migration: catch error and restore files

In case of migration error, restore original files, and print a message.

.dir-locals.el

@@ -0,0 +1,13 @@
+((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)
+                              (org-element-map . defun)
+                              (org-roam-with-temp-buffer . 1)
+                              (org-with-point-at . 1)
+                              (magit-insert-section . defun)
+                              (magit-section-case . 0)
+                              (->> . 1)
+                              (org-roam-with-file . 2)))))

.github/CONTRIBUTING.md

@@ -0,0 +1,34 @@
+# Contributing
+
+If you discover issues, have ideas for improvements or new features, please
+report them to the [issue tracker][1] of the repository or submit a pull
+request. Please, try to follow these guidelines when you do so.
+
+## Issue reporting
+
+* Check that the issue has not already been reported.
+* Check that the issue has not already been fixed in the latest code
+  (a.k.a. `develop`).
+* Be clear, concise and precise in your description of the problem.
+* Open an issue with a descriptive title and a summary in grammatically correct,
+  complete sentences.
+* Include any relevant code to the issue summary.
+* If you're reporting performance issues it'd be nice if you added some profiling data (Emacs has a built-in profiler).
+
+## Pull requests
+
+* Read [how to properly contribute to open source projects on Github][2].
+* Use a topic branch to easily amend a pull request later, if necessary.
+* Write [good commit messages][3].
+* Mention related tickets in the commit messages (e.g. `[Fix #N] Add missing autoload cookies`)
+* Update the [changelog][5].
+* Use the same coding conventions as the rest of the project.
+* Verify your Emacs Lisp code with `checkdoc` (<kbd>C-c ? d</kbd>).
+* Open a [pull request][4] that relates to *only* one subject with a clear title
+  and description in grammatically correct, complete sentences.
+
+[1]: https://github.com/jethrokuan/org-roam/issues
+[2]: http://gun.io/blog/how-to-github-fork-branch-and-pull-request
+[3]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
+[4]: https://help.github.com/articles/using-pull-requests
+[5]: https://github.com/jethrokuan/org-roam/blob/master/CHANGELOG.md

.github/FUNDING.yml

@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: [jethrokuan, zaeph]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+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

@@ -0,0 +1,43 @@
+---
+name: Bug Report
+about: Something's not working.
+title: ""
+labels: ""
+assignees: ""
+---
+
+### Description
+
+#### Steps to Reproduce
+
+<!--
+Example:
+
+1. Load Emacs
+2. Run `org-roam--build-cache-async`
+3. Run `org-roam-find-file`
+...
+-->
+
+#### 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 -->
+
+### Environment
+
+<!-- Please M-x org-roam-diagnostics and paste results here -->
+
+- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature Request
+about: Create a feature request to improve Org-roam
+title: ""
+labels: "enhancement"
+assignees: ""
+---
+
+### Brief Abstract
+
+### Long Description
+
+### Proposed Implementation (if any)
+
+### Please check the following:
+
+- [ ] No similar feature requests

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1 @@
+###### Motivation for this change

.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

@@ -0,0 +1,61 @@
+# * test.yml --- Test Emacs packages using makem.sh on GitHub Actions
+
+# https://github.com/alphapapa/makem.sh
+
+# Based on Steve Purcell's examples at
+# <https://github.com/purcell/setup-emacs/blob/master/.github/workflows/test.yml>,
+# <https://github.com/purcell/package-lint/blob/master/.github/workflows/test.yml>.
+
+# * License:
+
+# 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/>.
+
+# * Code:
+
+name: "CI"
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        emacs_version:
+          - 27.1
+          - snapshot
+    steps:
+      - uses: purcell/setup-emacs@master
+        with:
+          version: ${{ matrix.emacs_version }}
+
+      - uses: actions/checkout@v2
+
+      - name: Install Eldev
+        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
+
+      - name: Install dependencies
+        run: make prepare
+
+      - name: Lint
+        run: make lint
+
+      - name: Test
+        run: make test
+# Local Variables:
+# eval: (outline-minor-mode)
+# End:

.gitignore

@@ -0,0 +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

@@ -0,0 +1,359 @@
+# Changelog
+
+## 1.2.4 (TBD)
+
+### 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](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](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](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](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](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)
+
+## 0.1.1 (2020-02-15)
+
+Mostly a documentation/cleanup release.
+
+### New Features
+
+- [#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](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](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](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: -->

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

@@ -0,0 +1,29 @@
+.PHONY: clean
+clean:
+	eldev clean all
+
+.PHONY: prepare
+prepare:
+	eldev -C --unstable -p -dtT prepare
+
+.PHONY: lint
+lint:
+	eldev -C --unstable -T lint
+
+.PHONY: test
+test:
+	eldev -C --unstable -T test
+
+docs:
+	make -C doc all
+
+html:
+	make -C doc html-dir
+
+install: install-docs
+
+install-docs: docs
+	make -C doc install-docs
+
+install-info: info
+	make -C doc install-info

README.md

@@ -1,52 +1,114 @@
-[![Documentation Status](https://readthedocs.org/projects/org-roam/badge/?version=latest)](https://org-roam.readthedocs.io/en/latest/?badge=latest)
+# Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]
 
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
+<img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">
 
-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 is a plain-text knowledge management system. It brings some of
+[Roam's][roamresearch] more powerful features into the [Org-mode][org]
+ecosystem.
 
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem. 
+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.
 
-For more documentation, see [the documentation page](https://org-roam.readthedocs.io/en/latest/).
+- **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.
 
-## Understanding Roam
+<p align="center">
+  <img src="https://www.orgroam.com/img/screenshot.png" alt="Org-roam Screenshot" width="738">
+</p>
 
-To understand more about Roam, I recommend the following links:
+- **[Documentation][docs]**
+- **[Discourse][discourse]**
+- **[Slack][slack]**
+- **[Frequently Asked Questions][faq]**
+- **[Changelog](CHANGELOG.md)**
 
--   [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)
+## Installation
 
-## Project Status
+You can install `org-roam` using `package.el`:
 
-As of February 2020, it is in a very early stage of development. 
+```
+M-x package-install RET org-roam RET
+```
 
-## A Preview
+Here's a sample configuration with `use-package`:
 
-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.
+```emacs-lisp
+(use-package org-roam
+      :ensure t
+      :custom
+      (org-roam-directory (file-truename "/path/to/org-files/"))
+      :bind (("C-c n l" . org-roam-buffer-toggle)
+             ("C-c n f" . org-roam-node-find)
+             ("C-c n g" . org-roam-graph)
+             ("C-c n i" . org-roam-node-insert)
+             ("C-c n c" . org-roam-capture)
+             ;; Dailies
+             ("C-c n j" . org-roam-dailies-capture-today))
+      :config
+      (org-roam-setup)
+      ;; If using org-roam-protocol
+      (require 'org-roam-protocol))
+```
 
-![img](doc/images/org-roam-graph.gif)
+The `file-truename` function is only necessary when you use symbolic links
+inside `org-roam-directory`: Org-roam does not resolve symbolic links.
 
-## Knowledge Bases using Org-Roam
+Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
+graph-related functionality. It is recommended to install PCRE-enabled ripgrep
+for better performance and extended functionality.
+
+## 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))
+- [Alexey Shmalko](https://braindump.rasen.dev/)
+- [Sidharth Arya](https://sidhartharya.github.io/braindump/index.html)
 
 ## Contributing
 
 To report bugs and suggest new feature use the issue tracker. If you
 have some code which you would like to be merged, then open a pull
-request. Please also see CONTRIBUTING.md.
+request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
+
+## License
+
+Copyright © Jethro Kuan and contributors. Distributed under the GNU
+General Public License, Version 3.
 
