(release): Org-roam v1.2.0 (#802)

`org-roam-unlinked-references` uses rg to search for unlinked references. Regex courtesy of @angelsl.

Co-authored-by: Leo Vivier <leo.vivier+dev@gmail.com>

.dir-locals.el

@@ -1,4 +1,6 @@
 ;;; Directory Local Variables
 ;;; For more information see (info "(emacs) Directory Variables")
 
-((emacs-lisp-mode . ((eval . (require 'org-roam-dev)))))
+((emacs-lisp-mode
+  (eval . (require 'org-roam-dev))
+  (sentence-end-double-space . nil)))

.github/workflows/stale.yml

@@ -1,19 +0,0 @@
-name: Mark stale issues and pull requests
-
-on:
-  schedule:
-  - cron: "0 0 * * *"
-
-jobs:
-  stale:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/stale@v1
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-message: 'Stale issue message'
-        stale-pr-message: 'Stale pull request message'
-        stale-issue-label: 'no-issue-activity'
-        stale-pr-label: 'no-pr-activity'

.github/workflows/test.yml

@@ -54,9 +54,11 @@ jobs:
     # The "all" rule is not used, because it treats compilation warnings
     # as failures, so linting and testing are run as separate steps.
 
+    # org-roam-compat is excluded from linting because it contains
+    # symbols/aliases from other packages
     - name: Lint
       continue-on-error: false
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
+      run: ./makem.sh -vv --sandbox $SANDBOX_DIR --exclude org-roam-compat.el lint
 
     - name: Test
       if: always()  # Run test even if linting fails.

BACKERS.md

@@ -0,0 +1,5 @@
+# Backers
+
+Many thanks to the following backers, your contributions are greatly appreciated!
+
+- Nathan Tran

CHANGELOG.md

@@ -1,11 +1,38 @@
 # Changelog
 
+## 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_TAG` key add additional meta data to notes. For more information, see [here](https://org-roam.github.io/org-roam/manual/Tags.html#Tags).
+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://org-roam.github.io/org-roam/manual/Tags.html#Tags).
 
 As usual, this release comes with a multitude of bug-fixes and refactorings.
 

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/index.html

@@ -1,3 +1,175 @@
-<html>
+<!DOCTYPE html>
-  <h1>--> <a href="manual/index.html">MANUAL HERE</a> <--</h1>
+<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://org-roam.github.io/org-roam/manual/">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 class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/company-org-roam"
+            >company-org-roam</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/org-roam.org

@@ -1,20 +1,20 @@
-#+TITLE: Org-roam User Manual
+#+title: Org-roam User Manual
 :PREAMBLE:
-#+AUTHOR: Jethro Kuan
+#+author: Jethro Kuan
-#+EMAIL: jethrokuan95@gmail.com
+#+email: jethrokuan95@gmail.com
-#+DATE: 2020-2020
+#+date: 2020-2020
-#+LANGUAGE: en
+#+language: en
 
-#+TEXINFO_DIR_CATEGORY: Emacs
+#+texinfo_dir_category: Emacs
-#+TEXINFO_DIR_TITLE: Org-roam: (org-roam).
+#+texinfo_dir_title: Org-roam: (org-roam).
-#+TEXINFO_DIR_DESC: Rudimentary Roam Replica for Emacs.
+#+texinfo_dir_desc: Rudimentary Roam Replica for Emacs.
-#+SUBTITLE: for version 1.1.1
+#+subtitle: for version 1.2.0
 
-#+OPTIONS: H:4 num:3 toc:2 creator:t
+#+options: H:4 num:3 toc:2 creator:t
-#+PROPERTY: header-args :eval never
+#+property: header-args :eval never
-#+TEXINFO: @noindent
+#+texinfo: @noindent
 
-This manual is for Org-roam version 1.1.1.
+This manual is for Org-roam version 1.2.0.
 
 #+BEGIN_QUOTE
 Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>
@@ -55,13 +55,63 @@ Org-roam provides several benefits over other tooling:
 - Free and Open Source :: Org-roam is free and open-source, which means that if you feel unhappy with any part of Org-roam, you may choose to extend Org-roam, or open a PR.
 - Leverages the Org-mode ecosystem :: Over the years, Emacs and Org-mode has developed into a mature system for plain-text organization. Building upon Org-mode already puts Org-roam light-years ahead of many other solutions.
 - Built on Emacs :: Emacs is also a fantastic interface for editing text, and we can inherit many of the powerful text-navigation and editing packages available to Emacs.
+
+* A Brief Introduction to the Zettelkasten Method
+
+Org-roam provides utilities for maintaining a digital slip-box. This section
+aims to provide a brief introduction to the "slip-box", or "Zettelkasten"
+method. By providing some background on the method, we hope that the design
+decisions of Org-roam will become clear, and that will aid in using Org-roam
+appropriately. In this section we will also introduce terms commonly used within
+the Zettelkasten community, which will also commonly appear in the Org-roam
+forums and channels of discussion.
+
+The Zettelkasten method of note-taking is designed to increase research
+productivity: in particular, it acts as a research partner, where conversations
+with it may produce new and surprising lines of thought. This method is
+attributed to German sociologist Niklas Luhmann, who using the method had
+produced volumes of written works.
+
+In its paper form, the slip-box is simply a box of cards. These cards are small
+-- often only large enough to fit a single concept. The size limitation
+encourages ideas to be broken down into individual concepts. These ideas are
+explicitly linked together. The breakdown of ideas encourages tangential
+exploration of ideas, increasing the surface for thought. Making linking
+explicit between notes also encourages one to think about the connections
+between concepts.
+
+Org-roam is the slip-box, digitalized in Org-mode. Every zettel (card) is a
+plain-text, Org-mode file. These files are often placed in the same directory.
+In the same way one would maintain a paper slip-box, Org-roam makes it easy to
+create new zettels, pre-filling boilerplate content using a powerful templating
+system. Org-roam also facilitates the linking of zettels using Org-mode ~file:~
+links.
+
+A slip-box requires a method of quickly capturing ideas. These are called
+*fleeting notes*: they are simple reminders of information or ideas that will
+need to be processed later on, or trashed. This is typically accomplished using
+~org-capture~ (see info:org#capture), or using Org-roam's daily notes
+functionality (see [[*Daily Notes][Daily Notes]]). This provides a central inbox for collecting
+thoughts, to be processed later into permanent notes.
+
+Permanent notes are further split into two categories: *literature notes* and
+*concept notes*. Literature notes can be brief annotations on a particular
+source (e.g. book, website or paper), that you'd like to access later on.
+Concept notes require much more care in authoring: they need to be
+self-explanatory and detailed. Org-roam's templating system supports the
+addition of different templates to facilitate the creation of these notes.
+
 * Installation
-** _ :ignore:
+
-Org-roam can be installed using Emacs' package manager or manually from its development repository.
+Org-roam can be installed using Emacs' package manager or manually from its
+development repository.
 
 ** Installing from MELPA
 
-Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' package manager before, you may familiarize yourself with it by reading the documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the archives to =package-archives=:
+Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs'
+package manager before, you may familiarize yourself with it by reading the
+documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the
+archives to =package-archives=:
 
 - To use Melpa:
 
@@ -79,6 +129,13 @@ Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' pa
                '("melpa-stable" . "http://stable.melpa.org/packages/") t)
 #+END_SRC
 
+Org-roam also depends on a recent version of Org, which can be obtained in Org's
+package repository (see info:org#Installation). To use Org's ELPA archive:
+
+#+BEGIN_SRC emacs-lisp
+(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)
+#+END_SRC
+
 Once you have added your preferred archive, you need to update the
 local package list using:
 
@@ -97,7 +154,24 @@ Now see [[*Post-Installation Tasks][Post-Installation Tasks]].
 
