Org-roam V2 (#1401)

.dir-locals.el

@@ -1,6 +1,13 @@
-;;; Directory Local Variables
-;;; For more information see (info "(emacs) Directory Variables")
-
 ((emacs-lisp-mode
-  (eval . (require 'org-roam-dev))
+  (fill-column . 110)
-  (eval . (org-roam-dev-mode))))
+  (indent-tabs-mode . nil)
+  (elisp-lint-ignored-validators . ("byte-compile" "package-lint"))
+  (elisp-lint-indent-specs . ((describe . 1)
+                              (it . 1)
+                              (org-element-map . defun)
+                              (org-roam-with-temp-buffer . 1)
+                              (org-with-point-at . 1)
+                              (magit-insert-section . defun)
+                              (magit-section-case . 0)
+                              (->> . 1)
+                              (org-roam-with-file . 2)))))

.github/workflows/test.yml

@@ -34,39 +34,28 @@ jobs:
   build:
     runs-on: ubuntu-latest
     strategy:
-      fail-fast: false
       matrix:
         emacs_version:
+          - 27.1
           - snapshot
     steps:
-    - uses: purcell/setup-emacs@master
+      - uses: purcell/setup-emacs@master
-      with:
+        with:
-        version: ${{ matrix.emacs_version }}
+          version: ${{ matrix.emacs_version }}
 
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Create Sandbox Directory
+      - name: Install Eldev
-      run: |
+        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
-        SANDBOX_DIR=$(mktemp -d) || exit 1
-        echo "SANDBOX_DIR=$SANDBOX_DIR" >> $GITHUB_ENV
 
-    - name: Initialize Sandbox
+      - name: Install dependencies
-      run: |
+        run: make prepare
-        ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
 
-    # The "all" rule is not used, because it treats compilation warnings
+      - name: Lint
-    # as failures, so linting and testing are run as separate steps.
+        run: make lint
-
-    # 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 --exclude org-roam-compat.el lint
-
-    - name: Test
-      if: always()  # Run test even if linting fails.
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR test
 
+      - name: Test
+        run: make test
 # Local Variables:
 # eval: (outline-minor-mode)
 # End:

.gitignore

@@ -13,3 +13,4 @@
 /doc/stats/
 /config.mk
 /doc/manual.html
+/.eldev/

CHANGELOG.md

@@ -1,17 +1,21 @@
 # Changelog
+
 ## 1.2.4 (TBD)
 
 ### Added
+
 - [#1396](https://github.com/org-roam/org-roam/pull/1396) add option to choose between prepending, appending, and omitting `roam_tags` in file completion
 - [#1270](https://github.com/org-roam/org-roam/pull/1270) capture: create OLP if it does not exist. Removes need for OLP setup in `:head`.
 - [#1353](https://github.com/org-roam/org-roam/pull/1353) support file-level property drawers
 
 ### Changed
+
 - [#1352](https://github.com/org-roam/org-roam/pull/1352) prefer lower-case for roam_tag and roam_alias in interactive commands
 - [#1513](https://github.com/org-roam/org-roam/pull/1513) replaced hardcoded "svg" with defcustom org-roam-graph-filetype 
 - [#1540](https://github.com/org-roam/org-roam/pull/1540) allow `roam_tag` and `roam_alias` to be specified on multiple lines
 
 ### Fixed
+
 - [#1281](https://github.com/org-roam/org-roam/pull/1281) fixed idle-timer not instantiated on `org-roam-mode`
 - [#1308](https://github.com/org-roam/org-roam/pull/1308) fixed file renames corrupting database
 - [#1325](https://github.com/org-roam/org-roam/pull/1325) make titles and tags extracted unique per note
@@ -20,7 +24,7 @@
 - [#1347](https://github.com/org-roam/org-roam/pull/1347) allow use of `%a` element in regular Org-roam captures
 - [#1352](https://github.com/org-roam/org-roam/pull/1352) fixed org-roam-{tag/alias}-{add/delete} altering the original case of the Org property
 - [#1374](https://github.com/org-roam/org-roam/pull/1374) fix headline completions erroring out
-- [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file 
+- [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file
 - [#1403](https://github.com/org-roam/org-roam/issues/1403) fixed inconsistency between how we write and read props like alias and tags
 - [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
 - [#1542](https://github.com/org-roam/org-roam/issues/1542) fix files not excluded when `org-roam-list-files-commands` is nil
@@ -32,6 +36,7 @@ Primarily a stabilization and bug-fix release.
 Org-roam-dailies has also been revamped to include new features, see [this video](https://www.youtube.com/watch?v=1q9x2aZCJJ4) for a quick overview.
 
 ### Added
+
 - [#978](https://github.com/org-roam/org-roam/pull/978) Revamp org-roam-dailies
 - [#1183](https://github.com/org-roam/org-roam/pull/1183) Interactive functions for managing aliases and tags in Org-roam file, namely `org-roam-alias-add`, `org-roam-alias-delete`, `org-roam-tag-add`, and `org-roam-tag-delete`.
 - [#1215](https://github.com/org-roam/org-roam/pull/1215) Multiple `ROAM_KEY` keywords can now be specified in one file. This allows bibliographical entries to share the same note file.
@@ -40,9 +45,11 @@ Org-roam-dailies has also been revamped to include new features, see [this video
 - [#1264](https://github.com/org-roam/org-roam/pull/1264) add `org-roam-db-update-method` to control when the cache is rebuilt.
 
 ### Changed
+
 - [#1264](https://github.com/org-roam/org-roam/pull/1264) renamed `org-roam-update-db-idle-seconds` to `org-roam-db-idle-idle-seconds`
 
 ### Fixed
+
 - [#1074](https://github.com/org-roam/org-roam/issues/1074) fix `org-roam--extract-links` to handle content boundaries.
 - [#1193](https://github.com/org-roam/org-roam/issues/1193) fix `org-roam-db-build-cache` by not killing temporary buffer in `org-roam--extract-links`.
 - [#1195](https://github.com/org-roam/org-roam/issues/1195) fix ID face showing as invalid if within Org ID files, but not Org-roam's.

Eldev

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

Makefile

@@ -1,70 +1,29 @@
-# * makem.sh/Makefile --- Script to aid building and testing Emacs Lisp packages
+.PHONY: clean
+clean:
+	eldev clean all
 
-# This Makefile is from the makem.sh repo: <https://github.com/alphapapa/makem.sh>.
+.PHONY: prepare
+prepare:
+	eldev -C --unstable -p -dtT prepare
 
-# * Arguments
+.PHONY: lint
+lint:
+	eldev -C --unstable -T lint
 
-# For consistency, we use only var=val options, not hyphen-prefixed options.
+.PHONY: test
-
+test:
-# NOTE: I don't like duplicating the arguments here and in makem.sh,
+	eldev -C --unstable -T test
-# but I haven't been able to find a way to pass arguments which
-# conflict with Make's own arguments through Make to the script.
-# Using -- doesn't seem to do it.
-
-ifdef install-deps
-	INSTALL_DEPS = "--install-deps"
-endif
-ifdef install-linters
-	INSTALL_LINTERS = "--install-linters"
-endif
-
-ifdef sandbox
-	ifeq ($(sandbox), t)
-		SANDBOX = --sandbox
-	else
-		SANDBOX = --sandbox $(sandbox)
-	endif
-endif
-
-ifdef debug
-	DEBUG = "--debug"
-endif
-
-# ** Verbosity
-
-# Since the "-v" in "make -v" gets intercepted by Make itself, we have
-# to use a variable.
-
-verbose = $(v)
-
-ifneq (,$(findstring vv,$(verbose)))
-	VERBOSE = "-vv"
-else ifneq (,$(findstring v,$(verbose)))
-	VERBOSE = "-v"
-endif
-
-# * Rules
-
-# TODO: Handle cases in which "test" or "tests" are called and a
-# directory by that name exists, which can confuse Make.
-
-%:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS) $(@)
-
-.DEFAULT: init
-init:
-	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS)
 
 docs:
-	@$(MAKE) -C doc all
+	make -C doc all
 
 html:
-	@$(MAKE) -C doc html-dir
+	make -C doc html-dir
 
 install: install-docs
 
 install-docs: docs
-	@$(MAKE) -C doc install-docs
+	make -C doc install-docs
 
 install-info: info
-	@$(MAKE) -C doc install-info
+	make -C doc install-info

README.md

@@ -1,5 +1,5 @@
 # Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]
- 
+
 <img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">
 
 Org-roam is a plain-text knowledge management system. It brings some of
@@ -44,17 +44,19 @@ Here's a sample configuration with `use-package`:
 ```emacs-lisp
 (use-package org-roam
       :ensure t
-      :hook
-      (after-init . org-roam-mode)
       :custom
       (org-roam-directory (file-truename "/path/to/org-files/"))
-      :bind (:map org-roam-mode-map
+      :bind (("C-c n l" . org-roam-buffer-toggle)
-              (("C-c n l" . org-roam)
+             ("C-c n f" . org-roam-node-find)
-               ("C-c n f" . org-roam-find-file)
+             ("C-c n g" . org-roam-graph)
-               ("C-c n g" . org-roam-graph))
+             ("C-c n i" . org-roam-node-insert)
-              :map org-mode-map
+             ("C-c n c" . org-roam-capture)
-              (("C-c n i" . org-roam-insert))
+             ;; Dailies
-              (("C-c n I" . org-roam-insert-immediate))))
+             ("C-c n j" . org-roam-dailies-capture-today))
+      :config
+      (org-roam-setup)
+      ;; If using org-roam-protocol
+      (require 'org-roam-protocol))
 ```
 
 The `file-truename` function is only necessary when you use symbolic links

doc/org-roam.texi

@@ -25,13 +25,13 @@ General Public License for more details.
 
 @dircategory Emacs
 @direntry
-* Org-roam: (org-roam). Rudimentary Roam Replica for Emacs.
+* Org-roam: (org-roam). Roam Research for Emacs.
 @end direntry
 
 @finalout
 @titlepage
 @title Org-roam User Manual
-@subtitle for version 1.2.3
+@subtitle for version 2.0.0
 @author Jethro Kuan
 @page
 @vskip 0pt plus 1filll
@@ -44,10 +44,10 @@ General Public License for more details.
 
 @noindent
 
-This manual is for Org-roam version 1.2.3.
+This manual is for Org-roam version 2.0.0.
 
 @quotation
-Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@@gmail.com>
+Copyright (C) 2020-2021 Jethro Kuan <jethrokuan95@@gmail.com>
 
 You can redistribute this document and/or modify it under the terms of the GNU
 General Public License as published by the Free Software Foundation, either
@@ -67,13 +67,24 @@ General Public License for more details.
 * A Brief Introduction to the Zettelkasten Method::
 * Installation::
 * Getting Started::
-* Files::
+* Viewing the links::
+* Node Properties::
+* The Org-roam Buffer::
+* Styling Org-roam::
+* Completion::
+* Encryption::
+* Org-roam protocol::
+* Diagnosing and Repair::
+* Building Extensions::
+* The Org-mode Ecosystem::
+* Frequently Asked Questions::
+* Developer's Guide to Org-roam::
 * The Templating System::
 * Concepts and Configuration::
 * Inserting Links::
 * Completions::
 * Navigating Around::
-* Encryption::
+* Encryption: Encryption (1). 
 * Graphing::
 * Minibuffer Completion::
 * Roam Protocol::
@@ -91,31 +102,33 @@ General Public License for more details.
 @detailmenu
 --- The Detailed Node Listing ---
 
-A Brief Introduction to the Zettelkasten Method
-
-* Fleeting notes::
-* Permanent notes::
-
 Installation
 
 * Installing from MELPA::
 * Installing from Apt::
-* Installing from the Git Repository::
+* Installing from Source::
 * Post-Installation Tasks::
 
-Files
+Getting Started
 
-* File Titles::
+* The Org-roam Node::
-* File Tags::
+* Links between Nodes::
-* File Refs::
+* Setting up Org-roam::
+* Creating and Linking Nodes::
 
-File Titles
+Node Properties
 
-* Customizing Title Extraction::
+* Standard Org properties::
+* Aliases::
+* Refs::
 
-File Tags
+Building Extensions
 
-* Customizing Tag Extraction::
+* Public Interface::
+
+Developer's Guide to Org-roam
+
+* Org-roam's Design Principles::
 
 The Templating System
 
@@ -125,10 +138,9 @@ The Templating System
 Concepts and Configuration
 
 * Directories and Files::
-* The Org-roam Buffer::
+* The Org-roam Buffer: The Org-roam Buffer (1). 
 * Org-roam Files::
 * Org-roam Faces::
-* The Database::
 
 Completions
 
@@ -198,28 +210,24 @@ FAQ
 @node Introduction
 @chapter Introduction
 
-Org-roam is a tool for network thought. It reproduces some of @uref{https://roamresearch.com/, Roam
+Org-roam is a tool for networked thought. It reproduces some of @uref{https://roamresearch.com/, Roam
-Research's} @footnote{To understand more about Roam, a collection of links are available in @ref{Note-taking Workflows}.} features within the all-powerful @uref{https://orgmode.org/, Org-mode}.
+Research's} @footnote{To understand more about Roam, a collection of links are available in @ref{Note-taking Workflows}.} key features within @uref{https://orgmode.org/, Org-mode}.
 
-Org-roam is a solution for effortless non-hierarchical note-taking with
+Org-roam allows for effortless non-hierarchical note-taking: with Org-roam,
-Org-mode. With Org-roam, notes flow naturally, making note-taking fun and easy.
+notes flow naturally, making note-taking fun and easy. Org-roam augments the
-Org-roam keeps closely to Org syntax, and will work for anyone already using
+Org-mode syntax, and will work for anyone already using Org-mode for their
-Org-mode for their personal wiki.
+personal wiki.
 
-Org-roam gains its superpowers by leveraging the mature ecosystem around
+Org-roam leverages the mature ecosystem around Org-mode. For example, it has
-Org-mode. For example, it has first-class support for @uref{https://github.com/jkitchin/org-ref, org-ref} for citation
+first-class support for @uref{https://github.com/jkitchin/org-ref, org-ref} for citation management, and is able to
-management.
+piggyback off Org's excellent @LaTeX{} and source-block evaluation capabilities.
 
-Org-roam aims to implement the core features of Roam, leveraging the
+Org-roam provides these benefits over other tooling:
-mature ecosystem around Org-mode where possible. Eventually, we hope
-to further introduce features enabled by the Emacs ecosystem.
-
-Org-roam provides several benefits over other tooling:
 
 @itemize
 @item
-@strong{Privacy and Security:} Keep your personal wiki entirely offline and in your
+@strong{Privacy and Security:} Your personal wiki belongs only to you, entirely
-control. Encrypt your notes with GPG@.
+offline and in your control. Encrypt your notes with GPG@.
 
 @item
 @strong{Longevity of Plain Text:} Unlike web solutions like Roam Research, the notes
@@ -235,13 +243,13 @@ you feel unhappy with any part of Org-roam, you may choose to extend Org-roam,
 or open a pull request.
 
 @item
-@strong{Leverage the Org-mode ecosystem:} Over the years, Emacs and Org-mode has
+@strong{Leverage the Org-mode ecosystem:} Over the decades, 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.
 
 @item
-@strong{Built on Emacs:} Emacs is also a fantastic interface for editing text, and we
+@strong{Built on Emacs:} Emacs is also a fantastic interface for editing text, and
-can inherit many of the powerful text-navigation and editing packages
+Org-roam inherits many of the powerful text-navigation and editing packages
 available to Emacs.
 @end itemize
 
@@ -249,18 +257,18 @@ available to Emacs.
 @chapter Target Audience
 
 Org-roam is a tool that will appear unfriendly to anyone unfamiliar with Emacs
-and Org-mode, but is also extremely powerful to those willing to put effort in
+and Org-mode, but it is also extremely powerful to those willing to put effort
-mastering the intricacies of the tools. Org-roam stands on the shoulders on
+inn mastering the intricacies. Org-roam stands on the shoulders of giants. Emacs
-giants. Emacs was first created in 1976, and remains a top tier tool for editing
+was first created in 1976, and remains the tool of choice for many for editing
 text and designing textual interfaces. The malleability of Emacs allowed the
 creation of Org-mode, an all-purpose plain-text system for maintaining TODO
 lists, planning projects, and authoring documents. Both of these tools are
 incredibly vast and require significant time investment to master.
 
-Org-roam assumes basic familiarity with these tools. It is not difficult to get
+Org-roam assumes only basic familiarity with these tools. It is not difficult to
-up and running with basic text-editing functionality, but one will only fully
+get up and running with basic text-editing functionality, but one will only
-appreciate the power of building Roam functionality into Emacs and Org-mode when
+fully appreciate the power of building Roam functionality into Emacs and
-the usage of these tools become more advanced.
+Org-mode when the usage of these tools become more advanced.
 
 One key advantage to Org-roam is that building on top of Emacs gives it
 malleability. This is especially important for note-taking workflows. It is our
@@ -313,13 +321,7 @@ plain-text, Org-mode file. 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.
 
-@menu
+@strong{Fleeting notes}
-* Fleeting notes::
-* Permanent notes::
-@end menu
-
-@node Fleeting notes
-@section Fleeting notes
 
 A slip-box requires a method for quickly capturing ideas. These are called
 @strong{fleeting notes}: they are simple reminders of information or ideas that will
@@ -328,8 +330,7 @@ need to be processed later on, or trashed. This is typically accomplished using
 functionality (see @ref{Daily-notes}). This provides a central inbox for collecting
 thoughts, to be processed later into permanent notes.
 
-@node Permanent notes
+@strong{Permanent notes}
-@section 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
@@ -338,6 +339,9 @@ 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.
 
+For further reading on the Zettelkasten method, ``How to Take Smart Notes'' by
+Sonke Ahrens is a decent guide.
+
 @node Installation
 @chapter Installation
 
@@ -347,7 +351,7 @@ development repository.
 @menu
 * Installing from MELPA::
 * Installing from Apt::
-* Installing from the Git Repository::
+* Installing from Source::
 * Post-Installation Tasks::
 @end menu
 
@@ -416,8 +420,8 @@ apt-get install elpa-org-roam
 
 Org-roam will then be autoloaded into Emacs.
 
-@node Installing from the Git Repository
+@node Installing from Source
-@section Installing from the Git Repository
+@section Installing from Source
 
 You may install Org-roam directly from the repository on @uref{https://github.com/org-roam/org-roam, GitHub} if you like.
 This will give you access to the latest version hours or days before it appears
@@ -520,18 +524,19 @@ install-info /path/to/my/info/files/org-roam.info /path/to/my/info/files/dir
 @node Post-Installation Tasks
 @section Post-Installation Tasks
 
-Org-roam uses @code{emacsql-sqlite3}, which requires @code{sqlite3} to be located on
+Org-roam requires @code{sqlite3} to be locatable by Emacs (i.e. on @code{exec-path}).
-@code{exec-path}. Please ensure that @code{sqlite3} is installed appropriately on your
+Please ensure that @code{sqlite3} is installed appropriately on your operating
-operating system. You can verify that this is the case by executing:
+system. You can verify that this is the case by executing @footnote{Two easy ways to evaluate elisp: 1) Place the cursor after the closing
+paren and run @samp{M-x eval-last-sexp RET} or 2) Press @samp{C-c C-c} with your cursor in
+an Org file code block (like @samp{#+BEGIN_SRC emacs-lisp}).}:
 
 @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
+the path to the executable is not a member of the Emacs variable @code{exec-path}.
-variable @code{exec-path}. You may rectify this by manually adding the path within
+Rectify this by manually adding the path within your Emacs configuration:
-your Emacs configuration:
 
 @lisp
 (add-to-list 'exec-path "path/to/sqlite3")
@@ -540,283 +545,145 @@ your Emacs configuration:
 @node Getting Started
 @chapter Getting Started
 
-This short tutorial describes the essential commands used in Org-roam, to help
+@menu
-you get started.
+* The Org-roam Node::
+* Links between Nodes::
+* Setting up Org-roam::
+* Creating and Linking Nodes::
+@end menu
 
-First, it is important to understand how Org-roam was designed. Org-roam was
+@node The Org-roam Node
-built to support a workflow that was not possible with vanilla Org-mode. This
+@section The Org-roam Node
-flow is modelled after the @uref{https://zettelkasten.de/, Zettelkasten Method}, and many of @uref{https://roamresearch.com, Roam Research's}
+
-workflows. Org-roam does not magically make note-taking better -- this often
+We first begin with some terminology we'll use throughout the manual. We term
-requires a radical change in your current note-taking workflow. To understand
+the basic denomination in Org-roam a node. We define a node as follows:
-more about the methods and madness, see @ref{Note-taking Workflows}.
+
+@quotation
+A node is any headline or top level file with an ID@.
+
+@end quotation
+
+For example, with this example file content:
+
+@example
+:PROPERTIES:
+:ID:       foo
+:END:
+#+title: Foo
+
+* Bar
+:PROPERTIES:
+:ID:       bar
+:END:
+@end example
+
+We create two nodes:
+
+@itemize
+@item
+A file node ``Foo'' with id @code{foo}.
+
+@item
+A headline node ``Bar'' with id @code{bar}.
+@end itemize
+
+Headlines without IDs will not be considered Org-roam nodes. Org IDs can be
+added to files or headlines via the interactive command @code{M-x org-id-get-create}.
+
+@node Links between Nodes
+@section Links between Nodes
+
+We link between nodes using Org's standard ID link (e.g. @code{id:foo}). While only
+ID links will be considered during the computation of links between nodes,
+Org-roam caches all other links in the documents for external use.
+
+@node Setting up Org-roam
+@section Setting up Org-roam
+
+Org-roam's capabilities stem from its aggressive caching: it crawls all files
+within @code{org-roam-directory}, keeping a cache of all its links and nodes, while
+making sure that the cache is consistent.
 