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
+[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-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
+[issues]: https://github.com/org-roam/org-roam/issues
+[faq]: https://www.orgroam.com/manual.html#FAQ

default.mk

@@ -0,0 +1,106 @@
+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-buffer.el
+ELS += org-roam-capture.el
+ELS += org-roam-compat.el
+ELS += org-roam-completion.el
+ELS += org-roam-dailies.el
+ELS += org-roam-db.el
+ELS += org-roam.el
+ELS += org-roam-graph.el
+ELS += org-roam-macs.el
+ELS += 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/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

@@ -1,37 +0,0 @@
-## Ecosystem
-
-A number of packages work well combined with Org-Roam:
-
-### Deft
-[Deft](https://jblevins.org/projects/deft/) provides a nice
-interface for browsing and filtering org-roam notes.
-
-```
-(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/")
-  (deft-use-filename-as-title t))
-```
-
-### 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.
-
-```
-(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"))
-```

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-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">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-server"
+            >org-roam-server</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-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
+            >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

@@ -1,35 +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 (org-mode . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam")
-      :custom
-      (org-roam-directory "/path/to/org-files/")
-      (org-roam-link-representation 'title) ;; or keep it as 'id
-      :bind
-      ("C-c n l" . org-roam)      
-      ("C-c n t" . org-roam-today)
-      ("C-c n f" . org-roam-find-file)
-      ("C-c n i" . org-roam-insert)
-      ("C-c n g" . org-roam-show-graph))
-```
-
-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
-```
-
-```
-(add-to-list 'load-path "./elisp")
-(require 'org-roam)
-```
-
-[use-package]: https://github.com/jwiegley/use-package
-[straight]: https://github.com/raxod502/straight.el

doc/requirements.txt

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

doc/tour.md

@@ -1,20 +0,0 @@
-### A Tour of Org-Roam
-
-All of this starts from the note. A note is just a simple `.org` file
-in the directory. Any org file in the directory is considered part of
-the org-roam ecosystem. Notes are quickly linked together (and created
-if necessary) using `org-roam-insert`.
-
-![org-roam-insert](images/org-roam-insert.gif)
-
-Org-roam tracks all of these file links, and builds a cache
-asynchronously in the background. This cache is used to populate the
-backlinks buffer, which shows files that link to the current file, as
-well as some preview contents:
-
-![org-roam-buffer](images/org-roam-buffer.gif)
-
-These file links also form a graph. The generated graph is navigable
-in Emacs.
-
-![org-roam-graph](images/org-roam-graph.gif)