 ** TODO Installing from the Git Repository
 
-** TODO Post-Installation Tasks
+** Post-Installation Tasks
+
+Org-roam uses ~emacsql-sqlite3~, which requires ~sqlite3~ to be located on
+~exec-path~. Please ensure that ~sqlite3~ is installed appropriately on your
+operating system. You can verify that this is the case by executing:
+
+#+BEGIN_SRC emacs-lisp
+  (executable-find "sqlite3")
+#+END_SRC
+
+If you have ~sqlite3~ installed, and ~executable-find~ still reports ~nil~, then
+it is likely that the path to the executable is not a member of the Emacs
+variable ~exec-path~. You may rectify this by manually adding the path within
+your Emacs configuration:
+
+#+BEGIN_SRC emacs-lisp
+  (add-to-list 'exec-path "path/to/sqlite3")
+#+END_SRC
 
 * Getting Started
 
@@ -185,16 +259,16 @@ Org-roam calls =org-roam--extract-titles= to extract titles. It uses the
 variable =org-roam-title-sources=, to control how the titles are extracted. The
 title extraction methods supported are:
 
-1. ='title=: This extracts the title using the file =#+TITLE= property
+1. ='title=: This extracts the title using the file =#+title= property
 2. ='headline=: This extracts the title from the first headline in the Org file
-3. ='alias=: This extracts a list of titles using the =#ROAM_ALIAS= property.
+3. ='alias=: This extracts a list of titles using the =#+roam_alias= property.
    The aliases are space-delimited, and can be multi-worded using quotes
 
 Take for example the following org file:
 
 #+BEGIN_SRC org
-  #+TITLE: World War 2
+  #+title: World War 2
-  #+ROAM_ALIAS: "WWII" "World War II"
+  #+roam_alias: "WWII" "World War II"
 
   * Headline
 #+END_SRC
@@ -225,7 +299,7 @@ Org-roam calls =org-roam--extract-tags= to extract tags from files. It uses the
 variable =org-roam-tag-sources=, to control how tags are extracted. The tag
 extraction methods supported are:
 
-1. ='prop=: This extracts tags from the =#+ROAM_TAGS= property. Tags are space delimited, and can be multi-word using double quotes.
+1. ='prop=: This extracts tags from the =#+roam_tags= property. Tags are space delimited, and can be multi-word using double quotes.
 2. ='all-directories=: All sub-directories relative to =org-roam-directory= are
    extracted as tags. That is, if a file is located at relative path
    =foo/bar/file.org=, the file will have tags =foo= and =bar=.
@@ -251,8 +325,8 @@ Refs are unique identifiers for files. Each note can only have 1 ref.
 For example, a note for a website may contain a ref:
 
 #+BEGIN_SRC org
-  #+TITLE: Google
+  #+title: Google
-  #+ROAM_KEY: https://www.google.com/
+  #+roam_key: https://www.google.com/
 #+END_SRC
 
 These keys come in useful for when taking website notes, using the
@@ -262,8 +336,8 @@ Alternatively, add a ref for notes for a specific paper, using its
 [[https://github.com/jkitchin/org-ref][org-ref]] citation key:
 
 #+BEGIN_SRC org
-  #+TITLE: Neural Ordinary Differential Equations
+  #+title: Neural Ordinary Differential Equations
-  #+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
+  #+roam_key: cite:chen18_neural_ordin_differ_equat
 #+END_SRC
 
 The backlinks buffer will show any cites of this key: e.g.
@@ -287,7 +361,9 @@ org-roam's templating system works, it may be useful to look into basic usage of
 =org-capture=.
 
 Org-roam's templates can be customized by modifying the variable
-=org-roam-capture-templates=.
+=org-roam-capture-templates=. Just like the base =org-capture= this variable can
+contain multiple templates, in which case you will be prompted on which one to
+use when capturing a new note.
 
 ** Template Walkthrough
 
@@ -298,7 +374,7 @@ the default template, reproduced below.
   ("d" "default" plain (function org-roam--capture-get-point)
        "%?"
        :file-name "%<%Y%m%d%H%M%S>-${slug}"
-       :head "#+TITLE: ${title}\n"
+       :head "#+title: ${title}\n"
        :unnarrowed t)
 #+END_SRC
 
@@ -311,9 +387,12 @@ the default template, reproduced below.
 5. ="%?"= is the template inserted on each call to =org-roam-capture--capture=.
    This template means don't insert any content, but place the cursor
    here.
-6. =:file-name= is the file-name template for a new note, if it doesn't
+6. =:file-name= is the file-name template for a new note, if it doesn't yet
-   yet exist. This creates a file at path that looks like
+   exist. This creates a file at path that looks like
-   =/path/to/org-roam-directory/20200213032037-foo.org=.
+   =/path/to/org-roam-directory/20200213032037-foo.org=. This template also
+   allows you to specify if you want the note to go into a subdirectory. For
+   example, the template =private/${slug}= will create notes in
+   =/path/to/org-roam-directory/private=.
 7. =:head= contains the initial template to be inserted (once only), at
    the beginning of the file. Here, the title global attribute is
    inserted.
@@ -354,7 +433,7 @@ directly to provide its third argument to specify UTC.
   ("d" "default" plain (function org-roam--capture-get-point)
        "%?"
        :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
-       :head "#+TITLE: ${title}\n"
+       :head "#+title: ${title}\n"
        :unnarrowed t)
 #+END_SRC
 
@@ -466,7 +545,6 @@ number of password prompts, you may wish to cache the password.
 - Variable: org-roam-encrypt-files
 
   Whether to encrypt new files.  If true, create files with .org.gpg extension.
-
 * Graphing
 
 Org-roam provides graphing capabilities to explore interconnections between
@@ -692,7 +770,7 @@ in the generated graph.
 
 ** The =roam-ref= Protocol
 
-This protocol finds or creates a new note with a given =ROAM_KEY= (see [[*Anatomy of an Org-roam File][Anatomy of an Org-roam File]]):
+This protocol finds or creates a new note with a given ~roam_key~ (see [[*Anatomy of an Org-roam File][Anatomy of an Org-roam File]]):
 
 [[file:images/roam-ref.gif]]
 
@@ -706,26 +784,25 @@ javascript:location.href =
 + encodeURIComponent(document.title)
 #+END_SRC
 
-or as a keybinding in =qutebrowser=, adding the following to the =autoconfig.yml= file:
+or as a keybinding in ~qutebrowser~ in , using the ~config.py~ file (see
+[[https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc][Configuring qutebrowser]]):
 
-#+BEGIN_SRC yaml
+#+BEGIN_SRC python
-settings:
+config.bind("<Ctrl-r>", "spawn bash -c 'emacsclient \"org-protocol://roam-ref?template=r&ref={url:pretty}&title={title}\" '")
-  bindings.commands:
-    global:
-      normal:
-        gc: open javascript:void(location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title))
 #+END_SRC
 
-where =template= is the template key for a template in
+where ~template~ is the template key for a template in
-=org-roam-capture-ref-templates= (see [[*The Templating System][The Templating System]]). These templates
+~org-roam-capture-ref-templates~ (see [[*The Templating System][The Templating System]]). These templates
-should contain a =#+ROAM_KEY: ${ref}= in it.
+should contain a ~#+roam_key: ${ref}~ in it.
+
+* TODO Daily Notes
 
 * Diagnosing and Repairing Files
 
 Org-roam provides a utility for diagnosing and repairing problematic files via
-=org-roam-doctor=. By default, =org-roam-doctor= runs the check across all Org-roam
+~org-roam-doctor~. By default, ~org-roam-doctor~ runs the check on the current
-files, and this can take some time. To run the check only for the current file,
+Org-roam file. To run the check only for the current file, run =C-u M-x
-run =C-u M-x org-roam-doctor=.
+org-roam-doctor=, but note that this may take some time.
 
 - Function: org-roam-doctor &optional this-buffer
 
@@ -751,7 +828,6 @@ checker, to perform autofixes for the errors. For each error detected,
 =org-roam-doctor= will move the point to the current error, and pop-up a help
 window displaying the error message, as well as the list of actions that can be
 taken provided in =:actions=.
-
 * _ Copying
 :PROPERTIES:
 :COPYING:    t
@@ -858,7 +934,7 @@ to see all dated entries.
     :bind
     ("C-c n j" . org-journal-new-entry)
     :custom
-    (org-journal-date-prefix "#+TITLE: ")
+    (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"))
@@ -876,8 +952,7 @@ These are some plugins that make note-taking in Org-mode more enjoyable.
     :CUSTOM_ID: org-download
     :END:
 
-[[https://github.com/abo-abo/org-download][Org-download]] lets you
+[[https://github.com/abo-abo/org-download][Org-download]] lets you screenshot and yank images from the web into your notes:
-screenshot and yank images from the web into your notes:
 
 #+CAPTION: org-download
 [[file:images/org-download.gif]]
@@ -896,9 +971,7 @@ screenshot and yank images from the web into your notes:
     :CUSTOM_ID: mathpix.el
     :END:
 
-[[https://github.com/jethrokuan/mathpix.el][mathpix.el]] uses
+[[https://github.com/jethrokuan/mathpix.el][mathpix.el]] uses [[https://mathpix.com/][Mathpix's]] API to convert clips into latex equations:
-[[https://mathpix.com/][Mathpix's]] API to convert clips into latex
-equations:
 
 #+CAPTION: mathpix
 [[file:images/mathpix.gif]]
@@ -927,7 +1000,7 @@ etc.) within Org-mode.
     :CUSTOM_ID: bibliography
     :END:
 
-[[https://github.com/zaeph/org-roam-bibtex][org-roam-bibtex]] offers
+[[https://github.com/org-roam/org-roam-bibtex][org-roam-bibtex]] offers
 tight integration between
 [[https://github.com/jkitchin/org-ref][org-ref]],
 [[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
@@ -939,11 +1012,8 @@ tight integration between
     :CUSTOM_ID: spaced-repetition
     :END:
 
-[[https://github.com/l3kn/org-fc/][Org-fc]] is a spaced repetition
+[[https://github.com/l3kn/org-fc/][Org-fc]] is a spaced repetition system that scales well with a large number of
-system that scales well with a large number of files. Other alternatives
+files. Other alternatives include [[https://orgmode.org/worg/org-contrib/org-drill.html][org-drill]], and [[https://github.com/abo-abo/pamparam][pamparam]].
-include
-[[https://orgmode.org/worg/org-contrib/org-drill.html][org-drill]], and
-[[https://github.com/abo-abo/pamparam][pamparam]].
 
