v2.2.2 (#2171)

Create initial log module for working with Org logs

.dir-locals.el

@@ -0,0 +1,16 @@
+((emacs-lisp-mode
+  (fill-column . 110)
+  (indent-tabs-mode . nil)
+  (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
+  (elisp-lint-indent-specs . ((describe . 1)
+                              (it . 1)
+                              (thread-first . 0)
+                              (cl-flet . 1)
+                              (cl-flet* . 1)
+                              (org-element-map . defun)
+                              (org-roam-dolist-with-progress . 2)
+                              (org-roam-with-temp-buffer . 1)
+                              (org-with-point-at . 1)
+                              (magit-insert-section . defun)
+                              (magit-section-case . 0)
+                              (org-roam-with-file . 2)))))

.github/FUNDING.yml

@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: [jethrokuan]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,14 +1,15 @@
 ---
 name: Bug Report
 about: Something's not working.
-title: ''
-labels: ''
-assignees: 'jethrokuan'
+title: ""
+labels: ""
+assignees: ""
 ---
 
 ### Description
 
 #### Steps to Reproduce
+
 <!--
 Example:
 
@@ -18,13 +19,23 @@ Example:
 ...
 -->
 
+#### Backtrace
+<!--
+   Will help us track and understand issues faster.
+   How to provide a backtrace:
+   1. M-x toggle-debug-on-error
+   2. Trigger error. The debugger buffer should pop up.
+   3. Copy the contents of the debugger buffer and paste here
+-->
 
 #### Expected Results
+
 <!-- Example: File A is there -->
 
 #### Actual Results
+
 <!-- Example: File A is missing -->
 
-### Versions
-- Emacs (`C-h v emacs-version`): vX.X.X
-- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere
+### Environment
+
+<!-- Please M-x org-roam-diagnostics and paste results here -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,9 +1,9 @@
 ---
 name: Feature Request
 about: Create a feature request to improve Org-roam
-title: ''
-labels: 'enhancement'
-assignees: 'jethrokuan'
+title: ""
+labels: "enhancement"
+assignees: ""
 ---
 
 ### Brief Abstract
@@ -13,4 +13,5 @@ assignees: 'jethrokuan'
 ### Proposed Implementation (if any)
 
 ### Please check the following:
+
 - [ ] No similar feature requests

.github/workflows/docs.yml

@@ -0,0 +1,31 @@
+# * docs.yml --- Build the documentation and publish to Github Pages
+
+name: "Docs"
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install deps
+      run: |
+        sudo apt-get install texinfo
+
+    - name: Build docs
+      continue-on-error: false
+      run: make html
+
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@releases/v3
+      with:
+        ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: doc # The folder the action should deploy.
+        CLEAN: true

.github/workflows/test.yml

@@ -29,41 +29,33 @@ on:
   push:
     branches:
       - master
-      - develop
 
 jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
-      fail-fast: false
       matrix:
         emacs_version:
-          - 26.3
+          - 27.1
           - snapshot
     steps:
-    - uses: purcell/setup-emacs@master
-      with:
-        version: ${{ matrix.emacs_version }}
+      - uses: purcell/setup-emacs@master
+        with:
+          version: ${{ matrix.emacs_version }}
 
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Initialize sandbox
-      run: |
-        SANDBOX_DIR=$(mktemp -d) || exit 1
-        echo ::set-env name=SANDBOX_DIR::$SANDBOX_DIR
-        ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
+      - name: Install Eldev
+        run: curl -fsSL https://raw.github.com/org-roam/org-roam/master/github-eldev | sh
 
-    # The "all" rule is not used, because it treats compilation warnings
-    # as failures, so linting and testing are run as separate steps.
+      - name: Install dependencies
+        run: make prepare
 
-    - name: Lint
-      continue-on-error: true
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
-
-    - name: Test
-      if: always()  # Run test even if linting fails.
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR test
+      - name: Lint
+        run: make lint
 
+      - name: Test
+        run: make test
 # Local Variables:
 # eval: (outline-minor-mode)
 # End:

.gitignore

@@ -1,2 +1,16 @@
 /.sandbox/
 **/*.elc
+/doc/dir
+/doc/*.info
+/doc/*.pdf
+/doc/*.epub
+/doc/META_INF/
+/doc/OEBPS/
+/doc/dir
+/doc/epub.xml
+/doc/org-roam/
+/doc/mimetype
+/doc/stats/
+/config.mk
+/doc/manual.html
+/.eldev/

.readthedocs.yml

@@ -1,8 +0,0 @@
-version: 2
-mkdocs:
- configuration: mkdocs.yml
-formats: all
-python:
-  version: 3.7
-  install:
-    - requirements: doc/requirements.txt

BACKERS.md

@@ -0,0 +1,8 @@
+# Backers
+
+Many thanks to the following backers, your contributions are greatly appreciated!
+
+- Nathan Tran
+- Burke Libbey
+- forkrul
+- Andreas Stuhlmüller

CHANGELOG.md

@@ -1,93 +1,470 @@
 # Changelog
+## 2.2.2
+### 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
+### 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
+### 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
+### 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
+### 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
+
+### 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
+
+- [#1281](https://github.com/org-roam/org-roam/pull/1281) fixed idle-timer not instantiated on `org-roam-mode`
+- [#1308](https://github.com/org-roam/org-roam/pull/1308) fixed file renames corrupting database
+- [#1325](https://github.com/org-roam/org-roam/pull/1325) make titles and tags extracted unique per note
+- [#1327](https://github.com/org-roam/org-roam/pull/1327) preserve existing link description during automatic replacement
+- [#1346](https://github.com/org-roam/org-roam/pull/1346) prevent malformed path to `org-roam-index-file`
+- [#1347](https://github.com/org-roam/org-roam/pull/1347) allow use of `%a` element in regular Org-roam captures
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) fixed org-roam-{tag/alias}-{add/delete} altering the original case of the Org property
+- [#1374](https://github.com/org-roam/org-roam/pull/1374) fix headline completions erroring out
+- [#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 (13-11-2020)
+
+Primarily a stabilization and bug-fix release.
+
+Org-roam-dailies has also been revamped to include new features, see [this video](https://www.youtube.com/watch?v=1q9x2aZCJJ4) for a quick overview.
+
+### Added
+
+- [#978](https://github.com/org-roam/org-roam/pull/978) Revamp org-roam-dailies
+- [#1183](https://github.com/org-roam/org-roam/pull/1183) Interactive functions for managing aliases and tags in Org-roam file, namely `org-roam-alias-add`, `org-roam-alias-delete`, `org-roam-tag-add`, and `org-roam-tag-delete`.
+- [#1215](https://github.com/org-roam/org-roam/pull/1215) Multiple `ROAM_KEY` keywords can now be specified in one file. This allows bibliographical entries to share the same note file.
+- [#1238](https://github.com/org-roam/org-roam/pull/1238) Add `org-roam-prefer-id-links` variable to select linking method
+- [#1239](https://github.com/org-roam/org-roam/pull/1239) Allow `org-roam-protocol` to capture the webpage's selection, and add a toggle for storing the links to the pages
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) add `org-roam-db-update-method` to control when the cache is rebuilt.
+
+### Changed
+
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) renamed `org-roam-update-db-idle-seconds` to `org-roam-db-idle-idle-seconds`
+
+### Fixed
+
+- [#1074](https://github.com/org-roam/org-roam/issues/1074) fix `org-roam--extract-links` to handle content boundaries.
+- [#1193](https://github.com/org-roam/org-roam/issues/1193) fix `org-roam-db-build-cache` by not killing temporary buffer in `org-roam--extract-links`.
+- [#1195](https://github.com/org-roam/org-roam/issues/1195) fix ID face showing as invalid if within Org ID files, but not Org-roam's.
+- [#1199](https://github.com/org-roam/org-roam/issues/1199) make Org-roam link insertions respect `org-roam-link-title-format` everywhere.
+- [#1201](https://github.com/org-roam/org-roam/issues/1201) fix `org-roam-db-build-cache` failing in scenarios involving duplicate IDs and deleted files.
+- [#1226](https://github.com/org-roam/org-roam/issues/1226) only update relative path of file links
+- [#1232](https://github.com/org-roam/org-roam/issues/1232) fix incorrect title extractions from narrowed buffers
+- [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
+- [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
+
+## 1.2.2 (06-10-2020)
+
+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`.
+
+Org-roam now does not resolve symlinks. This significantly speeds up cache builds, but may result in some workflows breaking. In particular, Org-roam now cannot figure out if two distinct file paths in the Org-roam directory are the same file, and both files will be processed as if they were different files. This error seems to be unavoidable now that symlinks are not resolved, but this workflow is rare and should not affect most users.
+
+This change requires you to set `org-roam-directory` to the resolved path of a folder. That is:
+
+```elisp
+(setq org-roam-directory (file-truename "/path/to/directory/"))
+```
+
+### Breaking Changes
+
+- [#1164](https://github.com/org-roam/org-roam/pull/1164) Org-roam now stores the database in the user's Emacs directory by default
+- [#910](https://github.com/org-roam/org-roam/pull/910) Deprecate `company-org-roam`, using `completion-at-point` instead. To use this with company, add the `company-capf` backend instead.
+- [#1109](https://github.com/org-roam/org-roam/pull/1109) Org-roam now does not resolve symlinks.
+
+### Features
+
+- [#1163](https://github.com/org-roam/org-roam/pull/1163) Support file-level IDs introduced in Org 9.4
+- [#1093](https://github.com/org-roam/org-roam/pull/1093) Add `vanilla` org-roam-tag-source to extract buffer Org tags
+- [#1079](https://github.com/org-roam/org-roam/pull/1079) Add `org-roam-tag-face` to customize appearance of tags in interactive commands
+- [#1073](https://github.com/org-roam/org-roam/pull/1073) Rename file on title change, when `org-roam-rename-file-on-title-change` is non-nil.
+- [#1071](https://github.com/org-roam/org-roam/pull/1071) Update link descriptions on title changes, and clean-up rename file advice
+- [#1061](https://github.com/org-roam/org-roam/pull/1061) Speed up the extraction of file properties, headlines, and titles
+- [#1046](https://github.com/org-roam/org-roam/pull/1046) New user option to exclude files from Org-roam
+- [#1032](https://github.com/org-roam/org-roam/pull/1032) File changes are now propagated to the database on idle timer. This prevents large wait times during file saves.
+- [#974](https://github.com/org-roam/org-roam/pull/974) Protect region targeted by `org-roam-insert`
+- [#994](https://github.com/org-roam/org-roam/pull/994) Simplify org-roam-store-link
+- [#1062](https://github.com/org-roam/org-roam/pull/1062) Variable `org-roam-completions-everywhere` allows for completions everywhere from word at point
+- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`
+
+### Bugfixes
+
+- [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
+- [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
+
+## 1.2.1 (27-07-2020)
+
+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.
+
+We also added some new features that had been a long time coming:
+
+1. We made the backlinks more outline-friendly by also showing the outline hierarchy for a backlink (#863)
+2. We now support nested captures, which is crucial for `org-roam-protocol` (#966)
+
+### Breaking Changes
+
+- [#908](https://github.com/org-roam/org-roam/pull/908) Normalized titles in database. May break external packages that rely on unnormalized titles.
+
+### Features
+
+- [#814](https://github.com/org-roam/org-roam/pull/814) Implement `org-roam-insert-immediate`
+- [#833](https://github.com/org-roam/org-roam/pull/833) Add customization of file titles with `org-roam-title-to-slug-function`.
+- [#839](https://github.com/org-roam/org-roam/pull/839) Return selected file from `org-roam-insert`
+- [#847](https://github.com/org-roam/org-roam/pull/847) Add GC threshold `org-roam-db-gc-threshold` to temporarily change the threshold on expensive operations.
+- [#847](https://github.com/org-roam/org-roam/pull/847) Use sqlite3 transactions instead of storing the values to be inserted.
+- [#851](https://github.com/org-roam/org-roam/pull/851) Add `'first-directory'` option for `org-roam-tag-sources`
+- [#863](https://github.com/org-roam/org-roam/pull/863) Display outline hierarchy in backlinks buffer
+- [#898](https://github.com/org-roam/org-roam/pull/898) Add `org-roam-random-note` to browse a random note.
+- [#900](https://github.com/org-roam/org-roam/pull/900) Support and index all valid org links
+- [#966](https://github.com/org-roam/org-roam/pull/966) Enable nested captures
+
+### Bugfixes
+
+- [#854](https://github.com/org-roam/org-roam/pull/854) Warn instead of fail when duplicate refs and IDs exist.
+- [#857](https://github.com/org-roam/org-roam/pull/857) Fix tag extraction for symlinked directories.
+- [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
+- [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
+
+## 1.2.0 (12-06-2020)
+
+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.
+
+This is a major step forward. Supporting the in-file structure of Org-mode files means that we can interface with many of its core-features like TODOs, properties, priorities, etc. UX will have to be figured out, but this release ushers in a new age in terms of functionalities.
+
+We also add `org-roam-unlinked-references`, which naively finds text that could be references to the current Org-roam file.
+
+### Breaking Changes
+
+- [#701](https://github.com/org-roam/org-roam/pull/701) Use `emacsql-sqlite3` instead of `emacsql-sqlite` for better Windows compatibility. This requires the presence of the standard `sqlite3` binary on your machine.
+- [#750](https://github.com/org-roam/org-roam/pull/750) Deprecate `org-roam-buffer-no-delete-other-windows` in favour of `org-roam-buffer-window-parameters`.
+
+### Features
+
+- [#787](https://github.com/org-roam/org-roam/pull/787) Add `org-roam-unlinked-references`
+- [#783](https://github.com/org-roam/org-roam/pull/783) Add support for headlines
+- [#757](https://github.com/org-roam/org-roam/pull/757) Roam global properties are now case-insensitive
+- [#680](https://github.com/org-roam/org-roam/pull/680) , [#703](https://github.com/org-roam/org-roam/pull/703), [#708](https://github.com/org-roam/org-roam/pull/708) Add `org-roam-doctor` checkers for `ROAM_*` properties
+- [#664](https://github.com/org-roam/org-roam/pull/664) Add support for shelling out to `rg` and `find` in `org-roam--list-files`
+- [#679](https://github.com/org-roam/org-roam/pull/679), [#683](https://github.com/org-roam/org-roam/pull/683) Building of the graph now happens in a separate process
+
+### Bugfixes
+
+- [#714](https://github.com/org-roam/org-roam/pull/714) No longer print citelinks in backlinks buffer if there is no `ROAM_KEY` property or `org-ref` is not installed
+- [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
+- [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
+
+## 1.1.1 (18-05-2020)
+
+In this release, we added two new features:
+
+1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
+2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://www.orgroam.com/manual/Tags.html#Tags).
+
+As usual, this release comes with a multitude of bug-fixes and refactorings.
+
+### Breaking Changes
+
+- [#523](https://github.com/org-roam/org-roam/pull/523) remove `org-roam-completion-fuzzy-match` in favor of using completion mechanism's configuration options directly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Deprecate `org-roam-db--maybe-update`, in favour of `org-roam-db--update-maybe`
+- [#604](https://github.com/org-roam/org-roam/pull/604) Deprecate `org-roam-title-include-subdirs`, `org-roam-title-subdir-format` `org-roam-title-subdir-separator`, for a more general tagging system built on subdirectories
+
+### Bugfixes
+
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix backup files being tracked in database
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix external org files being tracked in database
+- [#537](https://github.com/org-roam/org-roam/pull/537) quote graphviz node and edge configuration options to allow multi-word configurations
+- [#545](https://github.com/org-roam/org-roam/pull/545) fix `org-roam--extract-links` to ensure that multiple citations (`cite:key1,key2`) are split correctly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Fix unlinked citations
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix rename-file advice not working for renaming to directories
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix links breaking within file on file movement
+
+### Features
+
+- [#538](https://github.com/org-roam/org-roam/pull/538) Optionally use text in first headline as title
+- [#553](https://github.com/org-roam/org-roam/pull/553) Add prefix argument to `org-roam-db-build-cache` for forcing rebuilds
+- [#560](https://github.com/org-roam/org-roam/pull/560) Apply 'error face to distinguish broken links
+- [#570](https://github.com/org-roam/org-roam/pull/570) Add `org-roam-doctor` to diagnose org-roam files
+- [#625](https://github.com/org-roam/org-roam/pull/625) Add `org-roam-title-sources` to control how titles are retrieved within notes
+- [#604](https://github.com/org-roam/org-roam/pull/604) Add a tagging system. `org-roam-tag-sources` controls how tags are retrieved from notes
+
+### Internal Changes
+
+- [#547](https://github.com/org-roam/org-roam/pull/547) Added `type` column to the `refs` table
+- [#606](https://github.com/org-roam/org-roam/pull/606) Added `org-roam-dev.el` for developer coding standards
+- [#622](https://github.com/org-roam/org-roam/pull/622) Online documentation now points to the Org-based documentation
+
+## 1.1.0 (21-04-2020)
+
+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:
+
+1. The codebase has been modularized into separate files, to ease future maintenance and adding of new features (mainly by [@progfolio](https://github.com/progfolio)). Because of these changes, we had to rename many functions and variables: the old names are kept for backwards compatibility, but you are encouraged to use the new function names. You'll receive a warning when you're calling the function with its obsolete name.
+2. [@kljohann](https://github.com/kljohann) did some fantastic work on graph generation: allowing building images for connected components within the graph up to a specified distance
+3. We also started supporting `org-ref` natively: cite links now show up in both the graph and the org-roam buffer.
+
+In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer).
+
+### Breaking Changes
+
+- [#385](https://github.com/org-roam/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
+- [#473](https://github.com/org-roam/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.
+
+### New Features
+
+- [#350](https://github.com/org-roam/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
+- [#359](https://github.com/org-roam/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
+- [#374](https://github.com/org-roam/org-roam/pull/374) Add support for `org-ref` `cite:` links
+- [#380](https://github.com/org-roam/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
+- [#385](https://github.com/org-roam/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
+- [#398](https://github.com/org-roam/org-roam/pull/398), [#418](https://github.com/org-roam/org-roam/pull/418) Add graph building for connected components
+- [#435](https://github.com/org-roam/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
+- [#439](https://github.com/org-roam/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
+- [#465](https://github.com/org-roam/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
+- [#488](https://github.com/org-roam/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
+- [#491](https://github.com/org-roam/org-roam/pull/491) Use TITLE as description when linking before first heading
+
+### Bugfixes
+
+- [#470](https://github.com/org-roam/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.
+
+### Internal Changes
+
+- [#363](https://github.com/org-roam/org-roam/pull/363), [#473](https://github.com/org-roam/org-roam/pull/473) Modularize org-roam features.
+- [#497](https://github.com/org-roam/org-roam/pull/497) Simplify `org-roam--list-files` implementation
+
+## 1.0.0 (23-03-2020)
+
+Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
+been stable for the most part.
+
+### New Features
+
+- [#269](https://github.com/org-roam/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
+- [#257](https://github.com/org-roam/org-roam/pull/257) Add a company-backend `company-org-roam`
+- [#284](https://github.com/org-roam/org-roam/pull/284), [#289](https://github.com/org-roam/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
+- [#289](https://github.com/org-roam/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
+- [#290](https://github.com/org-roam/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
+- [#296](https://github.com/org-roam/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`
+
+### Bugfixes
+
+- [#293](https://github.com/org-roam/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
+- [#275](https://github.com/org-roam/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
+
+## 1.0.0-rc1 (06-03-2020)
+
+This is a pre-release before the push to MELPA. It contains large
+internal changes, with little user-facing changes. Most notably, the
+backing storage has been changed to a SQLite database, and a
+templating system using `org-capture` is introduced.
+
+### Breaking Changes
+
+- [#200](https://github.com/org-roam/org-roam/pull/200) Move Org-roam cache into a SQLite database.
+- [#203](https://github.com/org-roam/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.
+
+### New Features
+
+- [#182](https://github.com/org-roam/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
+- [#216](https://github.com/org-roam/org-roam/pull/216) Adds templating functionality by extending org-capture.
+- [#232](https://github.com/org-roam/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
+- [#233](https://github.com/org-roam/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
+- [#247](https://github.com/org-roam/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
+- [#259](https://github.com/org-roam/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`
+
+### Bugfixes
+
+- [#207](https://github.com/org-roam/org-roam/pull/207), [#221](https://github.com/org-roam/org-roam/pull/221) small bugfixes to Org-roam graph generation
+- [#230](https://github.com/org-roam/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors
+
+### New Contributors
+
+- [@acowley][https://github.com/acowley]
+- [@teesloane][https://github.com/teesloane]
 
 ## 0.1.2 (2020-02-21)
 
 ### Breaking Changes
-* [#143][gh-143] `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
-* [#103][gh-103] Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+- [#143](https://github.com/org-roam/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+- [#103](https://github.com/org-roam/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
 
 ### New Features
-* [#145][gh-145] `org-roam-show-graph`: Fallback to Emacs SVG viewer
-* [#141][gh-141] add variable `org-roam-new-file-directory` for new Org-roam files
-* [#138][gh-138] add `org-roam-switch-to-buffer`
-* [#124][gh-124], [#141][gh-141] Maintain cache consistency on file rename and delete
-* [#87][gh-87], [#90][gh-90] Support encrypted Org files
-* [#110][gh-110] Add prefix to `org-roam-insert`, for inserting titles down-cased
-* [#99][gh-99] Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+- [#145](https://github.com/org-roam/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
+- [#141](https://github.com/org-roam/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
+- [#138](https://github.com/org-roam/org-roam/pull/138) add `org-roam-switch-to-buffer`
+- [#124](https://github.com/org-roam/org-roam/pull/124), [#141](https://github.com/org-roam/org-roam/pull/141) Maintain cache consistency on file rename and delete
+- [#87](https://github.com/org-roam/org-roam/pull/87), [#90](https://github.com/org-roam/org-roam/pull/90) Support encrypted Org files
+- [#110](https://github.com/org-roam/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
+- [#99](https://github.com/org-roam/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
 
 ### Changes
 
-* [#108][gh-108] Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+- [#108](https://github.com/org-roam/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
 
 ### Bugfixes
-* [#86][gh-86] Fix `org-roam--parse-content` incorrect `:to` computation for nested files
-* [#98][gh-98] Fix `org-roam--find-file` picking up temporary files
-* [#136][gh-136] Misc bugfixes
+
+- [#86](https://github.com/org-roam/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+- [#98](https://github.com/org-roam/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
+- [#136](https://github.com/org-roam/org-roam/pull/136) Misc bugfixes
 
 ### Internal
-* [#122][gh-122], [#128][gh-128] Improve performance of post-command-hook
-* [#92][gh-92], [#105][gh-105] Add tests for core functionality
+
+- [#122](https://github.com/org-roam/org-roam/pull/122), [#128](https://github.com/org-roam/org-roam/pull/128) Improve performance of post-command-hook
+- [#92](https://github.com/org-roam/org-roam/pull/92), [#105](https://github.com/org-roam/org-roam/pull/105) Add tests for core functionality
 
 ### New Contributors
-* [@frigge](https://github.com/frigge)
-* [@juergenhoetzel](https://github.com/juergenhoetzel)
-* [@chip2n](https://github.com/chip2n)
-* [@l3kn](https://github.com/l3kn)
-* [@jdormit](https://github.com/jdormit)
-* [@herbertjones](https://github.com/herbertjones)
-* [@CeleritasCelery](https://github.com/CeleritasCelery)
-* [@daniel-koudouna](https://github.com/daniel-koudouna)
+
+- [@frigge](https://github.com/frigge)
+- [@juergenhoetzel](https://github.com/juergenhoetzel)
+- [@chip2n](https://github.com/chip2n)
+- [@l3kn](https://github.com/l3kn)
+- [@jdormit](https://github.com/jdormit)
+- [@herbertjones](https://github.com/herbertjones)
+- [@CeleritasCelery](https://github.com/CeleritasCelery)
+- [@daniel-koudouna](https://github.com/daniel-koudouna)
 
 ## 0.1.1 (2020-02-15)
 
 Mostly a documentation/cleanup release.
 