 To first start using Org-roam, one needs to pick a location to store the
 Org-roam files. The directory that will contain your notes is specified by the
-variable @code{org-roam-directory}. This variable needs to be set before any calls to
+variable @code{org-roam-directory}. Org-roam searches recursively within
-Org-roam functions, including enabling @code{org-roam-mode}. For this tutorial,
+@code{org-roam-directory} for notes. This variable needs to be set before any calls
-create an empty directory, and set @code{org-roam-directory}:
+to Org-roam functions. For this tutorial, create an empty directory, and set
+@code{org-roam-directory}:
 
 @lisp
 (make-directory "~/org-roam")
 (setq org-roam-directory "~/org-roam")
 @end lisp
 
-We encourage using a flat hierarchy for storing notes, but some prefer using
+Next, we need to setup Org-roam to maintain cache consistency. This is achieved
-folders for storing specific kinds of notes (e.g. websites, papers). This is
+by running @code{M-x org-roam-setup}. To ensure that Org-roam is available on
-fine; Org-roam searches recursively within @code{org-roam-directory} for notes.
+startup, one can place this in their Emacs configuration:
-Instead of relying on the file hierarchy for any form of categorization, one
-should use links between files to establish connections between notes.
-
-Next, we need to enable the global minor mode @code{org-roam-mode}. This sets up
-Emacs with several hooks, building a cache that is kept consistent as your
-slip-box grows. We recommend starting @code{org-roam-mode} on startup:
 
 @lisp
-(add-hook 'after-init-hook 'org-roam-mode)
+(require 'org-roam)
+(org-roam-setup)
 @end lisp
 
 To build the cache manually, one can run @code{M-x org-roam-db-build-cache}. Cache
 builds may take a while the first time, but is often instantaneous in subsequent
 runs because it only reprocesses modified files.
 
-Let us now create our first note. Call @code{M-x org-roam-find-file}. This shows a
+@node Creating and Linking Nodes
-list of titles for notes that reside in @code{org-roam-directory}. It should show
+@section @strong{TODO} Creating and Linking Nodes
-nothing right now, since there are no notes in the directory. Entering the title
+
-of the note you wish to create, and pressing @code{RET} should begin the note
+Org-roam makes it easy to create notes and link them together. There are 2 main
+functions for creating nodes:
+
+@itemize
+@item
+@code{org-roam-node-insert}: creates a node if it does not exist, and inserts a
+link to the node at point.
+
+@item
+@code{org-roam-node-find}: creates a node if it does not exist, and visits the
+node.
+@end itemize
+
+Let's first try @code{org-roam-node-find}. Calling @code{M-x org-roam-node-find} will
+show a list of titles for nodes that reside in @code{org-roam-directory}. It should
+show nothing right now, since there are no notes in the directory. Enter the
+title of the note you wish to create, and press @code{RET}. This begins the note
 creation process. This process uses @code{org-capture}'s templating system, and can
 be customized (see @ref{The Templating System}). Using the default template, pressing
 @code{C-c C-c} finishes the note capture.
 
-By default, Org-roam updates the cache asynchronously in the background to
+Now that we have a node, we can try inserting a link to the node using @code{M-x
-avoid getting in the way of writing. Org-roam queues updates to the files,
+org-roam-node-insert}. This brings up the list of nodes, which should contain
-waits for you to be idle for 2 seconds, and then automatically triggers
+the node you just created. Selecting the node will insert an @code{id:} link to the
-updating the cache. After the cache has been updated, running @code{M-x
+node. If you instead entered a title that does not exist, you will once again be
-org-roam-find-file} again should show the note you have created, and selecting
+brought through the node creation process. To enable link auto-completion,
-that entry will bring you to that note @footnote{Depending on your completion framework, you may need to press TAB to
+see @ref{Completion}.
-see the list.}. One can customize the waiting
-time by setting @code{org-roam-db-update-idle-seconds}; or change the cache update
-to be triggered immediately after buffer save by setting
-@code{org-roam-db-update-method} to @code{'immediate}.
 
-For experienced @code{org-capture} users, the behavior of @code{M-x org-roam-find-file} 
+@node Viewing the links
-may seem unfamiliar: after finishing a capture with @code{C-c C-c}, you are returned  
+@chapter @strong{TODO} Viewing the links
-not to the original buffer from which you called @code{M-x org-roam-find-file}, but 
-to a buffer pointing to the note you just created. For the usual @code{org-capture} 
-behavior you can call @code{M-x org-roam-capture} instead of @code{M-x org-roam-find-file}. 
 
-Org-roam makes it easy to create notes, and link them together. To link notes
+Org-roam provides an interface to view relationships with other notes
-together, we call @code{M-x org-roam-insert}. This brings up a prompt with a list of
+(backlinks, reference links, unlinked references etc.). To pop up this info
-title for existing notes. Selecting an existing entry will create and insert a
+buffer, call @code{M-x org-roam-buffer}.
-link to the current file. Entering a non-existent title will create a new note
-with that title. Good usage of Org-roam requires liberally linking files: this
-facilitates building up a dense graph of inter-connected notes.
 
-Org-roam provides an interface to view backlinks. It shows backlinks for the
+@node Node Properties
-currently active Org-roam note, along with some surrounding context. To toggle
+@chapter @strong{TODO} Node Properties
-the visibility of this buffer, call @code{M-x org-roam}.
-
-For a visual representation of the notes and their connections, Org-roam also
-provides graphing capabilities, using Graphviz. It generates graphs with notes
-as nodes, and links between them as edges. The generated graph can be used to
-navigate to the files, but this requires some additional setup (see @ref{Roam Protocol}).
-
-@node Files
-@chapter Files
-
-In Org-roam, notes typically consist of multiple files, where each file is a
-zettel.
-
-While the bulk of Org-roam's functionality is built on top of vanilla Org-mode,
-Org-roam adds several Org-roam-specific keywords to support additional
-functionality.
-
-This section explains the important components of a file, and the extensions to
-Org-mode.
 
 @menu
-* File Titles::
+* Standard Org properties::
-* File Tags::
+* Aliases::
-* File Refs::
+* Refs::
 @end menu
 
-@node File Titles
+@node Standard Org properties
-@section File Titles
+@section @strong{TODO} Standard Org properties
 
-To easily find a note, a title needs to be prescribed to a note.
+@node Aliases
+@section @strong{TODO} Aliases
 
-A note can have many titles: this allows a note to be referred to by different
+@node Refs
-names, which is especially useful for topics or concepts with acronyms. For
+@section @strong{TODO} Refs
-example, for a note like ``World War 2'', it may be desirable to also refer to it
-using the acronym ``WWII''.
-
-Org-roam calls @code{org-roam--extract-titles} to extract titles. It uses the
-variable @code{org-roam-title-sources}, to control how the titles are extracted. The
-title extraction methods supported are:
-
-@itemize
-@item
-@code{'title}: This extracts the title using the file @code{#+title} property
-
-@item
-@code{'headline}: This extracts the title from the first headline in the Org file
-
-@item
-@code{'alias}: This extracts a list of titles using the @code{#+roam_alias} property.
-The aliases are space-delimited, and can be multi-worded using quotes.
-@end itemize
-
-Take for example the following org file:
-
-@example
-#+title: World War 2
-#+roam_alias: "WWII" "World War II"
-
-* Headline
-@end example
-
-@multitable {aaaaaaaaaaa} {aaaaaaaaaaaaaaaaaaaaaaaa}
-@headitem Method
-@tab Titles
-@item @code{'title}
-@tab '(``World War 2'')
-@item @code{'headline}
-@tab '(``Headline'')
-@item @code{'alias}
-@tab '(``WWII'' ``World War II'')
-@end multitable
-
-If no title is provided, Org-roam defaults to using the file-path.
-
-@menu
-* Customizing Title Extraction::
-@end menu
-
-@node Customizing Title Extraction
-@subsection Customizing Title Extraction
-
-To control how Org-roam extracts titles, customize @code{org-roam-title-sources}. If
-all methods of title extraction return no results, the file-name is used as the
-note's title.
-
-@defopt org-roam-title-sources
-
-The list of sources from which to retrieve a note title.
-Each element in the list is either:
-@end defopt
-
-@itemize
-@item
-a symbol -- this symbol corresponds to a title retrieval function, which
-returns the list of titles for the current buffer
-@itemize
-@item
-a list of symbols -- symbols in the list are treated as with (1). The
-return value of this list is the first symbol in the list returning a
-non-nil value.
-@end itemize
-
-The return results of the root list are concatenated.
-
-For example the setting: '((title headline) alias) means the following:
-
-@itemize
-@item
-Return the 'title + 'alias, if the title of current buffer is non-empty;
-
-@item
-Or return 'headline + 'alias otherwise.
-@end itemize
-
-The currently supported symbols are:
-
-@code{'title}
-The @code{#+title} property of org file.
-
-@code{'alias}
-The @code{#+roam_alias} property of the org file, using
-space-delimited strings.
-
-@code{'headline}
-The first headline in the org file.
-@end itemize
-
-Adding your own title extraction method requires two steps. First, define a
-method @code{(defun org-roam--extract-titles-foo () ...)}, where @code{foo} a
-self-prescribed name for the title extraction method. This method takes no
-arguments, and returns a list of strings (titles). Finally, push the symbol
-@code{foo} into @code{org-roam-title-sources}. You may need to rebuild the cache from
-scratch to re-process all files to pick up the new titles.
-
-@node File Tags
-@section File Tags
-
-Tags are used as meta-data for files: they facilitate interactions with notes
-where titles are insufficient. For example, tags allow for categorization of
-notes: differentiating between bibliographical and structure notes during
-interactive commands.
-
-By default, tags are extracted from the @code{#+roam_tags} property. To add
-additional extraction methods, see @ref{Customizing Tag Extraction}.
-
-@menu
-* Customizing Tag Extraction::
-@end menu
-
-@node Customizing Tag Extraction
-@subsection Customizing Tag Extraction
-
-Org-roam calls @code{org-roam--extract-tags} to extract tags from files. The variable
-@code{org-roam-tag-sources}, to control how tags are extracted.
-
-@defopt org-roam-tag-sources
-@end defopt
-
-Sources to obtain tags from.
-
-It should be a list of symbols representing any of the following extraction
-methods:
-
-@code{'prop}
-  Extract tags from the @code{#+roam_tags} property.
-  Tags are space delimited.
-  Tags may contain spaces if they are double-quoted.
-  e.g. @code{#+roam_tags: TAG "tag with spaces"}
-
-@code{'vanilla}
-  Extract vanilla org-mode tags, including @code{#+FILETAGS} and
-  inherited tags.
-
-@code{'all-directories}
-  Extract sub-directories relative to @code{org-roam-directory}.
-  That is, if a file is located at relative path foo/bar/file.org,
-  the file will have tags ``foo'' and ``bar''.
-
-@code{'last-directory}
-  Extract the last directory relative to `org-roam-directory'.
-  That is, if a file is located at relative path foo/bar/file.org,
-  the file will have tag \``bar\''.
-
-@code{'first-directory}
-  Extract the first directory relative to @code{org-roam-directory}.
-  That is, if a file is located at relative path foo/bar/file.org,
-  the file will have tag ``foo''
-
-By default, only the @code{'prop} extraction method is enabled. To enable the other
-extraction methods, you may modify @code{org-roam-tag-sources}, for example:
-
-@lisp
-(setq org-roam-tag-sources '(prop last-directory))
-@end lisp
-
-Adding your own tag extraction method requires two steps. First, define a method
-@code{(defun org-roam--extract-tags-foo (file) ...)}, where @code{foo} a self-prescribed
-name for the tag extraction method. This method takes the file path as an
-argument, and returns a list of strings (titles). Finally, push the symbol @code{foo}
-into @code{org-roam-tag-sources}. You may need to rebuild the cache from scratch to
-re-process all files to pick up the new tags.
-
-@node File Refs
-@section File Refs
 
 Refs are unique identifiers for files. For example, a note for a website may
 contain a ref:
@@ -849,6 +716,159 @@ You may assign multiple refs to a single file, for example when you want
 multiple papers in a series to share the same note, or an article has a citation
 key and a URL at the same time.
 
+@node The Org-roam Buffer
+@chapter @strong{TODO} The Org-roam Buffer
+
+@node Styling Org-roam
+@chapter @strong{TODO} Styling Org-roam
+
+@node Completion
+@chapter @strong{TODO} Completion
+
+@node Encryption
+@chapter @strong{TODO} Encryption
+
+@node Org-roam protocol
+@chapter @strong{TODO} Org-roam protocol
+
+@node Diagnosing and Repair
+@chapter @strong{TODO} Diagnosing and Repair
+
+@node Building Extensions
+@chapter @strong{TODO} Building Extensions
+
+@menu
+* Public Interface::
+@end menu
+
+@node Public Interface
+@section @strong{TODO} Public Interface
+
+Database (for developers)
+@itemize
+@item
+querying: (org-roam-db-query)
+
+@item
+updating full database: (org-roam-db-sync)
+
+@item
+update current file: (org-roam-db-update-file)
+
+@item
+remove file from database: (org-roam-db-clear-file)
+@end itemize
+
+Nodes:
+@itemize
+@item
+List all nodes
+
+@item
+Read a node in from completion
+
+@item
+Get node at point
+@end itemize
+
+Links:
+@itemize
+@item
+Get backlinks for node
+@end itemize
+
+Tags:
+@itemize
+@item
+Add tag to node
+
+@item
+delete tag for node
+
+@item
+Get tags for node
+@end itemize
+
+Aliases:
+@itemize
+@item
+Add alias to node
+
+@item
+Delete alias for node
+
+@item
+Get aliases for node
+@end itemize
+
+Ref:
+@itemize
+@item
+Add ref to node
+@end itemize
+
+Capture:
+
+Navigation:
+@itemize
+@item
+Find or create a node
+@end itemize
+
+@node The Org-mode Ecosystem
+@chapter @strong{TODO} The Org-mode Ecosystem
+
+@node Frequently Asked Questions
+@chapter @strong{TODO} Frequently Asked Questions
+
+@node Developer's Guide to Org-roam
+@chapter @strong{TODO} Developer's Guide to Org-roam
+
+@menu
+* Org-roam's Design Principles::
+@end menu
+
+@node Org-roam's Design Principles
+@section Org-roam's Design Principles
+
+Org-roam is primarily motivated by the need for a dual representation. We
+(humans) love operating in a plain-text environment. The syntax rules of
+Org-mode are simple and fit snugly within our brain. This also allows us to use
+the tools and packages we love to explore and edit our notes. Org-mode is simply
+the most powerful plain-text format available, with support for images, @LaTeX{},
+TODO planning and much more.
+
+But this plain-text format is simply ill-suited for exploration of these notes:
+plain-text is simply not amenable for answering large-scale, complex queries
+(e.g. how many tasks do I have that are due by next week?). Interfaces such as
+Org-agenda slow to a crawl when the number of files becomes unwieldy, which
+can quickly become the case.
+
+At its core, Org-roam provides a database abstraction layer, providing a dual
+representation of what's already available in plain-text. This allows us
+(humans) to continue working with plain-text, while programs can utilize the
+database layer to perform complex queries. These capabilities include, but are
+not limited to:
+
+@itemize
+@item
+link graph traversal and visualization
+
+@item
+Instantaneous SQL-like queries on headlines
+@itemize
+@item
+What are my TODOs, scheduled for X, or due by Y@?
+@end itemize
+@end itemize
+
+All of these functionality is powered by this database abstraction layer. Hence,
+at its core Org-roam's primary goal is to provide a resilient dual
+representation that is cheap to maintain, easy to understand, and is as
+up-to-date as it possibly can. Org-roam also then exposes an API to this
+database abstraction layer for users who would like to perform programmatic
+queries on their Org files.
+
 @node The Templating System
 @chapter The Templating System
 
@@ -918,7 +938,7 @@ The template is given a description of @code{"default"}.
 @code{(function org-roam--capture-get-point)} should not be changed.
 
 @item
-@code{"%?"} is the template inserted on each call to @code{org-roam-capture--capture}.
+@code{"%?"} is the template inserted on each call to @code{org-roam-capture-}.
 This template means don't insert any content, but place the cursor here.
 
 @item
@@ -990,10 +1010,9 @@ org-roam}.
 
 @menu
 * Directories and Files::
-* The Org-roam Buffer::
+* The Org-roam Buffer: The Org-roam Buffer (1). 
 * Org-roam Files::
 * Org-roam Faces::
-* The Database::
 @end menu
 
 @node Directories and Files
@@ -1021,7 +1040,7 @@ with multiple Org-roam instances.
 Files matching this regular expression are excluded from the Org-roam.
 @end defvar
 
-@node The Org-roam Buffer
+@node The Org-roam Buffer (1)
 @section The Org-roam Buffer
 
 The Org-roam buffer displays backlinks for the currently active Org-roam note.
@@ -1086,27 +1105,6 @@ The @code{org-roam-link-current} face corresponds to links to the same file it i
 The @code{org-roam-link-invalid} face is applied to links that are broken. These are
 links to files or IDs that cannot be found.
 
-@node The Database
-@section @strong{TODO} The Database
-
-Org-roam is backed by a Sqlite database.
-
-@defopt org-roam-db-update-method
-
-Method to update the Org-roam database.
-
-@code{'immediate}: Update the database immediately upon file changes.
-
-@code{'idle-timer}: Updates the database if dirty, if Emacs idles for
-@code{org-roam-db-update-idle-seconds}.
-@end defopt
-
-@defopt org-roam-db-update-idle-seconds
-
-Number of idle seconds before triggering an Org-roam database update. This is
-only valid if @code{org-roam-db-update-method} is @code{'idle-timer}.
-@end defopt
-
 @node Inserting Links
 @chapter Inserting Links
 
@@ -1194,7 +1192,7 @@ represents the cursor:
 @code{[[|]]}: completes for a file title
 
 @item
-@code{[[roam:]]}: completes for a file title
+@code{[[roam:|]]}: completes for a file title
 
 @item
 @code{[[*|]]}: completes for a headline within this file
@@ -1206,6 +1204,9 @@ represents the cursor:
 @code{[[roam:foo*|]]} completes a headline within the file with title ``foo''
 @end itemize
 
+If you don't see the literal display of your links like the above examples,
+call @code{M-x org-toggle-link-display}
+
 Completions account for the current input. For example, for @code{[[f|]]}, the
 completions (by default) only show for files with titles that start with ``f''.
 
@@ -1279,7 +1280,7 @@ title is @code{"Index"}.
 Opens the Index file in the current @code{org-roam-directory}.
 @end defun
 
-@node Encryption
+@node Encryption (1)
 @chapter Encryption
 
 One may wish to keep private, encrypted files. Org-roam supports encryption (via
@@ -1617,7 +1618,7 @@ in the generated graph.
 @node The roam-ref protocol
 @section The roam-ref protocol
 
-This protocol finds or creates a new note with a given @code{roam_key} (see @ref{Files}):
+This protocol finds or creates a new note with a given @code{roam_key}:
 
 @image{images/roam-ref,,,,gif}
 
@@ -1720,7 +1721,7 @@ template @code{j} will put its notes under the heading ‘Journal’.
 
 Create an entry in the daily note for today.
 
-When @code{goto} is non-nil, go the note without creating an entry.
+When @code{goto} is non-nil, go to the note without creating an entry.
 @end defun
 
 @defun @code{org-roam-dailies-find-today}
@@ -1986,22 +1987,6 @@ using @uref{https://github.com/raxod502/el-patch, el-patch}:
 
 (eval-when-compile
   (require 'el-patch))
-
-(use-package deft
-  ;; same as above...
-  :config/el-patch
-  (defun deft-parse-title (file contents)
-    "Parse the given FILE and CONTENTS and determine the title.
-If `deft-use-filename-as-title' is nil, the title is taken to
-be the first non-empty line of the FILE.  Else the base name of the FILE is
-used as title."
-    (el-patch-swap (if deft-use-filename-as-title
-                       (deft-base-filename file)
-                     (let ((begin (string-match "^.+$" contents)))
-                       (if begin
-                           (funcall deft-parse-title-function
-                                    (substring contents begin (match-end 0))))))
-                   (org-roam-db--get-title file))))
 @end lisp
 
 The Deft interface can slow down quickly when the number of files get huge.
@@ -2105,6 +2090,9 @@ file with the right @samp{#+roam_key}.
 @uref{https://www.leonrische.me/fc/index.html, Org-fc} is a spaced repetition system that scales well with a large number of
 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}.
 