 * FAQ
 ** How do I have more than one Org-roam directory?
@@ -964,9 +1034,12 @@ All files within that directory will be treated as their own separate
 set of Org-roam files. Remember to run =org-roam-db-build-cache= from a
 file within that directory, at least once.
 
-* _ :ignore:
+** How do I migrate from Roam Research?
+
+Fabio has produced a command-line tool that converts markdown files exported from Roam Research into Org-roam compatible markdown. More instructions are provided [[https://github.com/fabioberger/roam-migration][in the repository]].
+
 # Local Variables:
-# eval: (refill-mode +1)
+# eval: (require 'ol-info)
 # before-save-hook: org-make-toc
 # after-save-hook: (lambda nil (progn (require 'ox-texinfo nil t) (org-texinfo-export-to-info)))
 # indent-tabs-mode: nil

doc/org-roam.texi

@@ -31,7 +31,7 @@ General Public License for more details.
 @finalout
 @titlepage
 @title Org-roam User Manual
-@subtitle for version 1.1.1
+@subtitle for version 1.2.0
 @author Jethro Kuan
 @page
 @vskip 0pt plus 1filll
@@ -46,7 +46,7 @@ General Public License for more details.
 
 @noindent
 
-This manual is for Org-roam version 1.1.1.
+This manual is for Org-roam version 1.2.0.
 
 @quotation
 Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@@gmail.com>
@@ -65,6 +65,7 @@ General Public License for more details.
 
 @menu
 * Introduction::
+* A Brief Introduction to the Zettelkasten Method::
 * Installation::
 * Getting Started::
 * Anatomy of an Org-roam File::
@@ -75,17 +76,16 @@ General Public License for more details.
 * Graphing::
 * Org-roam Completion System::
 * Roam Protocol::
+* Daily Notes::
 * Diagnosing and Repairing Files::
 * Appendix::
 * FAQ::
-* _: _ (2). 
 
 @detailmenu
 --- The Detailed Node Listing ---
 
 Installation
 
-* _::
 * Installing from MELPA::
 * Installing from the Git Repository::
 * Post-Installation Tasks::
@@ -119,7 +119,7 @@ Graphing
 
 Roam Protocol
 
-* _: _ (1). 
+* _::
 * Installation: Installation (1). 
 * The @samp{roam-file} protocol::
 * The @samp{roam-ref} Protocol::
@@ -139,6 +139,7 @@ Ecosystem
 FAQ
 
 * How do I have more than one Org-roam directory?::
+* How do I migrate from Roam Research?::
 
 @end detailmenu
 @end menu
@@ -176,25 +177,71 @@ Over the years, Emacs and Org-mode has developed into a mature system for plain-
 Emacs is also a fantastic interface for editing text, and we can inherit many of the powerful text-navigation and editing packages available to Emacs.
 @end table
 
+@node A Brief Introduction to the Zettelkasten Method
+@chapter A Brief Introduction to the Zettelkasten Method
+
+Org-roam provides utilities for maintaining a digital slip-box. This section
+aims to provide a brief introduction to the ``slip-box'', or ``Zettelkasten''
+method. By providing some background on the method, we hope that the design
+decisions of Org-roam will become clear, and that will aid in using Org-roam
+appropriately. In this section we will also introduce terms commonly used within
+the Zettelkasten community, which will also commonly appear in the Org-roam
+forums and channels of discussion.
+
+The Zettelkasten method of note-taking is designed to increase research
+productivity: in particular, it acts as a research partner, where conversations
+with it may produce new and surprising lines of thought. This method is
+attributed to German sociologist Niklas Luhmann, who using the method had
+produced volumes of written works.
+
+In its paper form, the slip-box is simply a box of cards. These cards are small
+-- often only large enough to fit a single concept. The size limitation
+encourages ideas to be broken down into individual concepts. These ideas are
+explicitly linked together. The breakdown of ideas encourages tangential
+exploration of ideas, increasing the surface for thought. Making linking
+explicit between notes also encourages one to think about the connections
+between concepts.
+
+Org-roam is the slip-box, digitalized in Org-mode. Every zettel (card) is a
+plain-text, Org-mode file. These files are often placed in the same directory.
+In the same way one would maintain a paper slip-box, Org-roam makes it easy to
+create new zettels, pre-filling boilerplate content using a powerful templating
+system. Org-roam also facilitates the linking of zettels using Org-mode @code{file:}
+links.
+
+A slip-box requires a method of quickly capturing ideas. These are called
+@strong{fleeting notes}: they are simple reminders of information or ideas that will
+need to be processed later on, or trashed. This is typically accomplished using
+@code{org-capture} (see @ref{capture,,,org,}), or using Org-roam's daily notes
+functionality (see @ref{Daily Notes}). This provides a central inbox for collecting
+thoughts, to be processed later into permanent notes.
+
+Permanent notes are further split into two categories: @strong{literature notes} and
+@strong{concept notes}. Literature notes can be brief annotations on a particular
+source (e.g. book, website or paper), that you'd like to access later on.
+Concept notes require much more care in authoring: they need to be
+self-explanatory and detailed. Org-roam's templating system supports the
+addition of different templates to facilitate the creation of these notes.
+
 @node Installation
 @chapter Installation
 
+Org-roam can be installed using Emacs' package manager or manually from its
+development repository.
+
 @menu
-* _::
 * Installing from MELPA::
 * Installing from the Git Repository::
 * Post-Installation Tasks::
 @end menu
 
-@node _
-@section _ :ignore:
-
-Org-roam can be installed using Emacs' package manager or manually from its development repository.
-
 @node Installing from MELPA
 @section Installing from MELPA
 
-Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' package manager before, you may familiarize yourself with it by reading the documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the archives to @samp{package-archives}:
+Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs'
+package manager before, you may familiarize yourself with it by reading the
+documentation in the Emacs manual, see @ref{Packages,,,emacs,}. Then, add one of the
+archives to @samp{package-archives}:
 
 @itemize
 @item
@@ -218,6 +265,13 @@ To use Melpa-Stable:
              '("melpa-stable" . "http://stable.melpa.org/packages/") t)
 @end lisp
 
+Org-roam also depends on a recent version of Org, which can be obtained in Org's
+package repository (see @ref{Installation,,,org,}). To use Org's ELPA archive:
+
+@lisp
+(add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t)
+@end lisp
+
 Once you have added your preferred archive, you need to update the
 local package list using:
 
@@ -238,7 +292,24 @@ Now see @ref{Post-Installation Tasks}.
 @section @strong{TODO} Installing from the Git Repository
 
 @node Post-Installation Tasks
-@section @strong{TODO} Post-Installation Tasks
+@section Post-Installation Tasks
+
+Org-roam uses @code{emacsql-sqlite3}, which requires @code{sqlite3} to be located on
+@code{exec-path}. Please ensure that @code{sqlite3} is installed appropriately on your
+operating system. You can verify that this is the case by executing:
+
+@lisp
+(executable-find "sqlite3")
+@end lisp
+
+If you have @code{sqlite3} installed, and @code{executable-find} still reports @code{nil}, then
+it is likely that the path to the executable is not a member of the Emacs
+variable @code{exec-path}. You may rectify this by manually adding the path within
+your Emacs configuration:
+
+@lisp
+(add-to-list 'exec-path "path/to/sqlite3")
+@end lisp
 
 @node Getting Started
 @chapter Getting Started
@@ -337,19 +408,19 @@ title extraction methods supported are:
 
 @enumerate
 @item
-@samp{'title}: This extracts the title using the file @samp{#+TITLE} property
+@samp{'title}: This extracts the title using the file @samp{#+title} property
 @item
 @samp{'headline}: This extracts the title from the first headline in the Org file
 @item
-@samp{'alias}: This extracts a list of titles using the @samp{#ROAM_ALIAS} property.
+@samp{'alias}: This extracts a list of titles using the @samp{#+roam_alias} property.
 The aliases are space-delimited, and can be multi-worded using quotes
 @end enumerate
 
 Take for example the following org file:
 
 @example
-#+TITLE: World War 2
+#+title: World War 2
-#+ROAM_ALIAS: "WWII" "World War II"
+#+roam_alias: "WWII" "World War II"
 