 ### New Features
-* [#62][gh-62] Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
 
 ### Breaking Changes
-* [#62][gh-62] The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
 
 ### Changes
-* [#66][gh-66], [#68][gh-68]: Improved the quality of the package in preparation of submission to MELPA
-* [#73][gh-73]: Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
-* [#69][gh-69], [#72][gh-72], [#75][gh-75]: Major cleanup and de-duplication of code
+
+- [#66](https://github.com/org-roam/org-roam/pull/66), [#68](https://github.com/org-roam/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
+- [#73](https://github.com/org-roam/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
+- [#69](https://github.com/org-roam/org-roam/pull/69), [#72](https://github.com/org-roam/org-roam/pull/72), [#75](https://github.com/org-roam/org-roam/pull/75): Major cleanup and de-duplication of code
 
 ### Bugfixes
-* [#67][gh-67]: Fixed `org-roam--make-file` not creating files with extensions
-* [#71][gh-71], [#78][gh-78]: Fixed `org-roam-insert` not inserting correct paths
-* [#82][gh-82]: Fixed nested Org-roam files not being detected as part of Org-roam
 
-[gh-62]: https://github.com/jethrokuan/org-roam/pull/66
-[gh-66]: https://github.com/jethrokuan/org-roam/pull/66
-[gh-67]: https://github.com/jethrokuan/org-roam/pull/67
-[gh-68]: https://github.com/jethrokuan/org-roam/pull/68
-[gh-69]: https://github.com/jethrokuan/org-roam/pull/69
-[gh-71]: https://github.com/jethrokuan/org-roam/pull/71
-[gh-72]: https://github.com/jethrokuan/org-roam/pull/72
-[gh-73]: https://github.com/jethrokuan/org-roam/pull/73
-[gh-75]: https://github.com/jethrokuan/org-roam/pull/75
-[gh-78]: https://github.com/jethrokuan/org-roam/pull/78
-[gh-82]: https://github.com/jethrokuan/org-roam/pull/82
-[gh-86]: https://github.com/jethrokuan/org-roam/pull/86
-[gh-87]: https://github.com/jethrokuan/org-roam/pull/87
-[gh-90]: https://github.com/jethrokuan/org-roam/pull/90
-[gh-92]: https://github.com/jethrokuan/org-roam/pull/92
-[gh-98]: https://github.com/jethrokuan/org-roam/pull/98
-[gh-99]: https://github.com/jethrokuan/org-roam/pull/99
-[gh-103]: https://github.com/jethrokuan/org-roam/pull/103
-[gh-105]: https://github.com/jethrokuan/org-roam/pull/105
-[gh-108]: https://github.com/jethrokuan/org-roam/pull/108
-[gh-110]: https://github.com/jethrokuan/org-roam/pull/110
-[gh-122]: https://github.com/jethrokuan/org-roam/pull/122
-[gh-124]: https://github.com/jethrokuan/org-roam/pull/124
-[gh-128]: https://github.com/jethrokuan/org-roam/pull/128
-[gh-136]: https://github.com/jethrokuan/org-roam/pull/136
-[gh-138]: https://github.com/jethrokuan/org-roam/pull/138
-[gh-141]: https://github.com/jethrokuan/org-roam/pull/141
-[gh-142]: https://github.com/jethrokuan/org-roam/pull/142
-[gh-143]: https://github.com/jethrokuan/org-roam/pull/143
+- [#67](https://github.com/org-roam/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
+- [#71](https://github.com/org-roam/org-roam/pull/71), [#78](https://github.com/org-roam/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
+- [#82](https://github.com/org-roam/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
 
- # Local Variables:
- # eval: (auto-fill-mode -1)
- # End:
+<!-- Local Variables: -->
+<!-- eval: (auto-fill-mode -1) -->
+<!-- End: -->

Eldev

@@ -0,0 +1,29 @@
+; -*- mode: emacs-lisp; lexical-binding: t; no-byte-compile: t -*-
+
+;; explicitly set main file
+(setf eldev-project-main-file "org-roam.el")
+
+(eldev-use-package-archive 'gnu)
+(eldev-use-package-archive 'melpa-unstable)
+
+;; allow to load test helpers
+(eldev-add-loading-roots 'test "test/utils")
+
+;; Tell checkdoc not to demand two spaces after a period.
+(setq sentence-end-double-space nil)
+
+(setf eldev-lint-default '(elisp))
+(setf eldev-standard-excludes `(:or ,eldev-standard-excludes "org-roam-macs.el"))
+
+(with-eval-after-load 'elisp-lint
+  ;; We will byte-compile with Eldev.
+  (setf elisp-lint-ignored-validators '("package-lint" "fill-column")
+        enable-local-variables        :all))
+
+;; Teach linter how to properly indent emacsql vectors
+(eldev-add-extra-dependencies 'lint 'emacsql)
+(add-hook 'eldev-lint-hook
+          (lambda ()
+            (eldev-load-project-dependencies 'lint nil t)
+            (require 'emacsql)
+            (call-interactively #'emacsql-fix-vector-indentation)))

Makefile

@@ -1,56 +1,29 @@
-# * makem.sh/Makefile --- Script to aid building and testing Emacs Lisp packages
+.PHONY: clean
+clean:
+	eldev clean all
 
-# This Makefile is from the makem.sh repo: <https://github.com/alphapapa/makem.sh>.
+.PHONY: prepare
+prepare:
+	eldev -C --unstable -p -dtT prepare
 
-# * Arguments
+.PHONY: lint
+lint:
+	eldev -C --unstable -T lint
 
-# For consistency, we use only var=val options, not hyphen-prefixed options.
+.PHONY: test
+test:
+	eldev -C --unstable -T test
 
-# NOTE: I don't like duplicating the arguments here and in makem.sh,
-# but I haven't been able to find a way to pass arguments which
-# conflict with Make's own arguments through Make to the script.
-# Using -- doesn't seem to do it.
+docs:
+	make -C doc all
 
-ifdef install-deps
-	INSTALL_DEPS = "--install-deps"
-endif
-ifdef install-linters
-	INSTALL_LINTERS = "--install-linters"
-endif
+html:
+	make -C doc html-dir
 
-ifdef sandbox
-	ifeq ($(sandbox), t)
-		SANDBOX = --sandbox
-	else
-		SANDBOX = --sandbox $(sandbox)
-	endif
-endif
+install: install-docs
 
-ifdef debug
-	DEBUG = "--debug"
-endif
+install-docs: docs
+	make -C doc install-docs
 
-# ** Verbosity
-
-# Since the "-v" in "make -v" gets intercepted by Make itself, we have
-# to use a variable.
-
-verbose = $(v)
-
-ifneq (,$(findstring vv,$(verbose)))
-	VERBOSE = "-vv"
-else ifneq (,$(findstring v,$(verbose)))
-	VERBOSE = "-v"
-endif
-
-# * Rules
-
-# TODO: Handle cases in which "test" or "tests" are called and a
-# directory by that name exists, which can confuse Make.
-
-%:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS) $(@)
-
-.DEFAULT: init
-init:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS)
+install-info: info
+	make -C doc install-info

README.md

@@ -1,72 +1,235 @@
-[![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
-[![Documentation Status](https://readthedocs.org/projects/org-roam/badge/?version=latest)](https://org-roam.readthedocs.io/en/latest/?badge=latest)
-[![GitHub Release](https://img.shields.io/github/v/release/jethrokuan/org-roam)](https://img.shields.io/github/v/release/jethrokuan/org-roam)
+# Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]
 
-## Synopsis
+<img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">
 
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
-
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. Org-roam *enables* a note-taking workflow that
-is not fluid with vanilla Org-mode (more in [this blog
-post](https://blog.jethro.dev/posts/how_to_take_smart_notes_org/)).
-
-
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
+Org-roam is a plain-text knowledge management system. It brings some of
+[Roam's][roamresearch] more powerful features into the [Org-mode][org]
 ecosystem.
 
-Visit [the documentation
-page](https://org-roam.readthedocs.io/en/latest/) for a tutorial and
-more links.
+Org-roam borrows principles from the Zettelkasten method, providing a solution
+for non-hierarchical note-taking. It should also work as a plug-and-play
+solution for anyone already using Org-mode for their personal wiki.
 
-As of February 2020, it is in a very early stage of development. 
+- **Private and Secure**: Edit your personal wiki completely offline, entirely
+  in your control. Encrypt your notes with GPG. Take lasting notes in
+  plain-text.
+- **Networked Thought**: Connect notes and thoughts together with ease using
+  backlinks. Discover surprising and previously unseen connections in your notes
+  with the built-in graph visualization.
+- **Extensible and Powerful**: Leverage Emacs' fantastic text-editing interface,
+  and the mature Emacs and Org-mode ecosystem of packages.
+- **Free and Open Source**: Org-roam is licensed under the GNU General Public
+  License version 3 or later.
 
-## A Preview
+<p align="center">
+  <img src="https://www.orgroam.com/img/screenshot.png" alt="Org-roam Screenshot" width="738">
+</p>
 
-Here's a screenshot of `org-roam`. The `org-roam` buffer shows
-backlinks for the active org buffer in the left window, as well as the
-surrounding content in the backlink file. The backlink database is
-built asynchronously in the background, and is not noticeable to the
-end user. The graph is generated from the link structure, and can be
-used to navigate to the respective files.
-
-![img](doc/images/org-roam-graph.gif)
+- **[Documentation][docs]**
+- **[Discourse][discourse]**
+- **[Slack][slack]**
+- **[Frequently Asked Questions][faq]**
+- **[Changelog](CHANGELOG.md)**
 