+To use Anki for spaced repetition, @uref{https://github.com/louietan/anki-editor, anki-editor} allows you to write your cards in
+Org-mode, and sync your cards to Anki via @uref{https://github.com/FooSoft/anki-connect#installation, anki-connect}.
+
 @node FAQ
 @chapter FAQ
 

org-roam-buffer.el

@@ -1,357 +0,0 @@
-;;; org-roam-buffer.el --- Metadata buffer -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
-;; 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 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library provides the org-roam-buffer functionality for org-roam
-;;; Code:
-;;;; Library Requires
-(eval-when-compile (require 'subr-x))
-(require 'cl-lib)
-(require 'dash)
-(require 's)
-(require 'f)
-(require 'ol)
-(require 'org-element)
-(require 'org-roam-macs)
-
-(defvar org-roam-directory)
-(defvar org-link-frame-setup)
-(defvar org-return-follows-link)
-(defvar org-roam-backlinks-mode)
-(defvar org-roam-last-window)
-(defvar org-ref-cite-types) ;; in org-ref-core.el
-(defvar org-roam-mode)
-(defvar org-roam--org-link-bracket-typed-re)
-
-(declare-function org-roam-db--ensure-built   "org-roam-db")
-(declare-function org-roam-db--get-title      "org-roam-db")
-(declare-function org-roam-db-has-file-p      "org-roam-db")
-(declare-function org-roam--extract-refs      "org-roam")
-(declare-function org-roam--extract-titles    "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")
-(declare-function org-roam--find-file         "org-roam")
-(declare-function org-roam-format-link        "org-roam")
-(declare-function org-roam-link-get-path      "org-roam-link")
-
-(defcustom org-roam-buffer-position 'right
-  "Position of `org-roam' buffer.
-Valid values are
- * left,
- * right,
- * top,
- * bottom,
- * a function returning one of the above."
-  :type '(choice (const left)
-                 (const right)
-                 (const top)
-                 (const bottom)
-                 function)
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-width 0.33
-  "Width of `org-roam' buffer.
-Has an effect if and only if `org-roam-buffer-position' is `left' or `right'."
-  :type 'number
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-height 0.27
-  "Height of `org-roam' buffer.
-Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
-  :type 'number
-  :group 'org-roam)
-
-
-(defcustom org-roam-buffer "*org-roam*"
-  "Org-roam buffer name."
-  :type 'string
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-prepare-hook '(org-roam-buffer--insert-title
-                                          org-roam-buffer--insert-backlinks
-                                          org-roam-buffer--insert-ref-links)
-  "Hook run in the `org-roam-buffer' before it is displayed."
-  :type 'hook
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-preview-function #'org-roam-buffer--preview
-  "Function to obtain preview contents for a given link.
-The function takes in two arguments, the FILE containing the
-link, and the POINT of the link."
-  :type 'function
-  :group 'org-roam)
-
-(defcustom org-roam-buffer-window-parameters nil
-  "Additional window parameters for the `org-roam-buffer' side window.
-For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defvar org-roam-buffer--current nil
-  "Currently displayed file in `org-roam' buffer.")
-
-(defun org-roam-buffer--find-file (file)
-  "Open FILE in the window `org-roam' was called from."
-  (setq file (expand-file-name file))
-  (let ((last-window org-roam-last-window))
-    (if (window-valid-p last-window)
-        (progn (with-selected-window last-window
-                 (org-roam--find-file file))
-               (select-window last-window))
-      (org-roam--find-file file))))
-
-(defun org-roam-buffer--insert-title ()
-  "Insert the org-roam-buffer title."
-  (insert (propertize (org-roam-db--get-title
-                       (buffer-file-name org-roam-buffer--current))
-                      'font-lock-face
-                      'org-document-title)))
-
-(defun org-roam-buffer--preview (file point)
-  "Get preview content for FILE at POINT."
-  (save-excursion
-    (org-roam--with-temp-buffer file
-      (goto-char point)
-      (let ((elem (org-element-at-point)))
-        (or (org-element-property :raw-value elem)
-            (when-let ((begin (org-element-property :begin elem))
-                       (end (org-element-property :end elem)))
-              (string-trim (buffer-substring-no-properties begin end))))))))
-
-(defun org-roam-buffer--pluralize (string number)
-  "Conditionally pluralize STRING if NUMBER is above 1."
-  (let ((l (pcase number
-             ((pred (listp)) (length number))
-             ((pred (integerp)) number)
-             (wrong-type (signal 'wrong-type-argument
-                                 `((listp integerp)
-                                   ,wrong-type))))))
-    (concat string (when (> l 1) "s"))))
-
-(defun org-roam-buffer-expand-links (content orig-path)
-  "Crawl CONTENT for relative links and corrects them to be correctly displayed.
-ORIG-PATH is the path where the CONTENT originated."
-  (with-temp-buffer
-    (insert content)
-    (goto-char (point-min))
-    (let (link link-type)
-      (while (re-search-forward org-roam--org-link-bracket-typed-re (point-max) t)
-        (setq link-type (match-string 1)
-              link (match-string 2))
-        (when (and (string-equal link-type "file")
-                   (f-relative-p link))
-          (replace-match (org-roam-link-get-path (expand-file-name link (file-name-directory orig-path)))
-                         nil t nil 2))))
-    (buffer-string)))
-
-(defun org-roam-buffer--insert-ref-links ()
-  "Insert ref backlinks for the current buffer."
-  (when-let* ((refs (with-temp-buffer
-                      (insert-buffer-substring org-roam-buffer--current)
-                      (org-roam--extract-refs)))
-              (paths (mapcar #'cdr refs)))
-    (if-let* ((key-backlinks (mapcan #'org-roam--get-backlinks paths))
-              (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
-        (progn
-          (insert (let ((l (length key-backlinks)))
-                    (format "\n\n* %d %s\n"
-                            l (org-roam-buffer--pluralize "Ref Backlink" l))))
-          (dolist (group grouped-backlinks)
-            (let ((file-from (car group))
-                  (bls (cdr group)))
-              (insert (format "** %s\n"
-                              (org-roam-format-link file-from
-                                                    (org-roam-db--get-title file-from)
-                                                    "file")))
-              (dolist (backlink bls)
-                (pcase-let ((`(,file-from _ ,props) backlink))
-                  (insert (if-let ((content (funcall org-roam-buffer-preview-function file-from (plist-get props :point))))
-                              (propertize (org-roam-buffer-expand-links content file-from)
-                                          'help-echo "mouse-1: visit backlinked note"
-                                          'file-from file-from
-                                          'file-from-point (plist-get props :point))
-                            "")
-                          "\n\n"))))))
-      (insert "\n\n* No ref backlinks!"))))
-
-(defun org-roam-buffer--insert-backlinks ()
-  "Insert the org-roam-buffer backlinks string for the current buffer."
-  (let (props file-from)
-    (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
-              (titles (with-current-buffer org-roam-buffer--current
-                        (org-roam--extract-titles)))
-              (backlinks (org-roam--get-backlinks (push file-path titles)))
-              (grouped-backlinks (--group-by (nth 0 it) backlinks)))
-        (progn
-          (insert (let ((l (length backlinks)))
-                    (format "\n\n* %d %s\n"
-                            l (org-roam-buffer--pluralize "Backlink" l))))
-          (dolist (group grouped-backlinks)
-            (setq file-from (car group))
-            (setq props (mapcar (lambda (row) (nth 2 row)) (cdr group)))
-            (setq props (seq-sort-by (lambda (p) (plist-get p :point)) #'< props))
-            (insert (format "** %s\n"
-                            (org-roam-format-link file-from
-                                                  (org-roam-db--get-title file-from)
-                                                  "file")))
-            (dolist (prop props)
-              (insert "*** "
-                      (if-let ((outline (plist-get prop :outline)))
-                          (-> outline
-                              (string-join " > ")
-                              (org-roam-buffer-expand-links file-from))
-                        "Top")
-                      "\n"
-                      (if-let ((content (funcall org-roam-buffer-preview-function file-from (plist-get prop :point))))
-                          (propertize
-                           (s-trim (s-replace "\n" " " (org-roam-buffer-expand-links content file-from)))
-                           'help-echo "mouse-1: visit backlinked note"
-                           'file-from file-from
-                           'file-from-point (plist-get prop :point))
-                        "")
-                      "\n\n"))))
-      (insert "\n\n* No backlinks!"))))
-
-(defun org-roam-buffer-update ()
-  "Update the `org-roam-buffer'."
-  (interactive)
-  (org-roam-db--ensure-built)
-  (let* ((source-org-roam-directory org-roam-directory))
-    (with-current-buffer org-roam-buffer
-      ;; When dir-locals.el is used to override org-roam-directory,
-      ;; org-roam-buffer should have a different local org-roam-directory and
-      ;; default-directory, as relative links are relative from the overridden
-      ;; org-roam-directory.
-      (setq-local org-roam-directory source-org-roam-directory)
-      (setq-local default-directory source-org-roam-directory)
-      ;; Locally overwrite the file opening function to re-use the
-      ;; last window org-roam was called from
-      (setq-local org-link-frame-setup
-                  (cons '(file . org-roam--find-file) org-link-frame-setup))
-      (let ((inhibit-read-only t))
-        (erase-buffer)
-        (unless (eq major-mode 'org-mode)
-          (org-mode))
-        (unless org-roam-backlinks-mode
-          (org-roam-backlinks-mode))
-        (make-local-variable 'org-return-follows-link)
-        (setq org-return-follows-link t)
-        (run-hooks 'org-roam-buffer-prepare-hook)
-        (read-only-mode 1)))))
-
-
-(cl-defun org-roam-buffer--update-maybe (&key redisplay)
-  "Reconstructs `org-roam-buffer'.
-This needs to be quick or infrequent, because this is run at
-`post-command-hook'.  If REDISPLAY, force an update of
-`org-roam-buffer'."
-  (let ((buffer (window-buffer)))
-    (when (and (or redisplay
-                   (not (eq org-roam-buffer--current buffer)))
-               (eq 'visible (org-roam-buffer--visibility))
-               (buffer-file-name buffer)
-               (org-roam-db-has-file-p (buffer-file-name buffer)))
-      (setq org-roam-buffer--current buffer)
-      (org-roam-buffer-update))))
-
-;;;; Toggling the org-roam buffer
-(define-inline org-roam-buffer--visibility ()
-  "Return whether the current visibility state of the org-roam buffer.
-Valid states are 'visible, 'exists and 'none."
-  (declare (side-effect-free t))
-  (inline-quote
-   (cond
-    ((get-buffer-window org-roam-buffer) 'visible)
-    ((get-buffer org-roam-buffer) 'exists)
-    (t 'none))))
-
-(defun org-roam-buffer--set-width (width)
-  "Set the width of `org-roam-buffer' to `WIDTH'."
-  (unless (one-window-p)
-    (let ((window-size-fixed)
-          (w (max width window-min-width)))
-      (cond
-       ((> (window-width) w)
-        (shrink-window-horizontally  (- (window-width) w)))
-       ((< (window-width) w)
-        (enlarge-window-horizontally (- w (window-width))))))))
-
-(defun org-roam-buffer--set-height (height)
-  "Set the height of `org-roam-buffer' to `HEIGHT'."
-  (unless (one-window-p)
-    (let ((window-size-fixed)
-          (h (max height window-min-height)))
-      (cond
-       ((> (window-height) h)
-        (shrink-window  (- (window-height) h)))
-       ((< (window-height) h)
-        (enlarge-window (- h (window-height))))))))
-
-(defun org-roam-buffer--get-create ()
-  "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((position (if (functionp org-roam-buffer-position)
-                      (funcall org-roam-buffer-position)
-                    org-roam-buffer-position)))
-    (save-selected-window
-      (-> (get-buffer-create org-roam-buffer)
-          (display-buffer-in-side-window
-           `((side . ,position)
-             (window-parameters . ,org-roam-buffer-window-parameters)))
-          (select-window))
-      (pcase position
-        ((or 'right 'left)
-         (org-roam-buffer--set-width
-          (round (* (frame-width)  org-roam-buffer-width))))
-        ((or 'top  'bottom)
-         (org-roam-buffer--set-height
-          (round (* (frame-height) org-roam-buffer-height))))))))
-
-(defun org-roam-buffer-activate ()
-  "Activate display of the `org-roam-buffer'."
-  (interactive)
-  (unless org-roam-mode (org-roam-mode))
-  (setq org-roam-last-window (get-buffer-window))
-  (org-roam-buffer--get-create))
-
-(defun org-roam-buffer-deactivate ()
-  "Deactivate display of the `org-roam-buffer'."
-  (interactive)
-  (setq org-roam-last-window (get-buffer-window))
-  (delete-window (get-buffer-window org-roam-buffer)))
-
-(defun org-roam-buffer-toggle-display ()
-  "Toggle display of the `org-roam-buffer'."
-  (interactive)
-  (pcase (org-roam-buffer--visibility)
-    ('visible (org-roam-buffer-deactivate))
-    ((or 'exists 'none) (org-roam-buffer-activate))))
-
-(provide 'org-roam-buffer)
-
-;;; org-roam-buffer.el ends here

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: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,78 +34,7 @@
 ;;;; Library Requires
 
 ;;; Obsolete aliases (remove after next major release)
-;;;; Functions
+;;; Obsolete functions
-(define-obsolete-function-alias 'org-roam--capture-get-point 'org-roam-capture--get-point
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-build-cache 'org-roam-db-build-cache
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-sql         'org-roam-db-query
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--db-clear   'org-roam-db--clear
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-show-graph  'org-roam-graph-show
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--maybe-update-buffer
-  'org-roam-buffer--update-maybe "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--current-visibility
-  'org-roam-buffer--visibility "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-update         'org-roam-buffer-update
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-width     'org-roam-buffer--set-width
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-height    'org-roam-buffer--set-height
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam--set-up-buffer 'org-roam-buffer--get-create
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-today 'org-roam-dailies-today
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-tomorrow 'org-roam-dailies-tomorrow
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-yesterday 'org-roam-dailies-yesterday
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-date 'org-roam-dailies-date
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-graph-show  'org-roam-graph
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-graph-build 'org-roam-graph
-  "org-roam 1.0.0")
-(define-obsolete-function-alias 'org-roam-find-index 'org-roam-jump-to-index
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam--pluralize 'org-roam-buffer--pluralize
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam--capture 'org-roam-capture--capture
-  "org-roam 1.1.0")
-(define-obsolete-function-alias 'org-roam-db--clear 'org-roam-db-clear
-  "org-roam 1.2.0")
-(define-obsolete-function-alias 'org-roam-dailies-today 'org-roam-dailies-find-today
-  "org-roam 1.2.2")
-(define-obsolete-function-alias 'org-roam-dailies-yesterday 'org-roam-dailies-find-yesterday
-  "org-roam 1.2.2")
-(define-obsolete-function-alias 'org-roam-dailies-tomorrow 'org-roam-dailies-find-tomorrow
-  "org-roam 1.2.2")
-(define-obsolete-function-alias 'org-roam-dailies-date 'org-roam-dailies-find-date
-  "org-roam 1.2.2")
-
-;;;; Variables
-(define-obsolete-variable-alias 'org-roam-graphviz-extra-options
-  'org-roam-graph-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-grapher-extra-options
-  'org-roam-graph-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-graph-node-shape
-  'org-roam-graph-node-extra-config "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam--db-connection
-  'org-roam-db--connection "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam--current-buffer
-  'org-roam-buffer--current "org-roam 1.0.0")
-(define-obsolete-variable-alias 'org-roam-date-title-format
-  '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")
-(define-obsolete-variable-alias 'org-roam-update-db-idle-seconds
-  'org-roam-db-update-idle-seconds "org-roam 1.2.2")
-
-(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

@@ -5,9 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
-
 ;; This file is NOT part of GNU Emacs.
 
 ;; This program is free software; you can redistribute it and/or modify
@@ -27,90 +26,81 @@
 
 ;;; Commentary:
 ;;
-;; This library provides completion for org-roam.
+;; This library provides completion-at-point functions for Org-roam.
+;;
+;; The two main functions provided to capf are:
+;;
+;;    `org-roam-complete-link-at-point' provides completions to nodes
+;;    within link brackets
+;;
+;;    `org-roam-complete-everywhere' provides completions for nodes everywhere,
+;;    matching the symbol at point
+;;
 ;;; Code:
-;;;; Library Requires
 (require 'cl-lib)
-(require 's)
+(require 'org-element)
 
-(defvar helm-pattern)
+(declare-function org-roam--get-titles "org-roam")
-(declare-function helm "ext:helm")
-(declare-function helm-make-source "ext:helm-source" (name class &rest args) t)
 
-(defcustom org-roam-completion-system 'default
+(defcustom org-roam-completion-everywhere nil
-  "The completion system to be used by `org-roam'."
+  "When non-nil, provide link completion matching outside of Org links."
-  :type '(radio
-          (const :tag "Default" default)
-          (const :tag "Ido" ido)
-          (const :tag "Ivy" ivy)
-          (const :tag "Helm" helm)
-          (function :tag "Custom function"))
-  :group 'org-roam)
-
-(defcustom org-roam-completion-ignore-case t
-  "Whether to ignore case in Org-roam `completion-at-point' completions."
   :group 'org-roam
   :type 'boolean)
 
-(defun org-roam-completion--helm-candidate-transformer (candidates _source)
+(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
-  "Transforms CANDIDATES for Helm-based completing read.
+                                            #'org-roam-complete-everywhere)
-SOURCE is not used."
+  "List of functions to be used with `completion-at-point' for Org-roam.")
-  (let ((prefix (propertize "[?] "
-                            'face 'helm-ff-prefix)))
-    (cons (propertize helm-pattern
-                      'display (concat prefix helm-pattern))
-          candidates)))
 
-(cl-defun org-roam-completion--completing-read (prompt choices &key
+(defconst org-roam-bracket-completion-re
-                                                       require-match initial-input
+  "\\[\\[\\(\\(?:roam:\\)?\\)\\([^z-a]*\\)]]"
-                                                       action)
+  "Regex for completion within link brackets.
-  "Present a PROMPT with CHOICES and optional INITIAL-INPUT.
+We use this as a substitute for `org-link-bracket-re', because
-If REQUIRE-MATCH is t, the user must select one of the CHOICES.
+`org-link-bracket-re' requires content within the brackets for a match.")
-Return user choice."
+
-  (let (res)
+(defun org-roam-complete-everywhere ()
-    (setq res
+  "Provides completions for links for any word at point.
-          (cond
+This is a `completion-at-point' function, and is active when
-           ((eq org-roam-completion-system 'ido)
+`org-roam-completion-everywhere' is non-nil."
-            (let ((candidates (mapcar #'car choices)))
+  (when (and org-roam-completion-everywhere
-              (ido-completing-read prompt candidates nil require-match initial-input)))
+             (thing-at-point 'word)
-           ((eq org-roam-completion-system 'default)
+             (not (save-match-data (org-in-regexp org-link-any-re))))
-            (completing-read prompt choices nil require-match initial-input))
+    (let ((bounds (bounds-of-thing-at-point 'word)))
-           ((eq org-roam-completion-system 'ivy)
+      (list (car bounds) (cdr bounds)
-            (if (fboundp 'ivy-read)
+            (completion-table-dynamic
-                (ivy-read prompt choices
+             (lambda (_)
-                          :initial-input initial-input
+               (funcall #'org-roam--get-titles)))
-                          :preselect initial-input
+            :exit-function
-                          :require-match require-match
+            (lambda (str _status)
-                          :action (prog1 action
+              (delete-char (- (length str)))
-                                    (setq action nil))
+              (insert "[[roam:" str "]]"))))))
-                          :caller 'org-roam--completing-read)
+
-              (user-error "Please install ivy from \
+(defun org-roam-complete-link-at-point ()
-https://github.com/abo-abo/swiper")))
+  "Do appropriate completion for the link at point."
-           ((eq org-roam-completion-system 'helm)
+  (let (roam-p start end)
-            (unless (and (fboundp 'helm)
+    (when (org-in-regexp org-roam-bracket-completion-re 1)
-                         (fboundp 'helm-make-source))
+      (setq roam-p (not (string-blank-p (match-string 1)))
-              (user-error "Please install helm from \
+            start (match-beginning 2)
-https://github.com/emacs-helm/helm"))
+            end (match-end 2))
-            (let ((source (helm-make-source prompt 'helm-source-sync
+      (list start end
-                            :candidates (mapcar #'car choices)
+            (completion-table-dynamic
-                            :filtered-candidate-transformer
+             (lambda (_)
-                            (and (not require-match)
+               (funcall #'org-roam--get-titles)))
-                                 #'org-roam-completion--helm-candidate-transformer)))
+            :exit-function
-                  (buf (concat "*org-roam "
+            (lambda (str &rest _)
-                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
+              (delete-char (- 0 (length str)))
-                               "*")))
+              (insert (concat (unless roam-p "roam:")
-              (or (helm :sources source
+                              str))
-                        :action (if action
+              (forward-char 2))))))
-                                    (prog1 action
+
-                                      (setq action nil))
+(defun org-roam-complete-at-point ()
-                                  #'identity)
+  "."
-                        :prompt prompt
+  (run-hook-with-args-until-success 'org-roam-completion-functions))
-                        :input initial-input
+
-                        :buffer buf)
+(defun org-roam--register-completion-functions ()
-                  (keyboard-quit))))))
+  "."
-    (if action
+  (add-hook 'completion-at-point-functions #'org-roam-complete-at-point nil t))
-        (funcall action res)
+
-      res)))
+(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)
 
 (provide 'org-roam-completion)
 

org-roam-dailies.el

@@ -4,11 +4,11 @@
 ;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; 	Leo Vivier <leo.vivier+dev@gmail.com>
+;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -36,20 +36,23 @@
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
-(require 'org-roam-macs)
 (require 'f)
 