 * Headline
 @end example
@@ -388,7 +459,7 @@ extraction methods supported are:
 
 @enumerate
 @item
-@samp{'prop}: This extracts tags from the @samp{#+ROAM_TAGS} property. Tags are space delimited, and can be multi-word using double quotes.
+@samp{'prop}: This extracts tags from the @samp{#+roam_tags} property. Tags are space delimited, and can be multi-word using double quotes.
 @item
 @samp{'all-directories}: All sub-directories relative to @samp{org-roam-directory} are
 extracted as tags. That is, if a file is located at relative path
@@ -418,8 +489,8 @@ Refs are unique identifiers for files. Each note can only have 1 ref.
 For example, a note for a website may contain a ref:
 
 @example
-#+TITLE: Google
+#+title: Google
-#+ROAM_KEY: https://www.google.com/
+#+roam_key: https://www.google.com/
 @end example
 
 These keys come in useful for when taking website notes, using the
@@ -429,8 +500,8 @@ Alternatively, add a ref for notes for a specific paper, using its
 @uref{https://github.com/jkitchin/org-ref, org-ref} citation key:
 
 @example
-#+TITLE: Neural Ordinary Differential Equations
+#+title: Neural Ordinary Differential Equations
-#+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
+#+roam_key: cite:chen18_neural_ordin_differ_equat
 @end example
 
 The backlinks buffer will show any cites of this key: e.g.
@@ -464,7 +535,9 @@ org-roam's templating system works, it may be useful to look into basic usage of
 @samp{org-capture}.
 
 Org-roam's templates can be customized by modifying the variable
-@samp{org-roam-capture-templates}.
+@samp{org-roam-capture-templates}. Just like the base @samp{org-capture} this variable can
+contain multiple templates, in which case you will be prompted on which one to
+use when capturing a new note.
 
 @menu
 * Template Walkthrough::
@@ -481,7 +554,7 @@ the default template, reproduced below.
 ("d" "default" plain (function org-roam--capture-get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-$@{slug@}"
-     :head "#+TITLE: $@{title@}\n"
+     :head "#+title: $@{title@}\n"
      :unnarrowed t)
 @end lisp
 
@@ -501,9 +574,12 @@ The template is given a description of @samp{"default"}.
 This template means don't insert any content, but place the cursor
 here.
 @item
-@samp{:file-name} is the file-name template for a new note, if it doesn't
+@samp{:file-name} is the file-name template for a new note, if it doesn't yet
-yet exist. This creates a file at path that looks like
+exist. This creates a file at path that looks like
-@samp{/path/to/org-roam-directory/20200213032037-foo.org}.
+@samp{/path/to/org-roam-directory/20200213032037-foo.org}. This template also
+allows you to specify if you want the note to go into a subdirectory. For
+example, the template @samp{private/$@{slug@}} will create notes in
+@samp{/path/to/org-roam-directory/private}.
 @item
 @samp{:head} contains the initial template to be inserted (once only), at
 the beginning of the file. Here, the title global attribute is
@@ -548,7 +624,7 @@ directly to provide its third argument to specify UTC@.
 ("d" "default" plain (function org-roam--capture-get-point)
      "%?"
      :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--$@{slug@}\" (current-time) t)"
-     :head "#+TITLE: $@{title@}\n"
+     :head "#+title: $@{title@}\n"
      :unnarrowed t)
 @end lisp
 
@@ -840,13 +916,13 @@ Other options include @samp{'ido}, and @samp{'ivy}.
 @chapter Roam Protocol
 
 @menu
-* _: _ (1). 
+* _::
 * Installation: Installation (1). 
 * The @samp{roam-file} protocol::
 * The @samp{roam-ref} Protocol::
 @end menu
 
-@node _ (1)
+@node _
 @section _ :ignore:
 
 Org-roam extending @samp{org-protocol} with 2 protocols: the @samp{roam-file}
@@ -984,7 +1060,7 @@ in the generated graph.
 @node The @samp{roam-ref} Protocol
 @section The @samp{roam-ref} Protocol
 
-This protocol finds or creates a new note with a given @samp{ROAM_KEY} (see @ref{Anatomy of an Org-roam File}):
+This protocol finds or creates a new note with a given @code{roam_key} (see @ref{Anatomy of an Org-roam File}):
 
 @image{images/roam-ref,,,,gif}
 
@@ -998,27 +1074,27 @@ javascript:location.href =
 + encodeURIComponent(document.title)
 @end example
 
-or as a keybinding in @samp{qutebrowser}, adding the following to the @samp{autoconfig.yml} file:
+or as a keybinding in @code{qutebrowser} in , using the @code{config.py} file (see
+@uref{https://github.com/qutebrowser/qutebrowser/blob/master/doc/help/configuring.asciidoc, Configuring qutebrowser}):
 
 @example
-settings:
+config.bind("<Ctrl-r>", "spawn bash -c 'emacsclient \"org-protocol://roam-ref?template=r&ref=@{url:pretty@}&title=@{title@}\" '")
-  bindings.commands:
-    global:
-      normal:
-        gc: open javascript:void(location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title))
 @end example
 
-where @samp{template} is the template key for a template in
+where @code{template} is the template key for a template in
-@samp{org-roam-capture-ref-templates} (see @ref{The Templating System}). These templates
+@code{org-roam-capture-ref-templates} (see @ref{The Templating System}). These templates
-should contain a @samp{#+ROAM_KEY: $@{ref@}} in it.
+should contain a @code{#+roam_key: $@{ref@}} in it.
+
+@node Daily Notes
+@chapter @strong{TODO} Daily Notes
 
 @node Diagnosing and Repairing Files
 @chapter Diagnosing and Repairing Files
 
 Org-roam provides a utility for diagnosing and repairing problematic files via
-@samp{org-roam-doctor}. By default, @samp{org-roam-doctor} runs the check across all Org-roam
+@code{org-roam-doctor}. By default, @code{org-roam-doctor} runs the check on the current
-files, and this can take some time. To run the check only for the current file,
+Org-roam file. To run the check only for the current file, run @samp{C-u M-x
-run @samp{C-u M-x org-roam-doctor}.
+org-roam-doctor}, but note that this may take some time.
 
 @itemize
 @item
@@ -1167,7 +1243,7 @@ to see all dated entries.
   :bind
   ("C-c n j" . org-journal-new-entry)
   :custom
-  (org-journal-date-prefix "#+TITLE: ")
+  (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"))
@@ -1189,8 +1265,7 @@ These are some plugins that make note-taking in Org-mode more enjoyable.
 @node Org-download
 @unnumberedsubsubsec Org-download
 
-@uref{https://github.com/abo-abo/org-download, Org-download} lets you
+@uref{https://github.com/abo-abo/org-download, Org-download} lets you screenshot and yank images from the web into your notes:
-screenshot and yank images from the web into your notes:
 
 @float Figure
 @image{images/org-download,,,,gif}
@@ -1209,9 +1284,7 @@ screenshot and yank images from the web into your notes:
 @node mathpixel
 @unnumberedsubsubsec mathpix.el
 
-@uref{https://github.com/jethrokuan/mathpix.el, mathpix.el} uses
+@uref{https://github.com/jethrokuan/mathpix.el, mathpix.el} uses @uref{https://mathpix.com/, Mathpix's} API to convert clips into latex equations:
-@uref{https://mathpix.com/, Mathpix's} API to convert clips into latex
-equations:
 
 @float Figure
 @image{images/mathpix,,,,gif}
@@ -1238,7 +1311,7 @@ etc.) within Org-mode.
 @node Bibliography
 @unnumberedsubsubsec Bibliography
 
-@uref{https://github.com/zaeph/org-roam-bibtex, org-roam-bibtex} offers
+@uref{https://github.com/org-roam/org-roam-bibtex, org-roam-bibtex} offers
 tight integration between
 @uref{https://github.com/jkitchin/org-ref, org-ref},
 @uref{https://github.com/tmalsburg/helm-bibtex, helm-bibtex} and
@@ -1248,17 +1321,15 @@ tight integration between
 @node Spaced Repetition
 @unnumberedsubsubsec Spaced Repetition
 
-@uref{https://github.com/l3kn/org-fc/, Org-fc} is a spaced repetition
+@uref{https://github.com/l3kn/org-fc/, Org-fc} is a spaced repetition system that scales well with a large number of
-system that scales well with a large number of files. Other alternatives
+files. Other alternatives include @uref{https://orgmode.org/worg/org-contrib/org-drill.html, org-drill}, and @uref{https://github.com/abo-abo/pamparam, pamparam}.
-include
-@uref{https://orgmode.org/worg/org-contrib/org-drill.html, org-drill}, and
-@uref{https://github.com/abo-abo/pamparam, pamparam}.
 