mkdocs.yml

@@ -1,30 +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
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.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 +1,828 @@
+;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides capture functionality for org-roam
+;;; Code:
+;;;
+;;;; Library Requires
+(require 'org-capture)
+(eval-when-compile
+  (require 'org-roam-macs)
+  (require 'org-macs))
+(require 'org-roam-db)
+(require 'dash)
+(require 'cl-lib)
+
+;; Declarations
+(declare-function org-roam-ref-add "org-roam" (ref))
+(declare-function org-datetree-find-date-create "org-datetree" (date &optional keep-restriction))
+(declare-function org-datetree-find-month-create "org-datetree" (d &optional keep-restriction))
+
+(defvar org-roam-directory)
+
+(defvar org-roam-capture--node nil
+  "The node passed during an Org-roam capture.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defvar org-roam-capture--info nil
+  "A property-list of additional information passed to the Org-roam template.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defconst org-roam-capture--template-keywords (list :if-new :id :link-description :call-location
+                                                    :region :override-default-time)
+  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
+
+(defcustom org-roam-capture-templates
+  '(("d" "default" plain "%?"
+     :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
+                        "#+title: ${title}\n")
+     :unnarrowed t))
+  "Templates for the creation of new entries within Org-roam.
+
+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 :if-new property. This determines the
+location of the new node. The :if-new property contains a list, supporting
+the following options:
+
+   (file \"path/to/file\")
+       The file will be created, and prescribed an ID.
+
+   (file+head \"path/to/file\" \"head content\")
+       The file will be created, prescribed an ID, and head content will be
+       inserted into the file.
+
+   (file+olp \"path/to/file\" (\"h1\" \"h2\"))
+       The file will be created, prescribed an ID. The OLP (h1, h2) will be
+       created, and the point placed after.
+
+   (file+head+olp \"path/to/file\" \"head content\" (\"h1\" \"h2\"))
+       The file will be created, prescribed an ID. Head content will be
+       inserted at the start of the file. The OLP (h1, h2) will be created,
+       and the point placed after.
+
+   (file+datetree \"path/to/file\" day)
+       The file will be created, prescribed an ID. Head content will be
+       inserted at the start of the file. The datetree will be created,
+       available options are day, week, month.
+
+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 " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+(defvar org-roam-capture-new-node-hook (list #'org-roam-capture--insert-ref)
+  "Normal-mode hooks run when a new Org-roam node is created.
+The current point is the point of the new node.
+The hooks must not move the point.")
+
+(defcustom org-roam-capture-ref-templates
+  '(("r" "ref" plain "%?"
+     :if-new (file+head "${slug}.org"
+                        "#+title: ${title}")
+     :unnarrowed t))
+  "The Org-roam templates used during a capture from the roam-ref protocol.
+See `org-roam-capture-templates' for the template documentation."
+  :group 'org-roam
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+(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 (&rest stuff)
+  "Put properties from STUFF into the `org-roam-capture-template'."
+  (let ((p (plist-get org-capture-plist :org-roam)))
+    (while stuff
+      (setq p (plist-put p (pop stuff) (pop stuff))))
+    (setq org-capture-plist
+          (plist-put org-capture-plist :org-roam p))))
+
+;; FIXME: Pending upstream patch
+;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
+;;
+;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
+;; during the initialization of the Org-capture buffer. The value of
+;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
+;; However, the value for that particular capture is no longer accessible for
+;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
+;; cleaned up.
+;;
+;; This advice restores the global `org-capture-plist' during finalization, so
+;; the plist is valid during both initialization and finalization of the
+;; capture.
+(defun org-roam-capture--update-plist (&optional _)
+  "Update global plist from local var."
+  (setq org-capture-plist org-capture-current-plist))
+
+(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
+
+(defun org-roam-capture--finalize-find-file ()
+  "Visit the buffer after Org-capture is done.
+This function is to be called in the Org-capture finalization process.
+ID is unused."
+  (switch-to-buffer (org-capture-get :buffer)))
+
+(defun org-roam-capture--finalize-insert-link ()
+  "Insert a link to ID into the buffer where Org-capture was called.
+ID is the Org id of the newly captured content.
+This function is to be called in the Org-capture finalization process."
+  (when-let* ((mkr (org-roam-capture--get :call-location))
+              (buf (marker-buffer mkr)))
+    (with-current-buffer buf
+      (when-let ((region (org-roam-capture--get :region)))
+        (org-roam-unshield-region (car region) (cdr region))
+        (delete-region (car region) (cdr region))
+        (set-marker (car region) nil)
+        (set-marker (cdr region) nil))
+      (org-with-point-at mkr
+        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
+                                      (org-roam-capture--get :link-description)))))))
+
+(defun org-roam-capture--finalize ()
+  "Finalize the `org-roam-capture' process."
+  (when-let ((region (org-roam-capture--get :region)))
+    (org-roam-unshield-region (car region) (cdr region)))
+  (if org-note-abort
+      (when-let ((new-file (org-roam-capture--get :new-file)))
+        (org-roam-message "Deleting file for aborted capture %s" new-file)
+        (when (find-buffer-visiting new-file)
+          (kill-buffer (find-buffer-visiting new-file)))
+        (delete-file new-file))
+    (when-let* ((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--install-finalize ()
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
+  (when (org-roam-capture-p)
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
+
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
+
+(defun org-roam-capture--fill-template (template &optional org-capture-p)
+  "Expand TEMPLATE and return it.
+It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+also run Org-capture's template expansion."
+  (funcall (if org-capture-p #'org-capture-fill-template #'identity)
+           (org-roam-format
+            template
+            (lambda (key)
+              (let ((fn (intern 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 (completing-read (format "%s: " key) nil)))
+                      (plist-put org-roam-capture--info ksym r)
+                      r))))))))
+
+(defun org-roam-capture--insert-ref ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
+
+(defun org-roam-capture--goto-location ()
+  "Initialize the buffer, and goto the location of the new capture.
+Return the ID of the location."
+  (let (p)
+    (pcase (or (org-roam-capture--get :if-new)
+               (user-error "Template needs to specify `:if-new'"))
+      (`(file ,path)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (unless (file-exists-p path)
+         (org-roam-capture--put :new-file path))
+       (set-buffer (org-capture-target-buffer path))
+       (widen)
+       (setq p (goto-char (point-min))))
+      (`(file+olp ,path ,olp)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (set-buffer (org-capture-target-buffer path))
+       (unless (file-exists-p path)
+         (org-roam-capture--put :new-file 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 (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (set-buffer (org-capture-target-buffer path))
+       (unless (file-exists-p path)
+         (org-roam-capture--put :new-file path)
+         (insert (org-roam-capture--fill-template head t)))
+       (widen)
+       (setq p (goto-char (point-min))))
+      (`(file+head+olp ,path ,head ,olp)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (widen)
+       (set-buffer (org-capture-target-buffer path))
+       (unless (file-exists-p path)
+         (org-roam-capture--put :new-file path)
+         (insert (org-roam-capture--fill-template head t)))
+       (setq p (point-min))
+       (let ((m (org-roam-capture-find-or-create-olp olp)))
+         (goto-char m)))
+      (`(file+datetree ,path ,tree-type)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (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)))))
+    (prog1
+        ;; Setup `org-id' for the current capture target and return it back to
+        ;; the caller.
+        (save-excursion
+          (goto-char p)
+          (when-let* ((node org-roam-capture--node)
+                      (id (org-roam-node-id node)))
+            (org-entry-put p "ID" id))
+          (prog1
+              (org-id-get-create)
+            (run-hooks 'org-roam-capture-new-node-hook)))
+      ;; Adjust the point only after ID was generated and polluted to the
+      ;; current target in the capture buffer.
+      (org-roam-capture--adjust-point-for-capture-type))))
+
+(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))
+
+(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)
+       (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--get-node-from-ref (ref)
+  "Return the node from reference REF."
+  (save-match-data
+    (when (string-match org-link-plain-re ref)
+      (let ((type (match-string 1 ref))
+            (path (match-string 2 ref)))
+        (when-let ((id (caar (org-roam-db-query
+                              [:select [nodes:id]
+                               :from refs
+                               :left-join nodes
+                               :on (= refs:node-id nodes:id)
+                               :where (= refs:type $s1)
+                               :and (= refs:ref $s2)
+                               :limit 1]
+                              type path))))
+          (org-roam-populate (org-roam-node-create :id id)))))))
+
+(defun org-roam-capture--get-point ()
+  "Return exact point to file for org-capture-template.
+This function is used solely in Org-roam's capture templates: see
+`org-roam-capture-templates'."
+  (when (org-roam-capture--get :override-default-time)
+    (org-capture-put :default-time (org-roam-capture--get :override-default-time)))
+  (let ((id (cond ((plist-get org-roam-capture--info :ref)
+                   (if-let ((node (org-roam-capture--get-node-from-ref
+                                   (plist-get org-roam-capture--info :ref))))
+                       (progn
+                         (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+                         (goto-char (org-roam-node-point node))
+                         (widen)
+                         (org-end-of-subtree t t))
+                     (org-roam-capture--goto-location)))
+                  ((and (org-roam-node-file org-roam-capture--node)
+                        (org-roam-node-point org-roam-capture--node))
+                   (set-buffer (org-capture-target-buffer (org-roam-node-file org-roam-capture--node)))
+                   (goto-char (org-roam-node-point org-roam-capture--node))
+                   (widen)
+                   (org-end-of-subtree t t)
+                   (org-roam-node-id org-roam-capture--node))
+                  (t
+                   (org-roam-capture--goto-location)))))
+    (org-capture-put :template
+                     (org-roam-capture--fill-template (org-capture-get :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--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)
+    (`(,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--get-point ,body)
+               options
+               (list :org-roam org-roam-plist))))
+    (_
+     (signal 'invalid-template template))))
+
+;;;###autoload
+(cl-defun org-roam-capture- (&key goto keys node info props templates)
+  "Main entry point.
+GOTO and KEYS correspond to `org-capture' arguments.
+INFO is an alist for filling up Org-roam's capture templates.
+NODE is an `org-roam-node' construct containing information about the node.
+PROPS is a plist containing additional Org-roam properties for each template.
+TEMPLATES is a list of org-roam templates."
+  (let* ((props (plist-put props :call-location (point-marker)))
+         (org-capture-templates
+          (mapcar (lambda (template)
+                    (org-roam-capture--convert-template template props))
+                  (or templates org-roam-capture-templates)))
+         (org-roam-capture--node node)
+         (org-roam-capture--info info))
+    (when (and (not keys)
+               (= (length org-capture-templates) 1))
+      (setq keys (caar org-capture-templates)))
+    (org-capture goto keys)))
+
+;;;###autoload
+(defun org-roam-capture (&optional goto keys)
+  "Launches an `org-capture' process for a new or existing note.
+This uses the templates defined at `org-roam-capture-templates'.
+Arguments GOTO and KEYS see `org-capture'."
+  (interactive "P")
+  (let ((node (org-roam-node-read)))
+    (org-roam-capture- :goto goto
+                       :keys keys
+                       :node node
+                       :props '(:immediate-finish nil))))
+
+(provide 'org-roam-capture)
+
+;;; org-roam-capture.el ends here