 ## Installation
 
-The recommended method is using use-package and straight, or a similar package manager.
+Down below you will find basic installation instructions for how to quickly
+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`
+<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
-      :after org
-      :hook 
-      (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
-      :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-show-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
+  :straight t
+  ...)
 ```
 
-For more detailed installation instructions (including instructions for
-Spacemacs users), please see [the installation
-documentation](https://org-roam.readthedocs.io/en/develop/installation/).
+If you need to install the package directly from the source repository, instead
+of from MELPA, the next sample shows how to do so:
 
-## Knowledge Bases using Org-Roam
+```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 (9.4 is the minimal required version!)
+- emacsql
+- emacsql-sqlite
+- 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
+
+Before creating a new topic/issue, please be mindful of our time and ensure that
+it has not already been addressed on [GitHub][issues] or on
+[Discourse][discourse].
+
+- If you are new to Emacs and have problem setting up Org-roam, please ask your
+  question on [Slack, channel #how-do-i][slack].
+- For quick questions, please ask them on [Slack, channel
+  #troubleshooting][slack].
+- If something is not working as it should, or if you would like to suggest a
+  new feature, please [create a new issue][issues].
+- If you have questions about your workflow with the slip-box method, please
+  find a relevant topic on [Discourse][discourse], or create a new one.
+
+## Knowledge Bases using Org-roam
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-
-## Changelog
-
-A changelog is being maintained [here](CHANGELOG.md)
+- [Alexey Shmalko](https://www.alexeyshmalko.com/)
+- [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
 
 ## Contributing
 
@@ -77,8 +240,18 @@ request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
 ## License
 
 Copyright © Jethro Kuan and contributors. Distributed under the GNU
-General Public License, Version 3
+General Public License, Version 3.
 
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
-[badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
+[gpl3-badge]: https://img.shields.io/badge/license-GPL_3-green.svg
+[gpl3]: http://www.gnu.org/licenses/gpl-3.0.txt
+[melpa-badge]: https://melpa.org/packages/org-roam-badge.svg
+[melpa]: https://melpa.org/#/org-roam
+[release-badge]: https://img.shields.io/github/v/release/org-roam/org-roam
+[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
+[issues]: https://github.com/org-roam/org-roam/issues
+[faq]: https://www.orgroam.com/manual.html#FAQ

default.mk

@@ -0,0 +1,107 @@
+TOP := $(dir $(lastword $(MAKEFILE_LIST)))
+
+## User options ######################################################
+#
+# You can override these settings in "config.mk" or on the command
+# line.
+#
+# You might also want to set LOAD_PATH.  If you do, then it must
+# contain "-L .".
+#
+# If you don't do so, then the default is set in the "Load-Path"
+# section below.  The default assumes that all dependencies are
+# installed either at "../<DEPENDENCY>", or when using package.el
+# at "ELPA_DIR/<DEPENDENCY>-<HIGHEST-VERSION>".
+
+sharedir ?= $(HOME)/.local/share
+lispdir  ?= $(sharedir)/emacs/site-lisp/org-roam
+infodir  ?= $(sharedir)/info
+docdir   ?= $(sharedir)/doc/org-roam
+statsdir ?= $(TOP)/doc/stats
+
+CP       ?= install -p -m 644
+MKDIR    ?= install -p -m 755 -d
+RMDIR    ?= rm -rf
+TAR      ?= tar
+SED      ?= sed
+
+EMACSBIN ?= emacs
+BATCH     = $(EMACSBIN) -Q --batch $(LOAD_PATH)
+
+INSTALL_INFO     ?= $(shell command -v ginstall-info || printf install-info)
+MAKEINFO         ?= makeinfo
+MANUAL_HTML_ARGS ?= --css-ref /assets/page.css
+
+## Files #############################################################
+
+PKG       = org-roam
+PACKAGES  = org-roam
+
+TEXIPAGES = $(addsuffix .texi,$(PACKAGES))
+INFOPAGES = $(addsuffix .info,$(PACKAGES))
+HTMLFILES = $(addsuffix .html,$(PACKAGES))
+HTMLDIRS  = $(PACKAGES)
+PDFFILES  = $(addsuffix .pdf,$(PACKAGES))
+EPUBFILES = $(addsuffix .epub,$(PACKAGES))
+
+ELS = org-roam.el
+ELS += org-roam-capture.el
+ELS += org-roam-compat.el
+ELS += org-roam-db.el
+ELS += org-roam-mode.el
+ELS += org-roam-node.el
+ELS += org-roam-utils.el
+ELS += extensions/org-roam-dailies.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
+
+## Versions ##########################################################
+
+VERSION ?= $(shell test -e $(TOP).git && git describe --tags --abbrev=0 | cut -c2-)
+
+EMACS_VERSION = 26.1
+
+EMACSOLD := $(shell $(BATCH) --eval \
+  "(and (version< emacs-version \"$(EMACS_VERSION)\") (princ \"true\"))")
+ifeq "$(EMACSOLD)" "true"
+  $(error At least version $(EMACS_VERSION) of Emacs is required)
+endif
+
+## Load-Path #########################################################
+
+ifndef LOAD_PATH
+
+ELPA_DIR ?= $(HOME)/.emacs.d/elpa
+
+SYSTYPE := $(shell $(EMACSBIN) -Q --batch --eval "(princ system-type)")
+ifeq ($(SYSTYPE), windows-nt)
+  CYGPATH := $(shell cygpath --version 2>/dev/null)
+endif
+
+LOAD_PATH = -L $(TOP)
+
+# When making changes here, then don't forget to adjust "Makefile",
+# ".travis.yml", ".github/ISSUE_TEMPLATE/bug_report.md",
+# `magit-emacs-Q-command' and the "Installing from the Git Repository"
+# info node accordingly.  Also don't forget to "rgrep \b<pkg>\b".
+
+endif # ifndef LOAD_PATH
+
+ifndef ORG_LOAD_PATH
+ORG_LOAD_PATH  = $(LOAD_PATH)
+ORG_LOAD_PATH += -L $(TOP)../ox-texinfo-plus
+ORG_LOAD_PATH += -L $(TOP)../org-mode/contrib/lisp
+ORG_LOAD_PATH += -L $(TOP)../org-mode/lisp
+endif
+
+## Publish ###########################################################
+
+PUBLISH_TARGETS ?= html html-dir pdf epub
+
+DOCBOOK_XSL ?= /usr/share/xml/docbook/stylesheet/docbook-xsl/epub/docbook.xsl
+
+EPUBTRASH = epub.xml META-INF OEBPS

doc/AUTHORS.md

@@ -0,0 +1,37 @@
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+- Alexey Shmalko <rasen.dubi@gmail.com>
+- James Ravn <james@r-vn.org>
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Johann Klähn <johann@jklaehn.de>
+- Josh English <josh@joshenglish.com>
+- Jürgen Hötzel <juergen@archlinux.org>
+- Langston Barrett <langston.barrett@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+- Michael Glaesemann <grzm@seespotcode.net>
+- Michael Herold <github@michaeljherold.com>
+- Noboru <noboru.ota@gmail.com>
+- N V <44036031+progfolio@users.noreply.github.com>
+- Rafael Accácio Nogueira <raccacio@poli.ufrj.br>
+- Roland Coeurjoly <rolandcoeurjoly@gmail.com>
+- Sayan <dit7ya@users.noreply.github.com>
+- Tim Quelch <tim@tquelch.com>

doc/Makefile

@@ -0,0 +1,127 @@
+-include ../config.mk
+include ../default.mk
+
+###################################################################
+MANUAL_HTML_ARGS = --css-ref assets/page.css
+
+.PHONY: texi install clean AUTHORS.md stats
+
+all: info
+
+## Build #############################################################
+
+info: $(INFOPAGES) dir
+html: $(HTMLFILES)
+pdf:  $(PDFFILES)
+epub: $(EPUBFILES)
+
+%.info: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --no-split $< -o $@
+
+dir: org-roam.info
+	@printf "Generating dir\n"
+	@echo $^ | xargs -n 1 $(INSTALL_INFO) --dir=$@
+
+%.html: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<
+
+html-dir:
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam.html manual.html
+
+%.pdf: %.texi
+	@printf "Generating $@\n"
+	@texi2pdf --clean $< > /dev/null
+
+%.epub: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --docbook $< -o epub.xml
+	@xsltproc $(DOCBOOK_XSL) epub.xml 2> /dev/null
+	@echo "application/epub+zip" > mimetype
+	@zip -X --quiet --recurse-paths -0 $@ mimetype
+	@zip -X --quiet --recurse-paths -9 --no-dir-entries $@ META-INF OEBPS
+	@$(RMDIR) $(EPUBTRASH)
+
+## Install ###########################################################
+
+install: install-info install-docs
+
+install-docs: install-info
+	@$(MKDIR) $(DESTDIR)$(docdir)
+	$(CP) AUTHORS.md $(DESTDIR)$(docdir)
+
+install-info: info
+	@$(MKDIR) $(DESTDIR)$(infodir)
+	$(CP) $(INFOPAGES) $(DESTDIR)$(infodir)
+
+## Clean #############################################################
+
+clean:
+	@printf "Cleaning doc/*...\n"
+	@$(RMDIR) dir $(INFOPAGES) $(HTMLFILES) $(HTMLDIRS) $(PDFFILES)
+	@$(RMDIR) $(EPUBFILES) $(EPUBTRASH)
+
+## Release management ################################################
+
+ORG_ARGS  = --batch -Q $(ORG_LOAD_PATH)
+ORG_ARGS += -l ox-extra -l ox-texinfo+
+ORG_ARGS += --eval "(or (require 'org-man nil t) (require 'ol-man))"
+ORG_EVAL  = --eval "(ox-extras-activate '(ignore-headlines))"
+ORG_EVAL += --eval "(setq indent-tabs-mode nil)"
+ORG_EVAL += --eval "(setq org-src-preserve-indentation nil)"
+ORG_EVAL += --funcall org-texinfo-export-to-texinfo
+
+# This target first bumps version strings in the Org source.  The
+# necessary tools might be missing so other targets do not depend
+# on this target and it has to be run explicitly when appropriate.
+#
+#   AMEND=t make texi    Update manual to be amended to HEAD.
+#   VERSION=N make texi  Update manual for release.
+#
+texi:
+	@$(EMACSBIN) $(ORG_ARGS) $(PKG).org $(ORG_EVAL)
+	@printf "\n" >> $(PKG).texi
+	@rm -f $(PKG).texi~
+
+stats:
+	@printf "Generating statistics\n"
+	@gitstats -c style=/assets/stats.css -c max_authors=999 $(TOP) $(statsdir)
+
+authors: AUTHORS.md
+
+AUTHORS.md:
+	@printf "Generating AUTHORS.md..."
+	@test -e $(TOP).git \
+	&& (printf "$$AUTHORS_HEADER\n" > $@ \
+	&& git log --pretty=format:'- %aN <%aE>' | sort -u >> $@ \
+	&& printf "done\n" ; ) \
+	|| printf "FAILED (non-fatal)\n"
+
+# Templates ##########################################################
+
+define AUTHORS_HEADER
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+endef
+export AUTHORS_HEADER

doc/assets/page.css

@@ -0,0 +1,68 @@
+:root {
+  --border: #526980;
+  --code: #007;
+}
+
+body {
+    margin: 5ex 10ex;
+    max-width: 80ex;
+    line-height: 1.5;
+    font-family: sans-serif;
+}
+
+h1, h2, h3 {
+    font-weight: normal;
+}
+
+pre, code {
+    font-family: x, monospace;
+}
+
+pre {
+    padding: 1ex;
+    background: #eee;
+    border: solid 1px #ddd;
+    min-width: 0;
+    font-size: 80%;
+    overflow: auto;
+}
+
+code {
+    color: var(--code);
+}
+
+img {
+    max-width: 100%;
+}
+
+table {
+  border-collapse: collapse;
+  width: 100%;
+}
+
+pre.menu-comment {
+  background: none;
+  border: none;
+  font-family: sans-serif;
+  padding: 0;
+  margin: 0;
+  font-size: 100%;
+}
+
+thead {
+  border-bottom: 1px solid var(--border);
+}
+
+tfoot {
+  border-top: 1px solid var(--border);
+}
+
+blockquote {
+  margin-left: 1rem;
+  font-style: italic;
+  font-family: serif;
+  border-left: 3px solid;
+  border-left-color: currentcolor;
+  border-color: var(--text-color);
+  padding-left: 1em;
+}

doc/comparison.md

@@ -1,11 +0,0 @@
----
-title: "Comparing Org-Roam With Other Packages"
-metaTitle: "Comparing Org-Roam With Other Packages"
-metaDescription: "Comparing Org-Roam With Other Packages"
----
-
-# Org-brain
-
-# Zetteldeft
-
-# Org-zettelkasten

doc/configuration.md

@@ -1,121 +0,0 @@
-To ensure that Org-roam remains manageable, the number of
-configuration options is deliberately kept small. However, we have
-attempted to accommodate as many usage styles as possible.
-
-In this section, we'll go over the main customization options
-available to Org-Roam. This section is *crucial*. We need to exploit
-the flexibility of Emacs, and mould our tools exactly to our liking.
-
-All of Org-roam's customization options can be viewed via `M-x
-customize-group org-roam`.
-
-## Setting the Org-roam Directory
-
-Perhaps the single most important variable to set is
-`org-roam-directory`. Set `org-roam-directory` to the folder
-containing all your Org files:
-
-```emacs-lisp
-(setq org-roam-directory "/path/to/org/")
-```
-
-Every Org file, at any level of nesting, within `/path/to/org/` is
-considered part of the Org-roam ecosystem.
-
-## Org-roam Buffer
-
-The Org-roam buffer defaults to popping up from the right. You may
-choose to set it to pop up from the left with `(setq
-org-roam-buffer-position 'left)`.
-
-The Org-roam buffer name can also be renamed: e.g. `(setq
-org-roam-buffer "*my-buffer-name*")`.
-
-The Org-roam buffer width is adjustable via `org-roam-buffer-width`.
-The value of `org-roam-buffer-width` set as a percentage of the total
-frame width. For example:
-
-```emacs-lisp
-(setq org-roam-buffer-width 0.4)
-```
-
-Will result in the Org-roam buffer taking up 40% of the screen width.
-I have found this to be a good number.
-
-## Org-roam Links
-
-By default, links are inserted with the title as the link description.
-This can make them hard to distinguish from external links. If you
-wish, you may choose add special indicators for Org-roam links by
-tweaking `org-roam-link-title-format`, for example:
-
-```emacs-lisp
-(setq org-roam-link-title-format "R:%s")
-```
-
-## Org-roam Files
-
-These customization options revolve around the Org files created and
-managed by Org-roam.
-
-### Automatically Creating Files Using Timestamp
-
-A common hassle is ensuring that files are uniquely named within the
-Org-roam directory. Org-roam's default workflow utilizes the title of
-Org files in all of its main commands (`org-roam-insert`,
-`org-roam-find-file`). Hence, having any unique file name is a decent
-option, and the default workflow uses the timestamp as the filename.
-
-The format of the filename is controlled by the function
-`org-roam-file-name-function`, which defaults to a format like
-`YYYYMMDDHHMMSS_title_here.org`. You may choose to define your own
-function to change this.
-
-If you wish to be prompted to change the file name on creation, set
-`org-roam-filename-noconfirm` to `nil`:
-
-```emacs-lisp
-(setq org-roam-filename-noconfirm nil)
-```
-
-It is then the user's responsibility to ensure that the file names are
-unique.
-
-### Autopopulating Titles
-
-The default workflow uses the title of the Org file in several
-commands. The title is specified via the `#+TITLE:` attribute,
-typically near the top of the file. The option
-`org-roam-autopopulate-title` defaults to `t`. When true, the title
-attribute is automatically inserted into the files created via
-Org-roam commands. Setting it to `nil` will disable this behaviour.
-
-### Encryption
-
-Encryption (via GPG) can be enabled for all new files by setting
-`org-roam-encrypt-files` to `t`. When enabled, new files are created
-with the .org.gpg extension and decryption are handled automatically
-by EasyPG. Note that this causes Emacs to ask for password when the
-cache is built (if you have an encrypted file in `org-roam-directory`)
-as well as each time a new file is created. It might be a good idea to
-cache the password in order to make this more managable.
-
-## Org-roam Graph Viewer
-
-Org-roam generates an SVG image using
-[Graphviz](https://graphviz.org/). To setup graph navigation, see the
-[Graph Setup](graph_setup.md) page.
-
-Org-roam tries its best to locate the Graphviz executable from your
-PATH, but if it fails to do so, you may set it manually:
-
-```
-(setq org-roam-graphviz-executable "/path/to/dot")
-```
-
-Org-roam also attempts to use Firefox (located on PATH) to view the
-SVG, you may choose to set it to any compatible program:
-
-```
-(setq org-roam-graph-viewer "/path/to/image-viewer")
-```

doc/css/styles.css

@@ -0,0 +1,85 @@
+body {
+  margin: 20px;
+  background: #303030;
+  color: #f5f5f5;
+  font-size: 1.6rem;
+  font-weight: 300;
+}
+
+.container {
+  max-width: 800px;
+}
+
+.nav {
+  margin-top: 5rem;
+}
+
+.nav-item a {
+  /* color: #797979; */
+  color: #bebebe;
+  text-decoration: none;
+  font-family: "Consolas", "Monaco", "Menlo", monospace;
+}
+
+.nav-item a:hover {
+  cursor: pointer;
+  /* color: #4d4a4a; */
+  color: #dcdcdc;
+  border: none;
+}
+
+.hero {
+  color: #f5f5f5;
+}
+
+.hero div {
+  margin-bottom: 5rem;
+}
+
+.hero h3 {
+  /* font-family: "Edelsans", sans-serif; */
+  font-size: 5rem;
+  margin-bottom: 0;
+}
+
+.hero h5 {
+  margin-top: 1rem;
+  margin-bottom: 0;
+  /* font-weight: 200; */
+  font-weight: 250;
+}
+
+.grid-demo-col {
+  background: #e4e4e4;
+}
+
+a {
+  color: #cd86ff;
+}
+
+a:hover {
+  color: #dbb9f3;
+}
+
+img {
+  max-width: 100%;
+}
+
+.footer-links {
+  font-size: 1.5rem;
+  color: #f5f5f5;
+  text-decoration: none;
+  font-weight: 250;
+}
+
+.header {
+  font-weight: 200;
+}
+
+#footer {
+  margin-bottom: 3rem;
+}
+
+#footer h5 {
+  margin-bottom: 1.5rem;
+}

doc/ecosystem.md

@@ -1,126 +0,0 @@
-A number of packages work well combined with Org-Roam:
-
-## Deft
-
-[Deft][deft] provides a nice interface for browsing and filtering
-org-roam notes.
-
-```emacs-lisp
-(use-package deft
-  :after org
-  :bind
-  ("C-c n d" . deft)
-  :custom
-  (deft-recursive t)
-  (deft-use-filter-string-for-filename t)
-  (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/"))
-```
-
-If the title of the Org file is not the first line, you might not get
-nice titles. You may choose to patch this to use `org-roam`'s
-functionality. Here I'm using [el-patch](https://github.com/raxod502/el-patch):
-
-```emacs-lisp
-(use-package el-patch
-  :straight (:host github
-                   :repo "raxod502/el-patch"
-                   :branch "develop"))
-
-(eval-when-compile
-  (require 'el-patch))
-
-(use-package deft
-  ;; same as above...
-  :config/el-patch
-  (defun deft-parse-title (file contents)
-    "Parse the given FILE and CONTENTS and determine the title.
-If `deft-use-filename-as-title' is nil, the title is taken to
-be the first non-empty line of the FILE.  Else the base name of the FILE is
-used as title."
-    (el-patch-swap (if deft-use-filename-as-title
-                       (deft-base-filename file)
-                     (let ((begin (string-match "^.+$" contents)))
-                       (if begin
-                           (funcall deft-parse-title-function
-                                    (substring contents begin (match-end 0))))))
-                   (org-roam--get-title-or-slug file))))
-```
-
-The Deft interface can slow down quickly when the number of files get
-huge. [Notdeft][notdeft] is a fork of Deft that uses an external
-search engine and indexer.
-
-## Org-journal
-
-[Org-journal](https://github.com/bastibe/org-journal) is a more
-powerful alternative to the simple function `org-roam-today`. It
-provides better journaling capabilities, and a nice calendar interface
-to see all dated entries.
-
-```emacs-lisp
-(use-package org-journal
-  :bind
-  ("C-c n j" . org-journal-new-entry)
-  :custom
-  (org-journal-date-prefix "#+TITLE: ")
-  (org-journal-file-format "%Y-%m-%d.org")
-  (org-journal-dir "/path/to/org-roam-files/")
-  (org-journal-date-format "%A, %d %B %Y"))
-```
-
-## Note-taking Add-ons
-
-These are some plugins that make note-taking in Org-mode more
-enjoyable.
-
-### Org-download
-
-[Org-download][org-download] lets you screenshot and yank images from
-the web into your notes:
-
-![org-download](images/org-download.gif)
-
-```emacs-lisp
-(use-package org-download
-  :after org
-  :bind
-  (:map org-mode-map
-        (("s-Y" . org-download-screenshot)
-         ("s-y" . org-download-yank))))
-```
-
-### mathpix.el
-
-[mathpix.el][mathpix-el] uses [Mathpix's](https://mathpix.com/) API to convert clips into
-latex equations:
-
-![mathpix](images/mathpix.gif)
-
-```emacs-lisp
-(use-package mathpix.el
-  :straight (:host github :repo "jethrokuan/mathpix.el")
-  :custom ((mathpix-app-id "app-id")
-           (mathpix-app-key "app-key"))
-  :bind
-  ("C-x m" . mathpix-screenshot))
-```
-
-### Org-noter / Interleave
-
-[Org-noter][org-noter] and [Interleave][interleave] are both projects
-that allow synchronised annotation of documents (PDF, EPUB etc.)
-within Org-mode.
-
-### Org-ref
-
-[Org-ref][org-ref] does citation and bibliography management in
-Org-mode, and a great tool for scientific notes.
-
-[deft]: https://jblevins.org/projects/deft/
-[notdeft]: https://github.com/hasu/notdeft
-[org-download]: https://github.com/abo-abo/org-download
-[mathpix-el]: https://github.com/jethrokuan/mathpix.el
-[org-noter]: https://github.com/weirdNox/org-noter
-[interleave]: https://github.com/rudolfochrist/interleave
-[org-ref]: https://github.com/jkitchin/org-ref

doc/graph_setup.md

@@ -1,78 +0,0 @@
-The setup is similar to that of org-protocol. Here `roam://` links are
-defined, and need to be associated with an application. 
-
-The gist of the setup is setting up a Bash script to trim off the
-`roam://` prefix from the link, causing the desktop application to
-call `emacsclient path/to/org-roam-file.org`.
-
-## Linux
-
-Create a desktop application. I place mine in
-`~/.local/share/applications/roam.desktop`:
-
-```
-[Desktop Entry]
-Name=Org-Roam Client
-Exec=/home/jethro/.local/bin/launch_emacs %u
-Icon=emacs-icon
-Type=Application
-Terminal=false
-MimeType=x-scheme-handler/roam
-```
-
-Note the `Exec` key is set to a bash script poorly named
-`launch_emacs`. You can set it to whatever you want.
-
-Create the corresponding bash script, and make it executable. Here's
-how it looks like:
-
-```bash
-#!/usr/bin/env bash
-emacsclient "${1#*:}"
-```
-
-Finally, associate `roam://` links with the desktop application by
-running in your shell:
-
-```bash
-xdg-mime default roam.desktop x-scheme-handler/roam
-```
-
-## Mac OS
-
-One solution to this, recommended in [Issue
-#115](https://github.com/jethrokuan/org-roam/issues/115), is to use
-[Platypus](https://github.com/sveinbjornt/Platypus). Here are the
-instructions for setting up with Platypus and Chrome:
-
-1. Create an executable `launch-emacs.sh` script:
-
-```sh
-#!/usr/bin/env bash
-/usr/local/bin/emacsclient --no-wait "${1#*:}"
-```
-
-2. Install and launch Platypus (with [Homebrew](https://brew.sh/)):
-
-```sh
-brew cask install playtpus
-```
-
-3. Playtpus settings:
-
-- App Name: `OrgRoam`
-- Script Type: `env` and `/usr/bin/env`
-- Script Path: `/path/to/your/launch-emacs.sh`
-- Tick Accept dropped items and click Settings
-- Tick Accept dropped files
-- Tick Register as URI scheme handler
-- Add `roam` as a protocol
-- Create the app
-
-To disable the "confirm" prompt in Chrome, you can also make Chrome
-show a checkbox to tick, so that the `OrgRoam` app will be used
-without confirmation. To do this, run in a shell:
-
-```sh
-defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
-```

doc/htmlxref.cnf

@@ -0,0 +1,15 @@
+# https://www.gnu.org/software/texinfo/manual/texinfo/html_node/HTML-Xref-Configuration.html
+
+EMACS = https://www.gnu.org/software/emacs/manual
+
+auth		mono	${EMACS}/html_mono/auth.html
+auth		node	${EMACS}/html_node/auth/
+
+ediff		mono	${EMACS}/html_mono/ediff.html
+ediff		node	${EMACS}/html_node/ediff/
+
+elisp		mono	${EMACS}/html_mono/elisp.html
+elisp		node	${EMACS}/html_node/elisp/
+
+emacs		mono	${EMACS}/html_mono/emacs.html
+emacs		node	${EMACS}/html_node/emacs/

doc/index.html

@@ -0,0 +1,168 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="description" content="An Effortless PKM System." />
+    <meta name="author" content="Org-roam Contributors" />
+
+    <title>Org-roam</title>
+
+    <link rel="stylesheet" href="https://unpkg.com/wingcss" />
+    <link rel="stylesheet" type="text/css" href="./css/styles.css" />
+
+    <script src="https://code.iconify.design/1/1.0.6/iconify.min.js"></script>
+  </head>
+
+  <body>
+    <section class="hero container center text-center">
+      <div>
+        <img src="./img/logo.png" alt="Org-roam Logo" height="200" />
+        <h3>Org-roam</h3>
+        <h5>A plain-text personal knowledge management system.</h5>
+      </div>
+    </section>
+
+    <section class="container center">
+      <div>
+        <img src="./img/screenshot.png" alt="screenshot" />
+      </div>
+    </section>
+
+    <section id="features" class="container center">
+      <div>
+        <h3 class="header">FEATURES</h3>
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="fxemoji:lock"></iconify-icon> &nbsp;
+              Private and Secure
+            </h5>
+            <p class="content">
+              Edit your personal wiki completely offline, entirely in your
+              control. Encrypt your notes with GPG. Take lasting notes in
+              plain-text.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="flat-color-icons:link"></iconify-icon>
+              &nbsp; Make Connections
+            </h5>
+            <p class="content">
+              Connect notes and thoughts together with ease using backlinks.
+              Discover surprising and previously unseen connections in your
+              notes with the built-in graph visualization.
+            </p>
+          </div>
+        </div>
+
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="twemoji:puzzle-piece"></iconify-icon>
+              &nbsp; Extensible and Powerful
+            </h5>
+            <p class="content">
+              Leverage Emacs' fantastic text-editing interface, and the mature
+              Emacs and Org-mode ecosystem of packages.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="logos:git-icon"></iconify-icon> &nbsp;
+              Free and Open Source
+            </h5>
+            <p class="content">
+              Org-roam is licensed under the GNU General Public License version
+              3 or later. You are free to extend its functionality and
+              contribute back. Find
+              us <a href="https://github.com/org-roam/org-roam">here</a>.
+            </p>
+          </div>
+        </div>
+      </div>
+    </section>
+    
+    <section id="links" class="container">
+      <div>
+        <h3 class="header">LINKS</h3> New to Emacs and Org-mode, and trying to
+        find your way around? Org-roam has an inclusive community of users
+        passionate about Personal Knowledge Management -- we're happy to help!
+        You can find us on Discourse and Slack.
+        
+        <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>
+          </ul>
+      </div>
+    </section>
+
+    <section id="footer" class="row container">
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Ecosystem</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-bibtex"
+            >org-roam-bibtex</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-ui"
+            >org-roam-ui</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Resources</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc"
+            >Open Issues</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/releases"
+            >Releases</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Connect</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-wuoize1z-x3UyQnQ0WHF0RhuEQ2NLnQ"
+            >Slack</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://org-roam.discourse.group/"
+            >Discourse</a
+          >
+        </div>
+      </div>
+    </section>
+  </body>
+</html>

doc/index.md

@@ -1,41 +0,0 @@
-![org-roam][org-roam-intro-image]
-
-## What is Org-Roam?
-
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
-
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. To understand more about Roam, I recommend
-the following links:
-
--   [Building a second brain in
-    Roam](https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)
--   [Roam: Why I Love It and How I Use
-    It](https://www.nateliason.com/blog/roam)
-
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem. 
-
-## Why build Org-Roam?