 @node FAQ
 @chapter FAQ
 
 @menu
 * How do I have more than one Org-roam directory?::
+* How do I migrate from Roam Research?::
 @end menu
 
 @node How do I have more than one Org-roam directory?
@@ -1280,8 +1351,10 @@ All files within that directory will be treated as their own separate
 set of Org-roam files. Remember to run @samp{org-roam-db-build-cache} from a
 file within that directory, at least once.
 
-@node _ (2)
+@node How do I migrate from Roam Research?
-@chapter _ :ignore:
+@section How do I migrate from Roam Research?
+
+Fabio has produced a command-line tool that converts markdown files exported from Roam Research into Org-roam compatible markdown. More instructions are provided @uref{https://github.com/fabioberger/roam-migration, in the repository}.
 
 Emacs 28.0.50 (Org mode 9.4)
 @bye

mkdocs.yml

@@ -1,40 +0,0 @@
-site_name: "Org-roam"
-repo_url: https://github.com/org-roam/org-roam/
-edit_uri: edit/master/doc/
-copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
-docs_dir: doc
-extra:
-  social:
-    - type: 'slack'
-      link: 'https://join.slack.com/t/orgroam/shared_invite/zt-clh0g0tx-j8xg1kVxnrWdKt16gmSGPQ'
-nav:
-- Home: index.md
-- A Tour of Org-roam: tour.md
-- Installation: installation.md
-- Configuration: configuration.md
-- Anatomy of an Org-roam file: anatomy.md
-- The Templating System: templating.md
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.md
-- "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Roam Protocol": roam_protocol.md
-- "Appendix: Org Export": org_export.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-buffer.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -41,12 +41,14 @@
 (defvar org-roam-backlinks-mode)
 (defvar org-roam-last-window)
 (defvar org-ref-cite-types) ;; in org-ref-core.el
+(defvar org-roam-mode)
 
 (declare-function org-roam-db--ensure-built   "org-roam-db")
 (declare-function org-roam--extract-ref       "org-roam")
 (declare-function org-roam--get-title-or-slug "org-roam")
 (declare-function org-roam--get-backlinks     "org-roam")
 (declare-function org-roam-backlinks-mode     "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
 (defcustom org-roam-buffer-position 'right
   "Position of `org-roam' buffer.
@@ -86,10 +88,10 @@ Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
   :type 'hook
   :group 'org-roam)
 
-(defcustom org-roam-buffer-no-delete-other-windows nil
+(defcustom org-roam-buffer-window-parameters nil
-  "The `no-delete-other-windows' parameter of the `org-roam-buffer' window.
+  "Additional window parameters for the `org-roam-buffer' side window.
-When non-nil, the window will not be closed when deleting other windows."
+For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
-  :type 'boolean
+  :type '(alist)
   :group 'org-roam)
 
 (defvar org-roam-buffer--current nil
@@ -114,32 +116,32 @@ When non-nil, the window will not be closed when deleting other windows."
 
 (defun org-roam-buffer--insert-citelinks ()
   "Insert citation backlinks for the current buffer."
-  (if-let* ((ref (with-temp-buffer
+  (when-let ((org-ref-p (require 'org-ref nil t)) ;; Ensure that org-ref is present
-                   (insert-buffer-substring org-roam-buffer--current)
+             (ref (cdr (with-temp-buffer
-                   (org-roam--extract-ref)))
+                        (insert-buffer-substring org-roam-buffer--current)
-            (org-ref-p (require 'org-ref nil t)) ; Ensure that org-ref is present
+                        (org-roam--extract-ref)))))
-            (key-backlinks (org-roam--get-backlinks (cdr ref)))
+    (if-let* ((key-backlinks (org-roam--get-backlinks ref))
-            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
+              (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
-      (progn
+        (progn
-        (insert (let ((l (length key-backlinks)))
+          (insert (let ((l (length key-backlinks)))
-                  (format "\n\n* %d %s\n"
+                    (format "\n\n* %d %s\n"
-                          l (org-roam-buffer--pluralize "Cite backlink" l))))
+                            l (org-roam-buffer--pluralize "Cite backlink" l))))
-        (dolist (group grouped-backlinks)
+          (dolist (group grouped-backlinks)
-          (let ((file-from (car group))
+            (let ((file-from (car group))
-                (bls (cdr group)))
+                  (bls (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
+              (insert (format "** [[file:%s][%s]]\n"
-                            file-from
+                              file-from
-                            (org-roam--get-title-or-slug file-from)))
+                              (org-roam--get-title-or-slug file-from)))
-            (dolist (backlink bls)
+              (dolist (backlink bls)
-              (pcase-let ((`(,file-from _ ,props) backlink))
+                (pcase-let ((`(,file-from _ ,props) backlink))
-                (insert (propertize
+                  (insert (propertize
-                         (s-trim (s-replace "\n" " "
+                           (s-trim (s-replace "\n" " "
-                                            (plist-get props :content)))
+                                              (plist-get props :content)))
-                         'help-echo "mouse-1: visit backlinked note"
+                           'help-echo "mouse-1: visit backlinked note"
-                         'file-from file-from
+                           'file-from file-from
-                         'file-from-point (plist-get props :point)))
+                           'file-from-point (plist-get props :point)))
-                (insert "\n\n"))))))
+                  (insert "\n\n"))))))
-    (insert "\n\n* No cite backlinks!")))
+      (insert "\n\n* No cite backlinks!"))))
 
 (defun org-roam-buffer--insert-backlinks ()
   "Insert the org-roam-buffer backlinks string for the current buffer."
@@ -242,8 +244,7 @@ Valid states are 'visible, 'exists and 'none."
 
 (defun org-roam-buffer--get-create ()
   "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((window (get-buffer-window))
+  (let ((position
-        (position
          (if (member org-roam-buffer-position '(right left top bottom))
              org-roam-buffer-position
            (let ((text-quoting-style 'grave))
@@ -251,21 +252,24 @@ Valid states are 'visible, 'exists and 'none."
                     "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
                     org-roam-buffer-position))
            'right)))
-    (-> (get-buffer-create org-roam-buffer)
+    (save-selected-window
-        (display-buffer-in-side-window
+      (-> (get-buffer-create org-roam-buffer)
-         `((side . ,position)
+          (display-buffer-in-side-window
-           (window-parameters . ((no-delete-other-windows . ,org-roam-buffer-no-delete-other-windows)))))
+           `((side . ,position)
-        (select-window))
+             (window-parameters . ,org-roam-buffer-window-parameters)))
-    (pcase position
+          (select-window))
-      ((or 'right 'left)
+      (pcase position
-       (org-roam-buffer--set-width  (round (* (frame-width)  org-roam-buffer-width))))
+        ((or 'right 'left)
-      ((or 'top  'bottom)
+         (org-roam-buffer--set-width
-       (org-roam-buffer--set-height (round (* (frame-height) org-roam-buffer-height)))))
+          (round (* (frame-width)  org-roam-buffer-width))))
-    (select-window window)))
+        ((or 'top  'bottom)
+         (org-roam-buffer--set-height
+          (round (* (frame-height) org-roam-buffer-height))))))))
 
 (defun org-roam-buffer-toggle-display ()
   "Toggle display of the `org-roam-buffer'."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (setq org-roam-last-window (get-buffer-window))
   (pcase (org-roam-buffer--visibility)
     ('visible (delete-window (get-buffer-window org-roam-buffer)))

org-roam-capture.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -38,17 +38,19 @@
 ;; Declarations
 (defvar org-roam-encrypt-files)
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function  org-roam--get-title-path-completions "org-roam")
 (declare-function  org-roam--get-ref-path-completions   "org-roam")
 (declare-function  org-roam--file-path-from-id          "org-roam")
 (declare-function  org-roam--format-link                "org-roam")
 (declare-function  org-roam--title-to-slug              "org-roam")
+(declare-function  org-roam-mode                        "org-roam")
 (declare-function  org-roam-completion--completing-read "org-roam-completion")
 
 (defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
   "The default file name format for Org-roam templates.")
 
-(defvar org-roam-capture--header-default "#+TITLE: ${title}\n"
+(defvar org-roam-capture--header-default "#+title: ${title}\n"
   "The default capture header for Org-roam templates.")
 