 ;;;; Declarations
-(defvar org-roam-mode)
 (defvar org-roam-directory)
 (defvar org-roam-file-extensions)
-(declare-function org-roam--org-file-p        "org-roam")
+(declare-function org-roam-file-p        "org-roam")
-(declare-function org-roam--find-file         "org-roam")
+
-(declare-function org-roam-mode               "org-roam")
+;;;; Faces
+(defface org-roam-dailies-calendar-note
+  '((t :inherit (org-link) :underline nil))
+  "Face for dates with a daily-note in the calendar."
+  :group 'org-roam-faces)
 
 ;;;; Customizable variables
 (defcustom org-roam-dailies-directory "daily/"
-  "Path to daily-notes."
+  "Path to daily-notes.
+This path is relative to `org-roam-directory'."
   :group 'org-roam
   :type 'string)
 
@@ -59,120 +62,117 @@
   :type 'hook)
 
 (defcustom org-roam-dailies-capture-templates
-  `(("d" "default" entry (function org-roam-capture--get-point)
+  `(("d" "default" entry
      "* %?"
-     :file-name ,(concat org-roam-dailies-directory "%<%Y-%m-%d>")
+     :if-new (file+head "%<%Y-%m-%d>.org"
-     :head "#+title: %<%Y-%m-%d>\n"))
+                        "#+title: %<%Y-%m-%d>\n")))
-  "Capture templates for daily-notes in Org-roam."
+  "Capture templates for daily-notes in Org-roam.
+See `org-roam-capture-templates' for the template documentation."
   :group 'org-roam
-  ;; Adapted from `org-capture-templates'
+  :type '(repeat
-  :type
+          (choice (list :tag "Multikey description"
-  `(repeat
+                        (string :tag "Keys       ")
-    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                        (string :tag "Description"))
-                    "%?"
+                  (list :tag "Template entry"
-                    :file-name ,(concat org-roam-dailies-directory
+                        (string :tag "Keys           ")
-					"%<%Y-%m-%d>")
+                        (string :tag "Description    ")
-                    :head "#+title: %<%Y-%m-%d>\n"
+                        (choice :tag "Capture Type   " :value entry
-                    :unnarrowed t)
+                                (const :tag "Org entry" entry)
-      (list :tag "Multikey description"
+                                (const :tag "Plain list item" item)
-        (string :tag "Keys       ")
+                                (const :tag "Checkbox item" checkitem)
-        (string :tag "Description"))
+                                (const :tag "Plain text" plain)
-      (list :tag "Template entry"
+                                (const :tag "Table line" table-line))
-        (string :tag "Keys              ")
+                        (choice :tag "Template       "
-        (string :tag "Description       ")
+                                (string)
-        (choice :tag "Type              "
+                                (list :tag "File"
-         (const :tag "Plain" plain)
+                                      (const :format "" file)
-         (const :tag "Entry (for creating headlines)" entry))
+                                      (file :tag "Template file"))
-        (const :format "" #'org-roam-capture--get-point)
+                                (list :tag "Function"
-        (choice :tag "Template          "
+                                      (const :format "" function)
-          (string :tag "String"
+                                      (function :tag "Template function")))
-                  :format "String:\n            \
+                        (plist :inline t
-Template string   :\n%v")
+                               ;; Give the most common options as checkboxes
-          (list :tag "File"
+                               :options (((const :format "%v " :if-new)
-            (const :format "" file)
+                                          (choice :tag "Node location"
-            (file :tag "Template file     "))
+                                                  (list :tag "File"
-          (list :tag "Function"
+                                                        (const :format "" file)
-            (const :format "" function)
+                                                        (string :tag "  File"))
-            (function :tag "Template function ")))
+                                                  (list :tag "File & Head Content"
-        (const :format "File name format  :" :file-name)
+                                                        (const :format "" file+head)
-        (string :format " %v" :value ,(concat org-roam-dailies-directory
+                                                        (string :tag "  File")
-					      "%<%Y-%m-%d>"))
+                                                        (string :tag "  Head Content"))
-        (const :format "Header format     :" :head)
+                                                  (list :tag "File & Outline path"
-        (string :format " %v" :value "#+title: ${title}\n")
+                                                        (const :format "" file+olp)
-        (plist :inline t
+                                                        (string :tag "  File")
-               :tag "Options"
+                                                        (list :tag "Outline path"
-          ;; Give the most common options as checkboxes
+                                                              (repeat (string :tag "Headline"))))
-               :options
+                                                  (list :tag "File & Head Content & Outline path"
-               (((const :tag "Outline path" :olp)
+                                                        (const :format "" file+head+olp)
-                 (repeat :tag "Headings"
+                                                        (string :tag "  File")
-                   (string :tag "Heading")))
+                                                        (string :tag "  Head Content")
-                ((const :format "%v " :unnarrowed) (const t))
+                                                        (list :tag "Outline path"
-                ((const :format "%v " :prepend) (const t))
+                                                              (repeat (string :tag "Headline"))))))
-                ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :prepend) (const t))
-                ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
-                ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :jump-to-captured) (const t))
-                ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines) (const 1))
-                ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
-                ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
-                ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-in) (const t))
-                ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
-                ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
-                ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :time-prompt) (const t))
-                ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :tree-type) (const week))
-                ((const :format "%v " :kill-buffer) (const t))))))))
+                                         ((const :format "%v " :unnarrowed) (const t))
-
+                                         ((const :format "%v " :table-line-pos) (string))
-;;;; Utilities
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
-(defun org-roam-dailies-directory--get-absolute-path ()
-  "Get absolute path to `org-roam-dailies-directory'."
-  (expand-file-name org-roam-dailies-directory org-roam-directory))
 
+;;;###autoload
 (defun org-roam-dailies-find-directory ()
   "Find and open `org-roam-dailies-directory'."
   (interactive)
-  (org-roam--find-file (org-roam-dailies-directory--get-absolute-path)))
+  (find-file (expand-file-name org-roam-dailies-directory org-roam-directory)))
 
 (defun org-roam-dailies--daily-note-p (&optional file)
   "Return t if FILE is an Org-roam daily-note, nil otherwise.
-
 If FILE is not specified, use the current buffer's file-path."
-  (when-let ((path (or file
+  (when-let ((path (expand-file-name
-                       (-> (buffer-base-buffer)
+                    (or file
-                           (buffer-file-name))))
+                        (buffer-file-name (buffer-base-buffer)))))
-             (directory (org-roam-dailies-directory--get-absolute-path)))
+             (directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
     (setq path (expand-file-name path))
     (save-match-data
       (and
-       (org-roam--org-file-p path)
+       (org-roam-file-p path)
        (f-descendant-of-p path directory)))))
 
 (defun org-roam-dailies--capture (time &optional goto)
   "Capture an entry in a daily-note for TIME, creating it if necessary.
-
 When GOTO is non-nil, go the note without creating an entry."
-  (unless org-roam-mode (org-roam-mode))
+  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory)))
-  (let ((org-roam-capture-templates (--> org-roam-dailies-capture-templates
+    (org-roam-capture- :goto (when goto '(4))
-                                         (if goto (list (car it)) it)))
+                       :node (org-roam-node-create)
-        (org-roam-capture--info (list (cons 'time time)))
+                       :templates org-roam-dailies-capture-templates
-        (org-roam-capture--context 'dailies))
+                       :props (list :override-default-time time)))
-    (org-roam-capture--capture (when goto '(4)))))
+  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))
 
 ;;;; Commands
 ;;; Today
+;;;###autoload
 (defun org-roam-dailies-capture-today (&optional goto)
   "Create an entry in the daily-note for today.
-
 When GOTO is non-nil, go the note without creating an entry."
   (interactive "P")
-  (org-roam-dailies--capture (current-time) goto)
+  (org-roam-dailies--capture (current-time) goto))
-  (when goto
-    (run-hooks 'org-roam-dailies-find-file-hook)))
 
-(defun org-roam-dailies-find-today ()
+;;;###autoload
+(defun org-roam-dailies-goto-today ()
   "Find the daily-note for today, creating it if necessary."
   (interactive)
   (org-roam-dailies-capture-today t))
 
 ;;; Tomorrow
+;;;###autoload
 (defun org-roam-dailies-capture-tomorrow (n &optional goto)
   "Create an entry in the daily-note for tomorrow.
 
@@ -183,7 +183,8 @@ creating an entry."
   (interactive "p")
   (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
 
-(defun org-roam-dailies-find-tomorrow (n)
+;;;###autoload
+(defun org-roam-dailies-goto-tomorrow (n)
   "Find the daily-note for tomorrow, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
@@ -192,6 +193,7 @@ future."
   (org-roam-dailies-capture-tomorrow n t))
 
 ;;; Yesterday
+;;;###autoload
 (defun org-roam-dailies-capture-yesterday (n &optional goto)
   "Create an entry in the daily-note for yesteday.
 
@@ -201,7 +203,8 @@ When GOTO is non-nil, go the note without creating an entry."
   (interactive "p")
   (org-roam-dailies-capture-tomorrow (- n) goto))
 
-(defun org-roam-dailies-find-yesterday (n)
+;;;###autoload
+(defun org-roam-dailies-goto-yesterday (n)
   "Find the daily-note for yesterday, creating it if necessary.
 
 With numeric argument N, use the daily-note N days in the
@@ -210,68 +213,46 @@ future."
   (org-roam-dailies-capture-tomorrow (- n) t))
 
 ;;; Calendar
-(defvar org-roam-dailies-calendar-hook (list 'org-roam-dailies-calendar-mark-entries)
-  "Hooks to run when showing the `org-roam-dailies-calendar'.")
-
-(defun org-roam-dailies-calendar--install-hook ()
-  "Install Org-roam-dailies hooks to calendar."
-  (add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
-  (add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
-
-(defun org-roam-dailies-calendar--run-hook ()
-  "Run Org-roam-dailies hooks to calendar."
-  (run-hooks 'org-roam-dailies-calendar-hook)
-  (remove-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar--run-hook)
-  (remove-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar--run-hook))
-
 (defun org-roam-dailies-calendar--file-to-date (&optional file)
   "Convert FILE to date.
-
 Return (MONTH DAY YEAR)."
   (let ((file (or file
-                  (-> (buffer-base-buffer)
+                  (buffer-base-buffer (buffer-file-name)))))
-                      (buffer-file-name)))))
     (cl-destructuring-bind (_ _ _ d m y _ _ _)
-        (-> file
+        (org-parse-time-string
-            (file-name-nondirectory)
+         (file-name-sans-extension
-            (file-name-sans-extension)
+          (file-name-nondirectory file)))
-            (org-parse-time-string))
       (list m d y))))
 
 (defun org-roam-dailies-calendar--date-to-time (date)
-  "Convert DATE as returned from the calendar (MONTH DAY YEAR) to a time."
+  "Convert DATE as returned from then calendar (MONTH DAY YEAR) to a time."
   (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
 
 (defun org-roam-dailies-calendar-mark-entries ()
   "Mark days in the calendar for which a daily-note is present."
-  (when (file-exists-p (org-roam-dailies-directory--get-absolute-path))
+  (when (file-exists-p (expand-file-name org-roam-dailies-directory org-roam-directory))
     (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
                           (org-roam-dailies--list-files)))
       (when (calendar-date-is-visible-p date)
         (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
 
 ;;; Date
+;;;###autoload
 (defun org-roam-dailies-capture-date (&optional goto prefer-future)
   "Create an entry in the daily-note for a date using the calendar.
-
 Prefer past dates, unless PREFER-FUTURE is non-nil.
-
 With a `C-u' prefix or when GOTO is non-nil, go the note without
 creating an entry."
   (interactive "P")
-  (org-roam-dailies-calendar--install-hook)
+  (let ((time (let ((org-read-date-prefer-future prefer-future))
-  (let* ((time-str (let ((org-read-date-prefer-future prefer-future))
+                (org-read-date t t nil (if goto
-                     (org-read-date nil nil nil (if goto
+                                           "Find daily-note: "
-                                                    "Find daily-note: "
+                                         "Capture to daily-note: ")))))
-                                                  "Capture to daily-note: "))))
+    (org-roam-dailies--capture time goto)))
-         (time (org-read-date nil t time-str)))
-    (org-roam-dailies--capture time goto)
-    (when goto
-      (run-hooks 'org-roam-dailies-find-file-hook))))
 
-(defun org-roam-dailies-find-date (&optional prefer-future)
+;;;###autoload
+(defun org-roam-dailies-goto-date (&optional prefer-future)
   "Find the daily-note for a date using the calendar, creating it if necessary.
-
 Prefer past dates, unless PREFER-FUTURE is non-nil."
   (interactive)
   (org-roam-dailies-capture-date t prefer-future))
@@ -280,8 +261,8 @@ Prefer past dates, unless PREFER-FUTURE is non-nil."
 (defun org-roam-dailies--list-files (&rest extra-files)
   "List all files in `org-roam-dailies-directory'.
 EXTRA-FILES can be used to append extra files to the list."
-  (let ((dir (org-roam-dailies-directory--get-absolute-path))
+  (let ((dir (expand-file-name org-roam-dailies-directory org-roam-directory))
-	(regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
     (append (--remove (let ((file (file-name-nondirectory it)))
                         (when (or (auto-save-file-name-p file)
                                   (backup-file-name-p file)
@@ -290,7 +271,7 @@ EXTRA-FILES can be used to append extra files to the list."
                       (directory-files-recursively dir regexp))
             extra-files)))
 
-(defun org-roam-dailies-find-next-note (&optional n)
+(defun org-roam-dailies-goto-next-note (&optional n)
   "Find next daily-note.
 
 With numeric argument N, find note N days in the future. If N is
@@ -305,27 +286,30 @@ negative, find note N days in the past."
                             (string= (buffer-file-name (buffer-base-buffer)) candidate))
                           dailies))
          note)
-      (unless position
+    (unless position
-        (user-error "Can't find current note file - have you saved it yet?"))
+      (user-error "Can't find current note file - have you saved it yet?"))
-      (pcase n
+    (pcase n
-        ((pred (natnump))
+      ((pred (natnump))
-         (when (eq position (- (length dailies) 1))
+       (when (eq position (- (length dailies) 1))
-           (user-error "Already at newest note")))
+         (user-error "Already at newest note")))
-        ((pred (integerp))
+      ((pred (integerp))
-         (when (eq position 0)
+       (when (eq position 0)
-             (user-error "Already at oldest note"))))
+         (user-error "Already at oldest note"))))
-      (setq note (nth (+ position n) dailies))
+    (setq note (nth (+ position n) dailies))
-      (find-file note)
+    (find-file note)
-      (run-hooks 'org-roam-dailies-find-file-hook)))
+    (run-hooks 'org-roam-dailies-find-file-hook)))
 
-(defun org-roam-dailies-find-previous-note (&optional n)
+(defun org-roam-dailies-goto-previous-note (&optional n)
   "Find previous daily-note.
 
 With numeric argument N, find note N days in the past. If N is
 negative, find note N days in the future."
   (interactive "p")
   (let ((n (if n (- n) -1)))
-    (org-roam-dailies-find-next-note n)))
+    (org-roam-dailies-goto-next-note n)))
+
+(add-hook 'calendar-today-visible-hook #'org-roam-dailies-calendar-mark-entries)
+(add-hook 'calendar-today-invisible-hook #'org-roam-dailies-calendar-mark-entries)
 
 ;;;; Bindings
 (defvar org-roam-dailies-map (make-sparse-keymap)
@@ -333,16 +317,35 @@ negative, find note N days in the future."
 
 (define-prefix-command 'org-roam-dailies-map)
 
-(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-find-today)
+(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-goto-today)
-(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-find-yesterday)
+(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-goto-yesterday)
-(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-find-tomorrow)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-goto-tomorrow)
 (define-key org-roam-dailies-map (kbd "n") #'org-roam-dailies-capture-today)
-(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-find-next-note)
+(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-goto-next-note)
-(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-find-previous-note)
+(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-goto-previous-note)
-(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-find-date)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-goto-date)
 (define-key org-roam-dailies-map (kbd "v") #'org-roam-dailies-capture-date)
 (define-key org-roam-dailies-map (kbd ".") #'org-roam-dailies-find-directory)
 
+(define-obsolete-function-alias
+  'org-roam-dailies-find-today
+  'org-roam-dailies-goto-today "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-yesterday
+  'org-roam-dailies-goto-yesterday "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-tomorrow
+  'org-roam-dailies-goto-tomorrow "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-next-note
+  'org-roam-dailies-goto-next-note "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-previous-note
+  'org-roam-dailies-goto-previous-note "org-roam 2.0")
+(define-obsolete-function-alias
+  'org-roam-dailies-find-date
+  'org-roam-dailies-goto-date "org-roam 2.0")
+
 (provide 'org-roam-dailies)
 
 ;;; org-roam-dailies.el ends here

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: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,37 +27,31 @@
 
 ;;; Commentary:
 ;;
-;; This library is provides the underlying database api to org-roam
+;; This library provides the underlying database api to org-roam.
 ;;
 ;;; Code:
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite3)
+(require 'emacsql-sqlite)
 (require 'seq)
 
 (eval-and-compile
   (require 'org-roam-macs)
   ;; For `org-with-wide-buffer'
   (require 'org-macs))
+(require 'org)
+(require 'ol)
+(require 'org-roam-utils)
 
+(defvar org-roam-find-file-hook)
 (defvar org-roam-directory)
-(defvar org-roam-enable-headline-linking)
 (defvar org-roam-verbose)
-(defvar org-roam-file-name)
-
 (defvar org-agenda-files)
 
-(declare-function org-roam--org-roam-file-p                "org-roam")
+(declare-function org-roam-id-at-point "org-roam")
-(declare-function org-roam--extract-titles                 "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
-(declare-function org-roam--extract-refs                   "org-roam")
+(declare-function org-roam-node-at-point "org-roam")
-(declare-function org-roam--extract-tags                   "org-roam")
-(declare-function org-roam--extract-ids                    "org-roam")
-(declare-function org-roam--extract-links                  "org-roam")
-(declare-function org-roam--list-all-files                 "org-roam")
-(declare-function org-roam--path-to-slug                   "org-roam")
-(declare-function org-roam--file-name-extension            "org-roam")
-(declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
 (defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
@@ -71,7 +65,7 @@ when used with multiple Org-roam instances."
 