org-roam-compat.el

@@ -0,0 +1,124 @@
+;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This file contains code needed for backward compatibility with older Emacsen
+;; and previous versions of org-roam.
+;;
+;;; Code:
+;;;; Library Requires
+
+;;; Backports
+;; REVIEW Remove when 26.x support is dropped. This is exact the same as
+;; `directory-files-recursively' from Emacs 26, but with FOLLOW-SYMLINKS
+;; parameter from Emacs 27.
+(defun org-roam--directory-files-recursively (dir regexp
+                                                  &optional include-directories predicate
+                                                  follow-symlinks)
+  "Return list of all files under directory DIR whose names match REGEXP.
+This function works recursively.  Files are returned in \"depth
+first\" order, and files from each directory are sorted in
+alphabetical order.  Each file name appears in the returned list
+in its absolute form.
+
+By default, the returned list excludes directories, but if
+optional argument INCLUDE-DIRECTORIES is non-nil, they are
+included.
+
+PREDICATE can be either nil (which means that all subdirectories
+of DIR are descended into), t (which means that subdirectories that
+can't be read are ignored), or a function (which is called with
+the name of each subdirectory, and should return non-nil if the
+subdirectory is to be descended into).
+
+If FOLLOW-SYMLINKS is non-nil, symbolic links that point to
+directories are followed.  Note that this can lead to infinite
+recursion."
+  (let* ((result nil)
+         (files nil)
+         (dir (directory-file-name dir))
+         ;; When DIR is "/", remote file names like "/method:" could
+         ;; also be offered.  We shall suppress them.
+         (tramp-mode (and tramp-mode (file-remote-p (expand-file-name dir)))))
+    (dolist (file (sort (file-name-all-completions "" dir)
+                        'string<))
+      (unless (member file '("./" "../"))
+        (if (directory-name-p file)
+            (let* ((leaf (substring file 0 (1- (length file))))
+                   (full-file (concat dir "/" leaf)))
+              ;; Don't follow symlinks to other directories.
+              (when (and (or (not (file-symlink-p full-file))
+                             (and (file-symlink-p full-file)
+                                  follow-symlinks))
+                         ;; Allow filtering subdirectories.
+                         (or (eq predicate nil)
+                             (eq predicate t)
+                             (funcall predicate full-file)))
+                (let ((sub-files
+                       (if (eq predicate t)
+                           (condition-case nil
+                               (org-roam--directory-files-recursively
+                                full-file regexp include-directories
+                                predicate follow-symlinks)
+                             (file-error nil))
+                         (org-roam--directory-files-recursively
+                          full-file regexp include-directories
+                          predicate follow-symlinks))))
+                  (setq result (nconc result sub-files))))
+              (when (and include-directories
+                         (string-match regexp leaf))
+                (setq result (nconc result (list full-file)))))
+          (when (string-match regexp file)
+            (push (concat dir "/" file) files)))))
+    (nconc result (nreverse files))))
+
+;;; Obsolete aliases (remove after next major release)
+(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")
+
+;;; Obsolete functions
+
+(provide 'org-roam-compat)
+
+;;; org-roam-compat.el ends here

org-roam-completion.el

@@ -0,0 +1,107 @@
+;;; org-roam-completion.el --- Completion features -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides completion-at-point functions for Org-roam.
+;;
+;; The two main functions provided to capf are:
+;;
+;;    `org-roam-complete-link-at-point' provides completions to nodes
+;;    within link brackets
+;;
+;;    `org-roam-complete-everywhere' provides completions for nodes everywhere,
+;;    matching the symbol at point
+;;
+;;; Code:
+(require 'cl-lib)
+(require 'org-element)
+
+(declare-function org-roam--get-titles "org-roam")
+
+(defcustom org-roam-completion-everywhere nil
+  "When non-nil, provide link completion matching outside of Org links."
+  :group 'org-roam
+  :type 'boolean)
+
+(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
+                                            #'org-roam-complete-everywhere)
+  "List of functions to be used with `completion-at-point' for Org-roam.")
+
+(defconst org-roam-bracket-completion-re
+  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*\\)]]"
+  "Regex for completion within link brackets.
+We use this as a substitute for `org-link-bracket-re', because
+`org-link-bracket-re' requires content within the brackets for a match.")
+
+(defun org-roam-complete-everywhere ()
+  "Provides completions for links for any word at point.
+This is a `completion-at-point' function, and is active when
+`org-roam-completion-everywhere' is non-nil."
+  (when (and org-roam-completion-everywhere
+             (thing-at-point 'word)
+             (not (save-match-data (org-in-regexp org-link-any-re))))
+    (let ((bounds (bounds-of-thing-at-point 'word)))
+      (list (car bounds) (cdr bounds)
+            (completion-table-dynamic
+             (lambda (_)
+               (funcall #'org-roam--get-titles)))
+            :exit-function
+            (lambda (str _status)
+              (delete-char (- (length str)))
+              (insert "[[roam:" str "]]"))))))
+
+(defun org-roam-complete-link-at-point ()
+  "Do appropriate completion for the link at point."
+  (let (roam-p start end)
+    (when (org-in-regexp org-roam-bracket-completion-re 1)
+      (setq roam-p (not (string-blank-p (match-string 1)))
+            start (match-beginning 2)
+            end (match-end 2))
+      (list start end
+            (completion-table-dynamic
+             (lambda (_)
+               (funcall #'org-roam--get-titles)))
+            :exit-function
+            (lambda (str &rest _)
+              (delete-char (- 0 (length str)))
+              (insert (concat (unless roam-p "roam:")
+                              str))
+              (forward-char 2))))))
+
+(defun org-roam-complete-at-point ()
+  "."
+  (run-hook-with-args-until-success 'org-roam-completion-functions))
+
+(defun org-roam--register-completion-functions ()
+  "."
+  (add-hook 'completion-at-point-functions #'org-roam-complete-at-point nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)
+
+(provide 'org-roam-completion)
+
+;;; org-roam-completion.el ends here

org-roam-dailies.el

@@ -0,0 +1,332 @@
+;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;;
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;;      Leo Vivier <leo.vivier+dev@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides functionality for creating daily-notes. This is a
+;; concept borrowed from Roam Research.
+;;
+;;; Code:
+;;; Library Requires
+(require 'org-capture)
+(require 'org-roam-capture)
+(require 'f)
+
+;;;; Declarations
+(defvar org-roam-directory)
+(defvar org-roam-file-extensions)
+(declare-function org-roam-file-p        "org-roam")
+
+;;;; Faces
+(defface org-roam-dailies-calendar-note
+  '((t :inherit (org-link) :underline nil))
+  "Face for dates with a daily-note in the calendar."
+  :group 'org-roam-faces)
+
+;;;; Customizable variables
+(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
+     "* %?"
+     :if-new (file+head "%<%Y-%m-%d>.org"
+                        "#+title: %<%Y-%m-%d>\n")))
+  "Capture templates for daily-notes in Org-roam.
+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 " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat (string :tag "Headline"))))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+;;;###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)))
+
+(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)
+       (f-descendant-of-p path directory)))))
+
+(defun org-roam-dailies--capture (time &optional goto)
+  "Capture an entry in a daily-note for TIME, creating it if necessary.
+When GOTO is non-nil, go the note without creating an entry."
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
+    (org-roam-capture- :goto (when goto '(4))
+                       :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)))
+
+;;;; Commands
+;;; Today
+;;;###autoload
+(defun org-roam-dailies-capture-today (&optional goto)
+  "Create an entry in the daily-note for today.
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-today ()
+  "Find the daily-note for today, creating it if necessary."
+  (interactive)
+  (org-roam-dailies-capture-today t))
+
+;;; Tomorrow
+;;;###autoload
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+  "Create an entry in the daily-note for tomorrow.
+
+With numeric argument N, use the daily-note N days in the future.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "p")
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-tomorrow (n)
+  "Find the daily-note for tomorrow, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow n t))
+
+;;; Yesterday
+;;;###autoload
+(defun org-roam-dailies-capture-yesterday (n &optional goto)
+  "Create an entry in the daily-note for yesteday.
+
+With numeric argument N, use the daily-note N days in the past.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) goto))
+
+;;;###autoload
+(defun org-roam-dailies-goto-yesterday (n)
+  "Find the daily-note for yesterday, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) t))
+
+;;; Calendar
+(defun org-roam-dailies-calendar--file-to-date (&optional file)
+  "Convert FILE to date.
+Return (MONTH DAY YEAR)."
+  (let ((file (or file
+                  (buffer-base-buffer (buffer-file-name)))))
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (org-parse-time-string
+         (file-name-sans-extension
+          (file-name-nondirectory file)))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar--date-to-time (date)
+  "Convert DATE as returned from then calendar (MONTH DAY YEAR) to a time."
+  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
+    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
+                          (org-roam-dailies--list-files)))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
+;;; Date
+;;;###autoload
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+  "Create an entry in the daily-note for a date using the calendar.
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "P")
+  (let ((time (let ((org-read-date-prefer-future prefer-future))
+                (org-read-date t t nil (if goto
+                                           "Find daily-note: "
+                                         "Capture to daily-note: ")))))
+    (org-roam-dailies--capture time goto)))
+
+;;;###autoload
+(defun org-roam-dailies-goto-date (&optional prefer-future)
+  "Find the daily-note for a date using the calendar, creating it if necessary.
+Prefer past dates, unless PREFER-FUTURE is non-nil."
+  (interactive)
+  (org-roam-dailies-capture-date t prefer-future))
+
+;;; Navigation
+(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-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)))
+
+(add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar-mark-entries)
+(add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar-mark-entries)
+
+;;;; 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