 (defvar org-roam-capture--file-path nil
@@ -83,7 +85,7 @@ note with the given `ref'.")
   '(("d" "default" plain (function org-roam-capture--get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-${slug}"
-     :head "#+TITLE: ${title}\n"
+     :head "#+title: ${title}\n"
      :unnarrowed t))
   "Capture templates for Org-roam.
 The capture templates are an extension of
@@ -108,8 +110,8 @@ applies.
   '(("r" "ref" plain (function org-roam-capture--get-point)
      ""
      :file-name "${slug}"
-     :head "#+TITLE: ${title}
+     :head "#+title: ${title}
-#+ROAM_KEY: ${ref}\n"
+#+roam_key: ${ref}\n"
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
 Details on how to specify for the template is given in `org-roam-capture-templates'.")
@@ -265,8 +267,9 @@ This function is used solely in Org-roam's capture templates: see
                      ('ref
                       (let ((completions (org-roam--get-ref-path-completions))
                             (ref (cdr (assoc 'ref org-roam-capture--info))))
-                        (or (cdr (assoc ref completions))
+                        (if-let ((pl (cdr (assoc ref completions))))
-                            (org-roam-capture--new-file))))
+                            (plist-get pl :path)
+                          (org-roam-capture--new-file))))
                      (_ (error "Invalid org-roam-capture-context")))))
     (org-roam-capture--expand-template)
     (org-roam-capture--put :file-path file-path)
@@ -329,6 +332,7 @@ GOTO and KEYS argument have the same functionality as
   "Launches an `org-capture' process for a new or existing note.
 This uses the templates defined at `org-roam-capture-templates'."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (when (org-roam-capture--in-process-p)
     (user-error "Nested Org-roam capture processes not supported"))
   (let* ((completions (org-roam--get-title-path-completions))
@@ -336,7 +340,7 @@ This uses the templates defined at `org-roam-capture-templates'."
                                                                 completions))
          (res (cdr (assoc title-with-keys completions)))
          (title (or (plist-get res :title) title-with-keys))
-         (file-path (plist-get res :file-path)))
+         (file-path (plist-get res :path)))
     (let ((org-roam-capture--info (list (cons 'title title)
                                         (cons 'slug (org-roam--title-to-slug title))
                                         (cons 'file file-path)))

org-roam-compat.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -80,6 +80,9 @@
 (define-obsolete-function-alias 'org-roam-db--maybe-update 'org-roam-db--update-maybe
   "org-roam 1.1.0")
 
+(when (version< (org-version) "9.3")
+  (defalias 'org-link-make-string 'org-make-link-string))
+
 ;;;; Variables
 (define-obsolete-variable-alias 'org-roam-graphviz-extra-options
   'org-roam-graph-extra-config "org-roam 1.0.0")
@@ -95,6 +98,8 @@
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-date-filename-format
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
+(make-obsolete-variable 'org-roam-buffer-no-delete-other-windows
+  'org-roam-buffer-window-parameters "org-roam 1.1.1")
 
 (provide 'org-roam-compat)
 

org-roam-completion.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 

org-roam-dailies.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -41,11 +41,13 @@
      ""
      :immediate-finish t
      :file-name "%<%Y-%m-%d>"
-     :head "#+TITLE: %<%Y-%m-%d>"))
+     :head "#+title: %<%Y-%m-%d>"))
   "Capture templates for daily notes in Org-roam.")
 
 ;; Declarations
+(defvar org-roam-mode)
 (declare-function org-roam--file-path-from-id "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
 (defun org-roam-dailies--file-for-time (time)
   "Create and find file for TIME."
@@ -59,18 +61,21 @@
 (defun org-roam-dailies-today ()
   "Create and find the daily note for today."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (current-time)))
 
 (defun org-roam-dailies-tomorrow (n)
   "Create and find the daily note for tomorrow.
 With numeric argument N, use N days in the future."
   (interactive "p")
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
 
 (defun org-roam-dailies-yesterday (n)
   "Create and find the file for yesterday.
 With numeric argument N, use N days in the past."
   (interactive "p")
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies-tomorrow (- n)))
 
 (defun org-roam-dailies-date ()

org-roam-db.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -33,23 +33,26 @@
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite)
+(require 'emacsql-sqlite3)
+(require 'seq)
 (require 'org-roam-macs)
 
 (defvar org-roam-directory)
 (defvar org-roam-verbose)
+(defvar org-roam-file-name)
 
 (declare-function org-roam--org-roam-file-p                "org-roam")
 (declare-function org-roam--extract-titles                 "org-roam")
 (declare-function org-roam--extract-ref                    "org-roam")
 (declare-function org-roam--extract-tags                   "org-roam")
+(declare-function org-roam--extract-headlines              "org-roam")
 (declare-function org-roam--extract-links                  "org-roam")
 (declare-function org-roam--list-all-files                 "org-roam")
 (declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
 (defcustom org-roam-db-location nil
-  "Location of the Org-roam database.
+  "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
@@ -57,11 +60,7 @@ when used with multiple Org-roam instances."
   :type 'string
   :group 'org-roam)
 
-(defconst org-roam-db--version 5)
+(defconst org-roam-db--version 6)
-(defconst org-roam-db--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.")
@@ -69,8 +68,7 @@ when used with multiple Org-roam instances."
 ;;;; Core Functions
 (defun org-roam-db--get ()
   "Return the sqlite db file."
-  (interactive "P")
+    (or org-roam-db-location
-  (or org-roam-db-location
       (expand-file-name "org-roam.db" org-roam-directory)))
 
 (defun org-roam-db--get-connection ()
@@ -87,7 +85,7 @@ Performs a database upgrade when required."
     (let* ((db-file (org-roam-db--get))
            (init-db (not (file-exists-p db-file))))
       (make-directory (file-name-directory db-file) t)
-      (let ((conn (emacsql-sqlite db-file)))
+      (let ((conn (emacsql-sqlite3 db-file)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
         (puthash (file-truename org-roam-directory)
                  conn
@@ -123,6 +121,10 @@ SQL can be either the emacsql vector representation, or a string."
       (hash :not-null)
       (meta :not-null)])
 
+    (headlines
+     [(id :unique :primary-key)
+      (file :not-null)])
+
     (links
      [(from :not-null)
       (to :not-null)
@@ -227,6 +229,13 @@ This is equivalent to removing the node from the graph."
     :values $v1]
    (list (vector file titles))))
 
+(defun org-roam-db--insert-headlines (headlines)
+  "Insert HEADLINES into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into headlines
+    :values $v1]
+   headlines))
+
 (defun org-roam-db--insert-tags (file tags)
   "Insert TAGS for a FILE into the Org-roam cache."
   (org-roam-db-query
@@ -263,12 +272,12 @@ This is equivalent to removing the node from the graph."
 If the file does not have any connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    connected_component(file) AS
@@ -285,12 +294,12 @@ This includes the file itself. If the file does not have any
 connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    -- Links are traversed in a breadth-first search.  In order to calculate the
@@ -336,12 +345,13 @@ connections, nil is returned."
 
 (defun org-roam-db--update-tags ()
   "Update the tags of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name)))
+  (let ((file (file-truename (buffer-file-name)))
-         (tags (org-roam--extract-tags)))
+        (tags (org-roam--extract-tags)))
     (org-roam-db-query [:delete :from tags
                         :where (= file $s1)]
                        file)
-    (org-roam-db--insert-tags file tags)))
+    (when tags
+      (org-roam-db--insert-tags file tags))))
 
 (defun org-roam-db--update-refs ()
   "Update the ref of the current buffer into the cache."
@@ -352,7 +362,7 @@ connections, nil is returned."
     (when-let ((ref (org-roam--extract-ref)))
       (org-roam-db--insert-ref file ref))))
 
-(defun org-roam-db--update-cache-links ()
+(defun org-roam-db--update-links ()
   "Update the file links of the current buffer in the cache."
   (let ((file (file-truename (buffer-file-name))))
     (org-roam-db-query [:delete :from links
@@ -361,6 +371,15 @@ connections, nil is returned."
     (when-let ((links (org-roam--extract-links)))
       (org-roam-db--insert-links links))))
 
+(defun org-roam-db--update-headlines ()
+  "Update the file headlines of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name))))
+    (org-roam-db-query [:delete :from headlines
+                        :where (= file $s1)]
+                       file)
+    (when-let ((headlines (org-roam--extract-headlines)))
+      (org-roam-db--insert-headlines headlines))))
+
 (defun org-roam-db--update-file (&optional file-path)
   "Update Org-roam cache for FILE-PATH."
   (when (org-roam--org-roam-file-p file-path)
@@ -373,7 +392,8 @@ connections, nil is returned."
           (org-roam-db--update-tags)
           (org-roam-db--update-titles)
           (org-roam-db--update-refs)
-          (org-roam-db--update-cache-links)
+          (org-roam-db--update-headlines)
+          (org-roam-db--update-links)
           (org-roam-buffer--update-maybe :redisplay t))))))
 