 (defcustom org-roam-db-gc-threshold gc-cons-threshold
   "The value to temporarily set the `gc-cons-threshold' threshold to.
-During large, heavy operations like `org-roam-db-build-cache',
+During large, heavy operations like `org-roam-db-sync',
 many GC operations happen because of the large number of
 temporary structures generated (e.g. parsed ASTs). Temporarily
 increasing `gc-cons-threshold' will help reduce the number of GC
@@ -84,34 +78,20 @@ value like `most-positive-fixnum'."
   :type 'int
   :group 'org-roam)
 
-(defconst org-roam-db--version 10)
+(defcustom org-roam-db-node-include-function (lambda () t)
+  "A custom function to check if the headline at point is a node."
+  :type 'function
+  :group 'org-roam)
+
+(defconst org-roam-db-version 16)
+(defconst org-roam--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
-(defvar org-roam-db-dirty nil
-  "Whether the org-roam database is dirty and requires an update.
-Contains pairs of `org-roam-directory' and `org-roam-db-location'
-so that multi-directories are updated.")
-
-(defcustom org-roam-db-update-method 'idle-timer
-  "Method to update the Org-roam database.
-
-`immediate'
-  Update the database immediately upon file changes.
-
-`idle-timer'
-  Updates the database if dirty, if Emacs idles for
-  `org-roam-db-update-idle-seconds'."
-  :type '(choice (const :tag "idle-timer" idle-timer)
-		 (const :tag "immediate" immediate))
-  :group 'org-roam)
-
-(defcustom org-roam-db-update-idle-seconds 2
-  "Number of idle seconds before triggering an Org-roam database update."
-  :type 'integer
-  :group 'org-roam)
-
 ;;;; Core Functions
 
 (defun org-roam-db--get-connection ()
@@ -127,7 +107,7 @@ Performs a database upgrade when required."
                (emacsql-live-p (org-roam-db--get-connection)))
     (let ((init-db (not (file-exists-p org-roam-db-location))))
       (make-directory (file-name-directory org-roam-db-location) t)
-      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
+      (let ((conn (emacsql-sqlite org-roam-db-location)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
         (puthash (expand-file-name org-roam-directory)
                  conn
@@ -137,72 +117,103 @@ Performs a database upgrade when required."
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
                (version (org-roam-db--upgrade-maybe conn version)))
           (cond
-           ((> version org-roam-db--version)
+           ((> version org-roam-db-version)
             (emacsql-close conn)
             (user-error
              "The Org-roam database was created with a newer Org-roam version.  "
              "You need to update the Org-roam package"))
-           ((< version org-roam-db--version)
+           ((< version org-roam-db-version)
             (emacsql-close conn)
             (error "BUG: The Org-roam database scheme changed %s"
                    "and there is no upgrade path")))))))
   (org-roam-db--get-connection))
 
 ;;;; Entrypoint: (org-roam-db-query)
+(define-error 'emacsql-constraint "SQL constraint violation")
 (defun org-roam-db-query (sql &rest args)
   "Run SQL query on Org-roam database with ARGS.
 SQL can be either the emacsql vector representation, or a string."
-  (if  (stringp sql)
+  (apply #'emacsql (org-roam-db) sql args))
-      (emacsql (org-roam-db) (apply #'format sql args))
+
-    (apply #'emacsql (org-roam-db) sql args)))
+(defun org-roam-db-query! (handler sql &rest args)
+  "Run SQL query on Org-roam database with ARGS.
+SQL can be either the emacsql vector representation, or a string.
+The query is expected to be able to fail, in this situation, run HANDLER."
+  (condition-case err
+      (org-roam-db-query sql args)
+    (emacsql-constraint
+     (funcall handler err))))
 
 ;;;; Schemata
 (defconst org-roam-db--table-schemata
   '((files
      [(file :unique :primary-key)
       (hash :not-null)
-      (meta :not-null)])
+      (atime :not-null)
+      (mtime :not-null)])
 
-    (ids
+    (nodes
-     [(id :unique :primary-key)
+     ([(id :not-null :primary-key)
-      (file :not-null)
+       (file :not-null)
-      (level :not-null)])
+       (level :not-null)
+       (pos :not-null)
+       todo
+       priority
+       (scheduled text)
+       (deadline text)
+       title
+       properties
+       olp]
+      (:foreign-key [file] :references files [file] :on-delete :cascade)))
 
-    (links
+    (aliases
-     [(source :not-null)
+     ([(node-id :not-null)
-      (dest :not-null)
+       alias]
-      (type :not-null)
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
-      (properties :not-null)])
-
-    (tags
-     [(file :unique :primary-key)
-      (tags)])
-
-    (titles
-     [(file :not-null)
-      title])
 
     (refs
-     [(ref :unique :not-null)
+     ([(node-id :not-null)
-      (file :not-null)
+       (ref :not-null)
-      (type :not-null)])))
+       (type :not-null)]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (tags
+     ([(node-id :not-null)
+       tag]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (links
+     ([(pos :not-null)
+       (source :not-null)
+       (dest :not-null)
+       (type :not-null)
+       (properties :not-null)]
+      (:foreign-key [source] :references nodes [id] :on-delete :cascade)))))
+
+(defconst org-roam-db--table-indices
+  '((alias-node-id aliases [node-id])
+    (refs-node-id refs [node-id])
+    (tags-node-id tags [node-id])))
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
   (emacsql-with-transaction db
-    (pcase-dolist (`(,table . ,schema) org-roam-db--table-schemata)
+    (emacsql db "PRAGMA foreign_keys = ON")
+    (pcase-dolist (`(,table ,schema) org-roam-db--table-schemata)
       (emacsql db [:create-table $i1 $S2] table schema))
-    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
+    (pcase-dolist (`(,index-name ,table ,columns) org-roam-db--table-indices)
+      (emacsql db [:create-index $i1 :on $i2 $S3] index-name table columns))
+    (emacsql db (format "PRAGMA user_version = %s" org-roam-db-version))))
 
 (defun org-roam-db--upgrade-maybe (db version)
   "Upgrades the database schema for DB, if VERSION is old."
   (emacsql-with-transaction db
     'ignore
-    (if (< version org-roam-db--version)
+    (if (< version org-roam-db-version)
         (progn
           (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
-                                    version org-roam-db--version))
+                                    version org-roam-db-version))
-          (org-roam-db-build-cache t))))
+          (org-roam-db-sync t))))
   version)
 
 (defun org-roam-db--close (&optional db)
@@ -219,268 +230,216 @@ the current `org-roam-directory'."
   (dolist (conn (hash-table-values org-roam-db--connection))
     (org-roam-db--close conn)))
 
-;;;; Timer-based updating
-(defvar org-roam-db-file-update-timer nil
-  "Timer for updating the database when dirty.")
-
-(defun org-roam-db-mark-dirty ()
-  "Mark the Org-roam database as dirty."
-  (add-to-list 'org-roam-db-dirty (list org-roam-directory org-roam-db-location)
-               nil #'equal))
-
-(defun org-roam-db-update-cache-on-timer ()
-  "Update the cache if the database is dirty.
-This function is called on `org-roam-db-file-update-timer'."
-  (pcase-dolist (`(,org-roam-directory ,org-roam-db-location) org-roam-db-dirty)
-    (org-roam-db-build-cache))
-  (setq org-roam-db-dirty nil))
-
 ;;;; Database API
-;;;;; Initialization
-(defun org-roam-db--initialized-p ()
-  "Whether the Org-roam cache has been initialized."
-  (and (file-exists-p org-roam-db-location)
-       (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
-          0)))
-
-(defun org-roam-db--ensure-built ()
-  "Ensures that Org-roam cache is built."
-  (unless (org-roam-db--initialized-p)
-    (error "[Org-roam] your cache isn't built yet! Please run org-roam-db-build-cache")))
-
 ;;;;; Clearing
-(defun org-roam-db-clear ()
+(defun org-roam-db-clear-all ()
   "Clears all entries in the Org-roam cache."
   (interactive)
   (when (file-exists-p org-roam-db-location)
     (dolist (table (mapcar #'car org-roam-db--table-schemata))
       (org-roam-db-query `[:delete :from ,table]))))
 
-(defun org-roam-db--clear-file (&optional file)
+(defun org-roam-db-clear-file (&optional file)
   "Remove any related links to the FILE.
-This is equivalent to removing the node from the graph."
+This is equivalent to removing the node from the graph.
+If FILE is nil, clear the current buffer."
   (setq file (or file (buffer-file-name (buffer-base-buffer))))
-  (dolist (table (mapcar #'car org-roam-db--table-schemata))
+  (org-roam-db-query [:delete :from files
-    (org-roam-db-query `[:delete :from ,table
+                      :where (= file $s1)]
-                         :where (= ,(if (eq table 'links) 'source 'file) $s1)]
+                     file))
-                       file)))
 
-;;;;; Inserting
+;;;;; Updating tables
-(defun org-roam-db--insert-meta (&optional update-p)
+(defun org-roam-db-insert-file ()
-  "Update the metadata of the current buffer into the cache.
+  "Update the files table for the current buffer.
-If UPDATE-P is non-nil, first remove the meta for the file in the database."
+If UPDATE-P is non-nil, first remove the file in the database."
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
+  (let* ((file (buffer-file-name))
          (attr (file-attributes file))
          (atime (file-attribute-access-time attr))
          (mtime (file-attribute-modification-time attr))
          (hash (org-roam-db--file-hash)))
-    (when update-p
-      (org-roam-db-query [:delete :from files
-                          :where (= file $s1)]
-                         file))
     (org-roam-db-query
      [:insert :into files
       :values $v1]
-     (list (vector file hash (list :atime atime :mtime mtime))))))
+     (list (vector file hash atime mtime)))))
 
-(defun org-roam-db--insert-titles (&optional update-p)
+(defun org-roam-db-get-scheduled-time ()
-  "Update the titles of the current buffer into the cache.
+  "Return the scheduled time at point in ISO8601 format."
-If UPDATE-P is non-nil, first remove titles for the file in the database.
+  (when-let ((time (org-get-scheduled-time (point))))
-Returns the number of rows inserted."
+    (org-format-time-string "%FT%T%z" time)))
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
-         (titles (or (org-roam--extract-titles)
-                     (list (org-roam--path-to-slug file))))
-         (rows (mapcar (lambda (title)
-                         (vector file title)) titles)))
-    (when update-p
-      (org-roam-db-query [:delete :from titles
-                          :where (= file $s1)]
-                         file))
-    (org-roam-db-query
-        [:insert :into titles
-         :values $v1]
-        rows)
-    (length rows)))
 
-(defun org-roam-db--insert-refs (&optional update-p)
+(defun org-roam-db-get-deadline-time ()
-  "Update the refs of the current buffer into the cache.
+  "Return the deadline time at point in ISO8601 format."
-If UPDATE-P is non-nil, first remove the ref for the file in the database."
+  (when-let ((time (org-get-deadline-time (point))))
-  (let ((file (or org-roam-file-name (buffer-file-name)))
+    (org-format-time-string "%FT%T%z" time)))
-        (count 0))
-    (when update-p
-      (org-roam-db-query [:delete :from refs
-                          :where (= file $s1)]
-                         file))
-    (when-let ((refs (org-roam--extract-refs)))
-      (dolist (ref refs)
-        (let ((key (cdr ref))
-              (type (car ref)))
-          (condition-case nil
-              (progn
-                (org-roam-db-query
-                 [:insert :into refs :values $v1]
-                 (list (vector key file type)))
-                (cl-incf count))
-            (error
-             (lwarn '(org-roam) :error
-                    (format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
-                            key
-                            file
-                            (caar (org-roam-db-query
-                                   [:select file :from refs
-                                    :where (= ref $v1)]
-                                   (vector key))))))))))
-    count))
 
-(defun org-roam-db--insert-links (&optional update-p)
+(defun org-roam-db-node-p ()
-  "Update the file links of the current buffer in the cache.
+  "Return t if headline at point is a node, else return nil."
-If UPDATE-P is non-nil, first remove the links for the file in the database.
+  (and (org-id-get)
-Return the number of rows inserted."
+       (not (cdr (assoc "ROAM_EXCLUDE" (org-entry-properties))))
-  (let ((file (or org-roam-file-name (buffer-file-name))))
+       (funcall org-roam-db-node-include-function)))
-    (when update-p
+
-      (org-roam-db-query [:delete :from links
+(defun org-roam-db-map-nodes (fns)
-                          :where (= source $s1)]
+  "Run FNS over all nodes in the current buffer."
-                         file))
+  (org-with-point-at 1
-    (if-let ((links (org-roam--extract-links)))
+    (org-map-entries
-        (progn
+     (lambda ()
-          (org-roam-db-query
+       (when (org-roam-db-node-p)
-           [:insert :into links
+         (dolist (fn fns)
+           (funcall fn)))))))
+
+(defun org-roam-db-map-links (fns)
+  "Run FNS over all links in the current buffer."
+  (org-with-point-at 1
+    (org-element-map (org-element-parse-buffer) 'link
+      (lambda (link)
+        (dolist (fn fns)
+          (funcall fn link))))))
+
+(defun org-roam-db-insert-file-node ()
+  "Insert the file-level node into the Org-roam cache."
+  (org-with-point-at 1
+    (when (and (= (org-outline-level) 0)
+               (org-roam-db-node-p))
+      (when-let ((id (org-id-get)))
+        (let* ((file (buffer-file-name (buffer-base-buffer)))
+               (title (org-link-display-format
+                       (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
+                                        #'string-equal))
+                           (file-relative-name file org-roam-directory))))
+               (pos (point))
+               (todo nil)
+               (priority nil)
+               (scheduled nil)
+               (deadline nil)
+               (level 0)
+               (aliases (org-entry-get (point) "ROAM_ALIASES"))
+               (tags org-file-tags)
+               (refs (org-entry-get (point) "ROAM_REFS"))
+               (properties (org-entry-properties))
+               (olp (org-get-outline-path)))
+          (org-roam-db-query!
+           (lambda (err)
+             (lwarn 'org-roam :warning "%s for %s (%s) in %s"
+                    (error-message-string err)
+                    title id file))
+           [:insert :into nodes
             :values $v1]
-           links)
+           (vector id file level pos todo priority
-          (length links))
+                   scheduled deadline title properties olp))
-      0)))
+          (when tags
-
-(defun org-roam-db--insert-ids (&optional update-p)
-  "Update the ids of the current buffer into the cache.
-If UPDATE-P is non-nil, first remove ids for the file in the database.
-Returns the number of rows inserted."
-  (let ((file (or org-roam-file-name (buffer-file-name))))
-    (when update-p
-      (org-roam-db-query [:delete :from ids
-                          :where (= file $s1)]
-                         file))
-    (if-let ((ids (org-roam--extract-ids file)))
-      (condition-case nil
-          (progn
             (org-roam-db-query
-             [:insert :into ids
+             [:insert :into tags
               :values $v1]
-             ids)
+             (mapcar (lambda (tag)
-            (length ids))
+                       (vector id (substring-no-properties tag)))
-        (error
+                     tags)))
-         (lwarn '(org-roam) :error
+          (when aliases
-                (format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
+            (org-roam-db-query
-                        (aref (car ids) 1)
+             [:insert :into aliases
-                        (string-join (mapcar (lambda (hl)
+              :values $v1]
-                                               (aref hl 0)) ids) "\n")))
+             (mapcar (lambda (alias)
-         0))
+                       (vector id alias))
-      0)))
+                     (split-string-and-unquote aliases))))
+          (when refs
+            (setq refs (split-string-and-unquote refs))
+            (let (rows)
+              (dolist (ref refs)
+                (if (string-match org-link-plain-re ref)
+                    (progn
+                      (push (vector id (match-string 2 ref)
+                                    (match-string 1 ref)) rows))
+                  (lwarn '(org-roam) :warning
+                         "%s:%s\tInvalid ref %s, skipping..."
+                         (buffer-file-name) (point) ref)))
+              (when rows
+                (org-roam-db-query
+                 [:insert :into refs
+                  :values $v1]
+                 rows)))))))))
 
-(defun org-roam-db--insert-tags (&optional update-p)
+(defun org-roam-db-insert-node-data ()
-  "Insert tags for the current buffer into the Org-roam cache.
+  "Insert node data for headline at point into the Org-roam cache."
-If UPDATE-P is non-nil, first remove tags for the file in the database.
+  (when-let ((id (org-id-get)))
-Return the number of rows inserted."
+    (let* ((file (buffer-file-name (buffer-base-buffer)))
-  (let* ((file (or org-roam-file-name (buffer-file-name)))
+           (heading-components (org-heading-components))
-         (tags (org-roam--extract-tags file)))
+           (pos (point))
-    (when update-p
+           (todo (nth 2 heading-components))
-      (org-roam-db-query [:delete :from tags
+           (priority (nth 3 heading-components))
-                          :where (= file $s1)]
+           (level (nth 1 heading-components))
-                         file))
+           (scheduled (org-roam-db-get-scheduled-time))
-    (if tags
+           (deadline (org-roam-db-get-deadline-time))
-        (progn (org-roam-db-query
+           (title (org-link-display-format (nth 4 heading-components)))
-                [:insert :into tags
+           (properties (org-entry-properties))
-                 :values $v1]
+           (olp (org-get-outline-path)))
-                (list (vector file tags)))
+      (org-roam-db-query!
-               1)
+       (lambda (err)
-      0)))
+         (lwarn 'org-roam :warning "%s for %s (%s) in %s"
+                (error-message-string err)
+                title id file))
+       [:insert :into nodes
+        :values $v1]
+       (vector id file level pos todo priority
+               scheduled deadline title properties olp)))))
+
+(defun org-roam-db-insert-aliases ()
+  "Insert aliases for node at point into Org-roam cache."
+  (when-let ((node-id (org-id-get))
+             (aliases (org-entry-get (point) "ROAM_ALIASES")))
+    (org-roam-db-query [:insert :into aliases
+                        :values $v1]
+                       (mapcar (lambda (alias)
+                                 (vector node-id alias))
+                               (split-string-and-unquote aliases)))))
+
+(defun org-roam-db-insert-tags ()
+  "Insert tags for node at point into Org-roam cache."
+  (when-let ((node-id (org-id-get))
+             (tags (org-get-tags)))
+    (org-roam-db-query [:insert :into tags
+                        :values $v1]
+                       (mapcar (lambda (tag)
+                                 (vector node-id (substring-no-properties tag))) tags))))
+
+(defun org-roam-db-insert-refs ()
+  "Insert refs for node at point into Org-roam cache."
+  (when-let* ((node-id (org-id-get))
+              (refs (org-entry-get (point) "ROAM_REFS"))
+              (refs (split-string-and-unquote refs)))
+    (let (rows)
+      (dolist (ref refs)
+        (save-match-data
+          (if (string-match org-link-plain-re ref)
+              (progn
+                (push (vector node-id (match-string 2 ref) (match-string 1 ref)) rows))
+            (lwarn '(org-roam) :warning
+                   "%s:%s\tInvalid ref %s, skipping..." (buffer-file-name) (point) ref))))
+      (org-roam-db-query [:insert :into refs
+                          :values $v1]
+                         rows))))
+
+(defun org-roam-db-insert-link (link)
+  "Insert link data for LINK at current point into the Org-roam cache."
+  (save-excursion
+    (goto-char (org-element-property :begin link))
+    (let ((type (org-element-property :type link))
+          (dest (org-element-property :path link))
+          (properties (list :outline (org-get-outline-path)))
+          (source (org-roam-id-at-point)))
+      (when source
+        (org-roam-db-query
+         [:insert :into links
+          :values $v1]
+         (vector (point) source dest type properties))))))
 
 ;;;;; Fetching
-(defun org-roam-db-has-file-p (file)
-  "Return t if FILE is in the database, nil otherwise."
-  (> (caar (org-roam-db-query [:select (funcall count) :from files
-                              :where (= file $s1)]
-                              file))
-     0))
-
 (defun org-roam-db--get-current-files ()
   "Return a hash-table of file to the hash of its file contents."
-  (let* ((current-files (org-roam-db-query [:select * :from files]))
+  (let ((current-files (org-roam-db-query [:select [file hash] :from files]))
-         (ht (make-hash-table :test #'equal)))
+        (ht (make-hash-table :test #'equal)))
     (dolist (row current-files)
       (puthash (car row) (cadr row) ht))
     ht))
 
-(defun org-roam-db--get-title (file)
-  "Return the main title of FILE from the cache."
-  (caar (org-roam-db-query [:select [title] :from titles
-                            :where (= file $s1)
-                            :limit 1]
-                           file)))
-
-(defun org-roam-db--get-tags ()
-  "Return all distinct tags from the cache."
-  (let ((rows (org-roam-db-query [:select :distinct [tags] :from tags]))
-        acc)
-    (dolist (row rows)
-      (dolist (tag (car row))
-        (unless (member tag acc)
-          (push tag acc))))
-    acc))
-
-(defun org-roam-db--connected-component (file)
-  "Return all files reachable from/connected to FILE, including the file itself.
-If the file does not have any connections, nil is returned."
-  (let* ((query "WITH RECURSIVE
-                   links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"dest\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"source\", \"dest\" FROM filelinks UNION
-                      SELECT \"dest\", \"source\" FROM filelinks UNION
-                      SELECT \"file\", \"source\" FROM citelinks UNION
-                      SELECT \"dest\", \"file\" FROM citelinks),
-                   connected_component(file) AS
-                     (SELECT link FROM links_of WHERE file = $s1
-                      UNION
-                      SELECT link FROM links_of JOIN connected_component USING(file))
-                   SELECT * FROM connected_component;")
-         (files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
-    files))
-
-(defun org-roam-db--links-with-max-distance (file max-distance)
-  "Return all files connected to FILE in at most MAX-DISTANCE steps.
-This includes the file itself. If the file does not have any
-connections, nil is returned."
-  (let* ((query "WITH RECURSIVE
-                   links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"dest\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"source\", \"dest\" FROM filelinks UNION
-                      SELECT \"dest\", \"source\" FROM filelinks UNION
-                      SELECT \"file\", \"source\" FROM citelinks UNION
-                      SELECT \"source\", \"file\" FROM citelinks),
-                   -- Links are traversed in a breadth-first search.  In order to calculate the
-                   -- distance of nodes and to avoid following cyclic links, the visited nodes
-                   -- are tracked in 'trace'.
-                   connected_component(file, trace) AS
-                     (VALUES($s1, json_array($s1))
-                      UNION
-                      SELECT lo.link, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.link) FROM
-                      connected_component AS cc JOIN links_of AS lo USING(file)
-                      WHERE (
-                        -- Avoid cycles by only visiting each file once.
-                        (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.link) == 0
-                        -- Note: BFS is cut off early here.
-                        AND json_array_length(cc.trace) < ($s2 + 1)))
-                   SELECT DISTINCT file, min(json_array_length(trace)) AS distance
-                   FROM connected_component GROUP BY file ORDER BY distance;")
-         ;; In principle the distance would be available in the second column.
-         (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
-    files))
-
 (defun org-roam-db--file-hash (&optional file-path)
   "Compute the hash of FILE-PATH, a file or current buffer."
   (if file-path
@@ -492,30 +451,9 @@ connections, nil is returned."
      (secure-hash 'sha1 (current-buffer)))))
 