-
-With Org-roam, you:
-
-1. Never have to leave Emacs.
-2. Can leverage all the powerful features of Org-mode: LaTeX, tables,
-   and the whole to-do ecosystem (org-agenda etc.)
-3. Be in full control your second brain, and access it offline. Never
-   share your data with anyone
-
-There are several packages that are similar to Org-roam, see the
-[Comparison](comparison.md) page for a detailed comparison.
-
-## Project Status
-
-As of February 2020, it is in a very early stage of development. 
-
-[org-roam-intro-image]: images/org-roam-intro.png
-[roamresearch]: https://www.roamresearch.com/
-[org]: https://orgmode.org/

doc/installation.md

@@ -1,93 +0,0 @@
-## Installation
-
-The recommended method is using [use-package][use-package] and
-[straight][straight], or a similar package manager.
-
-```
-(use-package org-roam
-      :after org
-      :hook 
-      (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
-      :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-show-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-If not using package.el, you can also clone it into your Emacs
-directory and add it to your load path:
-
-```
-git clone https://github.com/jethrokuan/org-roam/ ~/.emacs.d/elisp/org-roam
-```
-
-```
-(use-package org-roam
-      :after org
-      :load-path "elisp/"
-      :hook 
-      (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
-      :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-show-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-Or without use-package:
-
-```
-(add-to-list 'load-path "./elisp")
-(require 'org-roam)
-```
-
-There are a number of important configuration options, that greatly
-affect the Roam workflow. Do look through them at the
-[Configuration](configuration.md) page.
-
-[use-package]: https://github.com/jwiegley/use-package
-[straight]: https://github.com/raxod502/straight.el
-
-## Spacemacs
-If you are using Spacemacs, you can easily install org-roam by creating a simple layer that wraps org-roam. Paste the following into a new file `/.emacs.d/private/org-roam/packages.el`.
-```
-(defconst org-roam-packages
-  '((org-roam :location
-        (recipe :fetcher github :repo "jethrokuan/org-roam" :branch "develop"))))
-
-(defun org-roam/init-org-roam ()
-    (use-package org-roam
-        :after org
-        :hook
-        (after-init . org-roam-mode)
-        :custom
-        (org-roam-directory "/path/to/org-files/")
-        :init
-        (progn
-          (spacemacs/declare-prefix "ar" "org-roam")
-          (spacemacs/set-leader-keys
-            "arl" 'org-roam
-            "art" 'org-roam-today
-            "arf" 'org-roam-find-file
-            "arg" 'org-roam-show-graph)
-
-          (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
-          (spacemacs/set-leader-keys-for-major-mode 'org-mode
-            "rl" 'org-roam
-            "rt" 'org-roam-today
-            "rb" 'org-roam-switch-to-buffer
-            "rf" 'org-roam-find-file
-            "ri" 'org-roam-insert
-            "rg" 'org-roam-show-graph))))
-```
-
-Next, append `org-roam` to the `dotspacemacs-configuration-layers` list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or restart Emacs to load `org-roam`. It's functions are available under the prefix `SPC a r` and `, r` when visiting an org-mode buffer. 

doc/notetaking_workflow.md

@@ -1,20 +0,0 @@
-## Recommended Books
-- [How to Take Smart Notes][1]
-
-## Articles
-- [How to Take Smart Notes in Org-mode - Jethro Kuan][7]
-- [The Zettelkasten Method - LessWrong 2.0][3]
-- [Building a second brain in Roam][4]
-- [Roam: Why I Love It and How I Use It][5]
-- [Adam Keesling's Twitter Thread][6]
-
-## What to Do With Your Notes
-- [How to Use Roam to Outline a New Article in Under 20 Minutes][2]
-
-[1]: https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes?ac=1&from_search=true&qid=6L8iEE1FIA&rank=1
-[2]: https://www.youtube.com/watch?v=RvWic15iXjk
-[3]: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1
-[4]: https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might
-[5]: https://www.nateliason.com/blog/roam
-[6]: https://twitter.com/adam_keesling/status/1196864424725774336?s=20
-[7]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

doc/requirements.txt

@@ -1,2 +0,0 @@
-mkdocs-material==4.6.2
-pymdown-extensions==6.3

doc/tour.md

@@ -1,69 +0,0 @@
-Org-roam was built to support a workflow that was not possible with
-vanilla Org-mode. This flow is modelled after the [Zettelkasten
-method][zettelkasten], and many of [Roam Research][roam]'s workflows.
-Understanding this flow is crucial! Org-roam doesn't auto-magically
-make your note-taking better -- it's changing the note-taking workflow
-that does.
-
-To understand more the methods and madness, the [Note-Taking
-Workflow][appendix:ntw] page contains a page of useful references.
-I've also written [a post][jethro-blog-post] about how I use Org-roam.
-
-Without further ado, let's begin!
-
-## Building the Cache
-
-Assuming you've set `org-roam-directory` appropriately, running `M-x
-org-roam--build-cache-async` should build up the caches that will
-allow you to begin using Org-roam. I do this on startup:
-
-```emacs-lisp
-(add-hook 'after-init-hook 'org-roam--build-cache-async)
-```
-
-## Finding a Note
-
-`org-roam-find-file` shows you the list of notes you currently have in
-Org-roam. Selecting the title will bring you to the corresponding
-note. Entering a title of a note that does not yet exist will create a
-new note with that title.
-
-![org-roam-find-file](images/org-roam-find-file.gif)
-
-## Inserting Links
-
-Within your Org-roam notes, you are encouraged to liberally insert
-links to existing (or new) Org-roam notes with `org-roam-insert`.
-Entering a non-existent title will also create a new note with that
-title.
-
-![org-roam-insert](images/org-roam-insert-filetag.gif)
-
-It is crucial for good usage of Org-roam to insert links liberally,
-where you want them the notes to resurface!
-
-## The Org-roam Buffer
-
-All of Org-roam's operations are designed such that the built cache is
-a consistent view of the inter-connectivity between your notes. The
-Org-roam buffer shows backlinks: i.e. the files that link to the
-currently viewed file, along with some surrounding context. The
-Org-roam buffer will always show the backlinks for the current
-Org-roam file in view.
-
-![org-roam-buffer](images/org-roam-buffer.gif)
-
-## Exporting the Graph
-
-It's also possible to export the links as a graph, using graphviz. The
-generated graph is navigable in Emacs, but requires some additional
-setup, which I describe in the [Graph Appendix][appendix:graph-setup]
-page.
-
-![org-roam-graph](images/org-roam-graph.gif)
-
-[zettelkasten]: https://zettelkasten.de/
-[appendix:ntw]: notetaking_workflow.md
-[appendix:graph-setup]: graph_setup.md
-[roam]: https://www.roamresearch.com/
-[jethro-blog-post]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

extensions/org-roam-dailies.el

@@ -0,0 +1,366 @@
+;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;;
+;; Copyright © 2020-2022 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: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (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 provides functionality for creating daily-notes, or shortly
+;; "dailies". Dailies implemented here as a unique node per unique file, where
+;; 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)
+(require '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
+(defcustom org-roam-dailies-directory "daily/"
+  "Path to daily-notes.
+This path is relative to `org-roam-directory'."
+  :group 'org-roam
+  :type 'string)
+
+(defcustom org-roam-dailies-find-file-hook nil
+  "Hook that is run right after navigating to a daily-note."
+  :group 'org-roam
+  :type 'hook)
+
+(defcustom org-roam-dailies-capture-templates
+  `(("d" "default" entry
+     "* %?"
+     :target (file+head "%<%Y-%m-%d>.org"
+                        "#+title: %<%Y-%m-%d>\n")))
+  "Capture templates for daily-notes in Org-roam.
+Note that for daily files to show up in the calendar, they have to be of format
+\"org-time-string.org\".
+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))))))))
+
+;;; Commands
+;;;; Today
+;;;###autoload
+(defun org-roam-dailies-capture-today (&optional goto keys)
+  "Create an entry in the daily-note for today.
+When GOTO is non-nil, go the note without creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto 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))
+
+;;;; Tomorrow
+;;;###autoload
+(defun org-roam-dailies-capture-tomorrow (n &optional goto keys)
+  "Create an entry in the daily-note for tomorrow.
+
+With numeric argument N, use the daily-note N days in the future.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry.
+
+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))
+
+;;;###autoload
+(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.
+
+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))
+
+;;;; Yesterday
+;;;###autoload
+(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.
+
+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))
+
+;;;###autoload
+(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.
+
+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))
+
+;;;; Date
+;;;###autoload
+(defun org-roam-dailies-capture-date (&optional goto prefer-future keys)
+  "Create an entry in the daily-note for a date using the calendar.
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry.
+
+ELisp programs can set KEYS to a string associated with a template.
+In this case, interactive selection will be bypassed."
+  (interactive "P")
+  (let ((time (let ((org-read-date-prefer-future prefer-future))
+                (org-read-date nil t nil (if goto
+                                             "Find daily-note: "
+                                           "Capture to daily-note: ")))))
+    (org-roam-dailies--capture time goto keys)))
+
+;;;###autoload
+(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.
+
+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))
+
+;;;; Navigation
+(defun org-roam-dailies-goto-next-note (&optional n)
+  "Find next daily-note.
+
+With numeric argument N, find note N days in the future. If N is
+negative, find note N days in the past."
+  (interactive "p")
+  (unless (org-roam-dailies--daily-note-p)
+    (user-error "Not in a daily-note"))
+  (setq n (or n 1))
+  (let* ((dailies (org-roam-dailies--list-files))
+         (position
+          (cl-position-if (lambda (candidate)
+                            (string= (buffer-file-name (buffer-base-buffer)) candidate))
+                          dailies))
+         note)
+    (unless position
+      (user-error "Can't find current note file - have you saved it yet?"))
+    (pcase n
+      ((pred (natnump))
+       (when (eq position (- (length dailies) 1))
+         (user-error "Already at newest note")))
+      ((pred (integerp))
+       (when (eq position 0)
+         (user-error "Already at oldest note"))))
+    (setq note (nth (+ position n) dailies))
+    (find-file note)
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-goto-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)))
+
+(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 (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 "y") #'org-roam-dailies-goto-yesterday)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-goto-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 "b") #'org-roam-dailies-goto-previous-note)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-goto-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)
+
+(provide 'org-roam-dailies)
+
+;;; org-roam-dailies.el ends here

extensions/org-roam-export.el

@@ -0,0 +1,75 @@
+;;; org-roam-export.el --- Org-roam org-export tweaks -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (org "9.4") (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

@@ -0,0 +1,302 @@
+;;; org-roam-graph.el --- Basic graphing functionality for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (org "9.4") (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

@@ -0,0 +1,96 @@
+;;; org-roam-overlay.el --- Link overlay for [id:] links to Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (org "9.4") (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

@@ -0,0 +1,174 @@
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (org "9.4") (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

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

mkdocs.yml

@@ -1,33 +0,0 @@
-site_name: "Org-Roam: Roam + Org-Mode = ♥"
-repo_url: https://github.com/jethrokuan/org-roam/
-edit_uri: edit/master/doc/
-copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
-docs_dir: doc
-nav:
-- Home: index.md
-- A Tour of Org-Roam: tour.md
-- Installation: installation.md
-- Configuration: configuration.md
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.md
-- "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Graph Setup": graph_setup.md
-markdown_extensions:
-  - admonition
-  - pymdownx.betterem:
-      smart_enable: all
-  - pymdownx.caret
-  - pymdownx.critic
-  - pymdownx.details
-  - pymdownx.mark
-  - pymdownx.smartsymbols
-  - pymdownx.superfences
-  - pymdownx.tasklist:
-      custom_checkbox: true
-  - pymdownx.tilde
-
-theme:
-  name: 'material'
-  palette:
-    primary: 'deep purple'
-    accent: 'deep purple'

org-roam-capture.el

@@ -0,0 +1,829 @@
+;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (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 `org-capture' functionality for Org-roam. With this
+;; module the user can capture new nodes or capture new content to existing
+;; nodes.
+;;
+;;; Code:
+(require 'org-roam)
+
+;;;; Declarations
+(defvar org-end-time-was-given)
+
+;;; Options
+(defcustom org-roam-capture-templates
+  '(("d" "default" plain "%?"
+     :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                        "#+title: ${title}\n")
+     :unnarrowed t))
+  "Templates for the creation of new entries within Org-roam.
+
+Each entry is a list with the following items:
+
+keys   The keys that will select the template, as a string, characters only, for
+       example \"a\" for a template to be selected with a single key, or
+       \"bt\" for selection with two keys. When using several keys, keys
+       using the same prefix must be together in the list and preceded by a
+       2-element entry explaining the prefix key, for example:
+
+                   (\"b\" \"Templates for marking stuff to buy\")
+
+       The \"C\" key is used by default for quick access to the customization of
+       the template variable. But if you want to use that key for a template,
+       you can.
+
+description   A short string describing the template, which will be shown
+              during selection.
+
+type       The type of entry. Valid types are:
+               entry       an Org node, with a headline.  Will be filed
+                           as the child of the target entry or as a
+                           top level entry.  Its default template is:
+                             \"* %?\n %a\"
+               item        a plain list item, will be placed in the
+                           first plain list at the target location.
+                           Its default template is:
+                             \"- %?\"
+               checkitem   a checkbox item.  This differs from the
+                           plain list item only in so far as it uses a
+                           different default template.  Its default
+                           template is:
+                             \"- [ ] %?\"
+               table-line  a new line in the first table at target location.
+                           Its default template is:
+                             \"| %? |\"
+               plain       text to be inserted as it is.
+
+template     The template for creating the capture item.
+             If it is an empty string or nil, a default template based on
+             the entry type will be used (see the \"type\" section above).
+             Instead of a string, this may also be one of:
+
+                 (file \"/path/to/template-file\")
+                 (function function-returning-the-template)
+
+             in order to get a template from a file, or dynamically
+             from a function.
+
+The template contains a compulsory :target property. The :target property
+contains a list, where:
+  - The first element indicates the type of the target.
+  - The second element indicates the location of the captured node.
+  - And the rest of the list indicate the prefilled template, that will be
+    inserted and the position of the point will be adjusted for.
+    This behavior varies from type to type.
+
+The following options are supported for the :target property:
+
+   (file \"path/to/file\")
+       The file will be created, and prescribed an ID.
+
+   (file+head \"path/to/file\" \"head content\")
+       The file will be created, prescribed an ID, and head content will be
+       inserted if the node is a newly captured one.
+
+   (file+olp \"path/to/file\" (\"h1\" \"h2\"))
+       The file will be created, prescribed an ID. If the file doesn't contain
+       the outline path (h1, h2), it will be automatically created. The point
+       will be adjusted to the last element in the OLP.
+
+   (file+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.
+       If the file doesn't contain the outline path (h1, h2), it will be
+       automatically created. The point will be adjusted to the last element in
+       the OLP.
+
+   (file+datetree \"path/to/file\" 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:
+
+ :prepend            Normally newly captured information will be appended at
+                     the target location (last child, last table line,
+                     last list item...).  Setting this property will
+                     change that.
+
+ :immediate-finish   When set, do not offer to edit the information, just
+                     file it away immediately.  This makes sense if the
+                     template only needs information that can be added
+                     automatically.
+
+ :jump-to-captured   When set, jump to the captured entry when finished.
+
+ :empty-lines        Set this to the number of lines that should be inserted
+                     before and after the new item.  Default 0, only common
+                     other value is 1.
+
+ :empty-lines-before Set this to the number of lines that should be inserted
+                     before the new item.  Overrides :empty-lines for the
+                     number lines inserted before.
+
+ :empty-lines-after  Set this to the number of lines that should be inserted
+                     after the new item.  Overrides :empty-lines for the
+                     number of lines inserted after.
+
+ :clock-in           Start the clock in this item.
+
+ :clock-keep         Keep the clock running when filing the captured entry.
+
+ :clock-resume       Start the interrupted clock when finishing the capture.
+                     Note that :clock-keep has precedence over :clock-resume.
+                     When setting both to t, the current clock will run and
+                     the previous one will not be resumed.
+
+ :time-prompt        Prompt for a date/time to be used for date/week trees
+                     and when filling the template.
+
+ :tree-type          When `week', make a week tree instead of the month-day
+                     tree.  When `month', make a month tree instead of the
+                     month-day tree.
+
+ :unnarrowed         Do not narrow the target buffer, simply show the
+                     full buffer.  Default is to narrow it so that you
+                     only see the new stuff.
+
+ :table-line-pos     Specification of the location in the table where the
+                     new line should be inserted.  It should be a string like
+                     \"II-3\", meaning that the new line should become the
+                     third line before the second horizontal separator line.
+
+ :kill-buffer        If the target file was not yet visited by a buffer when
+                     capture was invoked, kill the buffer again after capture
+                     is finalized.
+
+ :no-save            Do not save the target file after finishing the capture.
+
+The template defines the text to be inserted.  Often this is an
+Org mode entry (so the first line should start with a star) that
+will be filed as a child of the target headline.  It can also be
+freely formatted text.  Furthermore, the following %-escapes will
+be replaced with content and expanded:
+
+  %[pathname] Insert the contents of the file given by
+              `pathname'.  These placeholders are expanded at the very
+              beginning of the process so they can be used to extend the
+              current template.
+  %(sexp)     Evaluate elisp `(sexp)' and replace it with the results.
+              Only placeholders pre-existing within the template, or
+              introduced with %[pathname] are expanded this way.  Since this
+              happens after expanding non-interactive %-escapes, those can
+              be used to fill the expression.
+  %<...>      The result of `format-time-string' on the ... format
+              specification.
+  %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.
+  %T          Time stamp as above, with date and time.
+  %u, %U      Like the above, but inactive time stamps.
+  %i          Initial content, copied from the active region.  If
+              there is text before %i on the same line, such as
+              indentation, and %i is not inside a %(sexp), that prefix
+              will be added before every line in the inserted text.
+  %a          Annotation, normally the link created with `org-store-link'.
+  %A          Like %a, but prompt for the description part.
+  %l          Like %a, but only insert the literal link.
+  %L          Like %l, but without brackets (the link content itself).
+  %c          Current kill ring head.
+  %x          Content of the X clipboard.
+  %k          Title of currently clocked task.
+  %K          Link to currently clocked task.
+  %n          User name (taken from the variable `user-full-name').
+  %f          File visited by current buffer when `org-capture' was called.
+  %F          Full path of the file or directory visited by current buffer.
+  %:keyword   Specific information for certain link types, see below.
+  %^g         Prompt for tags, with completion on tags in target file.
+  %^G         Prompt for tags, with completion on all tags in all agenda files.
+  %^t         Like %t, but prompt for date.  Similarly %^T, %^u, %^U.
+              You may define a prompt like: %^{Please specify birthday}t.
+              The default date is that of %t, see above.
+  %^C         Interactive selection of which kill or clip to use.
+  %^L         Like %^C, but insert as link.
+  %^{prop}p   Prompt the user for a value for property `prop'.
+              A default value can be specified like this:
+              %^{prop|default}p.
+  %^{prompt}  Prompt the user for a string and replace this sequence with it.
+              A default value and a completion table can be specified like this:
+              %^{prompt|default|completion2|completion3|...}.
+  %?          After completing the template, position cursor here.
+  %\\1 ... %\\N Insert the text entered at the nth %^{prompt}, where N
+              is a number, starting from 1.
+
+Apart from these general escapes, you can access information specific to
+the link type that is created.  For example, calling `org-capture' in emails
+or in Gnus will record the author and the subject of the message, which you
+can access with \"%:from\" and \"%:subject\", respectively.  Here is a
+complete list of what is recorded for each link type.
+
+Link type               |  Available information
+------------------------+------------------------------------------------------
+bbdb                    |  %:type %:name %:company
+vm, wl, mh, mew, rmail, |  %:type %:subject %:message-id
+gnus                    |  %:from %:fromname %:fromaddress
+                        |  %:to   %:toname   %:toaddress
+                        |  %:fromto (either \"to NAME\" or \"from NAME\")
+                        |  %:date %:date-timestamp (as active timestamp)
+                        |  %:date-timestamp-inactive (as inactive timestamp)
+gnus                    |  %:group, for messages also all email fields
+eww, w3, w3m            |  %:type %:url
+info                    |  %:type %:file %:node
+calendar                |  %:type %:date
+
+When you need to insert a literal percent sign in the template,
+you can escape ambiguous cases with a backward slash, e.g., \\%i.
+
+In addition to all of the above, Org-roam supports additional
+substitutions within its templates. \"${foo}\" will look for the
+foo property in the Org-roam node (see the `org-roam-node'). If
+the property does not exist, the user will be prompted to fill in
+the string value.
+
+Org-roam templates are NOT compatible with regular Org capture:
+they rely on additional hacks and hooks to achieve the
+streamlined user experience in Org-roam."
+  :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))))))))
+
+(defcustom org-roam-capture-new-node-hook nil
+  "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."
+  :group 'org-roam
+  :type 'hook)
+
+(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
+valid for the capture (i.e. initialization, and finalization of
+the capture)."
+  (plist-get org-capture-plist :org-roam))
+
+(defun org-roam-capture--get (keyword)
+  "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)
+  "Set property PROP to VALUE in the `org-roam-capture-template'."
+  (let ((p (plist-get org-capture-plist :org-roam)))
+    (setq org-capture-plist
+          (plist-put org-capture-plist
+                     :org-roam
+                     (plist-put p prop value)))))
+
+;;;; Capture target
+(defun org-roam-capture--prepare-buffer ()
+  "Prepare the capture buffer for the current Org-roam based capture template.
+This function will initialize and setup the capture buffer,
+position the point to the current :target (and if necessary,
+create it if it doesn't exist), and place the point for further
+processing by `org-capture'.
+
+Note: During the capture process this function is run by
+`org-capture-set-target-location', as a (function ...) based
+capture target."
+  (let ((id (cond ((run-hook-with-args-until-success 'org-roam-capture-preface-hook))
+                  (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 ()
+  "Initialize the buffer, and goto the location of the new capture.
+Return the ID of the location."
+  (let (p new-file-p)
+    (pcase (org-roam-capture--get-target)
+      (`(file ,path)
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
+       (when new-file-p (org-roam-capture--put :new-file path))
+       (set-buffer (org-capture-target-buffer path))
+       (widen)
+       (setq p (goto-char (point-min))))
+      (`(file+olp ,path ,olp)
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
+       (when new-file-p (org-roam-capture--put :new-file path))
+       (set-buffer (org-capture-target-buffer path))
+       (setq p (point-min))
+       (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)
+             new-file-p (org-roam-capture--new-file-p path))
+       (set-buffer (org-capture-target-buffer path))