 (defun org-roam-db-build-cache (&optional force)
@@ -385,39 +405,53 @@ If FORCE, force a rebuild of the cache from scratch."
   (org-roam-db) ;; To initialize the database, no-op if already initialized
   (let* ((org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         all-files all-links all-titles all-refs all-tags)
+         all-files all-headlines all-links all-titles all-refs all-tags)
+    ;; Two-step building
+    ;; First step: Rebuild files and headlines
     (dolist (file org-roam-files)
       (let* ((attr (file-attributes file))
              (atime (file-attribute-access-time attr))
              (mtime (file-attribute-modification-time attr)))
-        (org-roam--with-temp-buffer
+        (org-roam--with-temp-buffer file
-          (insert-file-contents file)
           (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
             (unless (string= (gethash file current-files)
                              contents-hash)
               (org-roam-db--clear-file file)
               (push (vector file contents-hash (list :atime atime :mtime mtime))
                     all-files)
-              (when-let (links (org-roam--extract-links file))
+              (when-let (headlines (org-roam--extract-headlines file))
-                (push links all-links))
+                (push headlines all-headlines)))))))
-              (when-let (tags (org-roam--extract-tags file))
-                (push (vector file tags) all-tags))
-              (let ((titles (org-roam--extract-titles)))
-                (push (vector file titles)
-                      all-titles))
-              (when-let* ((ref (org-roam--extract-ref))
-                          (type (car ref))
-                          (key (cdr ref)))
-                (setq all-refs (cons (vector key file type) all-refs))))
-            (remhash file current-files)))))
-    (dolist (file (hash-table-keys current-files))
-      ;; These files are no longer around, remove from cache...
-      (org-roam-db--clear-file file))
     (when all-files
       (org-roam-db-query
        [:insert :into files
         :values $v1]
        all-files))
+    (when all-headlines
+      (org-roam-db-query
+       [:insert :into headlines
+        :values $v1]
+       all-headlines))
+    ;; Second step: Rebuild the rest
+    (dolist (file org-roam-files)
+      (org-roam--with-temp-buffer file
+        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+          (unless (string= (gethash file current-files)
+                           contents-hash)
+            (when-let (links (org-roam--extract-links file))
+              (push links all-links))
+            (when-let (tags (org-roam--extract-tags file))
+              (push (vector file tags) all-tags))
+            (let ((titles (org-roam--extract-titles)))
+              (push (vector file titles)
+                    all-titles))
+            (when-let* ((ref (org-roam--extract-ref))
+                        (type (car ref))
+                        (key (cdr ref)))
+              (setq all-refs (cons (vector key file type) all-refs))))
+          (remhash file current-files))))
+    (dolist (file (hash-table-keys current-files))
+      ;; These files are no longer around, remove from cache...
+      (org-roam-db--clear-file file))
     (when all-links
       (org-roam-db-query
        [:insert :into links
@@ -439,13 +473,15 @@ If FORCE, force a rebuild of the cache from scratch."
         :values $v1]
        all-refs))
     (let ((stats (list :files (length all-files)
+                       :headlines (length all-headlines)
                        :links (length all-links)
                        :tags (length all-tags)
                        :titles (length all-titles)
                        :refs (length all-refs)
                        :deleted (length (hash-table-keys current-files)))))
-      (org-roam-message "files: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
+      (org-roam-message "files: %s, headlines: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
                         (plist-get stats :files)
+                        (plist-get stats :headlines)
                         (plist-get stats :links)
                         (plist-get stats :tags)
                         (plist-get stats :titles)

org-roam-dev.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,7 +34,6 @@
 ;;; Code:
 (require 'emacsql)
 (emacsql-fix-vector-indentation)
-(setq-local sentence-end-double-space nil)
 (provide 'org-roam-dev)
 
 ;;; org-roam-dev.el ends here

org-roam-doctor.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -44,15 +44,20 @@
 ;; Library Requires
 (require 'cl-lib)
 (require 'org)
-(require 'org-roam-macs)
 (require 'org-element)
+(require 's)
+(require 'dash)
+(require 'org-roam-macs)
 
 (declare-function org-roam-insert "org-roam")
 (declare-function org-roam--get-roam-buffers "org-roam")
 (declare-function org-roam--list-all-files "org-roam")
 (declare-function org-roam--org-roam-file-p "org-roam")
+(declare-function org-roam--str-to-list "org-roam")
+(declare-function org-roam-mode "org-roam")
 
 (defvar org-roam-verbose)
+(defvar org-roam-mode)
 
 (cl-defstruct (org-roam-doctor-checker (:copier nil))
   (name 'missing-checker-name)
@@ -66,7 +71,78 @@
     :description "Fix broken links."
     :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
                ("r" . ("Replace link" . org-roam-doctor--replace-link))
-               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))))
+               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-roam-props
+    :description "Check #+roam_* properties.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-tags
+    :description "Check #+roam_tags.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-alias
+    :description "Check #+roam_alias.")))
+
+(defconst org-roam-doctor--supported-roam-properties
+  '("roam_tags" "roam_alias" "roam_key")
+  "List of supported Org-roam properties.")
+
+(defun org-roam-doctor-check-roam-props (ast)
+  "Checker for detecting invalid #+roam_* properties.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (let ((key (org-element-property :key kw)))
+          (when (and (string-prefix-p "ROAM_" key t)
+                     (not (member (downcase key) org-roam-doctor--supported-roam-properties)))
+            (push
+             `(,(org-element-property :begin kw)
+               ,(concat "Possible mispelled key: "
+                        (prin1-to-string key)
+                        "\nOrg-roam supports the following keys: "
+                        (s-join ", " org-roam-doctor--supported-roam-properties)))
+             reports)))))
+    reports))
+
+(defun org-roam-doctor-check-tags (ast)
+  "Checker for detecting invalid #+roam_tags.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_tags" nil t)
+          (let ((tags (org-element-property :value kw)))
+            (condition-case nil
+                (org-roam--str-to-list tags)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse tags: "
+                           tags
+                           (when (s-contains? "," tags)
+                             "\nCheck that your tags are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-check-alias (ast)
+  "Checker for detecting invalid #+roam_alias.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
+          (let ((aliases (org-element-property :value kw)))
+            (condition-case nil
+              (org-roam--str-to-list aliases)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse aliases: "
+                           aliases
+                           (when (s-contains? "," aliases)
+                             "\nCheck that your aliases are not comma-separated.")))
+                reports)))))))
+    reports))
 
 (defun org-roam-doctor-broken-links (ast)
   "Checker for detecting broken links.
@@ -207,6 +283,7 @@ CHECKER is a org-roam-doctor checker instance."
   "Perform a check on the current buffer to ensure cleanliness.
 If CHECKALL, run the check for all Org-roam files."
   (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
   (let ((files (if checkall
                   (org-roam--list-all-files)
                 (unless (org-roam--org-roam-file-p)

org-roam-graph.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -37,8 +37,10 @@
 
 ;;;; Declarations
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function org-roam--org-roam-file-p  "org-roam")
 (declare-function org-roam--path-to-slug     "org-roam")
+(declare-function org-roam-mode              "org-roam")
 
 ;;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
@@ -163,7 +165,7 @@ The Org-roam database titles table is read, to obtain the list of titles.
 The links table is then read to obtain all directed links, and formatted
 into a digraph."
   (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer
+  (org-roam--with-temp-buffer nil
     (let* ((nodes (org-roam-db-query node-query))
            (edges-query
             `[:with selected :as [:select [file] :from ,node-query]
@@ -217,24 +219,31 @@ into a digraph."
       (insert "}")
       (buffer-string))))
 
-(defun org-roam-graph--build (&optional node-query)
+(defun org-roam-graph--build (&optional node-query callback)
-  "Generate a graph showing the relations between nodes in NODE-QUERY."
+  "Generate a graph showing the relations between nodes in NODE-QUERY.
-  (let ((name org-roam-graph-executable))
+Execute CALLBACK when process exits successfully.
-    (unless (stringp name)
+CALLBACK is passed the graph file as its sole argument."
-      (user-error "`org-roam-graph-executable' is not a string"))
+  (unless (stringp org-roam-graph-executable)
-    (unless (executable-find org-roam-graph-executable)
+    (user-error "`org-roam-graph-executable' is not a string"))
-      (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+  (unless (executable-find org-roam-graph-executable)
-                          "Please adjust `org-roam-graph-executable'")
+    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
-                  name))
+                        "Please adjust `org-roam-graph-executable'")
-    (let* ((node-query (or node-query
+                org-roam-graph-executable))
-                           `[:select [file titles]
+  (let* ((node-query (or node-query
-                             :from titles
+                         `[:select [file titles] :from titles
-                             ,@(org-roam-graph--expand-matcher 'file t)]))
+                           ,@(org-roam-graph--expand-matcher 'file t)]))
-           (graph (org-roam-graph--dot node-query))
+         (graph      (org-roam-graph--dot node-query))
-           (temp-dot (make-temp-file "graph." nil ".dot" graph))
+         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
-           (temp-graph (make-temp-file "graph." nil ".svg")))
+         (temp-graph (make-temp-file "graph." nil ".svg")))
-      (call-process name nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
+    (org-roam-message "building graph")
-      temp-graph)))
+    (make-process
+     :name "*org-roam-graph--build-process*"
+     :buffer "*org-roam-graph--build-process*"
+     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-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."
@@ -249,9 +258,10 @@ into a digraph."
     ('nil (view-file file))
     (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
 