 ;;;;; Updating
-(defun org-roam-db--update-file (&optional file-path)
+;;;###autoload
-  "Update Org-roam cache for FILE-PATH.
+(defun org-roam-db-sync (&optional force)
-If the file does not exist anymore, remove it from the cache.
+  "Synchronize the cache state with the current Org files on-disk.
-If the file exists, update the cache with information."
-  (setq file-path (or file-path
-                      (buffer-file-name (buffer-base-buffer))))
-  (if (not (file-exists-p file-path))
-      (org-roam-db--clear-file file-path)
-    ;; save the file before performing a database update
-    (when-let ((buf (find-buffer-visiting file-path)))
-      (with-current-buffer buf
-        (save-buffer)))
-    (org-roam--with-temp-buffer file-path
-      (emacsql-with-transaction (org-roam-db)
-        (org-roam-db--insert-meta 'update)
-        (org-roam-db--insert-tags 'update)
-        (org-roam-db--insert-titles 'update)
-        (org-roam-db--insert-refs 'update)
-        (when org-roam-enable-headline-linking
-          (org-roam-db--insert-ids 'update))
-        (org-roam-db--insert-links 'update)))))
-
-(defun org-roam-db-build-cache (&optional force)
-  "Build the cache for `org-roam-directory'.
 If FORCE, force a rebuild of the cache from scratch."
   (interactive "P")
   (when force (delete-file org-roam-db-location))
@@ -525,109 +463,61 @@ If FORCE, force a rebuild of the cache from scratch."
          (org-agenda-files nil)
          (org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         (count-plist nil)
-         (deleted-count 0)
          (modified-files nil))
     (dolist (file org-roam-files)
       (let ((contents-hash (org-roam-db--file-hash file)))
         (unless (string= (gethash file current-files)
-                       contents-hash)
+                         contents-hash)
-          (push (cons file contents-hash) modified-files)))
+          (push file modified-files)))
       (remhash file current-files))
-    (dolist (file (hash-table-keys current-files))
+    (emacsql-with-transaction (org-roam-db)
-        ;; These files are no longer around, remove from cache...
+      (if (fboundp 'dolist-with-progress-reporter)
-        (org-roam-db--clear-file file)
+          (dolist-with-progress-reporter (file (hash-table-keys current-files))
-        (setq deleted-count (1+ deleted-count)))
+              "Clearing removed files..."
-    (setq count-plist (org-roam-db--update-files modified-files))
+            (org-roam-db-clear-file file))
-    (org-roam-message "total: Δ%s, files-modified: Δ%s, ids: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
+        (dolist (file (hash-table-keys current-files))
-                      (- (length org-roam-files) (plist-get count-plist :error-count))
+          (org-roam-db-clear-file file)))
-                      (plist-get count-plist :modified-count)
+      (if (fboundp 'dolist-with-progress-reporter)
-                      (plist-get count-plist :id-count)
+          (dolist-with-progress-reporter (file modified-files)
-                      (plist-get count-plist :link-count)
+              "Processing modified files..."
-                      (plist-get count-plist :tag-count)
+            (org-roam-db-update-file file))
-                      (plist-get count-plist :title-count)
+        (dolist (file modified-files)
-                      (plist-get count-plist :ref-count)
+          (org-roam-db-update-file file))))))
-                      deleted-count)))
 
-(defun org-roam-db--get-file-hash-from-db (&optional file-path)
+(defun org-roam-db-update-file (&optional file-path)
-  "Get hash from Org-roam database for FILE-PATH."
-  (setq file-path (or file-path
-                      (buffer-file-name (buffer-base-buffer))))
-  (caar (org-roam-db-query [:select hash :from files
-                              :where (= file $s1)] file-path)))
-
-(defun org-roam-db-update-file (file-path)
   "Update Org-roam cache for FILE-PATH.
 If the file does not exist anymore, remove it from the cache.
 If the file exists, update the cache with information."
+  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
   (let ((content-hash (org-roam-db--file-hash file-path))
-        (db-hash  (org-roam-db--get-file-hash-from-db file-path)))
+        (db-hash (caar (org-roam-db-query [:select hash :from files
+                                           :where (= file $s1)] file-path))))
     (unless (string= content-hash db-hash)
-      (org-roam-db--update-files (list (cons file-path content-hash)))
+      (org-roam-with-file file-path nil
-      (org-roam-message "Updated: %s" file-path))))
+        (save-excursion
+          (org-set-regexps-and-options 'tags-only)
+          (org-roam-db-clear-file)
+          (org-roam-db-insert-file)
+          (org-roam-db-insert-file-node)
+          (org-roam-db-map-nodes
+           (list #'org-roam-db-insert-node-data
+                 #'org-roam-db-insert-aliases
+                 #'org-roam-db-insert-tags
+                 #'org-roam-db-insert-refs))
+          (org-roam-db-map-links
+           (list #'org-roam-db-insert-link)))))))
 
-(defun org-roam-db--update-files (modified-files)
+(defun org-roam-db--update-on-save-h ()
-  "Update Org-roam cache for a list of MODIFIED-FILES.
+  "."
-FILES is a list of (file . hash) pairs."
+  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
-  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
-         (org-agenda-files nil)
-         (error-count 0)
-         (id-count 0)
-         (link-count 0)
-         (tag-count 0)
-         (title-count 0)
-         (ref-count 0)
-         (modified-count 0))
-    (pcase-dolist (`(,file . _) modified-files)
-      (org-roam-db--clear-file file))
-    ;; Process all the files for IDs first
-    ;;
-    ;; We do this so that link extraction is cheaper: this eliminates the need
-    ;; to read the file to check if the ID really exists
-    (pcase-dolist (`(,file . ,contents-hash) modified-files)
-      (let* ((attr (file-attributes file))
-             (atime (file-attribute-access-time attr))
-             (mtime (file-attribute-modification-time attr)))
-        (condition-case nil
-            (org-roam--with-temp-buffer file
-              (org-roam-db-query
-               [:insert :into files
-                :values $v1]
-               (vector file contents-hash (list :atime atime :mtime mtime)))
-              (when org-roam-enable-headline-linking
-                (setq id-count (+ id-count (org-roam-db--insert-ids)))))
-          (file-error
-           (setq error-count (1+ error-count))
-           (org-roam-db--clear-file file)
-           (lwarn '(org-roam) :warning
-                  "Skipping unreadable file while building cache: %s" file)))))
 
-    ;; Process titles, tags, links and ref links of file
+(add-hook 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
-    (pcase-dolist (`(,file . _) modified-files)
-      (org-roam-message "Processed %s/%s modified files..." modified-count (length modified-files))
-      (condition-case nil
-          (org-roam--with-temp-buffer file
-            (setq modified-count (1+ modified-count))
-            (setq link-count (+ link-count (org-roam-db--insert-links)))
-            (setq tag-count (+ tag-count (org-roam-db--insert-tags)))
-            (setq title-count (+ title-count (org-roam-db--insert-titles)))
-            (setq ref-count (+ ref-count (org-roam-db--insert-refs))))
-        (file-error
-         (setq error-count (1+ error-count))
-         (org-roam-db--clear-file file)
-         (lwarn '(org-roam) :warning
-                "Skipping unreadable file while building cache: %s" file))))
-    (list :error-count error-count :modified-count modified-count :id-count id-count :title-count title-count :tag-count tag-count :link-count link-count :ref-count ref-count)))
 
-(defun org-roam-db-update ()
+;; Diagnostic Interactives
-  "Update the database."
+(defun org-roam-db-diagnose-node ()
-  (pcase org-roam-db-update-method
+  "Print information about node at point."
-    ('immediate
+  (interactive)
-     (org-roam-db-update-file (buffer-file-name (buffer-base-buffer))))
+  (prin1 (org-roam-node-at-point)))
-    ('idle-timer
-     (org-roam-db-mark-dirty))
-    (_
-     (user-error "Invalid `org-roam-db-update-method'"))))
 
 (provide 'org-roam-db)
 

org-roam-dev.el

@@ -1,46 +0,0 @@
-;;; org-roam-dev.el --- Org-roam development code -mode -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
-;; 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 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library provides code for org-roam developers.
-;; It is intended to be loaded before editing org-roam source files.
-;; It ensures consistent application of various developer settings.
-;;
-;;; Code:
-(require 'emacsql)
-
-;;;###autoload
-(define-minor-mode org-roam-dev-mode
-  "Minor mode for setting the dev environment of Org-roam."
-  :lighter " ORD"
-  (when org-roam-dev-mode
-    (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

@@ -1,318 +0,0 @@
-;;; org-roam-doctor.el --- Linter for Org-roam files -*- coding: utf-8; lexical-binding: t; -*-
-;;
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
-;; 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 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-
-;;; Commentary:
-;;
-;; This library provides `org-roam-doctor', a utility for diagnosing and fixing
-;; Org-roam files. Running `org-roam-doctor' launches a list of checks defined
-;; by `org-roam-doctor--checkers'. Every checker is an instance of
-;; `org-roam-doctor-checker'.
-;;
-;; Each checker is given the Org parse tree (AST), and is expected to return a
-;; list of errors. The checker can also provide "actions" for auto-fixing errors
-;; (see `org-roam-doctor--remove-link' for an example).
-;;
-;; The UX experience is inspired by both org-lint and checkdoc, and their code
-;; is heavily referenced.
-;;
-;;; Code:
-;; Library Requires
-(require 'cl-lib)
-(require 'org)
-(require 'org-element)
-(require '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-mode "org-roam")
-
-(defvar org-roam-verbose)
-(defvar org-roam-mode)
-
-(defcustom org-roam-doctor-inhibit-startup t
-  "Inhibit `org-mode' startup when processing files with `org-doctor'.
-When non-nil, images and LaTeX preview will not be generated,
-tables will not be aligned, and headlines will not respect
-startup visability. This significantly improves performance when
-processing multiple files"
-  :type 'boolean
-  :group 'org-roam)
-
-(cl-defstruct (org-roam-doctor-checker (:copier nil))
-  (name 'missing-checker-name)
-  (description "")
-  (actions nil))
-
-(defconst org-roam-doctor--checkers
-  (list
-   (make-org-roam-doctor-checker
-    :name 'org-roam-doctor-broken-links
-    :description "Fix broken links."
-    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
-               ("r" . ("Replace link" . org-roam-doctor--replace-link))
-               ("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
-                (split-string-and-unquote 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
-              (split-string-and-unquote 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.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'link
-      (lambda (l)
-        (when (equal "file" (org-element-property :type l))
-          (let ((file (org-element-property :path l)))
-            (or (file-exists-p file)
-                (file-remote-p file)
-                (push
-                 `(,(org-element-property :begin l)
-                   ,(format (if (org-element-lineage l '(link))
-                                "Link to non-existent image file \"%s\"\
- in link description"
-                              "Link to non-existent local file \"%s\"")
-                            file))
-                 reports))))))
-    reports))
-
-(defun org-roam-doctor--check (buffer checkers)
-  "Check BUFFER for errors.
-CHECKERS is the list of checkers used."
-  (with-current-buffer buffer
-    (save-excursion
-      (goto-char (point-min))
-      (let* ((ast (org-element-parse-buffer))
-             (errors (sort (cl-mapcan
-                            (lambda (c)
-                              (mapcar
-                               (lambda (report)
-                                 (list (set-marker (make-marker) (car report))
-                                       (nth 1 report) c))
-                               (save-excursion
-                                 (funcall
-                                  (org-roam-doctor-checker-name c)
-                                  ast))))
-                            checkers)
-                           #'car-less-than-car)))
-        (dolist (e errors)
-          (pcase-let ((`(,m ,msg ,checker) e))
-            (switch-to-buffer buffer)
-            (goto-char m)
-            (org-reveal)
-            (undo-boundary)
-            (org-roam-doctor--resolve msg checker)
-            (set-marker m nil)))
-        errors))))
-
-;;; Actions
-(defun org-roam-doctor--recursive-edit ()
-  "Launch into a recursive edit."
-  (message "When you're done editing press C-M-c to continue.")
-  (recursive-edit))
-
-(defun org-roam-doctor--skip ()
-  "Skip the current error."
-  (org-roam-message "Skipping..."))
-
-(defun org-roam-doctor--replace-link ()
-  "Replace the current link with a new link."
-  (save-match-data
-    (unless (org-in-regexp org-link-bracket-re 1)
-      (user-error "No link at point"))
-    (let ((orig (buffer-string))
-          (p (point)))
-      (condition-case nil
-          (save-excursion
-            (replace-match "")
-            (org-roam-insert))
-        (quit (progn
-                (replace-buffer-contents orig)
-                (goto-char p)))))))
-
-(defun org-roam-doctor--replace-link-keep-label ()
-  "Replace the current link with a new link, keeping the current link's label."
-  (save-match-data
-    (unless (org-in-regexp org-link-bracket-re 1)
-      (user-error "No link at point"))
-    (let ((orig (buffer-string))
-          (p (point)))
-      (condition-case nil
-          (save-excursion
-            (let ((label (if (match-end 2)
-                             (match-string-no-properties 2)
-                           (org-link-unescape (match-string-no-properties 1)))))
-              (replace-match "")
-              (org-roam-insert nil nil label)))
-        (quit (progn
-                (replace-buffer-contents orig)
-                (goto-char p)))))))
-
-(defun org-roam-doctor--remove-link ()
-  "Unlink the text at point."
-  (unless (org-in-regexp org-link-bracket-re 1)
-    (user-error "No link at point"))
-  (save-excursion
-    (let ((label (if (match-end 2)
-                     (match-string-no-properties 2)
-                   (org-link-unescape (match-string-no-properties 1)))))
-      (delete-region (match-beginning 0) (match-end 0))
-      (insert label))))
-
-(defun org-roam-doctor--resolve (msg checker)
-  "Resolve an error.
-MSG is the error that was found, which is displayed in a help buffer.
-CHECKER is a org-roam-doctor checker instance."
-  (let ((actions (org-roam-doctor-checker-actions checker))
-        c)
-    (push '("e" . ("Edit" . org-roam-doctor--recursive-edit)) actions)
-    (push '("s" . ("Skip" . org-roam-doctor--skip)) actions)
-    (with-output-to-temp-buffer "*Org-roam-doctor Help*"
-      (mapc #'princ
-            (list "Error message:\n   " msg "\n\n"))
-      (dolist (action actions)
-        (princ (format "[%s]: %s\n"
-                       (car action)
-                       (cadr action))))
-      (princ "\n\n"))
-    (shrink-window-if-larger-than-buffer
-     (get-buffer-window "*Org-roam-doctor Help*"))
-    (message "Press key for command:")
-    (unwind-protect
-        (progn
-          (cl-loop
-           do (setq c (char-to-string (read-char-exclusive)))
-           until (assoc c actions)
-           do (message "Please enter a valid key for command:"))
-          (funcall (cddr (assoc c actions)))
-          (redisplay))
-      (when (get-buffer-window "*Org-roam-doctor Help*")
-        (delete-window (get-buffer-window "*Org-roam-doctor Help*"))
-        (kill-buffer "*Org-roam-doctor Help*")))))
-
-;;;###autoload
-(defun org-roam-doctor (&optional checkall)
-  "Perform a check on the current buffer to ensure cleanliness.
-If CHECKALL, run the check for all Org-roam files."
-  (interactive "P")
-  (unless org-roam-mode (org-roam-mode))
-  (let ((files (if checkall
-                  (org-roam--list-all-files)
-                (unless (org-roam--org-roam-file-p)
-                  (user-error "Not in an org-roam file"))
-                `(,(buffer-file-name)))))
-    (org-roam-doctor-start files org-roam-doctor--checkers)))
-
-(defun org-roam-doctor-start (files checkers)
-  "Lint FILES using CHECKERS."
-  (save-window-excursion
-    (let ((existing-buffers (org-roam--get-roam-buffers))
-          (org-inhibit-startup org-roam-doctor-inhibit-startup))
-      (dolist (f files)
-        (let ((buf (find-file-noselect f)))
-          (org-roam-doctor--check buf checkers)
-          (unless (memq buf existing-buffers)
-            (with-current-buffer buf
-              (save-buffer))
-            (kill-buffer buf))))))
-  (org-roam-message "Linting completed."))
-
-(provide 'org-roam-doctor)
-
-;;; org-roam-doctor.el ends here

org-roam-faces.el

@@ -1,77 +0,0 @@
-;;; org-roam-faces.el --- Face definitions -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
-;; Package-Requires: ((emacs "26.1"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-
-;; This file contains the face definitions for Org-roam.
-
-;;; Code:
-
-(defgroup org-roam-faces nil
-  "Faces used by Org-roam."
-  :group 'org-roam
-  :group 'faces)
-
-;;; Definitions
-(defface org-roam-link
-  '((t :inherit org-link))
-  "Face for Org-roam links."
-  :group 'org-roam-faces)
-
-(defface org-roam-tag
-  '((t :weight bold))
-  "Face for Org-roam tags in minibuffer commands."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-current
-  '((t :inherit org-link))
-  "Face for Org-roam links pointing to the current buffer."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-invalid
-  '((t :inherit (error org-link)))
-  "Face for Org-roam links that are not valid.
-This face is used for links without a destination."
-  :group 'org-roam-faces)
-
-(defface org-roam-link-shielded
-  '((t :inherit (warning org-link)))
-  "Face for Org-roam links that are shielded.
-This face is used on the region target by `org-roam-insertion'
-during an `org-roam-capture'."
-  :group 'org-roam-faces)
-
-(defface org-roam-dailies-calendar-note
-  '((t :inherit (org-roam-link) :underline nil))
-  "Face for dates with a daily-note in the calendar."
-  :group 'org-roam-faces)
-
-;;; _
-
-(provide 'org-roam-faces)
-
-;;; org-roam-faces.el ends here

org-roam-graph.el

@@ -1,12 +1,12 @@
 ;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
 
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,17 +31,12 @@
 ;;
 ;;; Code:
 (require 'xml) ;xml-escape-string
-(require 's)   ;s-truncate, s-replace
 (eval-and-compile
   (require 'org-roam-macs))
 (require 'org-roam-db)
 
 ;;;; 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")
@@ -74,31 +69,34 @@ Example:
   :type '(alist)
   :group 'org-roam)
 
+(defcustom org-roam-graph-edge-extra-config nil
+  "Extra edge options passed to graphviz.
+Example:
+ '((\"dir\" . \"back\"))"
+  :type '(alist)
+  :group 'org-roam)
+
 (defcustom org-roam-graph-node-extra-config
-  '(("shape"      . "underline")
+  '(("id" . (("style"      . "bold,rounded,filled")
-    ("style"      . "rounded,filled")
+             ("fillcolor"  . "#EEEEEE")
-    ("fillcolor"  . "#EEEEEE")
+             ("color"      . "#C9C9C9")
-    ("color"      . "#C9C9C9")
+             ("fontcolor"  . "#111111")))
-    ("fontcolor"  . "#111111"))
+    ("http" . (("style"      . "rounded,filled")
-  "Extra options for graphviz nodes.
+               ("fillcolor"  . "#EEEEEE")
-Example:
+               ("color"      . "#C9C9C9")
- '((\"color\" . \"skyblue\"))"
+               ("fontcolor"  . "#0A97A6")))
+    ("https" . (("shape"      . "rounded,filled")
+                ("fillcolor"  . "#EEEEEE")
+                ("color"      . "#C9C9C9")
+                ("fontcolor"  . "#0A97A6"))))
+  "Extra options for graphviz nodes."
   :type '(alist)
   :group 'org-roam)
 
-(defcustom org-roam-graph-edge-extra-config
+(defcustom org-roam-graph-link-hidden-types
-  '(("color" . "#333333"))
+  '("file")
-  "Extra options for graphviz edges.
+  "What sort of links to hide from the Org-roam graph."
-Example:
+  :type '(repeat string)
- '((\"dir\" . \"back\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-edge-cites-extra-config '(("color" . "red"))
-  "Extra options for graphviz edges for citation links.
-Example:
- '((\"dir\" . \"back\"))"
-  :type '(alist)
   :group 'org-roam)
 
 (defcustom org-roam-graph-max-title-length 100
@@ -119,45 +117,6 @@ All other values including nil will have no effect."
           (const :tag "no" nil))
   :group 'org-roam)
 
-(defcustom org-roam-graph-exclude-matcher nil
-  "Matcher for excluding nodes from the generated graph.
-Any nodes and links for file paths matching this string is
-excluded from the graph.
-
-If value is a string, the string is the only matcher.
-
-If value is a list, all file paths matching any of the strings
-are excluded."
-  :type '(choice
-          (string :tag "Matcher")
-          (list :tag "Matchers"))
-  :group 'org-roam)
-
-;;;; Functions
-(defun org-roam-graph--expand-matcher (col &optional negate where)
-  "Return the exclusion regexp from `org-roam-graph-exclude-matcher'.
-COL is the symbol to be matched against.  if NEGATE, add :not to sql query.
-set WHERE to true if WHERE query already exists."
-  (let ((matchers (pcase org-roam-graph-exclude-matcher
-                    ('nil nil)
-                    ((pred stringp) `(,(concat "%" org-roam-graph-exclude-matcher "%")))
-                    ((pred listp) (mapcar (lambda (m)
-                                            (concat "%" m "%"))
-                                          org-roam-graph-exclude-matcher))
-                    (_ (error "Invalid org-roam-graph-exclude-matcher"))))
-        res)
-    (dolist (match matchers)
-      (if where
-          (push :and res)
-        (push :where res)
-        (setq where t))
-      (push col res)
-      (when negate
-        (push :not res))
-      (push :like res)
-      (push match res))
-    (nreverse res)))
-
 (defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
   "Return dot string of form KEY=VAL for OPTION cons.
 If WRAP-KEY is non-nil it wraps the KEY.
@@ -166,71 +125,104 @@ If WRAP-VAL is non-nil it wraps the VAL."
           "="
           wrap-val (cdr option) wrap-val))
 