org-roam-db.el

@@ -0,0 +1,524 @@
+;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides the underlying database api to org-roam.
+;;
+;;; Code:
+;;;; Library Requires
+(eval-when-compile (require 'subr-x))
+(require 'emacsql)
+(require 'emacsql-sqlite)
+(require 'seq)
+
+(eval-and-compile
+  (require 'org-roam-macs)
+  ;; For `org-with-wide-buffer'
+  (require 'org-macs))
+(require 'org)
+(require 'ol)
+(require 'org-roam-utils)
+
+(defvar org-roam-find-file-hook)
+(defvar org-roam-directory)
+(defvar org-roam-verbose)
+(defvar org-agenda-files)
+
+(declare-function org-roam-id-at-point "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam-node-at-point "org-roam")
+
+;;;; Options
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
+  "The full path to file where the Org-roam database is stored.
+If this is non-nil, the Org-roam sqlite database is saved here.
+
+It is the user's responsibility to set this correctly, especially
+when used with multiple Org-roam instances."
+  :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 large, heavy operations like `org-roam-db-sync',
+many GC operations happen because of the large number of
+temporary structures generated (e.g. parsed ASTs). Temporarily
+increasing `gc-cons-threshold' will help reduce the number of GC
+operations, at the cost of temporary memory usage.
+
+This defaults to the original value of `gc-cons-threshold', but
+tweaking this number may lead to better overall performance. For
+example, to reduce the number of GCs, one may set it to a large
+value like `most-positive-fixnum'."
+  :type 'int
+  :group 'org-roam)
+
+(defcustom org-roam-db-node-include-function (lambda () t)
+  "A custom function to check if the headline at point is a node."
+  :type 'function
+  :group 'org-roam)
+
+(defconst org-roam-db-version 16)
+(defconst org-roam--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))
+
+(defvar org-roam-db--connection (make-hash-table :test #'equal)
+  "Database connection to Org-roam database.")
+
+;;;; Core Functions
+
+(defun org-roam-db--get-connection ()
+  "Return the database connection, if any."
+  (gethash (expand-file-name org-roam-directory)
+           org-roam-db--connection))
+
+(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 (emacsql-sqlite org-roam-db-location)))
+        (set-process-query-on-exit-flag (emacsql-process conn) nil)
+        (puthash (expand-file-name org-roam-directory)
+                 conn
+                 org-roam-db--connection)
+        (when init-db
+          (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)
+      (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)))
+
+    (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
+    (emacsql db "PRAGMA foreign_keys = ON")
+    (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
+      (emacsql db [:create-table $i1 $S2] table schema))
+    (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
+      (emacsql db [: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-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))
+         (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 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 a node, else return nil."
+  (and (org-id-get)
+       (not (cdr (assoc "ROAM_EXCLUDE" (org-entry-properties))))
+       (funcall org-roam-db-node-include-function)))
+
+(defun org-roam-db-map-nodes (fns)
+  "Run FNS over all nodes in the current buffer."
+  (org-with-point-at 1
+    (org-map-entries
+     (lambda ()
+       (when (org-roam-db-node-p)
+         (dolist (fn fns)
+           (funcall fn)))))))
+
+(defun org-roam-db-map-links (fns)
+  "Run FNS over all links in the current buffer."
+  (org-with-point-at 1
+    (org-element-map (org-element-parse-buffer) 'link
+      (lambda (link)
+        (dolist (fn fns)
+          (funcall fn link))))))
+
+(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-link-display-format
+                       (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
+                                        #'string-equal))
+                           (file-relative-name file org-roam-directory))))
+               (pos (point))
+               (todo nil)
+               (priority nil)
+               (scheduled nil)
+               (deadline nil)
+               (level 0)
+               (aliases (org-entry-get (point) "ROAM_ALIASES"))
+               (tags org-file-tags)
+               (refs (org-entry-get (point) "ROAM_REFS"))
+               (properties (org-entry-properties))
+               (olp (org-get-outline-path)))
+          (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)))
+          (when aliases
+            (org-roam-db-query
+             [:insert :into aliases
+              :values $v1]
+             (mapcar (lambda (alias)
+                       (vector id alias))
+                     (split-string-and-unquote aliases))))
+          (when refs
+            (setq refs (split-string-and-unquote refs))
+            (let (rows)
+              (dolist (ref refs)
+                (if (string-match org-link-plain-re ref)
+                    (progn
+                      (push (vector id (match-string 2 ref)
+                                    (match-string 1 ref)) rows))
+                  (lwarn '(org-roam) :warning
+                         "%s:%s\tInvalid ref %s, skipping..."
+                         (buffer-file-name) (point) ref)))
+              (when rows
+                (org-roam-db-query
+                 [:insert :into refs
+                  :values $v1]
+                 rows)))))))))
+
+(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 (org-link-display-format (nth 4 heading-components)))
+           (properties (org-entry-properties))
+           (olp (org-get-outline-path)))
+      (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")))
+    (org-roam-db-query [:insert :into aliases
+                        :values $v1]
+                       (mapcar (lambda (alias)
+                                 (vector node-id alias))
+                               (split-string-and-unquote aliases)))))
+
+(defun org-roam-db-insert-tags ()
+  "Insert tags for node at point into Org-roam cache."
+  (when-let ((node-id (org-id-get))
+             (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
+          (if (string-match org-link-plain-re ref)
+              (progn
+                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
+            (lwarn '(org-roam) :warning
+                   "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
+      (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))
+          (dest (org-element-property :path link))
+          (properties (list :outline (org-get-outline-path)))
+          (source (org-roam-id-at-point)))
+      (when source
+        (org-roam-db-query
+         [:insert :into links
+          :values $v1]
+         (vector (point) source dest type 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 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)))))
+
+;;;;; Updating
+;;;###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")
+  (when force (delete-file org-roam-db-location))
+  (org-roam-db--close) ;; Force a reconnect
+  (org-roam-db) ;; To initialize the database, no-op if already initialized
+  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
+         (org-agenda-files nil)
+         (org-roam-files (org-roam--list-all-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)
+      (if (fboundp 'dolist-with-progress-reporter)
+          (dolist-with-progress-reporter (file (hash-table-keys current-files))
+              "Clearing removed files..."
+            (org-roam-db-clear-file file))
+        (dolist (file (hash-table-keys current-files))
+          (org-roam-db-clear-file file)))
+      (if (fboundp 'dolist-with-progress-reporter)
+          (dolist-with-progress-reporter (file modified-files)
+              "Processing modified files..."
+            (org-roam-db-update-file file))
+        (dolist (file modified-files)
+          (org-roam-db-update-file file))))))
+
+(defun org-roam-db-update-file (&optional file-path)
+  "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."
+  (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))))
+    (unless (string= content-hash db-hash)
+      (org-roam-with-file file-path nil
+        (save-excursion
+          (org-set-regexps-and-options 'tags-only)
+          (org-roam-db-clear-file)
+          (org-roam-db-insert-file)
+          (org-roam-db-insert-file-node)
+          (org-roam-db-map-nodes
+           (list #'org-roam-db-insert-node-data
+                 #'org-roam-db-insert-aliases
+                 #'org-roam-db-insert-tags
+                 #'org-roam-db-insert-refs))
+          (org-roam-db-map-links
+           (list #'org-roam-db-insert-link)))))))
+
+(defun org-roam-db--update-on-save-h ()
+  "."
+  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
+
+;; Diagnostic Interactives
+(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-graph.el