-(defun org-roam-graph--build-connected-component (file &optional max-distance)
+(defun org-roam-graph--build-connected-component (file &optional max-distance callback)
   "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
+CALLBACK is passed to `org-roam-graph--build'."
   (let* ((file (file-truename file))
          (files (or (if (and max-distance (>= max-distance 0))
                         (org-roam-db--links-with-max-distance file max-distance)
@@ -260,7 +270,7 @@ If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
          (query `[:select [file titles]
                   :from titles
                   :where (in file [,@files])]))
-    (org-roam-graph--build query)))
+    (org-roam-graph--build query callback)))
 
 ;;;; Commands
 ;;;###autoload
@@ -275,6 +285,7 @@ ARG may be any of the following values:
   - `\\[universal-argument]' -   build the graph for FILE.
   - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
   (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
   (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
     (unless (or (not arg) (equal arg '(16)))
       (unless file
@@ -282,11 +293,9 @@ ARG may be any of the following values:
       (unless (org-roam--org-roam-file-p file)
         (user-error "\"%s\" is not an org-roam file" file)))
     (pcase arg
-      ('nil            (org-roam-graph--open (org-roam-graph--build node-query)))
+      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
-      ('(4)            (org-roam-graph--open (org-roam-graph--build-connected-component file)))
+      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
-      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component file (abs arg))))
+      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
-                         (when (>= arg 0)
-                           (org-roam-graph--open graph))))
       ('(16)           (org-roam-graph--build node-query))
       ('-              (org-roam-graph--build-connected-component file))
       (_ (user-error "Unrecognized ARG: %s" arg)))))

org-roam-macs.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -36,14 +36,18 @@
 
 (defvar org-roam-verbose)
 
-(defmacro org-roam--with-temp-buffer (&rest body)
+(defmacro org-roam--with-temp-buffer (file &rest body)
   "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'."
+Like `with-temp-buffer', but propagates `org-roam-directory'.
-  (declare (indent 0) (debug t))
+If FILE, set `org-roam-temp-file-name' to file 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))
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local org-roam-file-name ,file))
            ,@body)))))
 
 (defmacro org-roam--with-template-error (templates &rest body)

org-roam-protocol.el

@@ -4,7 +4,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.1
+;; Version: 1.2.0
 ;; Package-Requires: ((emacs "26.1") (org "9.3"))
 
 ;; This file is NOT part of GNU Emacs.

tests/roam-files/alias.org

@@ -1,2 +1,2 @@
-#+ROAM_ALIAS: "a1" "a 2"
+#+roam_alias: "a1" "a 2"
-#+TITLE: t1
+#+title: t1

tests/roam-files/bar.org

@@ -1,3 +1,3 @@
-#+TITLE: Bar
+#+title: Bar
 
 This is file bar. Bar links to [[file:nested/bar.org][Nested Bar]].

tests/roam-files/base.org

@@ -1 +1 @@
-#+TITLE: Base
+#+title: Base

tests/roam-files/foo.org

@@ -1,4 +1,4 @@
-#+TITLE: Foo
+#+title: Foo
 
 This is the foo file. It contains a link to [[file:bar.org][Bar]].
 

tests/roam-files/nested/bar.org

@@ -1,3 +1,3 @@
-#+TITLE: Nested Bar
+#+title: Nested Bar
 
 This file is nested, 1 level deeper. It links to both [[file:../foo.org][Foo]] and [[file:foo.org][Nested Foo]].

tests/roam-files/nested/deeply/deeply_nested_file.org

@@ -1 +1 @@
-#+TITLE: Deeply Nested File
+#+title: Deeply Nested File

tests/roam-files/nested/foo.org

@@ -1,3 +1,3 @@
-#+TITLE: Nested Foo
+#+title: Nested Foo
 
 This file has no links.

tests/roam-files/tags/no_tag.org

@@ -1,3 +1,3 @@
-#+TITLE: Tagless File
+#+title: Tagless File
 
-This file has no tags, and should not yield any tags on extracting via =#+ROAM_TAGS=.
+This file has no tags, and should not yield any tags on extracting via ~#+roam_tags~.

tests/roam-files/tags/tag.org

@@ -1,4 +1,4 @@
-#+ROAM_TAGS: "t1" "t2 with space" t3
+#+roam_tags: "t1" "t2 with space" t3
-#+TITLE: Tags
+#+title: Tags
 
 This file is used to test functionality for =(org-roam--extract-tags)=

tests/roam-files/titles/aliases.org

@@ -1 +1 @@
-#+ROAM_ALIAS: "roam" "alias"
+#+roam_alias: "roam" "alias"

tests/roam-files/titles/combination.org

@@ -1,4 +1,4 @@
-#+TITLE: TITLE PROP
+#+title: TITLE PROP
-#+ROAM_ALIAS: "roam" "alias"
+#+roam_alias: "roam" "alias"
 
 * Headline

tests/roam-files/titles/title.org

@@ -1 +1 @@
-#+TITLE: Title
+#+title: Title

tests/roam-files/unlinked.org

@@ -1,3 +1,3 @@
-#+TITLE: Unlinked
+#+title: Unlinked
 
 Nothing links here :(

tests/roam-files/web_ref.org

@@ -1 +1 @@
-#+ROAM_KEY: https://google.com/
+#+roam_key: https://google.com/

tests/test-org-roam.el

@@ -22,7 +22,6 @@
 ;;; Code:
 
 (require 'buttercup)
-(require 'with-simulated-input)
 (require 'org-roam)
 (require 'dash)
 
@@ -53,6 +52,25 @@
   (delete-file (org-roam-db--get))
   (org-roam-db--close))
 
+(describe "org-roam--str-to-list"
+  (it "nil"
+    (expect (org-roam--str-to-list nil)
+            :to-be
+            nil))
+  (it "\"multi word\" prop 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "prop \"multi word\" 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "errors on bad input"
+    (expect (org-roam--str-to-list 1)
+            :to-throw)
+    (expect (org-roam--str-to-list "\"hello")
+            :to-throw)))
+
 (describe "Title extraction"
   :var (org-roam-title-sources)
   (before-all
@@ -270,199 +288,6 @@
             :to-equal
             (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
-(xdescribe "org-roam-insert"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "temp1 -> foo"
-    (let ((buf (test-org-roam--find-file "temp1.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))
-
-  (it "temp2 -> nested/foo"
-    (let ((buf (test-org-roam--find-file "temp2.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "(nested) SPC Nested SPC Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))
-
-  (it "nested/temp3 -> foo"
-    (let ((buf (test-org-roam--find-file "nested/temp3.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))
-
-  (it "a/b/temp4 -> nested/foo"
-    (let ((buf (test-org-roam--find-file "a/b/temp4.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "(nested) SPC Nested SPC Foo RET"
-         (org-roam-insert))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))
-
-(xdescribe "rename file updates cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "foo -> new_foo"
-    (rename-file (test-org-roam--abs-path "foo.org")
-                 (test-org-roam--abs-path "new_foo.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (test-org-roam--abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (test-org-roam--abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../new_foo.org][Foo]]")))
-
-  (it "foo -> foo with spaces"
-    (rename-file (test-org-roam--abs-path "foo.org")
-                 (test-org-roam--abs-path "foo with spaces.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (test-org-roam--abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (test-org-roam--abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))
-
-  (it "no-title -> meaningful-title"
-    (rename-file (test-org-roam--abs-path "no-title.org")
-                 (test-org-roam--abs-path "meaningful-title.org"))
-    ;; File has no forward links
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "no-title.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "meaningful-title.org"))) :to-be 1)
-
-    ;; Links are updated with the appropriate name
-    (expect (with-temp-buffer
-              (insert-file-contents (test-org-roam--abs-path "meaningful-title.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
-
-  (it "web_ref -> hello"
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal
-            (list (list (test-org-roam--abs-path "web_ref.org"))))
-    (rename-file (test-org-roam--abs-path "web_ref.org")
-                 (test-org-roam--abs-path "hello.org"))
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal (list (list (test-org-roam--abs-path "hello.org"))))
-    (expect (caar (org-roam-db-query
-                   [:select [ref] :from refs
-                    :where (= file $s1)]
-                   (test-org-roam--abs-path "web_ref.org")))
-            :to-equal nil)))
-
-(xdescribe "delete file updates cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "delete foo"
-    (delete-file (test-org-roam--abs-path "foo.org"))
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 0))
-
-  (it "delete web_ref"
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
-    (delete-file (test-org-roam--abs-path "web_ref.org"))
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list))))
-
 (provide 'test-org-roam)
 
 ;;; test-org-roam.el ends here