1,16 +0,0 @@
-: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

@@ -1,63 +0,0 @@
-;;; test-org-roam-capture.el --- Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation, either version 3 of the License, or
-;; (at your option) any later version.
-
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(describe "org-roam-capture--fill-template"
-  (it "fills template without newline"
-    (expect
-     (org-roam-capture--fill-template "foo")
-     :to-equal "foo"))
-
-  (it "fills template ensuring newline"
-    (expect
-     (org-roam-capture--fill-template "foo" 'ensure-newline)
-     :to-equal "foo\n"))
-
-  (it "fills template with newline"
-    (expect
-     (org-roam-capture--fill-template "foo\n")
-     :to-equal "foo\n"))
-
-  (it "fills template with two newlines"
-    (expect
-     (org-roam-capture--fill-template "foo\n\n")
-     :to-equal "foo\n\n")
-    (expect
-     (org-roam-capture--fill-template "foo\n\t\n")
-     :to-equal "foo\n\t\n"))
-
-  (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

@@ -1,120 +0,0 @@
-;;; 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

@@ -1,79 +0,0 @@
-;;; 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-link-replace.el

@@ -1,56 +0,0 @@
-;;; test-org-roam-link-replace.el --- Tests for Org-roam link replacement -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2025
-
-;; 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:
-;; Tests for commits fc86387 and 89dfaef - link replacement optimization
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-(require 'org-roam-node)
-
-(describe "org-roam-link-replace-all optimization"
-  (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-db-sync))
-  
-  (after-all
-    (org-roam-db--close)
-    (delete-file org-roam-db-location))
-
-  (it "only processes roam: links, not other bracket links"
-    (with-temp-buffer
-      (org-mode)
-      (insert "[[file:test.org][File]]\n[[roam:Foo]]\n[[https://example.com][Web]]")
-      (let ((replace-count 0)
-            (original-fn (symbol-function 'org-roam-link-replace-at-point)))
-        ;; Wrap the original function to count calls
-        (cl-letf (((symbol-function 'org-roam-link-replace-at-point)
-                   (lambda ()
-                     (cl-incf replace-count)
-                     (funcall original-fn))))
-          (org-roam-link-replace-all)
-          ;; Should only be called once, for the roam: link
-          (expect replace-count :to-equal 1)
-          (expect (buffer-string) :to-match "\\[\\[id:.*\\]\\[Foo\\]\\]"))))))
-
-(provide 'test-org-roam-link-replace)
-
-;;; test-org-roam-link-replace.el ends here

tests/test-org-roam-mode.el

@@ -1,39 +0,0 @@
-;;; 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") "/tmp/regex")
-            :to-equal
-            "rg --follow --only-matching --vimgrep --pcre2 --ignore-case --glob \"*.org\" --glob \"*.org.gpg\" --glob \"*.org.age\" --file /tmp/regex /tmp/org\\ roam")))
-
-(provide 'test-org-roam-mode)
-
-;;; test-org-roam-mode.el ends here

tests/test-org-roam-node.el

@@ -1,166 +0,0 @@
-;;; 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"
-  (it "demotes an entire org buffer"
-    ;; Use a temporary copy to avoid interfering with other tests
-    (let ((temp-file (make-temp-file "test-demoteable-" nil ".org")))
-      (copy-file "tests/roam-files/demoteable.org" temp-file t)
-      (find-file temp-file)
-      (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")
-      (kill-buffer)
-      (delete-file temp-file))))
-
-(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

@@ -1,64 +0,0 @@
-;;; test-org-roam-utils.el --- Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation, either version 3 of the License, or
-;; (at your option) any later version.
-
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(describe "org-roam-whitespace-content"
-  (it "extracts whitespace correctly"
-    (expect
-     (org-roam-whitespace-content "foo")
-     :to-equal "")
-    (expect
-     (org-roam-whitespace-content "foo\n")
-     :to-equal "\n")
-    (expect
-     (org-roam-whitespace-content "foo\n\t\n")
-     :to-equal "\n\t\n")))
-
-(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

@@ -24,58 +24,30 @@
 (require 'buttercup)
 (require 'org-roam)
 
-(defvar root-directory default-directory)
+(describe "org-roam-db-sync"
-
+  (before-all
-(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)
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory))
-    (find-file "tests/roam-files/family.org" nil)
+    (org-roam-setup))
-    (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")
-          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory)
-          org-roam-file-extensions '("org")
-          org-roam-file-exclude-regexp nil))
 
   (after-all
-    (org-roam-db--close)
+    (org-roam-teardown)
     (delete-file org-roam-db-location))
 
-  (it "gets files correctly"
+  (it "has the correct number of files"
-    (expect (length (org-roam-list-files)) :to-equal 9))
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
+            :to-equal
+            2))
 
-  (it "respects org-roam-file-extensions"
+  (it "has the correct number of nodes"
-    (setq org-roam-file-extensions '("md"))
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
-    (expect (length (org-roam-list-files)) :to-equal 1)
+            :to-equal
-    (setq org-roam-file-extensions '("org" "md"))
+            2))
-    (expect (length (org-roam-list-files)) :to-equal 10))
 
-  (it "respects org-roam-file-exclude-regexp"
+  (it "has the correct number of links"
-    (setq org-roam-file-exclude-regexp (regexp-quote "foo.org"))
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
-    (expect (length (org-roam-list-files)) :to-equal 8)))
+            :to-equal
-
+            1)))
-(describe "org-roam--list-files-search-globs"
-
-  (it "returns the correct list of globs"
-    (expect (org-roam--list-files-search-globs org-roam-file-extensions)
-            :to-have-same-items-as
-            '("\"*.org\"" "\"*.org.gpg\"" "\"*.org.age\""))))
 
 (provide 'test-org-roam)