+       (when new-file-p
+         (org-roam-capture--put :new-file path)
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+       (widen)
+       (setq p (goto-char (point-min))))
+      (`(file+head+olp ,path ,head ,olp)
+       (setq path (org-roam-capture--target-truepath path)
+             new-file-p (org-roam-capture--new-file-p path))
+       (set-buffer (org-capture-target-buffer path))
+       (widen)
+       (when new-file-p
+         (org-roam-capture--put :new-file path)
+         (insert (org-roam-capture--fill-template head 'ensure-newline)))
+       (setq p (point-min))
+       (let ((m (org-roam-capture-find-or-create-olp olp)))
+         (goto-char m)))
+      (`(file+datetree ,path ,tree-type)
+       (setq path (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))))
+         (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)))))
+    ;; Setup `org-id' for the current capture target and return it back to the
+    ;; caller.
+    (save-excursion
+      (goto-char p)
+      (if-let ((id (org-entry-get p "ID")))
+          (setf (org-roam-node-id org-roam-capture--node) id)
+        (org-entry-put p "ID" (org-roam-node-id org-roam-capture--node)))
+      (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.
+If OLP does not exist, create it. If anything goes wrong, throw
+an error, and if you need to do something based on this error,
+you can catch it with `condition-case'."
+  (let* ((level 1)
+         (lmin 1)
+         (lmax 1)
+         (start (point-min))
+         (end (point-max))
+         found flevel)
+    (unless (derived-mode-p 'org-mode)
+      (error "Buffer %s needs to be in Org mode" (current-buffer)))
+    (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))
+         (while (re-search-forward re end t)
+           (setq level (- (match-end 1) (match-beginning 1)))
+           (when (and (>= level lmin) (<= level lmax))
+             (setq found (match-beginning 0) flevel level cnt (1+ cnt))))
+         (when (> cnt 1)
+           (error "Heading not unique on level %d: %s" lmax heading))
+         (when (= cnt 0)
+           ;; 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))
+           (unless (= lmax 1)
+             (dotimes (_ level) (org-do-demote)))
+           (insert heading)
+           (setq end (point))
+           (goto-char start)
+           (while (re-search-forward re end t)
+             (setq level (- (match-end 1) (match-beginning 1)))
+             (when (and (>= level lmin) (<= level lmax))
+               (setq found (match-beginning 0) flevel level cnt (1+ cnt))))))
+       (goto-char found)
+       (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))))
+
+(defun org-roam-capture--adjust-point-for-capture-type (&optional pos)
+  "Reposition the point for template insertion dependently on the capture type.
+Return the newly adjusted position of `point'.
+
+POS is the current position of point (an integer) inside the
+currently active capture buffer, where the adjustment should
+start to begin from. If it's nil, then it will default to
+the current value of `point'."
+  (or pos (setq pos (point)))
+  (goto-char pos)
+  (let ((location-type (if (= pos 1) 'beginning-of-file 'heading-at-point)))
+    (and (eq location-type 'heading-at-point)
+         (cl-assert (org-at-heading-p)))
+    (pcase (org-capture-get :type)
+      (`plain
+       (cl-case location-type
+         (beginning-of-file
+          (if (org-capture-get :prepend)
+              (let ((el (org-element-at-point)))
+                (while (and (not (eobp))
+                            (memq (org-element-type el)
+                                  '(drawer property-drawer keyword comment comment-block horizontal-rule)))
+                  (goto-char (org-element-property :end el))
+                  (setq el (org-element-at-point))))
+            (goto-char (org-entry-end-position))))
+         (heading-at-point
+          (if (org-capture-get :prepend)
+              (org-end-of-meta-data t)
+            (goto-char (org-entry-end-position))))))))
+  (point))
+
+;;; Capture implementation
+(add-hook 'org-roam-capture-preface-hook #'org-roam-capture--try-capture-to-ref-h)
+(defun org-roam-capture--try-capture-to-ref-h ()
+  "Try to capture to an existing node that match the ref."
+  (when-let ((node (and (plist-get org-roam-capture--info :ref)
+                        (org-roam-node-from-ref
+                         (plist-get org-roam-capture--info :ref)))))
+    (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+    (goto-char (org-roam-node-point node))
+    (widen)
+    (org-roam-node-id node)))
+
+(add-hook 'org-roam-capture-new-node-hook #'org-roam-capture--insert-captured-ref-h)
+(defun org-roam-capture--insert-captured-ref-h ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
+;;;; Finalizers
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize-h)
+(defun org-roam-capture--install-finalize-h ()
+  "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."
+  (when-let ((region (org-roam-capture--get :region)))
+    (org-roam-unshield-region (car region) (cdr region)))
+  (if org-note-abort
+      (when-let ((new-file (org-roam-capture--get :new-file))
+                 (_ (yes-or-no-p "Delete file for aborted capture?")))
+        (when (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)))
+        (org-roam-unshield-region (car region) (cdr region))
+        (delete-region (car region) (cdr region))
+        (set-marker (car region) nil)
+        (set-marker (cdr region) nil))
+      (let* ((id (org-roam-capture--get :id))
+             (description (org-roam-capture--get :link-description))
+             (link (org-link-make-string (concat "id:" id)
+                                         description)))
+        (if (eq (point) (marker-position mkr))
+            (insert link)
+          (org-with-point-at mkr
+            (insert 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)
+     template)
+    ((or `(,key ,desc ,type ignore ,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
+         (let* ((key (pop rest))
+                (val (pop rest))
+                (custom (member key org-roam-capture--template-keywords)))
+           (when (and custom
+                      (not val))
+             (user-error "Invalid capture template format: %s\nkey %s cannot be nil" template key))
+           (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)
+               options
+               (list :org-roam org-roam-plist))))
+    (_
+     (signal 'invalid-template template))))
+
+
+(provide 'org-roam-capture)
+
+;;; org-roam-capture.el ends here

org-roam-compat.el

@@ -0,0 +1,241 @@
+;;; org-roam-compat.el --- Backward compatibility code -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1"))
+
+;; 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 file is dedicated to maintain backward compatibility with older older
+;; Emacsen and Org-roam versions.
+;;
+;;; Code:
+(require 'org-roam)
+
+;;; Backports
+;; REVIEW Remove when 26.x support is dropped. This is exact the same as
+;; `directory-files-recursively' from Emacs 26, but with FOLLOW-SYMLINKS
+;; 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-compat.el ends here

org-roam-db.el

@@ -0,0 +1,789 @@
+;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (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 the underlying database API to Org-roam.
+;;
+;;; Code:
+(require 'org-roam)
+(defvar org-outline-path-cache)
+
+;;; Options
+(defcustom org-roam-database-connector 'sqlite
+  "The database connector used by Org-roam.
+This must be set before `org-roam' is loaded.  To use an alternative
+connector you must install the respective package explicitly.
+The default is `sqlite', which uses the `emacsql-sqlite' library
+that is being maintained in the same repository as `emacsql'
+itself.
+If you are using Emacs 29, then the recommended connector is
+`sqlite-builtin', which uses the new builtin support for SQLite.
+You need to install the `emacsql-sqlite-builtin' package to use
+this connector.
+If you are using an older Emacs release, then the recommended
+connector is `sqlite-module', which uses the module provided by
+the `sqlite3' package.  This is very similar to the previous
+connector and the built-in support in Emacs 29 derives from this
+module.  You need to install the `emacsql-sqlite-module' package
+to use this connector.
+For the time being `libsqlite3' is still supported.  Do not use
+this, it is an older version of the `sqlite-module' connector
+from before the connector and the package were renamed.
+For the time being `sqlite3' is also supported.  Do not use this.
+This uses the third-party `emacsql-sqlite3' package, which uses
+the official `sqlite3' cli tool, which is not intended
+to be used like this.  See https://nullprogram.com/blog/2014/02/06/."
+  :package-version '(forge . "0.3.0")
+  :group 'forge
+  :type '(choice (const sqlite)
+                 (const sqlite-builtin)
+                 (const sqlite-module)
+                 (const :tag "libsqlite3 (OBSOLETE)" libsqlite3)
+                 (const :tag "sqlite3 (BROKEN)" sqlite3)))
+
+(defcustom org-roam-db-location (locate-user-emacs-file "org-roam.db")
+  "The path to file where the Org-roam database is stored.
+
+It is the user's responsibility to set this correctly, especially
+when used with multiple Org-roam instances."
+  :type 'string
+  :group 'org-roam)
+
+(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
+perform garbage collection because of the large number of
+temporary structures generated (e.g. parsed ASTs).
+
+`gc-cons-threshold' is temporarily set to
+`org-roam-db-gc-threshold' during this operation, and increasing
+`gc-cons-threshold' will help reduce the number of GC operations,
+at the cost of memory usage. Tweaking this value may lead to
+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)
+  "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 18)
+
+(defvar org-roam-db--connection (make-hash-table :test #'equal)
+  "Database connection to Org-roam database.")
+
+;;; 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))
+           org-roam-db--connection))
+
+(declare-function emacsql-sqlite "ext:emacsql-sqlite")
+(declare-function emacsql-sqlite3 "ext:emacsql-sqlite3")
+(declare-function emacsql-libsqlite3 "ext:emacsql-libsqlite3")
+(declare-function emacsql-sqlite-builtin "ext:emacsql-sqlite-builtin")
+(declare-function emacsql-sqlite-module "ext:emacsql-sqlite-module")
+
+(defun org-roam-db--conn-fn ()
+  "Return the function for creating the database connection."
+  (cl-case org-roam-database-connector
+    (sqlite
+     (progn
+       (require 'emacsql-sqlite)
+       #'emacsql-sqlite))
+    (sqlite-builtin
+     (progn
+       (require 'emacsql-sqlite-builtin)
+       #'emacsql-sqlite-builtin))
+    (sqlite-module
+     (progn
+       (require 'emacsql-sqlite-module)
+       #'emacsql-sqlite-module))
+    (libsqlite3
+     (progn
+       (require 'emacsql-libsqlite3)
+       #'emacsql-libsqlite3))
+    (sqlite3
+     (progn
+       (require 'emacsql-sqlite3)
+       #'emacsql-sqlite3))))
+
+(defun org-roam-db ()
+  "Entrypoint to the Org-roam sqlite database.
+Initializes and stores the database, and the database connection.
+Performs a database upgrade when required."
+  (unless (and (org-roam-db--get-connection)
+               (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 (funcall (org-roam-db--conn-fn) org-roam-db-location)))
+        (emacsql conn [:pragma (= foreign_keys ON)])
+        (when-let* ((process (emacsql-process conn))
+                    (_ (processp process)))
+          (set-process-query-on-exit-flag process nil))
+        (puthash (expand-file-name (file-name-as-directory org-roam-directory))
+                 conn
+                 org-roam-db--connection)
+        (when init-db
+          (org-roam-db--init conn))
+        (let* ((version (caar (emacsql conn "PRAGMA user_version")))
+               (version (org-roam-db--upgrade-maybe conn version)))
+          (cond
+           ((> version org-roam-db-version)
+            (emacsql-close conn)
+            (user-error
+             "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)
+            (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)
+(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))
+
+(defun org-roam-db-query! (handler sql &rest args)
+  "Run SQL query on Org-roam database with ARGS.
+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)
+      (atime :not-null)
+      (mtime :not-null)])
+
+    (nodes
+     ([(id :not-null :primary-key)
+       (file :not-null)
+       (level :not-null)
+       (pos :not-null)
+       todo
+       priority
+       (scheduled text)
+       (deadline text)
+       title
+       properties
+       olp]
+      (:foreign-key [file] :references files [file] :on-delete :cascade)))
+
+    (aliases
+     ([(node-id :not-null)
+       alias]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (citations
+     ([(node-id :not-null)
+       (cite-key :not-null)
+       (pos :not-null)
+       properties]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (refs
+     ([(node-id :not-null)
+       (ref :not-null)
+       (type :not-null)]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (tags
+     ([(node-id :not-null)
+       tag]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (links
+     ([(pos :not-null)
+       (source :not-null)
+       (dest :not-null)
+       (type :not-null)
+       (properties :not-null)]
+      (:foreign-key [source] :references nodes [id] :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
+    (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 [: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)
+        (progn
+          (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
+                                    version org-roam-db-version))
+          (org-roam-db-sync t))))
+  version)
+
+(defun org-roam-db--close (&optional db)
+  "Closes the database connection for database DB.
+If DB is nil, closes the database connection for the database in
+the current `org-roam-directory'."
+  (unless db
+    (setq db (org-roam-db--get-connection)))
+  (when (and db (emacsql-live-p db))
+    (emacsql-close db)))
+
+(defun org-roam-db--close-all ()
+  "Closes all database connections made by Org-roam."
+  (dolist (conn (hash-table-values org-roam-db--connection))
+    (org-roam-db--close conn)))
+
+;;; Database API
+;;;; Clearing
+(defun org-roam-db-clear-all ()
+  "Clears all entries in the Org-roam cache."
+  (interactive)
+  (when (file-exists-p org-roam-db-location)
+    (dolist (table (mapcar #'car org-roam-db--table-schemata))
+      (org-roam-db-query `[:delete :from ,table]))))
+
+(defun org-roam-db-clear-file (&optional file)
+  "Remove any related links to the FILE.
+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
+                      :where (= file $s1)]
+                     file))
+
+;;;; Updating tables
+
+(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 (cadr (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 ()
+  "Update the files table for the current buffer.
+If UPDATE-P is non-nil, first remove the file in the database."
+  (let* ((file (buffer-file-name))
+         (file-title (org-roam-db--file-title))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (org-roam-db--file-hash)))
+    (org-roam-db-query
+     [:insert :into files
+      :values $v1]
+     (list (vector file file-title hash atime mtime)))))
+
+(defun org-roam-db-get-scheduled-time ()
+  "Return the scheduled time at point in ISO8601 format."
+  (when-let ((time (org-get-scheduled-time (point))))
+    (org-format-time-string "%FT%T%z" time)))
+
+(defun org-roam-db-get-deadline-time ()
+  "Return the deadline time at point in ISO8601 format."
+  (when-let ((time (org-get-deadline-time (point))))
+    (org-format-time-string "%FT%T%z" time)))
+
+(defun org-roam-db-node-p ()
+  "Return t if headline at point is an Org-roam node, else return nil."
+  (and (org-id-get)
+       (not (org-entry-get (point) "ROAM_EXCLUDE"))
+       (funcall org-roam-db-node-include-function)))
+
+(defun org-roam-db-map-nodes (fns)
+  "Run FNS over all nodes in the current buffer."
+  (org-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)
+      ;; `re-search-forward' let the cursor one character after the link, we need to go backward one char to
+      ;; make the point be on the link.
+      (backward-char)
+      (let* ((element (org-element-context))
+             (type (org-element-type element))
+             link bounds)
+        (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 bounds (org-in-regexp org-link-any-re))
+               (setq link (buffer-substring-no-properties
+                           (car bounds)
+                           (cdr bounds))))
+          (with-temp-buffer
+            (delay-mode-hooks (org-mode))
+            (insert link)
+            (setq link (org-element-context)))))
+        (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)
+               (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))
+               (pos (point))
+               (todo nil)
+               (priority nil)
+               (scheduled nil)
+               (deadline nil)
+               (level 0)
+               (tags org-file-tags)
+               (properties (org-entry-properties))
+               (olp nil))
+          (org-roam-db-query!
+           (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))
+          (when tags
+            (org-roam-db-query
+             [:insert :into tags
+              :values $v1]
+             (mapcar (lambda (tag)
+                       (vector id (substring-no-properties tag)))
+                     tags)))
+          (org-roam-db-insert-aliases)
+          (org-roam-db-insert-refs))))))
+
+(cl-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)))
+           (heading-components (org-heading-components))
+           (pos (point))
+           (todo (nth 2 heading-components))
+           (priority (nth 3 heading-components))
+           (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)
+                      (progn (lwarn 'org-roam :warning "Node in %s:%s:%s has no title, skipping..."
+                                    file
+                                    (line-number-at-pos)
+                                    (1+ (- (point) (line-beginning-position))))
+                             (cl-return-from org-roam-db-insert-node-data))))
+           (properties (org-entry-properties))
+           (olp (org-get-outline-path nil 'use-cache))
+           (title (org-link-display-format title)))
+      (org-roam-db-query!
+       (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))
+              (aliases (org-entry-get (point) "ROAM_ALIASES"))
+              (aliases (split-string-and-unquote aliases)))
+    (org-roam-db-query [:insert :into aliases
+                        :values $v1]
+                       (mapcar (lambda (alias)
+                                 (vector node-id alias))
+                               aliases))))
+
+(defun org-roam-db-insert-tags ()
+  "Insert tags for node at point into Org-roam cache."
+  (when-let ((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))))
+
+(defun org-roam-db-insert-refs ()
+  "Insert refs for node at point into Org-roam cache."
+  (when-let* ((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
+                 (string-prefix-p "@" ref)
+                 (push (vector node-id (substring ref 1) "cite") rows))
+                (;; [cite:@citeKey]
+                 (string-prefix-p "[cite:" ref)
+                 (condition-case nil
+                     (let ((cite-obj (org-cite-parse-objects ref)))
+                       (org-element-map cite-obj 'citation-reference
+                         (lambda (cite)
+                           (let ((key (org-element-property :key cite)))
+                             (push (vector node-id key "cite") rows)))))
+                   (error
+                    (lwarn '(org-roam) :warning
+                           "%s:%s\tInvalid cite %s, skipping..." (buffer-file-name) (point) ref))))
+                (;; https://google.com, cite:citeKey
+                 ;; Note: we use string-match here because it matches any link: e.g. [[cite:abc][abc]]
+                 ;; But this form of matching is loose, and can accept invalid links e.g. [[cite:abc]
+                 (string-match org-link-plain-re ref)
+                 (let ((link-type (match-string 1 ref))
+                       (path (match-string 2 ref)))
+                   (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))
+          (path (org-element-property :path link))
+          (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)))))
+      ;; 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
+          :values $v1]
+         (vector source key (point) properties))))))
+
+;;;; 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]))
+        (ht (make-hash-table :test #'equal)))
+    (dolist (row current-files)
+      (puthash (car row) (cadr row) ht))
+    ht))
+
+(defun org-roam-db--file-hash (&optional file-path)
+  "Compute the hash of FILE-PATH, a file or current buffer."
+  ;; If it is a GPG encrypted file, we always want to compute the hash
+  ;; for the GPG encrypted file (undecrypted)
+  (when (and (not file-path) (equal "gpg" (file-name-extension (buffer-file-name))))
+    (setq file-path (buffer-file-name)))
+  (if file-path
+      (with-temp-buffer
+        (set-buffer-multibyte nil)
+        (insert-file-contents-literally file-path)
+        (secure-hash 'sha1 (current-buffer)))
+    (org-with-wide-buffer
+     (secure-hash 'sha1 (current-buffer)))))
+
+;;;; Synchronization
+(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-refresh-category-properties)
+           (org-roam-db-clear-file)
+           (org-roam-db-insert-file)
+           (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) ;; 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))
+         (current-files (org-roam-db--get-current-files))
+         (modified-files nil))
+    (dolist (file org-roam-files)
+      (let ((contents-hash (org-roam-db--file-hash file)))
+        (unless (string= (gethash file current-files)
+                         contents-hash)
+          (push file modified-files)))
+      (remhash file current-files))
+    (emacsql-with-transaction (org-roam-db)
+      (org-roam-dolist-with-progress (file (hash-table-keys current-files))
+          "Clearing removed files..."
+        (org-roam-db-clear-file file))
+      (org-roam-dolist-with-progress (file modified-files)
+          "Processing modified files..."
+        (condition-case err
+            (org-roam-db-update-file file 'no-require)
+          (error
+           (org-roam-db-clear-file file)
+           (lwarn 'org-roam :error "Failed to process %s with error %s, skipping..."
+                  file (error-message-string err))))))))
+
+;;;###autoload
+(define-minor-mode org-roam-db-autosync-mode
+  "Global minor mode to keep your Org-roam session automatically synchronized.
+Through the session this will continue to setup your
+buffers (that are Org-roam file visiting), keep track of the
+related changes, maintain cache consistency and incrementally
+update the currently active database.
+
+If you need to manually trigger resync of the currently active
+database, see `org-roam-db-sync' command."
+  :group 'org-roam
+  :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)
+      (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)
+      (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
+(defun org-roam-db-autosync-enable ()
+  "Activate `org-roam-db-autosync-mode'."
+  (org-roam-db-autosync-mode +1))
+
+(defun org-roam-db-autosync-disable ()
+  "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--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)
+  (prin1 (org-roam-node-at-point)))
+
+(provide 'org-roam-db)
+
+;;; org-roam-db.el ends here

org-roam-id.el

@@ -0,0 +1,117 @@
+;;; org-roam-id.el --- ID-related utilities for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (magit-section "3.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This module provides ID-related facilities using the Org-roam database.
+;;
+;;; Code:
+(require 'org-id)
+
+(defun org-roam-id-at-point ()
+  "Return the ID at point, if any.
+Recursively traverses up the headline tree to find the
+first encapsulating ID."
+  (org-with-wide-buffer
+   (org-back-to-heading-or-point-min t)
+   (while (and (not (org-roam-db-node-p))
+               (not (bobp)))
+     (org-roam-up-heading-or-point-min))
+   (when (org-roam-db-node-p)
+     (org-id-get))))
+
+(defun org-roam-id-find (id &optional markerp)
+  "Return the location of the entry with the id ID using the Org-roam db.
+The return value is a cons cell (file-name . position), or nil
+if there is no entry with that ID.
+With optional argument MARKERP, return the position as a new marker."
+  (cond
+   ((symbolp id) (setq id (symbol-name id)))
+   ((numberp id) (setq id (number-to-string id))))
+  (let ((node (org-roam-populate (org-roam-node-create :id id))))
+    (when-let ((file (org-roam-node-file node)))
+      (if markerp
+          (unwind-protect
+              (let ((buffer (or (find-buffer-visiting file)
+                                (find-file-noselect file))))
+                (with-current-buffer buffer
+                  (move-marker (make-marker) (org-roam-node-point node) buffer))))
+        (cons (org-roam-node-file node)
+              (org-roam-node-point node))))))
+
+(defun org-roam-id-open (id _)
+  "Go to the entry with id ID.
+Like `org-id-open', but additionally uses the Org-roam database."
+  (org-mark-ring-push)
+  (let ((m (or (org-roam-id-find id 'marker)
+               (org-id-find id 'marker)))
+        cmd)
+    (unless m
+      (error "Cannot find entry with ID \"%s\"" id))
+    ;; Use a buffer-switching command in analogy to finding files
+    (setq cmd
+          (or
+           (cdr
+            (assq
+             (cdr (assq 'file org-link-frame-setup))
+             '((find-file . switch-to-buffer)
+               (find-file-other-window . switch-to-buffer-other-window)
+               (find-file-other-frame . switch-to-buffer-other-frame))))
+           'switch-to-buffer-other-window))
+    (if (not (equal (current-buffer) (marker-buffer m)))
+        (funcall cmd (marker-buffer m)))
+    (goto-char m)
+    (move-marker m nil)
+    (org-show-context)))
+
+(org-link-set-parameters "id" :follow #'org-roam-id-open)
+
+;;;###autoload
+(defun org-roam-update-org-id-locations (&rest directories)
+  "Scan Org-roam files to update `org-id' related state.
+This is like `org-id-update-id-locations', but will automatically
+use the currently bound `org-directory' and `org-roam-directory'
+along with DIRECTORIES (if any), where the lookup for files in
+these directories will be always recursive.
+
+Note: Org-roam doesn't have hard dependency on
+`org-id-locations-file' to lookup IDs for nodes that are stored
+in the database, but it still tries to properly integrates with
+`org-id'. This allows the user to cross-reference IDs outside of
+the current `org-roam-directory', and also link with \"id:\"
+links to headings/files within the current `org-roam-directory'
+that are excluded from identification in Org-roam as
+`org-roam-node's, e.g. with \"ROAM_EXCLUDE\" property."
+  (interactive)
+  (cl-loop for dir in (cons org-roam-directory directories)