@@ -0,0 +1,281 @@
+;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides graphing functionality for org-roam.
+;;
+;;; Code:
+(require 'xml) ;xml-escape-string
+(eval-and-compile
+  (require 'org-roam-macs))
+(require 'org-roam-db)
+
+;;;; Declarations
+(defvar org-roam-directory)
+
+;;;; 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" . (("shape"      . "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)
+
+(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--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 = $s1 UNION
+   SELECT dest FROM links_of JOIN connected_component USING(source))
+SELECT source, dest, type FROM links WHERE source IN connected_component OR dest IN connected_component;"
+            "
+WITH RECURSIVE
+  links_of(source, dest) AS
+  (SELECT source, dest FROM links UNION
+   SELECT dest, source FROM links),
+  connected_component(source, trace) AS
+  (VALUES ($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 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 (&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 (org-roam--nodes-table))
+        (seen-nodes (list))
+        (edges (or edges (org-roam-db-query [:select :distinct [source dest type] :from links]))))
+    (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--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 (org-roam-truncate org-roam-graph-max-title-length title))
+                                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                   (_ title)))))
+          (setq node-id (org-roam-node-id node)
+                node-properties `(("label"   . ,shortened-title)
+                                  ("URL"     . ,(concat "org-protocol://roam-node?node="
+                                                        (url-hexify-string (org-roam-node-id node))))
+                                  ("tooltip" . ,(xml-escape-string title)))))
+      (setq node-id node
+            node-properties (append `(("label" . ,(concat type ":" node)))
+                                    (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--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--build-process*"
+     :buffer "*org-roam-graph--build-process*"
+     :command `(,org-roam-graph-executable ,temp-dot "-T" ,org-roam-graph-filetype "-o" ,temp-graph)
+     :sentinel (when callback
+                 (lambda (process _event)
+                   (when (= 0 (process-exit-status process))
+                     (funcall callback temp-graph)))))))
+
+(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)))))
+
+;;;; Commands
+;;;###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)))
+
+
+(provide 'org-roam-graph)
+
+;;; org-roam-graph.el ends here

org-roam-macs.el

@@ -0,0 +1,90 @@
+;;; org-roam-macs.el --- Macros/utility functions -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements macros used throughout org-roam.
+;;
+;;; Code:
+(defmacro org-roam-plist-map! (fn plist)
+  "Map FN over PLIST, modifying it in-place."
+  (declare (indent 1))
+  (let ((plist-var (make-symbol "plist"))
+        (k (make-symbol "k"))
+        (v (make-symbol "v")))
+    `(let ((,plist-var (copy-sequence ,plist)))
+       (while ,plist-var
+         (setq ,k (pop ,plist-var))
+         (setq ,v (pop ,plist-var))
+         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
+
+(defmacro org-roam-with-file (file keep-buf-p &rest body)
+  "Execute BODY within FILE.
+If FILE is nil, execute BODY in the current buffer.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (auto-mode-alist 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 (equal major-mode 'org-mode)
+         (delay-mode-hooks
+           (let ((org-inhibit-startup t)
+                 (org-agenda-files nil))
+             (org-mode))))
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+       (when (find-buffer-visiting ,file)
+         (kill-buffer (find-buffer-visiting ,file))))
+     res))
+
+(defmacro org-roam-with-temp-buffer (file &rest body)
+  "Execute BODY within a temp buffer.
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `default-directory' to FILE's directory and insert its contents."
+  (declare (indent 1) (debug t))
+  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
+    `(let ((,current-org-roam-directory org-roam-directory))
+       (with-temp-buffer
+         (let ((org-roam-directory ,current-org-roam-directory))
+           (delay-mode-hooks (org-mode))
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local default-directory (file-name-directory ,file)))
+           ,@body)))))
+
+(provide 'org-roam-macs)
+
+;;; org-roam-macs.el ends here

org-roam-migrate.el

@@ -0,0 +1,200 @@
+;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; 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:
+;;
+;;  To ease transition from v1 to v2, we provide various migration utilities.
+;;  This library helps convert v1 notes to v2, and informs the user.
+;;
+;;; Code:
+;;;; Dependencies
+;;;;
+;;; v1 breaking warning
+(require 'org-roam-db)
+
+(defvar org-roam-v2-ack nil)
+
+(unless org-roam-v2-ack
+  (lwarn 'org-roam :error "
+------------------------------------
+WARNING: You're now on Org-roam v2!
+------------------------------------
+
+You may have arrived here from a package upgrade. Please read the
+wiki entry at
+https://github.com/org-roam/org-roam/wiki/Hitchhiker's-Rough-Guide-to-Org-roam-V2
+for an overview of the major changes.
+
+Notes taken in v1 are incompatible with v1, but you can upgrade
+them to the v2 format via a simple command. To migrate your
+notes, run:
+
+  M-x org-roam-migrate-wizard
+
+If you wish to stay on v1, v1 is unfortunately not distributed on
+MELPA. See org-roam/org-roam-v1 on GitHub on how to install v1.
+
+If you've gone through the migration steps (if necessary), and
+know what you're doing set `org-roam-v2-ack' to `t' to disable
+this warning. You can do so by adding:
+
+(setq org-roam-v2-ack t)
+
+To your init file.
+
+"))
+
+;;;###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* ((parent-dir (f-parent org-roam-directory))
+           (backup-dir (expand-file-name "org-roam.bak" parent-dir))
+           (debug-dir (expand-file-name "org-roam.debug" parent-dir)))
+      (message "Backing up files to %s" backup-dir)
+      (copy-directory org-roam-directory backup-dir))
+    (condition-case err
+        (progn
+          ;; Convert v1 to v2
+          (dolist (f (org-roam--list-all-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-all-files))
+            (org-roam-with-file f nil
+              (org-roam-migrate-replace-file-links-with-id)
+              (save-buffer))))
+      (t
+       (rename-file org-roam-directory debug-dir)
+       (rename-file backup-dir org-roam-directory)
+       (lwarn 'org-roam :warning (format "The migration wizard failed with error:\n%s\n%s"
+                                         (error-message-string err)
+                                         "Your files have been restored, consider filing an issue.\n"))))))
+
+(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 (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" (string-join 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)) nil t)))))))
+
+(provide 'org-roam-migrate)
+;;; org-roam-migrate.el ends here