-(defun org-roam-graph--dot (node-query)
+(defun org-roam-graph--connected-component (id distance)
-  "Build the graphviz dot string for NODE-QUERY.
+  "Return the edges for all nodes reachable from/connected to ID.
-The Org-roam database titles table is read, to obtain the list of titles.
+DISTANCE is the maximum distance away from the root node."
-The links table is then read to obtain all directed links, and formatted
+  (let* ((query
-into a digraph."
+          (if (= distance 0)
-  (org-roam-db--ensure-built)
+              "
-  (org-roam--with-temp-buffer nil
+WITH RECURSIVE
-    (let* ((nodes (org-roam-db-query node-query))
+  links_of(source, dest) AS
-           (edges-query
+  (SELECT source, dest FROM links UNION
-            `[:with selected :as [:select [file] :from ,node-query]
+   SELECT dest, source FROM links),
-              :select :distinct [dest source] :from links
+   connected_component(source) AS
-              :where (and (in dest selected) (in source selected))])
+  (SELECT dest FROM links_of WHERE source = $s1 UNION
-           (edges-cites-query
+   SELECT dest FROM links_of JOIN connected_component USING(source))
-            `[:with selected :as [:select [file] :from ,node-query]
+SELECT source, dest, type FROM links WHERE source IN connected_component OR dest IN connected_component;"
-              :select :distinct [file source]
+            "
-              :from links :inner :join refs :on (and (= links:dest refs:ref)
+WITH RECURSIVE
-                                                     (= links:type "cite")
+  links_of(source, dest) AS
-                                                     (= refs:type "cite"))
+  (SELECT source, dest FROM links UNION
-              :where (and (in file selected) (in source selected))])
+   SELECT dest, source FROM links),
-           (edges       (org-roam-db-query edges-query))
+  connected_component(source, trace) AS
-           (edges-cites (org-roam-db-query edges-cites-query)))
+  (VALUES ($s1 , json_array($s1)) UNION
+   SELECT lo.dest, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.dest) FROM
+   connected_component AS cc JOIN links_of AS lo USING(source)
+   WHERE (
+    -- Avoid cycles by only visiting each node once.
+    (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.dest) == 0
+    -- Note: BFS is cut off early here.
+    AND json_array_length(cc.trace) < $s2)),
+  nodes(source) as (SELECT DISTINCT source
+   FROM connected_component GROUP BY source ORDER BY min(json_array_length(trace)))
+SELECT source, dest, type FROM links WHERE source IN nodes OR dest IN nodes;")))
+    (org-roam-db-query query id distance)))
+
+(defun org-roam-graph--dot (&optional edges all-nodes)
+  "Build the graphviz given the EDGES of the graph.
+If ALL-NODES, include also nodes without edges."
+  (let ((org-roam-directory-temp org-roam-directory)
+        (nodes-table (org-roam--nodes-table))
+        (seen-nodes (list))
+        (edges (or edges (org-roam-db-query [:select :distinct [source dest type] :from links]))))
+    (with-temp-buffer
+      (setq-local org-roam-directory org-roam-directory-temp)
       (insert "digraph \"org-roam\" {\n")
       (dolist (option org-roam-graph-extra-config)
         (insert (org-roam-graph--dot-option option) ";\n"))
-      (dolist (attribute '("node" "edge"))
+      (insert (format " edge [%s];\n"
-        (insert (format " %s [%s];\n" attribute
+                      (mapconcat (lambda (var)
-                        (mapconcat (lambda (var)
+                                   (org-roam-graph--dot-option var nil "\""))
-                                     (org-roam-graph--dot-option var nil "\""))
+                                 org-roam-graph-edge-extra-config
-                                   (symbol-value
+                                 ",")))
-                                    (intern (concat "org-roam-graph-" attribute "-extra-config")))
+      (pcase-dolist (`(,source ,dest ,type) edges)
-                                   ","))))
+        (unless (member type org-roam-graph-link-hidden-types)
-      (dolist (node nodes)
+          (pcase-dolist (`(,node ,node-type) `((,source "id")
-        (let* ((file (xml-escape-string (car node)))
+                                               (,dest ,type)))
-               (title (or (cadr node)
+            (unless (member node seen-nodes)
-                          (org-roam--path-to-slug file)))
+              (insert (org-roam-graph--format-node
-               (shortened-title (pcase org-roam-graph-shorten-titles
+                       (or (gethash node nodes-table) node) node-type))
-                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
+              (push node seen-nodes)))
-                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+          (insert (format "  \"%s\" -> \"%s\";\n"
-                                  (_ title)))
+                          (xml-escape-string source)
-               (shortened-title (org-roam-string-quote shortened-title))
+                          (xml-escape-string dest)))))
-               (title (org-roam-string-quote title))
+      (when all-nodes
-               (node-properties
+        (maphash (lambda (id node)
-                `(("label"   . ,shortened-title)
+                   (unless (member id seen-nodes)
-                  ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
+                     (insert (org-roam-graph--format-node node "id"))))
-                  ("tooltip" . ,(xml-escape-string title)))))
+                 nodes-table))
-          (insert
-           (format "  \"%s\" [%s];\n" file
-                   (mapconcat (lambda (n)
-                                (org-roam-graph--dot-option n nil "\""))
-                              node-properties ",")))))
-      (dolist (edge edges)
-        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
-                                  ,@(mapcar #'xml-escape-string edge)))))
-      (insert (format "  edge [%s];\n"
-                      (mapconcat #'org-roam-graph--dot-option
-                                 org-roam-graph-edge-cites-extra-config ",")))
-      (dolist (edge edges-cites)
-        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
-                                  ,@(mapcar #'xml-escape-string edge)))))
       (insert "}")
       (buffer-string))))
 
-(defun org-roam-graph--build (&optional node-query callback)
+(defun org-roam-graph--format-node (node type)
-  "Generate a graph showing the relations between nodes in NODE-QUERY.
+  "Return a graphviz NODE with TYPE.
-Execute CALLBACK when process exits successfully.
+Handles both Org-roam nodes, and string nodes (e.g. urls)."
+  (let (node-id node-properties)
+    (if (org-roam-node-p node)
+        (let* ((title (org-roam-quote-string (org-roam-node-title node)))
+               (shortened-title (org-roam-quote-string
+                                 (pcase org-roam-graph-shorten-titles
+                                   (`truncate (org-roam-truncate org-roam-graph-max-title-length title))
+                                   (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                   (_ title)))))
+          (setq node-id (org-roam-node-id node)
+                node-properties `(("label"   . ,shortened-title)
+                                  ("URL"     . ,(concat "org-protocol://roam-node?node="
+                                                        (url-hexify-string (org-roam-node-id node))))
+                                  ("tooltip" . ,(xml-escape-string title)))))
+      (setq node-id node
+            node-properties (append `(("label" . ,(concat type ":" node)))
+                                    (when (member type (list "http" "https"))
+                                      `(("URL" . ,(xml-escape-string (concat type ":" node))))))))
+    (format "\"%s\" [%s];\n"
+            node-id
+            (mapconcat (lambda (n)
+                         (org-roam-graph--dot-option n nil "\""))
+                       (append (cdr (assoc type org-roam-graph-node-extra-config))
+                               node-properties) ","))))
+
+(defun org-roam-graph--build (graph &optional callback)
+  "Generate the GRAPH, and execute CALLBACK when process exits successfully.
 CALLBACK is passed the graph file as its sole argument."
   (unless (stringp org-roam-graph-executable)
     (user-error "`org-roam-graph-executable' is not a string"))
@@ -238,12 +230,7 @@ CALLBACK is passed the graph file as its sole argument."
     (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
                         "Please adjust `org-roam-graph-executable'")
                 org-roam-graph-executable))
-  (let* ((node-query (or node-query
+  (let* ((temp-dot   (make-temp-file "graph." nil ".dot" graph))
-                         `[:select [file title] :from titles
-                           ,@(org-roam-graph--expand-matcher 'file t)
-                           :group :by file]))
-         (graph      (org-roam-graph--dot node-query))
-         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
          (temp-graph (make-temp-file "graph." nil (concat "." org-roam-graph-filetype))))
     (org-roam-message "building graph")
     (make-process
@@ -268,47 +255,26 @@ CALLBACK is passed the graph file as its sole argument."
     ('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 callback)
-  "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
-CALLBACK is passed to `org-roam-graph--build'."
-  (let* ((file (expand-file-name file))
-         (files (or (if (and max-distance (>= max-distance 0))
-                        (org-roam-db--links-with-max-distance file max-distance)
-                      (org-roam-db--connected-component file))
-                    (list file)))
-         (query `[:select [file title]
-                  :from titles
-                  :where (in file [,@files])]))
-    (org-roam-graph--build query callback)))
-
 ;;;; Commands
 ;;;###autoload
-(defun org-roam-graph (&optional arg file node-query)
+(defun org-roam-graph (&optional arg node)
-  "Build and possibly display a graph for FILE from NODE-QUERY.
+  "Build and possibly display a graph for NODE.
-If FILE is nil, default to current buffer's file name.
 ARG may be any of the following values:
   - nil       show the graph.
-  - `\\[universal-argument]'     show the graph for FILE.
+  - `\\[universal-argument]'     show the graph for NODE.
-  - `\\[universal-argument]' N   show the graph for FILE limiting nodes to N steps.
+  - `\\[universal-argument]' N   show the graph for NODE limiting nodes to N steps."
-  - `\\[universal-argument] \\[universal-argument]' build the graph.
+  (interactive
-  - `\\[universal-argument]' -   build the graph for FILE.
+   (list current-prefix-arg
-  - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
+         (and current-prefix-arg
-  (interactive "P")
+              (org-roam-node-at-point 'assert))))
-  (unless org-roam-mode (org-roam-mode))
+  (let ((graph (cl-typecase arg
-  (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
+                 (null (org-roam-graph--dot nil 'all-nodes))
-    (unless (or (not arg) (equal arg '(16)))
+                 (cons (org-roam-graph--dot (org-roam-graph--connected-component
-      (unless file
+                                             (org-roam-node-id node) 0)))
-        (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
+                 (integer (org-roam-graph--dot (org-roam-graph--connected-component
-      (unless (org-roam--org-roam-file-p file)
+                                                (org-roam-node-id node) (abs arg)))))))
-        (user-error "\"%s\" is not an org-roam file" file)))
+    (org-roam-graph--build graph #'org-roam-graph--open)))
-    (pcase arg
+
-      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
-      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
-      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
-      ('(16)           (org-roam-graph--build node-query))
-      ('-              (org-roam-graph--build-connected-component file))
-      (_ (user-error "Unrecognized ARG: %s" arg)))))
 
 (provide 'org-roam-graph)
 

org-roam-link.el

@@ -1,324 +0,0 @@
-;;; org-roam-link.el --- Custom links for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-;;                  Alan Carroll
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
-;; 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 "1.0.2"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This adds the custom `roam:' link to Org-roam. `roam:' links allow linking to
-;; Org-roam files via their titles and headlines.
-;;
-;;; Code:
-;;;; Dependencies
-
-(require 'ol)
-(require 'org-roam-compat)
-(require 'org-roam-macs)
-(require 'org-roam-db)
-
-(require 'org-element)
-
-(defvar org-roam-completion-ignore-case)
-(defvar org-roam-directory)
-(declare-function  org-roam--find-file                  "org-roam")
-(declare-function  org-roam-find-file                   "org-roam")
-(declare-function org-roam-format-link                  "org-roam")
-
-(defcustom org-roam-link-auto-replace t
-  "When non-nil, replace Org-roam's roam links with file/id equivalents."
-  :group 'org-roam
-  :type 'boolean)
-
-(defcustom org-roam-link-file-path-type 'relative
-  "How the path name in file links should be stored.
-Valid values are:
-
-relative  Relative to the current directory, i.e. the directory of the file
-          into which the link is being inserted.
-absolute  Absolute path, if possible with ~ for home directory.
-noabbrev  Absolute path, no abbreviation of home directory."
-  :group 'org-roam
-  :type '(choice
-          (const relative)
-          (const absolute)
-          (const noabbrev))
-  :safe #'symbolp)
-
-;;; the roam: link
-(org-link-set-parameters "roam"
-                         :follow #'org-roam-link-follow-link)
-
-(defun org-roam-link-follow-link (_path)
-  "Navigates to location in Org-roam link.
-This function is called by Org when following links of the type
-`roam'. While the path is passed, assume that the cursor is on
-the link."
-  (pcase-let ((`(,link-type ,loc ,desc ,mkr) (org-roam-link--get-location)))
-    (when (and org-roam-link-auto-replace loc desc)
-      (org-roam-link--replace-link link-type loc desc))
-    (pcase link-type
-      ("file"
-       (if loc
-           (org-roam--find-file loc)
-         (org-roam-find-file desc nil nil t)))
-      ("id"
-       (org-goto-marker-or-bmk mkr)))))
-
-;;; Retrieval Functions
-(defun org-roam-link--get-titles ()
-  "Return all titles within Org-roam."
-  (mapcar #'car (org-roam-db-query [:select [titles:title] :from titles])))
-
-(defun org-roam-link--get-headlines (&optional file with-marker use-stack)
-  "Return all outline headings for the current buffer.
-If FILE, return outline headings for passed FILE instead.
-If WITH-MARKER, return a cons cell of (headline . marker).
-If USE-STACK, include the parent paths as well."
-  (org-roam-with-file file (when with-marker 'keep)
-    (let* ((outline-level-fn outline-level)
-           (path-separator "/")
-           (stack-level 0)
-           stack cands name level marker)
-      (save-excursion
-        (goto-char (point-min))
-        (while (re-search-forward org-complex-heading-regexp nil t)
-          (save-excursion
-            (setq name (substring-no-properties (or (match-string 4) "")))
-            (setq marker (point-marker))
-            (when use-stack
-              (goto-char (match-beginning 0))
-              (setq level (funcall outline-level-fn))
-              ;; Update stack.  The empty entry guards against incorrect
-              ;; headline hierarchies, e.g. a level 3 headline
-              ;; immediately following a level 1 entry.
-              (while (<= level stack-level)
-                (pop stack)
-                (cl-decf stack-level))
-              (while (> level stack-level)
-                (push name stack)
-                (cl-incf stack-level))
-              (setq name (mapconcat #'identity
-                                    (reverse stack)
-                                    path-separator)))
-            (push (if with-marker
-                      (cons name marker)
-                    name) cands))))
-      (nreverse cands))))
-
-
-(defun org-roam-link--get-file-from-title (title &optional no-interactive)
-  "Return the file path corresponding to TITLE.
-When NO-INTERACTIVE, return nil if there are multiple options."
-  (let ((files (mapcar #'car (org-roam-db-query [:select [titles:file] :from titles
-                                                 :where (= titles:title $v1)]
-                                                (vector title)))))
-    (pcase files
-      ('nil nil)
-      (`(,file) file)
-      (_
-       (unless no-interactive
-         (completing-read "Select file: " files))))))
-
-(defun org-roam-link--get-id-from-headline (headline &optional file)
-  "Return (marker . id) correspondng to HEADLINE in FILE.
-If FILE is nil, get ID from current buffer.
-If there is no corresponding headline, return nil."
-  (save-excursion
-    (org-roam-with-file file 'keep
-      (let ((headlines (org-roam-link--get-headlines file 'with-markers)))
-        (when-let ((marker (cdr (assoc-string headline headlines))))
-          (goto-char marker)
-          (cons marker
-                (when org-roam-link-auto-replace
-                  (org-id-get-create))))))))
-
-;;; Path-related functions
-(defun org-roam-link-get-path (path &optional type)
-  "Return the PATH of the link to use.
-If TYPE is non-nil, create a link of TYPE. Otherwise, respect
-`org-link-file-path-type'."
-  (pcase (or type org-roam-link-file-path-type)
-      ('absolute
-       (abbreviate-file-name (expand-file-name path)))
-      ('noabbrev
-       (expand-file-name path))
-      ('relative
-       (file-relative-name path))))
-
-(defun org-roam-link--split-path (path)
-  "Splits PATH into title and headline.
-Return a list of the form (type title has-headline-p headline star-idx).
-type is one of `title', `headline', `title+headline'.
-title is the title component of the path.
-headline is the headline component of the path.
-star-idx is the index of the asterisk, if any."
-  (save-match-data
-    (let* ((star-index (string-match-p "\\*" path))
-           (title (substring-no-properties path 0 star-index))
-           (headline (if star-index
-                         (substring-no-properties path (+ 1 star-index))
-                       ""))
-           (type (cond ((not star-index)
-                        'title)
-                       ((= 0 star-index)
-                        'headline)
-                       (t 'title+headline))))
-      (list type title headline star-index))))
-
-(defun org-roam-link--get-location ()
-  "Return the location of the Org-roam fuzzy link at point.
-The location is returned as a list containing (link-type loc desc marker).
-nil is returned if there is no matching location.
-
-link-type is either \"file\" or \"id\".
-loc is the target location: e.g. a file path, or an id.
-marker is a marker to the headline, if applicable.
-
-desc is either the the description of the link under point, or
-the target of LINK (title or heading content)."
-  (let ((context (org-element-context))
-        mkr link-type desc loc)
-    (pcase (org-element-lineage context '(link) t)
-      (`nil (error "Not at an Org link"))
-      (link
-       (if (not (string-equal "roam" (org-element-property :type link)))
-           (error "Not at Org-roam link")
-         (setq desc (and (org-element-property :contents-begin link)
-                         (org-element-property :contents-end link)
-                         (buffer-substring-no-properties
-                          (org-element-property :contents-begin link)
-                          (org-element-property :contents-end link))))
-         (pcase-let ((`(,type ,title ,headline _) (org-roam-link--split-path
-                                                   (org-element-property :path link))))
-           (pcase type
-             ('title+headline
-              (let ((file (org-roam-link--get-file-from-title title)))
-                (if (not file)
-                    (org-roam-message "Cannot find matching file")
-                  (setq mkr (org-roam-link--get-id-from-headline headline file))
-                  (pcase mkr
-                    (`(,marker . ,target-id)
-                     (progn
-                       (setq mkr marker
-                             loc target-id
-                             desc (or desc headline)
-                             link-type "id")))
-                    (_ (org-roam-message "Cannot find matching id"))))))
-             ('title
-              (setq loc (org-roam-link--get-file-from-title title)
-                    link-type "file"
-                    desc (or desc title)))
-             ('headline
-              (setq mkr (org-roam-link--get-id-from-headline headline))
-              (pcase mkr
-                (`(,marker . ,target-id)
-                 (setq mkr marker
-                       loc target-id
-                       link-type "id"
-                       desc (or desc headline)))
-                (_ (org-roam-message "Cannot find matching headline")))))))))
-    (list link-type loc desc mkr)))
-
-;;; Conversion Functions
-(defun org-roam-link--replace-link (link-type loc &optional desc)
-  "Replace link at point with a vanilla Org link.
-LINK-TYPE is the Org link type, typically \"file\" or \"id\".
-LOC is path for the Org link.
-DESC is the link description."
-  (save-excursion
-    (save-match-data
-      (unless (org-in-regexp org-link-bracket-re 1)
-        (user-error "No link at point"))
-      (replace-match "")
-      (insert (org-roam-format-link loc desc link-type)))))
-
-(defun org-roam-link-replace-all ()
-  "Replace all roam links in the current buffer."
-  (interactive)
-  (save-excursion
-    (goto-char (point-min))
-    (while (re-search-forward org-link-bracket-re nil t)
-      (condition-case nil
-          (pcase-let ((`(,link-type ,loc ,desc _) (org-roam-link--get-location)))
-            (when (and link-type loc)
-              (org-roam-link--replace-link link-type loc desc)))
-        (error nil)))))
-
-(defun org-roam-link--replace-link-on-save ()
-  "Hook to replace all roam links on save."
-  (when org-roam-link-auto-replace
-    (org-roam-link-replace-all)))
-
-;;; Completion
-(defun org-roam-link-complete-at-point ()
-  "Do appropriate completion for the link at point."
-  (let ((end (point))
-        (start (point))
-        collection link-type headline-only-p)
-    (when (org-in-regexp org-link-bracket-re 1)
-      (setq start (match-beginning 1)
-            end (match-end 1))
-      (let ((context (org-element-context)))
-        (pcase (org-element-lineage context '(link) t)
-          (`nil nil)
-          (link
-           (setq link-type (org-element-property :type link))
-           (when (member link-type '("roam" "fuzzy"))
-             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
-             (pcase-let ((`(,type ,title _ ,star-idx)
-                          (org-roam-link--split-path (org-element-property :path link))))
-               (pcase type
-                 ('title+headline
-                  (when-let ((file (org-roam-link--get-file-from-title title t)))
-                    (setq collection (apply-partially #'org-roam-link--get-headlines file))
-                    (setq start (+ start star-idx 1))))
-                 ('title
-                  (setq collection #'org-roam-link--get-titles))
-                 ('headline
-                  (setq collection #'org-roam-link--get-headlines)
-                  (setq start (+ start star-idx 1))
-                  (setq headline-only-p t)))))))))
-    (when collection
-      (let ((prefix (buffer-substring-no-properties start end)))
-        (list start end
-              (if (functionp collection)
-                  (completion-table-case-fold
-                   (completion-table-dynamic
-                    (lambda (_)
-                      (cl-remove-if (apply-partially #'string= prefix)
-                                    (funcall collection))))
-                   (not org-roam-completion-ignore-case))
-                collection)
-              :exit-function
-              (lambda (str &rest _)
-                (delete-char (- 0 (length str)
-                                (if headline-only-p 1 0)))
-                (insert (concat (unless (string= link-type "roam") "roam:")
-                                (when headline-only-p "*")
-                                (org-link-escape str)))))))))
-
-(provide 'org-roam-link)
-;;; org-roam-link.el ends here

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: 1.2.3
+;; Version: 2.0.0
-;; 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 "1.0.2"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,30 +27,20 @@
 