+           for org-roam-directory = dir
+           nconc (org-roam-list-files) into files
+           finally (org-id-update-id-locations files org-roam-verbose)))
+
+(provide 'org-roam-id)
+
+;;; org-roam-id.el ends here

org-roam-log.el

@@ -0,0 +1,53 @@
+;;; org-roam-log.el --- Integrations with Org-log -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2022-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This module provides integrations with Org-log.
+;;
+;;; Code:
+(require 'org-roam)
+
+(defcustom org-roam-log-setup-hook nil
+  "Hook run when a log for an Org-roam file is setup."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam-log-p ()
+  "Return t if the log buffer is for an Org-roam file, nil otherwise."
+  (and org-log-note-marker
+       (org-roam-file-p (buffer-file-name (marker-buffer org-log-note-marker)))))
+
+(defun org-roam-log--setup ()
+  "Run hooks in `org-roam-log-setup-hook'."
+  (run-hooks 'org-roam-log-setup-hook))
+
+(add-hook 'org-roam-log-setup-hook #'org-roam--register-completion-functions-h)
+(add-hook 'org-log-buffer-setup-hook #'org-roam-log--setup)
+
+(provide 'org-roam-log)
+;;; org-roam-log.el ends here

org-roam-migrate.el

@@ -0,0 +1,168 @@
+;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (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

@@ -0,0 +1,697 @@
+;;; org-roam-mode.el --- Major mode for special Org-roam buffers -*- lexical-binding: t -*-
+
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (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 implements `org-roam-mode', which is a major mode that used by
+;; special Org-roam buffers to display various content in a section-like manner
+;; about the nodes and relevant to them information (e.g. backlinks) with which
+;; the user can interact with.
+;;
+;;; Code:
+(require 'org-roam)
+
+;;;; Declarations
+(defvar org-ref-buffer-hacked)
+
+;;; Options
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+                                        #'org-roam-reflinks-section)
+  "A list of sections for the `org-roam-mode' based buffers.
+Each section is a function that is passed the an `org-roam-node'
+for which the section will be constructed for as the first
+argument. Normally this node is `org-roam-buffer-current-node'.
+The function may also accept other optional arguments. Each item
+in the list is either:
+
+1. A function, which is called only with the `org-roam-node' as the argument
+2. A list, containing the function and the optional arguments.
+
+For example, one can add
+
+    (org-roam-backlinks-section :unique t)
+
+to the list to pass :unique t to the section-rendering function."
+  :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
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "DarkGoldenrod4"
+     :weight bold)
+    (((class color) (background  dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "LightGoldenrod2"
+     :weight bold))
+  "Face for the `header-line' in some Org-roam modes."
+  :group 'org-roam-faces)
+
+(defface org-roam-title
+  '((t :weight bold))
+  "Face for Org-roam titles."
+  :group 'org-roam-faces)
+
+(defface org-roam-olp
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the OLP of the node."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey80"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey25"
+     :foreground "grey70"))
+  "Face for preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-highlight
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey75"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey35"
+     :foreground "grey70"))
+  "Face for current preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-selection
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "salmon4")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "LightSalmon3"))
+  "Face for selected preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-region
+  `((t :inherit bold
+       ,@(and (>= emacs-major-version 27)
+              (list :extend (ignore-errors (face-attribute 'region :extend))))))
+  "Face used by `org-roam-highlight-preview-region-using-face'.
+
+This face is overlaid over text that uses other hunk faces,
+and those normally set the foreground and background colors.
+The `:foreground' and especially the `:background' properties
+should be avoided here.  Setting the latter would cause the
+loss of information.  Good properties to set here are `:weight'
+and `:slant'."
+  :group 'org-roam-faces)
+
+(defface org-roam-dim
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the dimmer part of the widgets."
+  :group 'org-roam-faces)
+
+;;; Major 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 (kbd "C-m") 'org-roam-buffer-visit-thing)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-refresh)
+    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.
+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
+(defvar org-roam-buffer-current-node nil
+  "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)
+  "Return the file at point in the current `org-roam-mode' based buffer.
+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))
+  (save-excursion (org-roam-buffer-render-contents)))
+
+(defun org-roam-buffer-render-contents ()
+  "Recompute and render the contents of an Org-roam buffer.
+Assumes that the current buffer is an `org-roam-mode' based
+buffer."
+  (let ((inhibit-read-only t))
+    (erase-buffer)
+    (org-roam-mode)
+    (setq-local default-directory org-roam-buffer-current-directory)
+    (setq-local org-roam-directory org-roam-buffer-current-directory)
+    (org-roam-buffer-set-header-line-format
+     (org-roam-node-title org-roam-buffer-current-node))
+    (magit-insert-section (org-roam)
+      (magit-insert-heading)
+      (dolist (section org-roam-mode-sections)
+        (pcase section
+          ((pred functionp)
+           (funcall section org-roam-buffer-current-node))
+          (`(,fn . ,args)
+           (apply fn (cons org-roam-buffer-current-node args)))
+          (_
+           (user-error "Invalid `org-roam-mode-sections' specification")))))
+    (run-hooks 'org-roam-buffer-postrender-functions)
+    (goto-char 0)))
+
+(defun org-roam-buffer-set-header-line-format (string)
+  "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 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 ()
+  "Toggle display of the persistent `org-roam-buffer'."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (quit-window nil (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--redisplay-h)))
+    ((or 'exists 'none)
+     (progn
+       (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'.
+Valid states are 'visible, 'exists and 'none."
+  (declare (side-effect-free t))
+  (inline-quote
+   (cond
+    ((get-buffer-window org-roam-buffer) 'visible)
+    ((get-buffer org-roam-buffer) 'exists)
+    (t 'none))))
+
+(defun org-roam-buffer-persistent-redisplay ()
+  "Recompute contents of the persistent `org-roam-buffer'.
+Has no effect when there's no `org-roam-node-at-point'."
+  (when-let ((node (org-roam-node-at-point)))
+    (unless (equal node org-roam-buffer-current-node)
+      (setq org-roam-buffer-current-node node
+            org-roam-buffer-current-directory org-roam-directory)
+      (with-current-buffer (get-buffer-create org-roam-buffer)
+        (org-roam-buffer-render-contents)
+        (add-hook 'kill-buffer-hook #'org-roam-buffer--persistent-cleanup-h nil t)))))
+
+(defun org-roam-buffer--persistent-cleanup-h ()
+  "Clean-up global state thats dedicated for the persistent `org-roam-buffer'."
+  (setq-default org-roam-buffer-current-node nil
+                org-roam-buffer-current-directory nil))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--setup-redisplay-h)
+(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-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))
+  source-node target-node
+  point properties)
+
+(cl-defmethod org-roam-populate ((backlink org-roam-backlink))
+  "Populate BACKLINK from database."
+  (setf (org-roam-backlink-source-node backlink)
+        (org-roam-populate (org-roam-backlink-source-node backlink))
+        (org-roam-backlink-target-node backlink)
+        (org-roam-populate (org-roam-backlink-target-node backlink)))
+  backlink)
+
+(cl-defun org-roam-backlinks-get (node &key unique)
+  "Return the backlinks for NODE.
+
+ When UNIQUE is nil, show all positions where references are found.
+ When UNIQUE is t, limit to unique sources."
+  (let* ((sql (if unique
+                  [:select :distinct [source dest pos properties]
+                   :from links
+                   :where (= dest $s1)
+                   :and (= type "id")
+                   :group :by source
+                   :having (funcall min pos)]
+                [:select [source dest pos properties]
+                 :from links
+                 :where (= dest $s1)
+                 :and (= type "id")]))
+         (backlinks (org-roam-db-query sql (org-roam-node-id node))))
+    (cl-loop for backlink in backlinks
+             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
+                       (org-roam-populate
+                        (org-roam-backlink-create
+                         :source-node (org-roam-node-create :id source-id)
+                         :target-node (org-roam-node-create :id dest-id)
+                         :point pos
+                         :properties properties))))))
+
+(defun org-roam-backlinks-sort (a b)
+  "Default sorting function for backlinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-backlink-source-node a))
+           (org-roam-node-title (org-roam-backlink-source-node b))))
+
+(cl-defun org-roam-backlinks-section (node &key (unique nil))
+  "The backlinks section for NODE.
+
+When UNIQUE is nil, show all positions where references are found.
+When UNIQUE is t, limit to unique sources."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node :unique unique))))
+    (magit-insert-section (org-roam-backlinks)
+      (magit-insert-heading "Backlinks:")
+      (dolist (backlink backlinks)
+        (org-roam-node-insert-section
+         :source-node (org-roam-backlink-source-node backlink)
+         :point (org-roam-backlink-point backlink)
+         :properties (org-roam-backlink-properties backlink)))
+      (insert ?\n))))
+
+;;;; Reflinks
+(cl-defstruct (org-roam-reflink (:constructor org-roam-reflink-create)
+                                (:copier nil))
+  source-node ref
+  point properties)
+
+(cl-defmethod org-roam-populate ((reflink org-roam-reflink))
+  "Populate REFLINK from database."
+  (setf (org-roam-reflink-source-node reflink)
+        (org-roam-populate (org-roam-reflink-source-node reflink)))
+  reflink)
+
+(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]
+                                  :from refs
+                                  :left-join links
+                                  :where (= refs:node-id $s1)
+                                  :and (= links:dest refs:ref)
+                                  :union
+                                  :select :distinct [refs:ref citations:node-id
+                                                     citations:pos citations:properties]
+                                  :from refs
+                                  :left-join citations
+                                  :where (= refs:node-id $s1)
+                                  :and (= citations:cite-key refs:ref)]
+                                 (org-roam-node-id node)))
+        links)
+    (pcase-dolist (`(,ref ,source-id ,pos ,properties) refs)
+      (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)
+  "Default sorting function for reflinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-reflink-source-node a))
+           (org-roam-node-title (org-roam-reflink-source-node b))))
+
+(defun org-roam-reflinks-section (node)
+  "The reflinks section for NODE."
+  (when-let ((refs (org-roam-node-refs node))
+             (reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+    (magit-insert-section (org-roam-reflinks)
+      (magit-insert-heading "Reflinks:")
+      (dolist (reflink reflinks)
+        (org-roam-node-insert-section
+         :source-node (org-roam-reflink-source-node reflink)
+         :point (org-roam-reflink-point reflink)
+         :properties (org-roam-reflink-properties reflink)))
+      (insert ?\n))))
+
+;;;; Grep
+(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)
+    map)
+  "Keymap for Org-roam grep result sections.")
+
+(defclass org-roam-grep-section (magit-section)
+  ((keymap :initform 'org-roam-grep-map)
+   (file :initform nil)
+   (row :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)
+  "Visit FILE at row ROW (if any) and column COL (if any). Return the buffer.
+With OTHER-WINDOW non-nil (in interactive calls set with
+`universal-argument') display the buffer in another window
+instead."
+  (interactive (list (org-roam-buffer-file-at-point t)
+                     current-prefix-arg
+                     (oref (magit-current-section) row)
+                     (oref (magit-current-section) col)))
+  (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))
+      (when row
+        (forward-line (1- row)))
+      (when col
+        (forward-char (1- col))))
+    (when (org-invisible-p) (org-show-context))
+    buf))
+
+;;;; Unlinked references
+(defvar org-roam-unlinked-references-result-re
+  (rx (group (one-or-more anything))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (zero-or-more anything)))
+  "Regex for the return result of a ripgrep query.")
+
+(defun org-roam-unlinked-references-preview-line (file row)
+  "Return the preview line from FILE.
+This is the ROW within FILE."
+  (with-temp-buffer
+    (insert-file-contents file)
+    (forward-line (1- row))
+    (buffer-substring-no-properties
+     (save-excursion
+       (beginning-of-line)
+       (point))
+     (save-excursion
+       (end-of-line)
+       (point)))))
+
+(defun org-roam-unlinked-references-section (node)
+  "The unlinked references section for NODE.
+References from FILE are excluded."
+  (when (and (executable-find "rg")
+             (not (string-match "PCRE2 is not available"
+                                (shell-command-to-string "rg --pcre2-version"))))
+    (let* ((titles (cons (org-roam-node-title node)
+                         (org-roam-node-aliases node)))
+           (rg-command (concat "rg -L -o --vimgrep -P -i "
+                               (mapconcat (lambda (glob) (concat "-g " glob))
+                                          (org-roam--list-files-search-globs org-roam-file-extensions)
+                                          " ")
+                               (format " '\\[([^[]]++|(?R))*\\]%s' "
+                                       (mapconcat (lambda (title)
+                                                    (format "|(\\b%s\\b)" (shell-quote-argument title)))
+                                                  titles ""))
+                               org-roam-directory))
+           (results (split-string (shell-command-to-string rg-command) "\n"))
+           f row col match)
+      (magit-insert-section (unlinked-references)
+        (magit-insert-heading "Unlinked References:")
+        (dolist (line results)
+          (save-match-data
+            (when (string-match org-roam-unlinked-references-result-re line)
+              (setq f (match-string 1 line)
+                    row (string-to-number (match-string 2 line))
+                    col (string-to-number (match-string 3 line))
+                    match (match-string 4 line))
+              (when (and match
+                         (not (file-equal-p (org-roam-node-file node) f))
+                         (member (downcase match) (mapcar #'downcase titles)))
+                (magit-insert-section section (org-roam-grep-section)
+                  (oset section file f)
+                  (oset section row row)
+                  (oset section col col)
+                  (insert (propertize (format "%s:%s:%s"
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil t)
+                                              row col) 'font-lock-face 'org-roam-dim)
+                          " "
+                          (org-roam-fontify-like-in-org-mode
+                           (org-roam-unlinked-references-preview-line f row))
+                          "\n"))))))
+        (insert ?\n)))))
+
+(provide 'org-roam-mode)
+;;; org-roam-mode.el ends here

org-roam-utils.el

@@ -1,12 +1,12 @@
-;;; org-roam-utils.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-utils.el --- Utilities for Org-roam -*- lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 0.1.2
-;; Package-Requires: ((emacs "26.1"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,143 +27,468 @@
 
 ;;; Commentary:
 ;;
-;; This library is an attempt at injecting Roam functionality into Org-mode.
-;; This is achieved primarily through building caches for forward links,
-;; backward links, and file titles.
+;; This library provides definitions for utilities that used throughout the
+;; whole package.
 ;;
 ;;; Code:
 
-(require 'org)
-(require 'org-element)
-(require 'subr-x)
-(require 'cl-lib)
+(require 'org-roam)
 
-(defun org-roam--file-name-extension (filename)
-  "Return file name extension for FILENAME.
+(defun org-roam-require (libs)
+  "Require LIBS."
+  (dolist (lib libs)
+    (require lib nil 'noerror)))
 
-Like file-name-extension, but does not strip version number."
+;;; String utilities
+;; TODO Refactor this.
+(defun org-roam-replace-string (old new s)
+  "Replace OLD with NEW in S."
+  (declare (pure t) (side-effect-free t))
+  (replace-regexp-in-string (regexp-quote old) new s t t))
+
+(defun org-roam-quote-string (s)
+  "Quotes string S."
+  (->> s
+       (org-roam-replace-string "\\" "\\\\")
+       (org-roam-replace-string "\"" "\\\"")))
+
+(defun org-roam-word-wrap (len s)
+  "If S is longer than LEN, wrap the words with newlines."
+  (declare (side-effect-free t))
   (save-match-data
-    (let ((file (file-name-nondirectory filename)))
-      (if (and (string-match "\\.[^.]*\\'" file)
-                     (not (eq 0 (match-beginning 0))))
-          (substring file (+ (match-beginning 0) 1))))))
+    (with-temp-buffer
+      (insert s)
+      (let ((fill-column len))
+        (fill-region (point-min) (point-max)))
+      (buffer-substring (point-min) (point-max)))))
 
-(defun org-roam--org-file-p (path)
-  "Check if PATH is pointing to an org file."
-  (let ((ext (org-roam--file-name-extension path)))
-    (or (string= ext "org")
-        (and
-         (string= ext "gpg")
-         (string= (org-roam--file-name-extension (file-name-sans-extension path)) "org")))))
+(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--find-files (dir)
-  "Return all `org-roam' files in `DIR'."
-  (if (file-exists-p dir)
-      (let ((files (directory-files dir t "." t))
-            (dir-ignore-regexp (concat "\\(?:"
-                                       "\\."
-                                       "\\|\\.\\."
-                                       "\\)$"))
-            result)
-        (dolist (file files)
-          (cond
-           ((file-directory-p file)
-            (when (not (string-match dir-ignore-regexp file))
-              (setq result (append (org-roam--find-files file) result))))
-           ((and (file-readable-p file)
-                 (org-roam--org-file-p file))
-            (setq result (cons (file-truename file) result)))))
-        result)))
+(defun org-roam-whitespace-content (s)
+  "Return the whitespace content at the end of S."
+  (with-temp-buffer
+    (let ((c 0))
+      (insert s)
+      (skip-chars-backward " \t\n")
+      (buffer-substring-no-properties
+       (point) (point-max)))))
 
-(defun org-roam--parse-content (&optional file-path)
-  "Parse the current buffer, and return a list of items for processing."
-  (org-element-map (org-element-parse-buffer) 'link
-    (lambda (link)
-      (let ((type (org-element-property :type link))
-            (path (org-element-property :path link))
-            (start (org-element-property :begin link)))
-        (when (and (string= type "file")
-                   (org-roam--org-file-p path))
-          (goto-char start)
-          (let* ((element (org-element-at-point))
-                 (begin (or (org-element-property :content-begin element)
-                            (org-element-property :begin element)))
-                 (content (or (org-element-property :raw-value element)
-                              (buffer-substring
-                               begin
-                               (or (org-element-property :content-end element)
-                                   (org-element-property :end element)))))
-                 (content (string-trim content))
-                 (file-path (or file-path
-                                (file-truename (buffer-file-name (current-buffer))))))
-            (list :from file-path
-                  :to (file-truename (expand-file-name path (file-name-directory file-path)))
-                  :properties (list :content content :point begin))))))))
+(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 (point-at-bol) (progn (forward-line) (point)))
+        (forward-line)))
+    (buffer-string)))
 
-(cl-defun org-roam--insert-item (item &key forward backward)
-  "Insert ITEM into FORWARD and BACKWARD cache.
+;;; 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)
 
-ITEM is of the form: (:from from-path :to to-path :properties (:content preview-content :point point))."
-  (pcase-let ((`(:from ,p-from :to ,p-to :properties ,props) item))
-    ;; Build forward-links
-    (let ((links (gethash p-from forward)))
-      (if links
-          (puthash p-from
-                   (if (member p-to links)
-                       links
-                     (cons p-to links)) forward)
-        (puthash p-from (list p-to) forward)))
-    ;; Build backward-links
-    (let ((contents-hash (gethash p-to backward)))
-      (if contents-hash
-          (if-let ((contents-list (gethash p-from contents-hash)))
-              (let ((updated (cons props contents-list)))
-                (puthash p-from updated contents-hash)
-                (puthash p-to contents-hash backward))
+(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 (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))
+           (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)
+  "Fontify string S like in Org mode.
+Like `org-fontify-like-in-org-mode', but supports `org-ref'."
+  ;; NOTE: pretend that the temporary buffer created by `org-fontify-like-in-org-mode' to
+  ;; fontify a `cite:' reference has been hacked by org-ref, whatever that means;
+  ;;
+  ;; `org-ref-cite-link-face-fn', which is used to supply a face for `cite:' links, calls
+  ;; `hack-dir-local-variables' rationalizing that `bibtex-completion' would throw some warnings
+  ;; otherwise.  This doesn't seem to be the case and calling this function just before
+  ;; `org-font-lock-ensure' (alias of `font-lock-ensure') actually instead of fixing the alleged
+  ;; warnings messes the things so badly that `font-lock-ensure' crashes with error and doesn't let
+  ;; org-roam to proceed further. I don't know what's happening there exactly but disabling this hackery
+  ;; fixes the crashing.  Fortunately, org-ref provides the `org-ref-buffer-hacked' switch, which we use
+  ;; here to make it believe that the buffer was hacked.
+  ;;
+  ;; This is a workaround for `cite:' links and does not have any effect on other ref types.
+  ;;
+  ;; `org-ref-buffer-hacked' is a buffer-local variable, therefore we inline
+  ;; `org-fontify-like-in-org-mode' here
+  (with-temp-buffer
+    (insert s)
+    (let ((org-ref-buffer-hacked t))
+      (org-mode)
+      (org-font-lock-ensure)
+      (buffer-string))))
+
+;;;; Shielding regions
+(defface org-roam-shielded
+  '((t :inherit (warning)))
+  "Face for regions that are shielded (marked as read-only).
+This face is used on the region target by org-roam-insertion
+during an `org-roam-capture'."
+  :group 'org-roam-faces)
+
+(defun org-roam-shield-region (beg end)
+  "Shield region against modifications.
+BEG and END are markers for the beginning and end regions.
+REGION must be a cons-cell containing the marker to the region
+beginning and maximum values."
+  (add-text-properties beg end
+                       '(font-lock-face org-roam-shielded
+                                        read-only t)
+                       (marker-buffer beg)))
+
+(defun org-roam-unshield-region (beg end)
+  "Unshield the shielded REGION.
+BEG and END are markers for the beginning and end regions."
+  (let ((inhibit-read-only t))
+    (remove-text-properties beg end
+                            '(font-lock-face org-roam-shielded
+                                             read-only t)
+                            (marker-buffer beg))))
+
+;;; Org-mode utilities
+;;;; Motions
+(defun org-roam-up-heading-or-point-min ()
+  "Fixed version of Org's `org-up-heading-or-point-min'."
+  (ignore-errors (org-back-to-heading t))
+  (let ((p (point)))
+    (if (< 1 (funcall outline-level))
+        (progn
+          (org-up-heading-safe)
+          (when (= (point) p)
+            (goto-char (point-min))))
+      (unless (bobp) (goto-char (point-min))))))
+
+;;;; Keywords
+(defun org-roam-get-keyword (name &optional file bound)
+  "Return keyword property NAME from an org FILE.
+FILE defaults to current file.
+Only scans up to BOUND bytes of the document."
+  (unless bound
+    (setq bound 1024))
+  (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)
+  "Return keyword property NAME in current buffer.
+If BOUND, scan up to BOUND bytes of the buffer."
+  (save-excursion
+    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
+      (goto-char (point-min))
+      (when (re-search-forward re bound t)
+        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
+
+(defun org-roam-end-of-meta-data (&optional full)
+  "Like `org-end-of-meta-data', but supports file-level metadata.
+
+When FULL is non-nil but not t, skip planning information,
+properties, clocking lines and logbook drawers.
+
+When optional argument FULL is t, skip everything above, and also
+skip keywords."
+  (org-back-to-heading-or-point-min t)
+  (when (org-at-heading-p) (forward-line))
+  ;; Skip planning information.
+  (when (looking-at-p org-planning-line-re) (forward-line))
+  ;; Skip property drawer.
+  (when (looking-at org-property-drawer-re)
+    (goto-char (match-end 0))
+    (forward-line))
+  ;; When FULL is not nil, skip more.
+  (when (and full (not (org-at-heading-p)))
+    (catch 'exit
+      (let ((end (save-excursion (outline-next-heading) (point)))
+            (re (concat "[ \t]*$" "\\|" org-clock-line-re)))
+        (while (not (eobp))
+          (cond ;; Skip clock lines.
+           ((looking-at-p re) (forward-line))
+           ;; Skip logbook drawer.
+           ((looking-at-p org-logbook-drawer-re)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ((looking-at-p org-drawer-regexp)
+            (if (re-search-forward "^[ \t]*:END:[ \t]*$" end t)
+                (forward-line)
+              (throw 'exit t)))
+           ;; When FULL is t, skip keywords too.
+           ((and (eq full t)
+                 (looking-at-p org-keyword-regexp))
+            (forward-line))
+           (t (throw 'exit t))))))))
+
+(defun org-roam-set-keyword (key value)
+  "Set keyword KEY to VALUE.
+If the property is already set, it's value is replaced."
+  (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