org-roam-mode.el

@@ -0,0 +1,468 @@
+;;; org-roam-mode.el --- create and refresh Org-roam buffers -*- lexical-binding: t -*-
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements the abstract major-mode `org-roam-mode', from which
+;; almost all other Org-roam major-modes derive.
+;;
+;;; Code:
+(require 'magit-section)
+
+(require 'org-roam-utils)
+
+(defvar org-roam-directory)
+(defvar org-roam-find-file-hook)
+
+(declare-function org-roam-node-at-point "org-roam")
+
+;;; 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)
+
+;;; Variables
+(defvar org-roam-current-node nil
+  "The current node at point.")
+
+(defvar org-roam-current-directory nil
+  "The `org-roam-directory' value for the current node.")
+
+(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
+                                                 #'org-roam-reflinks-section)
+  "Functions which insert sections of the `org-roam-buffer'.
+Each function is called with one argument, which is the current org-roam node at point."
+  :group 'org-roam
+  :type 'hook)
+
+;;; The mode
+(defvar org-roam-mode-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map magit-section-mode-map)
+    (define-key map [C-return]  'org-roam-visit-thing)
+    (define-key map (kbd "C-m") 'org-roam-visit-thing)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-render)
+    map)
+  "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")
+
+(define-derived-mode org-roam-mode magit-section-mode "Org-roam"
+  "Major mode for Org-roam's buffer."
+  :group 'org-roam
+  (face-remap-add-relative 'header-line 'org-roam-header-line))
+
+;;; Key functions
+(defun org-roam-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-render ()
+  "Render the current node at point."
+  (interactive)
+  (when (derived-mode-p 'org-roam-mode)
+    (let ((inhibit-read-only t))
+      (erase-buffer)
+      (setq-local default-directory org-roam-current-directory)
+      (setq-local org-roam-directory org-roam-current-directory)
+      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+      (magit-insert-section (org-roam)
+        (magit-insert-heading)
+        (run-hook-with-args 'org-roam-mode-section-functions org-roam-current-node)))))
+
+(defun org-roam-buffer ()
+  "Launch an Org-roam buffer for the current node at point."
+  (interactive)
+  (if-let ((node (org-roam-node-at-point))
+           (source-org-roam-directory org-roam-directory))
+      (progn
+        (let ((buffer (get-buffer-create
+                       (concat "org-roam: "
+                               (file-relative-name (buffer-file-name) org-roam-directory)))))
+          (with-current-buffer buffer
+            (org-roam-mode)
+            (setq-local org-roam-current-node node)
+            (setq-local org-roam-current-directory source-org-roam-directory)
+            (org-roam-buffer-render))
+          (switch-to-buffer-other-window buffer)))
+    (user-error "No node at point")))
+
+;;; Persistent buffer
+(defvar org-roam-buffer "*org-roam*"
+  "The persistent Org-roam buffer name.")
+
+(defun org-roam-buffer--post-command-h ()
+  "Reconstructs the Org-roam buffer.
+This needs to be quick or infrequent, because this is run at
+`post-command-hook'.  If REDISPLAY, force an update of
+the Org-roam buffer."
+  (when (get-buffer-window org-roam-buffer)
+    (when-let ((node (org-roam-node-at-point)))
+      (unless (equal node org-roam-current-node)
+        (setq org-roam-current-node node)
+        (setq org-roam-current-directory org-roam-directory)
+        (org-roam-buffer-persistent-redisplay)))))
+
+(define-inline org-roam-buffer--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))))
+
+(defun org-roam-buffer-toggle ()
+  "Toggle display of the Org-roam buffer."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (delete-window (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--post-command-h)))
+    ((or 'exists 'none)
+     (progn
+       (setq org-roam-current-node (org-roam-node-at-point)
+             org-roam-current-directory org-roam-directory)
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (org-roam-buffer-persistent-redisplay)))))
+
+(defun org-roam-buffer-persistent-redisplay ()
+  "Recompute contents of the persistent Org-roam buffer.
+Has no effect when `org-roam-current-node' is nil."
+  (when org-roam-current-node
+    (with-current-buffer (get-buffer-create org-roam-buffer)
+      (let ((inhibit-read-only t))
+        (erase-buffer)
+        (org-roam-mode)
+        (setq-local default-directory org-roam-current-directory)
+        (setq-local org-roam-directory org-roam-current-directory)
+        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+        (magit-insert-section (org-roam)
+          (magit-insert-heading)
+          (dolist (fn org-roam-mode-section-functions)
+            (funcall fn org-roam-current-node)))))))
+
+(defun org-roam-buffer--redisplay ()
+  "."
+  (add-hook 'post-command-hook #'org-roam-buffer--post-command-h nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--redisplay)
+
+;;; Sections
+;;;; 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)
+
+(defun org-roam-backlinks-get (node)
+  "Return the backlinks for NODE."
+  (let ((backlinks (org-roam-db-query
+                    [:select [source dest pos properties]
+                     :from links
+                     :where (= dest $s1)
+                     :and (= type "id")]
+                    (org-roam-node-id node))))
+    (cl-loop for backlink in backlinks
+             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
+                       (org-roam-populate
+                        (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))))
+
+(defun org-roam-backlinks-section (node)
+  "The backlinks section for NODE."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+    (magit-insert-section (org-roam-backlinks)
+      (magit-insert-heading "Backlinks:")
+      (dolist (backlink backlinks)
+        (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 [ref] :from refs
+                                  :where (= node-id $s1)]
+                                 (org-roam-node-id node)))
+        links)
+    (pcase-dolist (`(,ref) refs)
+      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
+                                                     [:select [source pos properties]
+                                                      :from links
+                                                      :where (= dest $s1)]
+                                                     ref))
+        (push (org-roam-populate
+               (org-roam-reflink-create
+                :source-node (org-roam-node-create :id source-id)
+                :ref ref
+                :point pos
+                :properties properties)) links)))
+    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 (org-roam-node-refs node)
+    (let* ((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)))))
+
+;;;; Unlinked references
+(defvar org-roam-grep-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map org-roam-mode-map)
+    (define-key map [remap org-roam-visit-thing] 'org-roam-file-visit)
+    map)
+  "Keymap for Org-roam grep result sections.")
+
+(defclass org-roam-grep-section (magit-section)
+  ((keymap :initform 'org-roam-grep-map)
+   (file :initform nil)
+   (row :initform nil)
+   (col :initform nil)))
+
+(defun org-roam-file-at-point (&optional assert)
+  "Return the file at point.
+If ASSERT, throw an error."
+  (if-let ((file (magit-section-case
+                   (org-roam-node-section (org-roam-node-file (oref it node)))
+                   (org-roam-grep-section (oref it file))
+                   (org-roam-preview-section (oref it file)))))
+      file
+    (when assert
+      (user-error "No file at point"))))
+
+(defun org-roam-file-visit (file &optional other-window row col)
+  "Visits FILE.
+With a prefix argument OTHER-WINDOW, display the buffer in
+another window instead.
+If ROW, move to the row, and if COL move to the COL."
+  (interactive (list (org-roam-file-at-point t)
+                     current-prefix-arg
+                     (oref (magit-current-section) row)
+                     (oref (magit-current-section) col)))
+  (let ((buf (find-file-noselect file)))
+    (with-current-buffer buf
+      (widen)
+      (goto-char (point-min))
+      (when row
+        (forward-line (1- row)))
+      (when col
+        (forward-char (1- col))))
+    (funcall (if other-window
+                 #'switch-to-buffer-other-window
+               #'pop-to-buffer-same-window) buf)))
+
+(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-literally 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 -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 (f-equal-p (org-roam-node-file node) f))
+                         (member (downcase match) (mapcar #'downcase titles)))
+                (magit-insert-section section (org-roam-grep-section)
+                  (oset section file f)
+                  (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 "...")
+                                              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-overlay.el