-              (puthash p-from (list props) contents-hash)
-              (puthash p-to contents-hash backward)))
-        (let ((contents-hash (make-hash-table :test #'equal)))
-          (puthash p-from (list props) contents-hash)
-          (puthash p-to contents-hash backward))))))
+              (end-of-line)
+              (insert "\n"))
+          (forward-line)
+          (beginning-of-line))
+        (insert "#+" key ": " value "\n")))))
 
-(defun org-roam--extract-title ()
-  "Extract the title from `BUFFER'."
-  (org-element-map
-      (org-element-parse-buffer)
-      'keyword
-    (lambda (kw)
-      (when (string= (org-element-property :key kw) "TITLE")
-        (org-element-property :value kw)))
-    :first-match t))
+(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."
+  (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-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."
+  (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))
+
+(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))
+         gitdir topdir version)
+    (unless (and toplib (equal (file-name-nondirectory toplib) "org-roam-utils.el"))
+      (setq toplib (locate-library "org-roam-utils.el")))
+    (setq toplib (and toplib (org-roam--straight-chase-links toplib)))
+    (when toplib
+      (setq topdir (file-name-directory toplib)
+            gitdir (expand-file-name ".git" topdir)))
+    (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."
+  (interactive)
+  (with-current-buffer (switch-to-buffer-other-window (get-buffer-create "*org-roam diagnostics*"))
+    (erase-buffer)
+    (insert (propertize "Copy info below this line into issue:\n" 'face '(:weight bold)))
+    (insert (format "- Emacs: %s\n" (emacs-version)))
+    (insert (format "- Framework: %s\n"
+                    (condition-case _
+                        (completing-read "I'm using the following Emacs framework:"
+                                         '("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 "- sqlite-connector: %s" org-roam-database-connector))))
 
-(defun org-roam--build-cache (dir)
-  "Build the org-roam caches in DIR."
-  (let ((backward-links (make-hash-table :test #'equal))
-        (forward-links (make-hash-table :test #'equal))
-        (file-titles (make-hash-table :test #'equal)))
-    (let* ((org-roam-files (org-roam--find-files dir))
-           (file-items (mapcar (lambda (file)
-                                 (with-temp-buffer
-                                   (insert-file-contents file)
-                                   (org-roam--parse-content file))) org-roam-files)))
-      (dolist (items file-items)
-        (dolist (item items)
-          (org-roam--insert-item
-           item
-           :forward forward-links
-           :backward backward-links)))
-      (dolist (file org-roam-files)
-        (with-temp-buffer
-          (insert-file-contents file)
-          (when-let ((title (org-roam--extract-title)))
-            (puthash file title file-titles)))
-        org-roam-files))
-    (list
-     :forward forward-links
-     :backward backward-links
-     :titles file-titles)))
 
 (provide 'org-roam-utils)
-
 ;;; org-roam-utils.el ends here

org-roam.el

@@ -1,12 +1,12 @@
-;;; org-roam.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam.el --- A database abstraction layer for Org-mode -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2022 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 0.1.2
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (async "1.9.4"))
+;; Version: 2.2.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "3.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,680 +27,316 @@
 
 ;;; Commentary:
 ;;
-;; This library is an attempt at injecting Roam functionality into Org-mode.
-;; This is achieved primarily through building caches for forward links,
-;; backward links, and file titles.
+;; Org-roam is a Roam Research inspired Emacs package and is an addition to
+;; Org-mode to have a way to quickly process complex SQL-like queries over a
+;; large set of plain text Org-mode files. To achieve this Org-roam provides a
+;; database abstraction layer, the capabilities of which include, but are not
+;; limited to:
 ;;
+;; - Link graph traversal and visualization.
+;; - Instantaneous SQL-like queries on headlines
+;;   - What are my TODOs, scheduled for X, or due by Y?
+;; - Accessing the properties of a node, such as its tags, refs, TODO state or
+;;   priority.
+;;
+;; All of these functionality is powered by this layer. Hence, at its core
+;; Org-roam's primary goal is to provide a resilient dual representation of
+;; what's already available in plain text, while cached in a binary database,
+;; that is cheap to maintain, easy to understand, and is as up-to-date as it
+;; possibly can. For users who would like to perform arbitrary programmatic
+;; queries on their Org files Org-roam also exposes an API to this database
+;; abstraction layer.
+;;
+;; -----------------------------------------------------------------------------
+;;
+;; In order for the package to correctly work through your interactive session
+;; it's mandatory to add somewhere to your configuration the next form:
+;;
+;;     (org-roam-db-autosync-mode)
+;;
+;; The form can be called both, before or after loading the package, which is up
+;; to your preferences. If you call this before the package is loaded, then it
+;; will automatically load the package.
+;;
+;; -----------------------------------------------------------------------------
+;;
+;; This package also comes with a set of officially supported extensions that
+;; provide extra features. You can find them in the "extensions/" subdirectory.
+;; These extensions are not automatically loaded with `org-roam`, but they still
+;; will be lazy-loaded through their own `autoload's.
+;;
+;; Org-roam also has other extensions that don't come together with this package.
+;; Such extensions are distributed as their own packages, while also
+;; authored and maintained by different people on distinct repositories. The
+;; majority of them can be found at https://github.com/org-roam and MELPA.
 ;;
 ;;; Code:
-
-(eval-when-compile (require 'cl-lib))
 (require 'dash)
-(require 'org-element)
-(require 'async)
-(require 'subr-x)
-(require 's)
-(require 'f)
-(require 'org-roam-utils)
 
-;;; Customizations
+(require 'rx)
+(require 'seq)
+(require 'cl-lib)
+
+(require 'magit-section)
+
+(require 'emacsql)
+(require 'emacsql-sqlite)
+
+(require 'org)
+(require 'org-attach)                   ; To set `org-attach-id-dir'
+(require 'org-id)
+(require 'ol)
+(require 'org-element)
+(require 'org-capture)
+
+(require 'ansi-color) ; to strip ANSI color codes in `org-roam--list-files'
+
+(eval-when-compile
+  (require 'subr-x))
+
+;;; Options
 (defgroup org-roam nil
-  "Roam Research replica in Org-mode."
+  "A database abstraction layer for Org-mode."
   :group 'org
   :prefix "org-roam-"
-  :link '(url-link :tag "Github" "https://github.com/jethrokuan/org-roam")
-  :link '(url-link :tag "Online Manual" "https://org-roam.readthedocs.io/"))
+  :link '(url-link :tag "Github" "https://github.com/org-roam/org-roam")
+  :link '(url-link :tag "Online Manual" "https://www.orgroam.com/manual.html"))
+
+(defgroup org-roam-faces nil
+  "Faces used by Org-roam."
+  :group 'org-roam
+  :group 'faces)
+
+(defcustom org-roam-verbose t
+  "Echo messages that are not errors."
+  :type 'boolean
+  :group 'org-roam)
 
 (defcustom org-roam-directory (expand-file-name "~/org-roam/")
-  "Path to Org-roam files.
-
-All Org files, at any level of nesting, is considered part of the Org-roam."
+  "Default path to Org-roam files.
+All Org files, at any level of nesting, are considered part of the Org-roam."
   :type 'directory
   :group 'org-roam)
 
-(defcustom org-roam-new-file-directory nil
-  "Path to where new Org-roam files are created.
-
-If nil, default to the org-roam-directory (preferred)."
-  :type 'directory
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-position 'right
-  "Position of `org-roam' buffer.
-
-Valid values are
- * left,
- * right."
-  :type '(choice (const left)
-                 (const right))
-  :group 'org-roam)
-
-(defcustom org-roam-file-name-function #'org-roam--file-name-timestamp-title
-  "The function used to generate filenames.
-
-The function takes as parameter `TITLE', a string the user inputs."
+(defcustom org-roam-find-file-hook nil
+  "Hook run when an Org-roam file is visited."
   :group 'org-roam
-  :type '(choice (const :tag "Default" org-roam--file-name-timestamp-title)
-                 (function :tag "Personalized function")))
+  :type 'hook)
 
-(defcustom org-roam-link-title-format "%s"
-  "The format string used when inserting org-roam links that use their title."
-  :type 'string
+(defcustom org-roam-post-node-insert-hook nil
+  "Hook run when an Org-roam node is inserted as an Org link.
+Each function takes two arguments: the id of the node, and the link description."
+  :group 'org-roam
+  :type 'hook)
+
+(defcustom org-roam-file-extensions '("org")
+  "List of file extensions to be included by Org-Roam.
+While a file extension different from \".org\" may be used, the
+file still needs to be an `org-mode' file, and it is the user's
+responsibility to ensure that."
+  :type '(repeat string)
   :group 'org-roam)
 
-(defcustom org-roam-filename-noconfirm t
-  "Whether to prompt for confirmation of fil name for new files.
-
-If nil, always ask for filename."
-  :type 'boolean
+(defcustom org-roam-file-exclude-regexp (list org-attach-id-dir)
+  "Files matching this regular expression are excluded from the Org-roam."
+  :type '(choice
+          (repeat
+           (string :tag "Regular expression matching files to ignore"))
+          (string :tag "Regular expression matching files to ignore")
+          (const :tag "Include everything" nil))
   :group 'org-roam)
 
-(defcustom org-roam-autopopulate-title t "Whether to autopopulate the title."
-  :type 'boolean
-  :group 'org-roam)
+(defcustom org-roam-list-files-commands
+  (if (member system-type '(windows-nt ms-dos cygwin))
+      nil
+    '(find fd fdfind rg))
+  "Commands that will be used to find Org-roam files.
 
-(defcustom org-roam-buffer-width 0.33 "Width of `org-roam' buffer."
-  :type 'number
-  :group 'org-roam)
+It should be a list of symbols or cons cells representing any of the following
+supported file search methods.
 
-(defcustom org-roam-buffer "*org-roam*"
-  "Org-roam buffer name."
-  :type 'string
-  :group 'org-roam)
+The commands will be tried in order until an executable for a command is found.
+The Elisp implementation is used if no command in the list is found.
 
-(defcustom org-roam-encrypt-files nil
-  "Whether to encrypt new files. If true, create files with .org.gpg extension."
-  :type 'boolean
-  :group 'org-roam)
+  `find'
+    Use find as the file search method.
+    Example command:
+    find /path/to/dir -type f \( -name \"*.org\" -o -name \"*.org.gpg\" \)
 
-(defcustom org-roam-graph-viewer (executable-find "firefox")
-  "Path to executable for viewing SVG."
-  :type 'string
-  :group 'org-roam)
+  `fd'
+    Use fd as the file search method.
+    Example command: fd /path/to/dir/ --type file -e \".org\" -e \".org.gpg\"
 
-(defcustom org-roam-graphviz-executable (executable-find "dot")
-  "Path to graphviz executable."
-  :type 'string
-  :group 'org-roam)
+  `fdfind'
+    Same as `fd'. It's an alias that used in some OSes (e.g. Debian, Ubuntu)
 
-(defcustom org-roam-graph-max-title-length 100
-  "Maximum length of titles in graphviz graph nodes"
-  :type 'number
-  :group 'org-roam)
+  `rg'
+    Use ripgrep as the file search method.
+    Example command: rg /path/to/dir/ --files -g \"*.org\" -g \"*.org.gpg\"
 
-(defcustom org-roam-graph-node-shape "ellipse"
-  "Maximum length of titles in graphviz graph nodes"
-  :type 'string
-  :group 'org-roam)
+By default, `executable-find' will be used to look up the path to the
+executable. If a custom path is required, it can be specified together with the
+method symbol as a cons cell. For example: '(find (rg . \"/path/to/rg\"))."
+  :type '(set (const :tag "find" find)
+              (const :tag "fd" fd)
+              (const :tag "fdfind" fdfind)
+              (const :tag "rg" rg)
+              (const :tag "elisp" nil)))
 
-;;; Polyfills
-;; These are for functions I use that are only available in newer Emacs
+;;; Library
+(defun org-roam-file-p (&optional file)
+  "Return t if FILE is an Org-roam file, nil otherwise.
+If FILE is not specified, use the current buffer's file-path.
 
-;; Introduced in Emacs 27.1
-(unless (fboundp 'make-empty-file)
-  (defun make-empty-file (filename &optional parents)
-    "Create an empty file FILENAME.
-Optional arg PARENTS, if non-nil then creates parent dirs as needed.
+FILE is an Org-roam file if:
+- It's located somewhere under `org-roam-directory'
+- It has a matching file extension (`org-roam-file-extensions')
+- It doesn't match excluded regexp (`org-roam-file-exclude-regexp')"
+  (let* ((path (or file (buffer-file-name (buffer-base-buffer))))
+         (ext (when path (org-roam--file-name-extension path)))
+         (ext (if (string= ext "gpg")
+                  (org-roam--file-name-extension (file-name-sans-extension path))
+                ext))
+         (org-roam-dir-p (org-roam-descendant-of-p path org-roam-directory))
+         (valid-file-ext-p (member ext org-roam-file-extensions))
+         (match-exclude-regexp-p
+          (cond
+           ((not org-roam-file-exclude-regexp) nil)
+           ((stringp org-roam-file-exclude-regexp)
+            (string-match-p org-roam-file-exclude-regexp path))
+           ((listp org-roam-file-exclude-regexp)
+            (let (is-match)
+              (dolist (exclude-re org-roam-file-exclude-regexp)
+                (setq is-match (or is-match (string-match-p exclude-re path))))
+              is-match)))))
+    (save-match-data
+      (and
+       path
+       org-roam-dir-p
+       valid-file-ext-p
+       (not match-exclude-regexp-p)))))
 
-If called interactively, then PARENTS is non-nil."
-    (interactive
-     (let ((filename (read-file-name "Create empty file: ")))
-       (list filename t)))
-    (when (and (file-exists-p filename) (null parents))
-      (signal 'file-already-exists `("File exists" ,filename)))
-    (let ((paren-dir (file-name-directory filename)))
-      (when (and paren-dir (not (file-exists-p paren-dir)))
-        (make-directory paren-dir parents)))
-    (write-region "" nil filename nil 0)))
+(defun org-roam-list-files ()
+  "Return a list of all Org-roam files under `org-roam-directory'.
+See `org-roam-file-p' for how each file is determined to be as
+part of Org-Roam."
+  (org-roam--list-files (expand-file-name org-roam-directory)))
 
-;;; Dynamic variables
-(defvar org-roam-cache-initialized nil
-  "Boolean value indicating whether the cache is initialized.")
+(defun org-roam-buffer-p (&optional buffer)
+  "Return t if BUFFER is for an Org-roam file.
+If BUFFER is not specified, use the current buffer."
+  (let ((buffer (or buffer (current-buffer)))
+        path)
+    (with-current-buffer buffer
+      (and (derived-mode-p 'org-mode)
+           (setq path (buffer-file-name (buffer-base-buffer)))
+           (org-roam-file-p path)))))
 
-(defvar org-roam-forward-links-cache (make-hash-table :test #'equal)
-  "Cache containing forward links.")
-
-(defvar org-roam-backward-links-cache (make-hash-table :test #'equal)
-  "Cache containing backward-links.")
-
-(defvar org-roam-titles-cache (make-hash-table :test #'equal)
-  "Cache containing titles for org-roam files.")
-
-(defvar org-roam--current-buffer nil
-  "Currently displayed file in `org-roam' buffer.")
-
-(defvar org-roam-last-window nil
-  "Last window `org-roam' was called from.")
-
-;;; Utilities
-(defun org-roam--ensure-cache-built ()
-  "Ensures that org-roam cache is built."
-  (unless org-roam-cache-initialized
-    (org-roam--build-cache-async)
-    (user-error "Your Org-Roam cache isn't built yet! Please wait")))
-
-(defun org-roam--org-roam-file-p (&optional file)
-  "Return t if FILE is part of org-roam system, defaulting to the name of the current buffer. Else, return nil."
-  (let ((path (or file
-                  (buffer-file-name (current-buffer)))))
-    (and path
-         (org-roam--org-file-p path)
-         (f-descendant-of-p (file-truename path)
-                            (file-truename org-roam-directory)))))
-
-(defun org-roam--get-title-from-cache (file)
-  "Return title of `FILE' from the cache."
-  (or (gethash file org-roam-titles-cache)
-      (progn
-        (unless org-roam-cache-initialized
-          (user-error "The Org-Roam caches aren't built! Please run org-roam--build-cache-async"))
-        nil)))
-
-(defun org-roam--find-all-files ()
-  "Return all org-roam files."
-  (org-roam--find-files (file-truename org-roam-directory)))
-
-(defun org-roam--make-new-file-path (id &optional absolute)
-  "Make new file path from identifier `ID'.
-
-If `ABSOLUTE', return an absolute file-path. Else, return a relative file-path."
-  (let ((absolute-file-path (file-truename
-                             (expand-file-name
-                              (if org-roam-encrypt-files
-                                  (concat id ".org.gpg")
-                                (concat id ".org"))
-                              (or org-roam-new-file-directory
-                                  org-roam-directory)))))
-    (if absolute
-        absolute-file-path
-      (file-relative-name absolute-file-path
-                          (file-truename org-roam-directory)))))
-
-(defun org-roam--get-title-or-slug (file-path)
-  "Convert `FILE-PATH' to the file title, if it exists. Else, return the path."
-  (or (org-roam--get-title-from-cache file-path)
-      (-> file-path
-          (file-relative-name (file-truename org-roam-directory))
-          (file-name-sans-extension))))
-
-(defun org-roam--title-to-slug (title)
-  "Convert TITLE to a filename-suitable slug."
-  (let* ((s (s-downcase title))
-         (s (replace-regexp-in-string "[^a-zA-Z0-9_ ]" "" s))
-         (s (s-split " " s))
-         (s (s-join "_" s)))
-    s))
-
-(defun org-roam--file-name-timestamp-title (title)
-  "Return a file name (without extension) for new files.
-
-It uses TITLE and the current timestamp to form a unique title."
-  (let ((timestamp (format-time-string "%Y%m%d%H%M%S" (current-time)))
-        (slug (org-roam--title-to-slug title)))
-    (format "%s_%s" timestamp slug)))
-
-;;; Creating org-roam files
-(defun org-roam--populate-title (file &optional title)
-  "Populate title line for FILE using TITLE, if provided.
-If not provided, derive the title from the file name."
-  (let ((title (or title
-                   (-> file
-                       (file-name-nondirectory)
-                       (file-name-sans-extension)
-                       (split-string "_")
-                       (string-join " ")
-                       (s-titleize)))))
-    (write-region
-     (concat
-      "#+TITLE: "
-      title
-      "\n\n")
-     nil file nil)))
-
-(defun org-roam--make-file (file-path &optional title)
-  "Create an org-roam file at FILE-PATH, optionally setting the TITLE attribute."
-  (if (file-exists-p file-path)
-      (error (format "Aborting, file already exists at %s" file-path))
-    (make-empty-file file-path t)
-    (if org-roam-autopopulate-title
-        (org-roam--populate-title file-path title))
-    (save-excursion
-      (with-current-buffer (find-file-noselect file-path)
-        (org-roam--update-cache)))))
-
-(defun org-roam--new-file-named (slug)
-  "Create a new file named `SLUG'.
-`SLUG' is the short file name, without a path or a file extension."
-  (interactive "sNew filename (without extension): ")
-  (let ((file-path (org-roam--make-new-file-path slug t)))
-    (unless (file-exists-p file-path)
-      (org-roam--make-file file-path))
-    (find-file file-path)))
-
-(defun org-roam--get-new-id (title)
-  "Return a new ID, given the note TITLE."
-  (let* ((proposed-slug (funcall org-roam-file-name-function title))
-         (new-slug (if org-roam-filename-noconfirm
-                       proposed-slug
-                     (read-string "Enter ID (without extension): "
-                                  proposed-slug)))
-         (file-path (org-roam--make-new-file-path new-slug t)))
-    (if (file-exists-p file-path)
-        (user-error "There's already a file at %s")
-      new-slug)))
-
-(defun org-roam-new-file ()
-  "Quickly create a new file, using the current timestamp."
-  (interactive)
-  (org-roam--new-file-named (format-time-string "%Y%m%d%H%M%S" (current-time))))
-
-;;; Inserting org-roam links
-(defun org-roam-insert (prefix)
-  "Find an org-roam file, and insert a relative org link to it at point.
-
-If PREFIX, downcase the title before insertion."
-  (interactive "P")
-  (let* ((completions (mapcar (lambda (file)
-                                (list (org-roam--get-title-or-slug file)
-                                      file))
-                              (org-roam--find-all-files)))
-         (title (completing-read "File: " completions))
-         (absolute-file-path (or (cadr (assoc title completions))
-                                 (org-roam--make-new-file-path (org-roam--get-new-id title) t)))
-         (current-file-path (-> (or (buffer-base-buffer)
-                                    (current-buffer))
-                                (buffer-file-name)
-                                (file-truename)
-                                (file-name-directory))))
-    (unless (file-exists-p absolute-file-path)
-      (org-roam--make-file absolute-file-path title))
-    (insert (format "[[%s][%s]]"
-                    (concat "file:" (file-relative-name absolute-file-path
-                                                        current-file-path))
-                    (format org-roam-link-title-format (if prefix
-                                                           (downcase title)
-                                                         title))))))
-
-;;; Finding org-roam files
-(defun org-roam-find-file ()
-  "Find and open an org-roam file."
-  (interactive)
-  (let* ((completions (mapcar (lambda (file)
-                                (list (org-roam--get-title-or-slug file) file))
-                              (org-roam--find-all-files)))
-         (title-or-slug (completing-read "File: " completions))
-         (absolute-file-path (or (cadr (assoc title-or-slug completions))
-                                 (org-roam--make-new-file-path
-                                  (org-roam--get-new-id title-or-slug) t))))
-    (unless (file-exists-p absolute-file-path)
-      (org-roam--make-file absolute-file-path title-or-slug))
-    (find-file absolute-file-path)))
-
-(defun org-roam--get-roam-buffers ()
-  "Return a list of buffers that are org-roam files."
-  (--filter (and (with-current-buffer it (derived-mode-p 'org-mode))
-                 (buffer-file-name it)
-                 (org-roam--org-roam-file-p (buffer-file-name it)))
+(defun org-roam-buffer-list ()
+  "Return a list of buffers that are Org-roam files."
+  (--filter (org-roam-buffer-p it)
             (buffer-list)))
 
-(defun org-roam-switch-to-buffer ()
-  "Switch to an existing org-roam buffer using completing-read."
-  (interactive)
-  (let* ((roam-buffers (org-roam--get-roam-buffers))
-         (names-and-buffers (mapcar (lambda (buffer)
-                                      (cons (or (org-roam--get-title-from-cache
-                                                 (buffer-file-name buffer))
-                                                (buffer-name buffer))
-                                            buffer))
-                                    roam-buffers)))
-    (unless roam-buffers
-      (error "No roam buffers."))
-    (when-let ((name (completing-read "Choose a buffer: " names-and-buffers)))
-      (switch-to-buffer (cdr (assoc name names-and-buffers))))))
+(defun org-roam--file-name-extension (filename)
+  "Return file name extension for FILENAME.
+Like `file-name-extension', but does not strip version number."
+  (save-match-data
+    (let ((file (file-name-nondirectory filename)))
+      (if (and (string-match "\\.[^.]*\\'" file)
+               (not (eq 0 (match-beginning 0))))
+          (substring file (+ (match-beginning 0) 1))))))
 
-;;; Building the org-roam cache
-(defun org-roam--build-cache-async ()
-  "Builds the caches asychronously."
-  (interactive)
-  (async-start
-   `(lambda ()
-      (setq load-path ',load-path)
-      (package-initialize)
-      (require 'org-roam-utils)
-      ,(async-inject-variables "org-roam-directory")
-      (org-roam--build-cache org-roam-directory))
-   (lambda (cache)
-     (setq org-roam-forward-links-cache (plist-get cache :forward))
-     (setq org-roam-backward-links-cache (plist-get cache :backward))
-     (setq org-roam-titles-cache (plist-get cache :titles))
-     (setq org-roam-cache-initialized t)
-     (message "Org-roam cache built!"))))
+(defun org-roam--list-files (dir)
+  "Return all Org-roam files located recursively within DIR.
+Use external shell commands if defined in `org-roam-list-files-commands'."
+  (let (path exe)
+    (cl-dolist (cmd org-roam-list-files-commands)
+      (pcase cmd
+        (`(,e . ,path)
+         (setq path (executable-find path)
+               exe  (symbol-name e)))
+        ((pred symbolp)
+         (setq path (executable-find (symbol-name cmd))
+               exe (symbol-name cmd)))
+        (wrong-type
+         (signal 'wrong-type-argument
+                 `((consp symbolp)
+                   ,wrong-type))))
+      (when path (cl-return)))
+    (if-let* ((files (when path
+                       (let ((fn (intern (concat "org-roam--list-files-" exe))))
+                         (unless (fboundp fn) (user-error "%s is not an implemented search method" fn))
+                         (funcall fn path (format "\"%s\"" dir)))))
+              (files (seq-filter #'org-roam-file-p files))
+              (files (mapcar #'expand-file-name files))) ; canonicalize names
+        files
+      (org-roam--list-files-elisp dir))))
 
-(defun org-roam--clear-cache ()
-  "Clears all entries in the caches."
-  (interactive)
-  (setq org-roam-cache-initialized nil)
-  (setq org-roam-forward-links-cache (make-hash-table :test #'equal))
-  (setq org-roam-backward-links-cache (make-hash-table :test #'equal))
-  (setq org-roam-titles-cache (make-hash-table :test #'equal)))
+(defun org-roam--shell-command-files (cmd)
+  "Run CMD in the shell and return a list of files.
+If no files are found, an empty list is returned."
+  (--> cmd
+       (shell-command-to-string it)
+       (ansi-color-filter-apply it)
+       (split-string it "\n")
+       (seq-filter (lambda (s)
+                     (not (or (null s) (string= "" s)))) it)))
 
-(defun org-roam--clear-file-from-cache (&optional filepath)
-  "Remove any related links to the file.
+(defun org-roam--list-files-search-globs (exts)
+  "Given EXTS, return a list of search globs.
+E.g. (\".org\") => (\"*.org\" \"*.org.gpg\")"
+  (cl-loop for e in exts
+           append (list (format "\"*.%s\"" e)
+                        (format "\"*.%s.gpg\"" e))))
 
-This is equivalent to removing the node from the graph."
-  (let* ((path (or filepath
-                   (buffer-file-name (current-buffer))))
-         (file (file-truename path)))
-    ;; Step 1: Remove all existing links for file
-    (when-let ((forward-links (gethash file org-roam-forward-links-cache)))
-      ;; Delete backlinks to file
-      (dolist (link forward-links)
-        (when-let ((backward-links (gethash link org-roam-backward-links-cache)))
-          (remhash file backward-links)
-          (puthash link backward-links org-roam-backward-links-cache)))
-      ;; Clean out forward links
-      (remhash file org-roam-forward-links-cache))
-    ;; Step 2: Remove from the title cache
-    (remhash file org-roam-titles-cache)))
+(defun org-roam--list-files-find (executable dir)
+  "Return all Org-roam files under DIR, using \"find\", provided as EXECUTABLE."
+  (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
+         (names (string-join (mapcar (lambda (glob) (concat "-name " glob)) globs) " -o "))
+         (command (string-join `(,executable "-L" ,dir "-type f \\(" ,names "\\)") " ")))
+    (org-roam--shell-command-files command)))
 
-(defun org-roam--update-cache-title ()
-  "Insert the title of the current buffer into the cache."
-  (when-let ((title (org-roam--extract-title)))
-    (puthash (file-truename (buffer-file-name (current-buffer)))
-             title
-             org-roam-titles-cache)))
+(defun org-roam--list-files-fd (executable dir)
+  "Return all Org-roam files under DIR, using \"fd\", provided as EXECUTABLE."
+  (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
+         (extensions (string-join (mapcar (lambda (glob) (concat "-e " (substring glob 2 -1))) globs) " "))
+         (command (string-join `(,executable "-L" "--type file" ,extensions "." ,dir) " ")))
+    (org-roam--shell-command-files command)))
 
-(defun org-roam--update-cache ()
-  "Update org-roam caches for the current buffer file."
-  (save-excursion
-    (org-roam--clear-file-from-cache)
-    ;; Insert into title cache
-    (org-roam--update-cache-title)
-    ;; Insert new items
-    (let ((items (org-roam--parse-content)))
-      (dolist (item items)
-        (org-roam--insert-item
-         item
-         :forward org-roam-forward-links-cache
-         :backward org-roam-backward-links-cache)))
-    ;; Rerender buffer
-    (org-roam--maybe-update-buffer :redisplay t)))
+(defalias 'org-roam--list-files-fdfind #'org-roam--list-files-fd)
 
-;;; Org-roam daily notes
-(defun org-roam-today ()
-  "Create the file for today."
-  (interactive)
-  (org-roam--new-file-named (format-time-string "%Y-%m-%d" (current-time))))
+(defun org-roam--list-files-rg (executable dir)
+  "Return all Org-roam files under DIR, using \"rg\", provided as EXECUTABLE."
+  (let* ((globs (org-roam--list-files-search-globs org-roam-file-extensions))
+         (command (string-join `(,executable "-L" ,dir "--files"
+                                             ,@(mapcar (lambda (glob) (concat "-g " glob)) globs)) " ")))
+    (org-roam--shell-command-files command)))
 
-(defun org-roam-tomorrow ()
-  "Create the file for tomorrow."
-  (interactive)
-  (org-roam--new-file-named (format-time-string "%Y-%m-%d" (time-add 86400 (current-time)))))
+(declare-function org-roam--directory-files-recursively "org-roam-compat")
 
-(defun org-roam-date ()
-  "Create the file for any date using the calendar."
-  (interactive)
-  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
-    (org-roam--new-file-named (format-time-string "%Y-%m-%d" time))))
-
-;;; Org-roam buffer
-(define-derived-mode org-roam-backlinks-mode org-mode "Backlinks"
-  "Major mode for the org-roam backlinks buffer
-
-Bindings:
-\\{org-roam-backlinks-mode-map}")
-
-(define-key org-roam-backlinks-mode-map [mouse-1] 'org-roam-jump-to-backlink)
-(define-key org-roam-backlinks-mode-map (kbd "RET") 'org-roam-jump-to-backlink)
-
-(defun org-roam-jump-to-backlink ()
-  "Jumps to original file and location of the backlink content snippet at point"
-  (interactive)
-  (let ((file-from (get-text-property (point) 'file-from))
-        (p (get-text-property (point) 'file-from-point)))
-    (when (and file-from p)
-      (find-file file-from)
-      (goto-char p)
-      (org-show-context))))
-
-(defun org-roam--find-file (file)
-  "Open FILE in the window `org-roam' was called from."
-  (if (and org-roam-last-window (window-valid-p org-roam-last-window))
-      (progn (with-selected-window org-roam-last-window
-               (find-file file))
-             (select-window org-roam-last-window))
-    (find-file file)))
-
-(defun org-roam-update (file-path)
-  "Show the backlinks for given org file for file at `FILE-PATH'."
-  (org-roam--ensure-cache-built)
-  (let ((buffer-title (org-roam--get-title-or-slug file-path)))
-    (with-current-buffer org-roam-buffer
-      ;; Locally overwrite the file opening function to re-use the
-      ;; last window org-roam was called from
-      (setq-local
-       org-link-frame-setup
-       (cons '(file . org-roam--find-file) org-link-frame-setup))
-      (let ((inhibit-read-only t))
-        (erase-buffer)
-        (when (not (eq major-mode 'org-roam-backlinks-mode))
-          (org-roam-backlinks-mode))
-        (make-local-variable 'org-return-follows-link)
-        (setq org-return-follows-link t)
-        (insert
-         (propertize buffer-title 'font-lock-face 'org-document-title))
-        (if-let ((backlinks (gethash file-path org-roam-backward-links-cache)))
-            (progn
-              (insert (format "\n\n* %d Backlinks\n"
-                              (hash-table-count backlinks)))
-              (maphash (lambda (file-from contents)
-                         (insert (format "** [[file:%s][%s]]\n"
-                                         file-from
-                                         (org-roam--get-title-or-slug file-from)))
-                         (dolist (properties contents)
-                           (let ((content (propertize
-                                           (s-trim (s-replace "\n" " "
-                                                              (plist-get properties :content)))
-                                           'font-lock-face 'org-block
-                                           'help-echo "mouse-1: visit backlinked note"
-                                           'file-from file-from
-                                           'file-from-point (plist-get properties :point))))
-                             (insert (format "%s \n\n" content)))))
-                       backlinks))
-          (insert "\n\n* No backlinks!")))
-      (read-only-mode 1))))
-
-;;; Building the Graphviz graph
-(defun org-roam-build-graph ()
-  "Build graphviz graph output."
-  (org-roam--ensure-cache-built)
-  (with-temp-buffer
-	(insert "digraph {\n")
-	(dolist (file (org-roam--find-all-files))
-	  (let ((title (org-roam--get-title-or-slug file)))
-		(let ((shortened-title (s-truncate org-roam-graph-max-title-length title)))
-		  (insert
-		   (format "  \"%s\" [label=\"%s\", shape=%s, URL=\"roam://%s\", tooltip=\"%s\"];\n"
-				   title
-				   shortened-title
-				   org-roam-graph-node-shape
-				   file
-				   title
-				   )))))
-	  (maphash
-	   (lambda (from-link to-links)
-		 (dolist (to-link to-links)
-		   (insert (format "  \"%s\" -> \"%s\";\n"
-						   (org-roam--get-title-or-slug from-link)
-						   (org-roam--get-title-or-slug to-link)))))
-	   org-roam-forward-links-cache)
-	  (insert "}")
-	  (buffer-string)))
-
-(defun org-roam-show-graph ()
-  "Generate the org-roam graph in SVG format, and display it using `org-roam-graph-viewer'."
-  (interactive)
-  (unless org-roam-graphviz-executable
-    (setq org-roam-graphviz-executable (executable-find "dot")))
-  (unless org-roam-graphviz-executable
-    (user-error "Can't find graphviz executable. Please check if it is in your path"))
-  (declare (indent 0))
-  (let ((temp-dot (expand-file-name "graph.dot" temporary-file-directory))
-        (temp-graph (expand-file-name "graph.svg" temporary-file-directory))
-        (graph (org-roam-build-graph)))
-    (with-temp-file temp-dot
-      (insert graph))
-    (call-process org-roam-graphviz-executable nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
-    (if (and org-roam-graph-viewer (executable-find org-roam-graph-viewer))
-	(call-process org-roam-graph-viewer nil 0 nil temp-graph)
-      (view-file temp-graph))))
-
-;;; Org-roam minor mode
-(cl-defun org-roam--maybe-update-buffer (&key redisplay)
-  "Update `org-roam-buffer' with the necessary information.
-This needs to be quick/infrequent, because this is run at
-`post-command-hook'."
-  (let ((buffer (window-buffer)))
-    (when (and (or redisplay
-                   (not (eq org-roam--current-buffer buffer)))
-               (eq 'visible (org-roam--current-visibility))
-               (buffer-local-value 'buffer-file-truename buffer))
-      (setq org-roam--current-buffer buffer)
-      (org-roam-update (expand-file-name
-                        (buffer-local-value 'buffer-file-truename buffer))))))
-
-(defun org-roam--find-file-hook-function ()
-  "Called by `find-file-hook' when `org-roam-mode' is on."
-  (when (org-roam--org-roam-file-p)
-    (add-hook 'post-command-hook #'org-roam--maybe-update-buffer nil t)
-    (add-hook 'after-save-hook #'org-roam--update-cache nil t)))
-
-(defvar org-roam-mode-map
-  (make-sparse-keymap)
-  "Keymap for org-roam commands.")
-
-(defun org-roam--delete-file-advice (file &optional _trash)
-  "Advice for maintaining cache consistency during file deletes."
-  (org-roam--clear-file-from-cache (file-truename file)))
-
-(defun org-roam--rename-file-advice (file new-file &rest args)
-  "Rename backlinks of FILE to refer to NEW-FILE."
-  (when (and (not (auto-save-file-name-p file))
-             (not (auto-save-file-name-p new-file))
-             (org-roam--org-roam-file-p new-file))
-    (org-roam--ensure-cache-built)
-    (org-roam--clear-file-from-cache file)
-
-    (let* ((files (gethash file org-roam-backward-links-cache nil))
-           (path (file-truename file))
-           (new-path (file-truename new-file))
-           (slug (org-roam--get-title-or-slug file))
-           (old-title (format org-roam-link-title-format slug))
-           (new-slug (or (org-roam--get-title-from-cache path)
-                         (org-roam--get-title-or-slug new-path)))
-           (new-title (format org-roam-link-title-format new-slug)))
-      (when files
-        (maphash (lambda (file-from props)
-                   (let* ((file-dir (file-name-directory file-from))
-                          (relative-path (file-relative-name new-path file-dir))
-                          (old-relative-path (file-relative-name path file-dir))
-                          (slug-regex (regexp-quote (format "[[file:%s][%s]]" old-relative-path old-title)))
-                          (named-regex (concat
-                                        (regexp-quote (format "[[file:%s][" old-relative-path))
-                                        "\\(.*\\)"
-                                        (regexp-quote "]]"))))
-                     (with-temp-file file-from
-                       (insert-file-contents file-from)
-                       (while (re-search-forward slug-regex  nil t)
-                         (replace-match (format "[[file:%s][%s]]" relative-path new-title)))
-                       (goto-char (point-min))
-                       (while (re-search-forward named-regex nil t)
-                         (replace-match (format "[[file:%s][\\1]]" relative-path))))
-                     (save-window-excursion
-                       (find-file file-from)
-                       (org-roam--update-cache))))
-                 files))
-      (save-window-excursion
-        (find-file new-path)
-        (org-roam--update-cache)))))
-
-;;;###autoload
-(define-minor-mode org-roam-mode
-  "Minor mode for Org-roam.
-
-When called interactively, toggle `org-roam-mode'. with prefix ARG, enable `org-roam-mode'
-if ARG is posiwive, otherwise disable it.
-
-When called from Lisp, enable `org-roam-mode' if ARG is omitted, nil, or positive.
-If ARG is `toggle', toggle `org-roam-mode'. Otherwise, behave as if called interactively."
-  :lighter "Org-Roam "
-  :keymap  org-roam-mode-map
-  :group 'org-roam
-  :require 'org-roam
-  :global t
-  (cond
-   (org-roam-mode
-    (unless org-roam-cache-initialized
-      (org-roam--build-cache-async))
-    (add-hook 'find-file-hook #'org-roam--find-file-hook-function)
-    (advice-add 'rename-file :after #'org-roam--rename-file-advice)
-    (advice-add 'delete-file :before #'org-roam--delete-file-advice))
-   (t
-    (remove-hook 'find-file-hook #'org-roam--find-file-hook-function)
-    (advice-remove 'rename-file #'org-roam--rename-file-advice)
-    (advice-remove 'delete-file #'org-roam--delete-file-advice)
-    ;; Disable local hooks for all org-roam buffers
-    (dolist (buf (org-roam--get-roam-buffers))
-      (with-current-buffer buf
-        (remove-hook 'post-command-hook #'org-roam--maybe-update-buffer t)
-        (remove-hook 'after-save-hook #'org-roam--update-cache t))))))
+(defun org-roam--list-files-elisp (dir)
+  "Return all Org-roam files under DIR, using Elisp based implementation."
+  (let ((regex (concat "\\.\\(?:"(mapconcat
+                                  #'regexp-quote org-roam-file-extensions
+                                  "\\|" )"\\)\\(?:\\.gpg\\)?\\'"))
+        result)
+    (dolist (file (org-roam--directory-files-recursively dir regex nil nil t) result)
+      (when (and (file-readable-p file)
+                 (org-roam-file-p file))
+        (push file result)))))
 
+;;; Package bootstrap
 (provide 'org-roam)
 
-;;; Show/hide the org-roam buffer
-(define-inline org-roam--current-visibility ()
-  "Return whether the current visibility state of the org-roam buffer.
-Valid states are 'visible, 'exists and 'none."
-  (declare (side-effect-free t))
-  (inline-quote
-   (cond
-    ((get-buffer-window org-roam-buffer) 'visible)
-    ((get-buffer org-roam-buffer) 'exists)
-    (t 'none))))
+(cl-eval-when (load eval)
+  (require 'org-roam-compat)
+  (require 'org-roam-utils)
+  (require 'org-roam-db)
+  (require 'org-roam-node)
+  (require 'org-roam-id)
+  (require 'org-roam-capture)
+  (require 'org-roam-mode)
+  (require 'org-roam-log)
+  (require 'org-roam-migrate))
 
-(defun org-roam--set-width (width)
-  "Set the width of the org-roam buffer to `WIDTH'."
-  (unless (one-window-p)
-    (let ((window-size-fixed)
-          (w (max width window-min-width)))
-      (cond
-       ((> (window-width) w)
-        (shrink-window-horizontally  (- (window-width) w)))
-       ((< (window-width) w)
-        (enlarge-window-horizontally (- w (window-width))))))))
-
-(defun org-roam--setup-buffer ()
-  "Setup the `org-roam' buffer at the `org-roam-buffer-position'."
-  (let ((window (get-buffer-window)))
-    (-> (get-buffer-create org-roam-buffer)
-        (display-buffer-in-side-window
-         `((side . ,org-roam-buffer-position)))
-        (select-window))
-    (org-roam--set-width
-     (round (* (frame-width)
-               org-roam-buffer-width)))
-    (select-window window)))
-
-(defun org-roam ()
-  "Pops up the window `org-roam-buffer' accordingly."
-  (interactive)
-  (setq org-roam-last-window (get-buffer-window))
-  (pcase (org-roam--current-visibility)
-    ('visible (delete-window (get-buffer-window org-roam-buffer)))
-    ('exists (org-roam--setup-buffer))
-    ('none (org-roam--setup-buffer))))
 ;;; org-roam.el ends here
-
-;; Local Variables:
-;; outline-regexp: ";;;+ "
-;; End:

tests/roam-files/bar.org

@@ -0,0 +1,6 @@
+:PROPERTIES:
+:ID:       440795d0-70c1-4165-993d-aebd5eef7a24
+:END:
+#+title: Bar
+
+[[id:884b2341-b7fe-434d-848c-5282c0727861][Foo]]

tests/roam-files/f1.org

@@ -1,7 +0,0 @@
-#+TITLE: File 1
-
-link to [[file:nested/f1.org][Nested File 1]] 
-link to [[file:f2.org][File 2]]
-
-Arbitrary [[https://google.com][HTML]] link
-Arbitrary text

tests/roam-files/f2.org

@@ -1,3 +0,0 @@
-#+TITLE: File 2
-
-This file has no links.

tests/roam-files/f3.org

@@ -1,5 +0,0 @@
-#+TITLE: File 3
-
-This file has a link to an file with no title.
-
-[[file:no-title.org][no-title]]

tests/roam-files/foo.org

@@ -0,0 +1,4 @@
+:PROPERTIES:
+:ID:       884b2341-b7fe-434d-848c-5282c0727861
+:END:
+#+title: Foo

tests/roam-files/nested/f1.org

@@ -1,4 +0,0 @@
-#+TITLE: Nested File 1
-
-Link to [[file:f2.org][Nested File 2]]
-Link to [[file:../f1.org][File 1]]

tests/roam-files/nested/f2.org

@@ -1,3 +0,0 @@
-#+TITLE: Nested File 2
-
-Link to [[file:f1.org][Nested File 1]]

tests/roam-files/no-title.org

@@ -1 +0,0 @@
-no title in this file :O

tests/roam-files/roam-exclude.org

@@ -0,0 +1,7 @@
+: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/test-org-roam-capture.el

@@ -0,0 +1,56 @@
+;;; 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 "expands templates when it's a function"
+    (expect
+     (org-roam-capture--fill-template (lambda () "foo"))
+     :to-equal "foo")))
+
+(provide 'test-org-roam-capture)

tests/test-org-roam-utils.el

@@ -0,0 +1,39 @@
+;;; test-org-roam-utils.el --- Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(describe "org-roam-whitespace-content"
+  (it "extracts whitespace correctly"
+    (expect
+     (org-roam-whitespace-content "foo")
+     :to-equal "")
+    (expect
+     (org-roam-whitespace-content "foo\n")
+     :to-equal "\n")
+    (expect
+     (org-roam-whitespace-content "foo\n\t\n")
+     :to-equal "\n\t\n")))
+
+(provide 'test-org-roam-utils)

tests/test-org-roam.el

@@ -1,9 +1,9 @@
-;;; test-org-roam.el --- Tests for org-roam -*- lexical-binding: t; -*-
+;;; test-org-roam.el --- Tests for Org-roam -*- lexical-binding: t; -*-
 
 ;; Copyright (C) 2020 Jethro Kuan
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup) (with-simulated-input))
+;; 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
@@ -19,212 +19,65 @@
 ;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 ;;; Commentary:
-
-;;
-
 ;;; Code:
 
-;;;; Requirements
-
 (require 'buttercup)
-(require 'with-simulated-input)
 (require 'org-roam)
-(require 'dash)
 
-(defun abs-path (file-path)
-  (file-truename (expand-file-name file-path org-roam-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))
 
-(defun org-roam--test-find-new-file (path)
-  (let ((path (abs-path path)))
-    (make-directory (file-name-directory path) t)
-    (find-file path)))
+  (it "gets files correctly"
+    (expect (length (org-roam-list-files))
+            :to-equal 3))
 
-(defvar org-roam--tests-directory (file-truename (concat default-directory "tests/roam-files"))
-  "Directory containing org-roam test org files.")
+  (it "respects org-roam-file-extensions"
+    (setq org-roam-file-extensions '("md"))
+    (expect (length (org-roam-list-files)) :to-equal 1)
+    (setq org-roam-file-extensions '("org" "md"))
+    (expect (length (org-roam-list-files)) :to-equal 4))
 
-(defun org-roam--test-init ()
-  (let ((original-dir org-roam--tests-directory)
-        (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
-    (copy-directory original-dir new-dir)
-    (setq org-roam-directory new-dir))
-  (org-roam-mode +1))
+  (it "respects org-roam-file-exclude-regexp"
+    (setq org-roam-file-exclude-regexp (regexp-quote "foo.org"))
+    (expect (length (org-roam-list-files)) :to-equal 2)))
 
-(defun org-roam--test-build-cache ()
-  "Builds the caches synchronously."
-  (let ((cache (org-roam--build-cache org-roam-directory)))
-    (setq org-roam-forward-links-cache (plist-get cache :forward))
-    (setq org-roam-backward-links-cache (plist-get cache :backward))
-    (setq org-roam-titles-cache (plist-get cache :titles))
-    (setq org-roam-cache-initialized t)))
+(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))
 
-;;; Tests
-(describe "org-roam--build-cache-async"
-          (it "initializes correctly"
-              (org-roam--test-init)
-              (expect org-roam-cache-initialized :to-be nil)
-              (expect (hash-table-count org-roam-forward-links-cache) :to-be 0)
-              (expect (hash-table-count org-roam-backward-links-cache) :to-be 0)
-              (expect (hash-table-count org-roam-titles-cache) :to-be 0)
+  (after-all
+    (org-roam-db--close)
+    (delete-file org-roam-db-location))
 
-              (org-roam--build-cache-async)
-              (sleep-for 3) ;; Because it's async
+  (it "has the correct number of files"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
+            :to-equal
+            3))
 
-              ;; Caches should be populated
-              (expect org-roam-cache-initialized :to-be t)
-              (expect (hash-table-count org-roam-forward-links-cache) :to-be 4)
-              (expect (hash-table-count org-roam-backward-links-cache) :to-be 5)
-              (expect (hash-table-count org-roam-titles-cache) :to-be 5)
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
+            :to-equal
+            2))
 
-              ;; Forward cache
-              (let ((f1 (gethash (abs-path "f1.org") org-roam-forward-links-cache))
-                    (f2 (gethash (abs-path "f2.org") org-roam-forward-links-cache))
-                    (nested-f1 (gethash (abs-path "nested/f1.org") org-roam-forward-links-cache))
-                    (nested-f2 (gethash (abs-path "nested/f2.org") org-roam-forward-links-cache))
-                    (expected-f1 (list (abs-path "nested/f1.org")
-                                       (abs-path "f2.org")))
-                    (expected-nested-f1 (list (abs-path "nested/f2.org")
-                                              (abs-path "f1.org")))
-                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
+            :to-equal
+            1))
 
-                (expect f1 :to-have-same-items-as expected-f1)
-                (expect f2 :to-be nil)
-                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
-                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+  (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"))))
 
-              ;; Backward cache
-              (let ((f1 (hash-table-keys (gethash (abs-path "f1.org") org-roam-backward-links-cache)))
-                    (f2 (hash-table-keys (gethash (abs-path "f2.org") org-roam-backward-links-cache)))
-                    (nested-f1 (hash-table-keys(gethash (abs-path "nested/f1.org") org-roam-backward-links-cache)))
-                    (nested-f2 (hash-table-keys (gethash (abs-path "nested/f2.org") org-roam-backward-links-cache)))
-                    (expected-f1 (list (abs-path "nested/f1.org")))
-                    (expected-f2 (list (abs-path "f1.org")))
-                    (expected-nested-f1 (list (abs-path "nested/f2.org")
-                                              (abs-path "f1.org")))
-                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
-                (expect f1 :to-have-same-items-as expected-f1)
-                (expect f2 :to-have-same-items-as expected-f2)
-                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
-                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+(provide 'test-org-roam)
 
-              ;; Titles Cache
-              (expect (gethash (abs-path "f1.org") org-roam-titles-cache) :to-equal "File 1")
-              (expect (gethash (abs-path "f2.org") org-roam-titles-cache) :to-equal "File 2")
-              (expect (gethash (abs-path "nested/f1.org") org-roam-titles-cache) :to-equal "Nested File 1")
-              (expect (gethash (abs-path "nested/f2.org") org-roam-titles-cache) :to-equal "Nested File 2")
-              (expect (gethash (abs-path "no-title.org") org-roam-titles-cache) :to-be nil)))
-
-(describe "org-roam-insert"
-          (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
-
-          (it "temp1 -> f1"
-              (let ((buf (org-roam--test-find-new-file "temp1.org")))
-                (with-current-buffer buf
-                  (with-simulated-input
-                   "File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:f1.org")))
-
-          (it "temp2 -> nested/f1"
-              (let ((buf (org-roam--test-find-new-file "temp2.org")))
-                (with-current-buffer buf
-                  (with-simulated-input
-                   "Nested SPC File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:nested/f1.org")))
-
-          (it "nested/temp3 -> f1"
-              (let ((buf (org-roam--test-find-new-file "nested/temp3.org")))
-                (with-current-buffer buf
-                  (with-simulated-input
-                   "File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:../f1.org")))
-
-          (it "a/b/temp4 -> nested/f1"
-              (let ((buf (org-roam--test-find-new-file "a/b/temp4.org")))
-                (with-current-buffer buf
-                  (with-simulated-input
-                   "Nested SPC File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:../../nested/f1.org"))))
-
-(describe "rename file updates cache"
-          (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
-
-          (it "f1 -> new_f1"
-              (rename-file (abs-path "f1.org")
-                           (abs-path "new_f1.org"))
-              ;; Cache should be cleared of old file
-              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (hash-table-keys)
-                           (member (abs-path "f1.org"))) :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "new_f1.org"))) :not :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "new_f1.org"))
-                           (member (abs-path "nested/f1.org"))) :not :to-be nil)
-              ;; Links are updated
-              (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "nested/f1.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:../new_f1.org][File 1]]")))
-
-
-          (it "f1 -> f1 with spaces"
-              (rename-file (abs-path "f1.org")
-                           (abs-path "f1 with spaces.org"))
-              ;; Cache should be cleared of old file
-              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (hash-table-keys)
-                           (member (abs-path "f1.org"))) :to-be nil)
-              ;; Links are updated
-              (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "nested/f1.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:../f1 with spaces.org][File 1]]")))
-
-          (it "no-title -> meaningful-title"
-              (rename-file (abs-path "no-title.org")
-                           (abs-path "meaningful-title.org"))
-              ;; File has no forward links
-              (expect (gethash (abs-path "no-title.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (gethash (abs-path "meaningful-title.org")  org-roam-forward-links-cache) :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f3.org"))
-                           (member (abs-path "no-title.org"))) :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f3.org"))
-                           (member (abs-path "meaningful-title.org"))) :not :to-be nil)
-
-              ;; Links are updated with the appropriate name
-              (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "f3.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:meaningful-title.org][meaningful-title]]"))))
-
-(describe "delete file updates cache"
-          (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
-          (it "delete f1"
-              (delete-file (abs-path "f1.org"))
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f1.org"))) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (gethash (abs-path "f1.org"))) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (gethash (abs-path "nested/f2.org"))) :not :to-be nil)))
+;;; test-org-roam.el ends here