@@ -0,0 +1,98 @@
+;;; org-roam-overlay.el --- Link overlay for Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library 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.
+;;
+;;
+;;; Code:
+;;;; Dependencies
+
+(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

org-roam-protocol.el

@@ -0,0 +1,107 @@
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; We extend org-protocol, adding custom Org-roam handlers. The setup
+;; instructions for `org-protocol' can be found in org-protocol.el.
+;;
+;; We define 2 protocols:
+;;
+;; 1. "roam-node": This protocol simply opens the node given by the node ID
+;; 2. "roam-ref": This protocol creates or opens a note with the given REF
+;;
+;;; Code:
+(require 'org-protocol)
+(require 'org-roam)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'ol) ;; for org-link-decode
+
+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
+
+;;;; Functions
+(defun org-roam-protocol-open-ref (info)
+  "Process an org-protocol://roam-ref?ref= style url with INFO.
+
+It opens or creates a note with the given ref.
+
+  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
+        encodeURIComponent(location.href) + \\='&title=\\=' + \\
+        encodeURIComponent(document.title) + \\='&body=\\=' + \\
+        encodeURIComponent(window.getSelection())"
+  (unless (plist-get info :ref)
+    (user-error "No ref key provided"))
+  (org-roam-plist-map! (lambda (k v)
+                         (org-link-decode
+                          (if (equal k :ref)
+                              (org-protocol-sanitize-uri v)
+                            v))) info)
+  (when org-roam-protocol-store-links
+    (push (list (plist-get info :ref)
+                (plist-get info :title)) org-stored-links))
+  (org-link-store-props :type (and (string-match org-link-plain-re
+                                                 (plist-get info :ref))
+                                   (match-string 1 (plist-get info :ref)))
+                        :link (plist-get info :ref)
+                        :annotation (org-link-make-string (plist-get info :ref)
+                                                          (or (plist-get info :title)
+                                                              (plist-get info :ref)))
+                        :initial (or (plist-get info :body) ""))
+  (raise-frame)
+  (org-roam-capture-
+   :keys (plist-get info :template)
+   :node (org-roam-node-create :title (plist-get info :title))
+   :info (list :ref (plist-get info :ref)
+               :body (plist-get info :body))
+   :templates org-roam-capture-ref-templates)
+  nil)
+
+(defun org-roam-protocol-open-node (info)
+  "This handler simply opens the file with emacsclient.
+
+INFO is an alist containing additional information passed by the protocol URL.
+It should contain the FILE key, pointing to the path of the file to open.
+
+  Example protocol string:
+
+org-protocol://roam-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)
+
+(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

org-roam-utils.el

@@ -0,0 +1,296 @@
+;;; org-roam-utils.el --- Utilities for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements utility functions used throughout
+;; Org-roam.
+;;
+;;
+;;; Code:
+;;;; Library Requires
+(require 'dash)
+
+(eval-when-compile
+  (require 'org-roam-macs)
+  (require 'org-macs))
+
+(defvar org-roam-verbose)
+
+;; This is necessary to ensure all dependents on this module see
+;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
+;; regardless of whether Org is loaded before their compilation.
+(require 'org)
+
+;;;; String Utilities
+(defun org-roam-truncate (len s &optional ellipsis)
+  "If S is longer than LEN, cut it down and add ELLIPSIS to the end.
+
+The resulting string, including ellipsis, will be LEN characters
+long.
+
+When not specified, ELLIPSIS defaults to ‘...’."
+  (declare (pure t) (side-effect-free t))
+  (unless ellipsis
+    (setq ellipsis "..."))
+  (if (> (length s) len)
+      (format "%s%s" (substring s 0 (- len (length ellipsis))) ellipsis)
+    s))
+
+(defun org-roam-replace (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 "\\" "\\\\")
+    (org-roam-replace "\"" "\\\"")))
+
+;;;; Utility Functions
+(defun org-roam--list-interleave (lst separator)
+  "Interleaves elements in LST with SEPARATOR."
+  (when lst
+    (let ((new-lst (list (pop lst))))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
+
+(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))))))
+
+(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))))
+
+(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))))
+
+(defun org-roam-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)))
+
+;;; Keywords
+(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-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-literally file nil 0 bound)
+        (org-roam--get-keyword name))
+    (org-roam--get-keyword name bound)))
+
+;;; 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))))
+
+;;; Formatting
+(defun org-roam-format (template replacer)
+  "Format TEMPLATE with the function REPLACER.
+REPLACER takes an argument of the format variable and optionally
+an extra argument which is the EXTRA value from the call to
+`org-roam-format'.
+Adapted from `s-format'."
+  (let ((saved-match-data (match-data)))
+    (unwind-protect
+        (replace-regexp-in-string
+         "\\${\\([^}]+\\)}"
+         (lambda (md)
+           (let ((var (match-string 1 md))
+                 (replacer-match-data (match-data)))
+             (unwind-protect
+                 (let ((v (progn
+                            (set-match-data saved-match-data)
+                            (funcall replacer var))))
+                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
+               (set-match-data replacer-match-data)))) template
+         ;; Need literal to make sure it works
+         t t)
+      (set-match-data saved-match-data))))
+
+(defvar org-roam--cached-display-format nil)
+
+(defun org-roam--process-display-format (format)
+  "Pre-calculate minimal widths needed by the FORMAT string."
+  (or org-roam--cached-display-format
+      (setq org-roam--cached-display-format
+            (let* ((fields-width 0)
+                   (string-width
+                    (string-width
+                     (org-roam-format
+                      format
+                      (lambda (field)
+                        (setq fields-width
+                              (+ fields-width
+                                 (string-to-number
+                                  (or (cadr (split-string field ":"))
+                                      "")))))))))
+              (cons format (+ fields-width string-width))))))
+
+;;; for org-roam-demote-entire-buffer in org-roam-refile.el
+(defun org-roam--file-keyword-get (keyword)
+  "Pull a KEYWORD setting from the top of the file.
+
+Keyword must be specified in ALL CAPS."
+  (cadr (assoc keyword
+               (org-collect-keywords (list keyword)))))
+
+(defun org-roam--file-keyword-kill (keyword)
+  "Erase KEYWORD 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)))))
+
+(defun org-roam--kill-empty-buffer ()
+  "If the source buffer has been emptied, kill it.
+
+If the buffer is associated with a file, delete the file.
+
+If the buffer is associated with an in-process capture operation, abort the operation."
+  (when (eq (buffer-size) 0)
+    (if (buffer-file-name)
+        (delete-file (buffer-file-name)))
+    (set-buffer-modified-p nil)
+    (when (and org-capture-mode
+               (buffer-base-buffer (current-buffer)))
+      (org-capture-kill))
+    (kill-buffer (current-buffer))))
+
+;;; Diagnostics
+;;;###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* ((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)))
+
+;;;###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)))))
+
+(provide 'org-roam-utils)
+;;; org-roam-utils.el ends here

shell.nix

@@ -1,10 +0,0 @@
-let
-  pkgs = import <nixpkgs> {};
-in
-pkgs.mkShell {
-  name = "docs";
-  buildInput = with pkgs; [
-    mkdocs
-    python3Packages.alabaster
-  ];
-}

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/foo.org

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

tests/test-org-roam.el

@@ -0,0 +1,54 @@
+;;; 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))
+
+;; 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-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-setup))
+
+  (after-all
+    (org-roam-teardown)
+    (delete-file org-roam-db-location))
+
+  (it "has the correct number of files"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
+            :to-equal
+            2))
+
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
+            :to-equal
+            2))
+
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
+            :to-equal
+            1)))
+
+(provide 'test-org-roam)
+
+;;; test-org-roam.el ends here