 ;;; Commentary:
 ;;
-;; This library implements macros and utility functions used throughout
+;; This library implements macros used throughout org-roam.
-;; org-roam.
-;;
 ;;
 ;;; Code:
-;;;; Library Requires
+(defmacro org-roam-plist-map! (fn plist)
-(require 'dash)
+  "Map FN over PLIST, modifying it in-place."
-(require 's)
+  (declare (indent 1))
-
+  (let ((plist-var (make-symbol "plist"))
-(defvar org-roam-verbose)
+        (k (make-symbol "k"))
-
+        (v (make-symbol "v")))
-;; This is necessary to ensure all dependents on this module see
+    `(let ((,plist-var (copy-sequence ,plist)))
-;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
+       (while ,plist-var
-;; regardless of whether Org is loaded before their compilation.
+         (setq ,k (pop ,plist-var))
-(require 'org)
+         (setq ,v (pop ,plist-var))
-
+         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
-;;;; Utility Functions
-(defun org-roam--list-interleave (lst separator)
-  "Interleaves elements in LST with SEPARATOR."
-  (when lst
-    (let ((new-lst (list (pop lst))))
-      (dolist (it lst)
-        (nconc new-lst (list separator it)))
-      new-lst)))
 
 (defmacro org-roam-with-file (file keep-buf-p &rest body)
   "Execute BODY within FILE.
@@ -58,6 +48,7 @@ If FILE is nil, execute BODY in the current buffer.
 Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
   (declare (indent 2) (debug t))
   `(let* (new-buf
+          (auto-mode-alist nil)
           (buf (or (and (not ,file)
                         (current-buffer)) ;If FILE is nil, use current buffer
                    (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
@@ -66,6 +57,11 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
                      (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
           res)
      (with-current-buffer buf
+       (unless (equal major-mode 'org-mode)
+         (delay-mode-hooks
+           (let ((org-inhibit-startup t)
+                 (org-agenda-files nil))
+             (org-mode))))
        (setq res (progn ,@body))
        (unless (and new-buf (not ,keep-buf-p))
          (save-buffer)))
@@ -74,57 +70,21 @@ Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
          (kill-buffer (find-buffer-visiting ,file))))
      res))
 
-(defmacro org-roam--with-temp-buffer (file &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'.
-If FILE, set `org-roam-temp-file-name' to file and insert its contents."
+If FILE, set `default-directory' to FILE's directory and insert its contents."
   (declare (indent 1) (debug t))
   (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory)
+         (let ((org-roam-directory ,current-org-roam-directory))
-               (org-mode-hook nil)
+           (delay-mode-hooks (org-mode))
-               (org-inhibit-startup t))
-           (org-mode)
            (when ,file
              (insert-file-contents ,file)
-             (setq-local org-roam-file-name ,file)
              (setq-local default-directory (file-name-directory ,file)))
            ,@body)))))
 
-(defun org-roam-message (format-string &rest args)
-  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
-  (when org-roam-verbose
-    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
-
-(defun org-roam-string-quote (str)
-  "Quote STR."
-  (->> str
-       (s-replace "\\" "\\\\")
-       (s-replace "\"" "\\\"")))
-
-;;; Shielding regions
-(defun org-roam-shield-region (beg end)
-  "Shield REGION against modifications.
-REGION must be a cons-cell containing the marker to the region
-beginning and maximum values."
-  (when (and beg end)
-    (add-text-properties beg end
-                           '(font-lock-face org-roam-link-shielded
-                                            read-only t)
-                           (marker-buffer beg))
-    (cons beg end)))
-
-(defun org-roam-unshield-region (beg end)
-  "Unshield the shielded REGION."
-  (when (and beg end)
-    (let ((inhibit-read-only t))
-      (remove-text-properties beg end
-                              '(font-lock-face org-roam-link-shielded
-                                               read-only t)
-                              (marker-buffer beg)))
-    (cons beg end)))
-
 (provide 'org-roam-macs)
 
 ;;; org-roam-macs.el ends here

org-roam-migrate.el

@@ -0,0 +1,192 @@
+;;; org-roam-migrate.el --- Migration utilities from v1 to v2 -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;;  To ease transition from v1 to v2, we provide various migration utilities.
+;;  This library helps convert v1 notes to v2, and informs the user.
+;;
+;;; Code:
+;;;; Dependencies
+;;;;
+;;; v1 breaking warning
+(require 'org-roam-db)
+
+(defvar org-roam-v2-ack nil)
+
+(unless org-roam-v2-ack
+  (lwarn 'org-roam :error "
+------------------------------------
+WARNING: You're now on Org-roam v2!
+------------------------------------
+
+You may have arrived here from a package upgrade. Please read the
+wiki entry at
+https://github.com/org-roam/org-roam/wiki/Hitchhiker's-Rough-Guide-to-Org-roam-V2
+for an overview of the major changes.
+
+Notes taken in v1 are incompatible with v1, but you can upgrade
+them to the v2 format via a simple command. To migrate your
+notes, run:
+
+  M-x org-roam-migrate-wizard
+
+If you wish to stay on v1, v1 is unfortunately not distributed on
+MELPA. See org-roam/org-roam-v1 on GitHub on how to install v1.
+
+If you've gone through the migration steps (if necessary), and
+know what you're doing set `org-roam-v2-ack' to `t' to disable
+this warning. You can do so by adding:
+
+(setq org-roam-v2-ack t)
+
+To your init file.
+
+"))
+
+;;;###autoload
+(defun org-roam-migrate-wizard ()
+  "Migrate all notes from to be compatible with Org-roam v2.
+1. Convert all notes from v1 format to v2.
+2. Rebuild the cache.
+3. Replace all file links with ID links."
+  (interactive)
+  (when (yes-or-no-p "Org-roam will now convert all your notes from v1 to v2.
+This will take a while. Are you sure you want to do this?")
+    ;; Back up notes
+    (let ((backup-dir (expand-file-name "org-roam.bak"
+                                        (file-name-directory (directory-file-name org-roam-directory)))))
+      (message "Backing up files to %s" backup-dir)
+      (copy-directory org-roam-directory backup-dir))
+
+    ;; Convert v1 to v2
+    (dolist (f (org-roam--list-all-files))
+      (org-roam-with-file f nil
+        (org-roam-migrate-v1-to-v2)))
+    ;; Rebuild cache
+    (org-roam-db-sync 'force)
+
+    ;;Replace all file links with ID links
+    (dolist (f (org-roam--list-all-files))
+      (org-roam-with-file f nil
+        (org-roam-migrate-replace-file-links-with-id)
+        (save-buffer)))))
+
+(defun org-roam-migrate-v1-to-v2 ()
+  "Convert the current buffer to v2 format."
+  ;; Create file level ID
+  (org-with-point-at 1
+    (org-id-get-create))
+  ;; Replace roam_key into properties drawer roam_ref
+  (when-let* ((refs (mapcan #'split-string-and-unquote
+                            (cdar (org-collect-keywords '("roam_key"))))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (dolist (ref refs)
+          (org-roam-ref-add ref))
+        (while (re-search-forward "^#\\+roam_key:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+
+  ;; Replace roam_alias into properties drawer roam_aliases
+  (when-let* ((aliases (mapcan #'split-string-and-unquote
+                               (cdar (org-collect-keywords '("roam_alias"))))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (dolist (alias aliases)
+          (org-roam-alias-add alias))
+        (while (re-search-forward "^#\\+roam_alias:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+
+  ;; Replace #+roam_tags into #+filetags
+  (org-with-point-at 1
+    (let* ((roam-tags (org-roam-migrate-get-prop-list "ROAM_TAGS"))
+           (file-tags (org-roam-migrate-get-prop-list "FILETAGS"))
+           (tags (append roam-tags file-tags))
+           (tags (seq-map (lambda (tag)
+                            (replace-regexp-in-string
+                             "[^[:alnum:]_@#%]"
+                             "_"
+                             tag)) tags))
+           (tags (seq-uniq tags)))
+      (when tags
+        (org-roam-migrate-prop-set "filetags" (string-join tags " "))))
+    (let ((case-fold-search t))
+      (org-with-point-at 1
+        (while (re-search-forward "^#\\+roam_tags:" (point-max) t)
+          (beginning-of-line)
+          (kill-line 1)))))
+  (save-buffer))
+
+(defun org-roam-migrate-get-prop-list (keyword)
+  "Return prop list for KEYWORD."
+  (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase keyword)))
+        lst)
+    (goto-char (point-min))
+    (while (re-search-forward re 2048 t)
+      (setq lst (append lst (split-string-and-unquote
+                             (buffer-substring-no-properties
+                              (match-beginning 1) (match-end 1))))))
+    lst))
+
+(defun org-roam-migrate-prop-set (name value)
+  "Set a file property called NAME to VALUE in buffer file.
+If the property is already set, replace its value."
+  (setq name (downcase name))
+  (org-with-point-at 1
+    (let ((case-fold-search t))
+      (if (re-search-forward (concat "^#\\+" name ":\\(.*\\)")
+                             (point-max) t)
+          (replace-match (concat "#+" name ": " value) 'fixedcase)
+        (while (and (not (eobp))
+                    (looking-at "^[#:]"))
+          (if (save-excursion (end-of-line) (eobp))
+              (progn
+                (end-of-line)
+                (insert "\n"))
+            (forward-line)
+            (beginning-of-line)))
+        (insert "#+" name ": " value "\n")))))
+
+(defun org-roam-migrate-replace-file-links-with-id ()
+  "Replace all file: links with ID links in current buffer."
+  (org-with-point-at 1
+    (while (re-search-forward org-link-bracket-re nil t)
+      (let* ((mdata (match-data))
+             (path (match-string 1))
+             (desc (match-string 2)))
+        (when (string-prefix-p "file:" path)
+          (setq path (expand-file-name (substring path 5)))
+          (when-let ((node-id (caar (org-roam-db-query [:select [id] :from nodes
+                                                        :where (= file $s1)
+                                                        :and (= level 0)] path))))
+            (set-match-data mdata)
+            (replace-match (org-link-make-string (concat "id:" node-id) desc))))))))
+
+(provide 'org-roam-migrate)
+;;; org-roam-migrate.el ends here

org-roam-mode.el

@@ -0,0 +1,468 @@
+;;; org-roam-mode.el --- create and refresh Org-roam buffers -*- lexical-binding: t -*-
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements the abstract major-mode `org-roam-mode', from which
+;; almost all other Org-roam major-modes derive.
+;;
+;;; Code:
+(require 'magit-section)
+
+(require 'org-roam-utils)
+
+(defvar org-roam-directory)
+(defvar org-roam-find-file-hook)
+
+(declare-function org-roam-node-at-point "org-roam")
+
+;;; Faces
+(defface org-roam-header-line
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "DarkGoldenrod4"
+     :weight bold)
+    (((class color) (background  dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :foreground "LightGoldenrod2"
+     :weight bold))
+  "Face for the `header-line' in some Org-roam modes."
+  :group 'org-roam-faces)
+
+(defface org-roam-title
+  '((t :weight bold))
+  "Face for Org-roam titles."
+  :group 'org-roam-faces)
+
+(defface org-roam-olp
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the OLP of the node."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey80"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey25"
+     :foreground "grey70"))
+  "Face for preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-highlight
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey75"
+     :foreground "grey30")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :background "grey35"
+     :foreground "grey70"))
+  "Face for current preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-heading-selection
+  `((((class color) (background light))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "salmon4")
+    (((class color) (background dark))
+     ,@(and (>= emacs-major-version 27) '(:extend t))
+     :inherit org-roam-preview-heading-highlight
+     :foreground "LightSalmon3"))
+  "Face for selected preview headings."
+  :group 'org-roam-faces)
+
+(defface org-roam-preview-region
+  `((t :inherit bold
+       ,@(and (>= emacs-major-version 27)
+              (list :extend (ignore-errors (face-attribute 'region :extend))))))
+  "Face used by `org-roam-highlight-preview-region-using-face'.
+
+This face is overlaid over text that uses other hunk faces,
+and those normally set the foreground and background colors.
+The `:foreground' and especially the `:background' properties
+should be avoided here.  Setting the latter would cause the
+loss of information.  Good properties to set here are `:weight'
+and `:slant'."
+  :group 'org-roam-faces)
+
+(defface org-roam-dim
+  '((((class color) (background light)) :foreground "grey60")
+    (((class color) (background  dark)) :foreground "grey40"))
+  "Face for the dimmer part of the widgets."
+  :group 'org-roam-faces)
+
+;;; Variables
+(defvar org-roam-current-node nil
+  "The current node at point.")
+
+(defvar org-roam-current-directory nil
+  "The `org-roam-directory' value for the current node.")
+
+(defcustom org-roam-mode-section-functions (list #'org-roam-backlinks-section
+                                                 #'org-roam-reflinks-section)
+  "Functions which insert sections of the `org-roam-buffer'.
+Each function is called with one argument, which is the current org-roam node at point."
+  :group 'org-roam
+  :type 'hook)
+
+;;; The mode
+(defvar org-roam-mode-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map magit-section-mode-map)
+    (define-key map [C-return]  'org-roam-visit-thing)
+    (define-key map (kbd "C-m") 'org-roam-visit-thing)
+    (define-key map [remap revert-buffer] 'org-roam-buffer-render)
+    map)
+  "Parent keymap for all keymaps of modes derived from `org-roam-mode'.")
+
+(define-derived-mode org-roam-mode magit-section-mode "Org-roam"
+  "Major mode for Org-roam's buffer."
+  :group 'org-roam
+  (face-remap-add-relative 'header-line 'org-roam-header-line))
+
+;;; Key functions
+(defun org-roam-visit-thing ()
+  "This is a placeholder command.
+Where applicable, section-specific keymaps bind another command
+which visits the thing at point."
+  (interactive)
+  (user-error "There is no thing at point that could be visited"))
+
+(defun org-roam-buffer-render ()
+  "Render the current node at point."
+  (interactive)
+  (when (derived-mode-p 'org-roam-mode)
+    (let ((inhibit-read-only t))
+      (erase-buffer)
+      (setq-local default-directory org-roam-current-directory)
+      (setq-local org-roam-directory org-roam-current-directory)
+      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+      (magit-insert-section (org-roam)
+        (magit-insert-heading)
+        (run-hook-with-args 'org-roam-mode-section-functions org-roam-current-node)))))
+
+(defun org-roam-buffer ()
+  "Launch an Org-roam buffer for the current node at point."
+  (interactive)
+  (if-let ((node (org-roam-node-at-point))
+           (source-org-roam-directory org-roam-directory))
+      (progn
+        (let ((buffer (get-buffer-create
+                       (concat "org-roam: "
+                               (file-relative-name (buffer-file-name) org-roam-directory)))))
+          (with-current-buffer buffer
+            (org-roam-mode)
+            (setq-local org-roam-current-node node)
+            (setq-local org-roam-current-directory source-org-roam-directory)
+            (org-roam-buffer-render))
+          (switch-to-buffer-other-window buffer)))
+    (user-error "No node at point")))
+
+;;; Persistent buffer
+(defvar org-roam-buffer "*org-roam*"
+  "The persistent Org-roam buffer name.")
+
+(defun org-roam-buffer--post-command-h ()
+  "Reconstructs the Org-roam buffer.
+This needs to be quick or infrequent, because this is run at
+`post-command-hook'.  If REDISPLAY, force an update of
+the Org-roam buffer."
+  (when (get-buffer-window org-roam-buffer)
+    (when-let ((node (org-roam-node-at-point)))
+      (unless (equal node org-roam-current-node)
+        (setq org-roam-current-node node)
+        (setq org-roam-current-directory org-roam-directory)
+        (org-roam-buffer-persistent-redisplay)))))
+
+(define-inline org-roam-buffer--visibility ()
+  "Return whether the current visibility state of the org-roam buffer.
+Valid states are 'visible, 'exists and 'none."
+  (declare (side-effect-free t))
+  (inline-quote
+   (cond
+    ((get-buffer-window org-roam-buffer) 'visible)
+    ((get-buffer org-roam-buffer) 'exists)
+    (t 'none))))
+
+(defun org-roam-buffer-toggle ()
+  "Toggle display of the Org-roam buffer."
+  (interactive)
+  (pcase (org-roam-buffer--visibility)
+    ('visible
+     (progn
+       (delete-window (get-buffer-window org-roam-buffer))
+       (remove-hook 'post-command-hook #'org-roam-buffer--post-command-h)))
+    ((or 'exists 'none)
+     (progn
+       (setq org-roam-current-node (org-roam-node-at-point)
+             org-roam-current-directory org-roam-directory)
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (org-roam-buffer-persistent-redisplay)))))
+
+(defun org-roam-buffer-persistent-redisplay ()
+  "Recompute contents of the persistent Org-roam buffer.
+Has no effect when `org-roam-current-node' is nil."
+  (when org-roam-current-node
+    (with-current-buffer (get-buffer-create org-roam-buffer)
+      (let ((inhibit-read-only t))
+        (erase-buffer)
+        (org-roam-mode)
+        (setq-local default-directory org-roam-current-directory)
+        (setq-local org-roam-directory org-roam-current-directory)
+        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+        (magit-insert-section (org-roam)
+          (magit-insert-heading)
+          (dolist (fn org-roam-mode-section-functions)
+            (funcall fn org-roam-current-node)))))))
+
+(defun org-roam-buffer--redisplay ()
+  "."
+  (add-hook 'post-command-hook #'org-roam-buffer--post-command-h nil t))
+
+(add-hook 'org-roam-find-file-hook #'org-roam-buffer--redisplay)
+
+;;; Sections
+;;;; Backlinks
+(cl-defstruct (org-roam-backlink (:constructor org-roam-backlink-create)
+                                 (:copier nil))
+  source-node target-node
+  point properties)
+
+(cl-defmethod org-roam-populate ((backlink org-roam-backlink))
+  "Populate BACKLINK from database."
+  (setf (org-roam-backlink-source-node backlink)
+        (org-roam-populate (org-roam-backlink-source-node backlink))
+        (org-roam-backlink-target-node backlink)
+        (org-roam-populate (org-roam-backlink-target-node backlink)))
+  backlink)
+
+(defun org-roam-backlinks-get (node)
+  "Return the backlinks for NODE."
+  (let ((backlinks (org-roam-db-query
+                    [:select [source dest pos properties]
+                     :from links
+                     :where (= dest $s1)
+                     :and (= type "id")]
+                    (org-roam-node-id node))))
+    (cl-loop for backlink in backlinks
+             collect (pcase-let ((`(,source-id ,dest-id ,pos ,properties) backlink))
+                       (org-roam-populate
+                        (org-roam-backlink-create
+                         :source-node (org-roam-node-create :id source-id)
+                         :target-node (org-roam-node-create :id dest-id)
+                         :point pos
+                         :properties properties))))))
+
+(defun org-roam-backlinks-sort (a b)
+  "Default sorting function for backlinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-backlink-source-node a))
+           (org-roam-node-title (org-roam-backlink-source-node b))))
+
+(defun org-roam-backlinks-section (node)
+  "The backlinks section for NODE."
+  (when-let ((backlinks (seq-sort #'org-roam-backlinks-sort (org-roam-backlinks-get node))))
+    (magit-insert-section (org-roam-backlinks)
+      (magit-insert-heading "Backlinks:")
+      (dolist (backlink backlinks)
+        (org-roam-node-insert-section
+         :source-node (org-roam-backlink-source-node backlink)
+         :point (org-roam-backlink-point backlink)
+         :properties (org-roam-backlink-properties backlink)))
+      (insert ?\n))))
+
+;;;; Reflinks
+(cl-defstruct (org-roam-reflink (:constructor org-roam-reflink-create)
+                                (:copier nil))
+  source-node ref
+  point properties)
+
+(cl-defmethod org-roam-populate ((reflink org-roam-reflink))
+  "Populate REFLINK from database."
+  (setf (org-roam-reflink-source-node reflink)
+        (org-roam-populate (org-roam-reflink-source-node reflink)))
+  reflink)
+
+(defun org-roam-reflinks-get (node)
+  "Return the reflinks for NODE."
+  (let ((refs (org-roam-db-query [:select [ref] :from refs
+                                  :where (= node-id $s1)]
+                                 (org-roam-node-id node)))
+        links)
+    (pcase-dolist (`(,ref) refs)
+      (pcase-dolist (`(,source-id ,pos ,properties) (org-roam-db-query
+                                                     [:select [source pos properties]
+                                                      :from links
+                                                      :where (= dest $s1)]
+                                                     ref))
+        (push (org-roam-populate
+               (org-roam-reflink-create
+                :source-node (org-roam-node-create :id source-id)
+                :ref ref
+                :point pos
+                :properties properties)) links)))
+    links))
+
+(defun org-roam-reflinks-sort (a b)
+  "Default sorting function for reflinks A and B.
+Sorts by title."
+  (string< (org-roam-node-title (org-roam-reflink-source-node a))
+           (org-roam-node-title (org-roam-reflink-source-node b))))
+
+(defun org-roam-reflinks-section (node)
+  "The reflinks section for NODE."
+  (when (org-roam-node-refs node)
+    (let* ((reflinks (seq-sort #'org-roam-reflinks-sort (org-roam-reflinks-get node))))
+      (magit-insert-section (org-roam-reflinks)
+        (magit-insert-heading "Reflinks:")
+        (dolist (reflink reflinks)
+          (org-roam-node-insert-section
+           :source-node (org-roam-reflink-source-node reflink)
+           :point (org-roam-reflink-point reflink)
+           :properties (org-roam-reflink-properties reflink)))
+        (insert ?\n)))))
+
+;;;; Unlinked references
+(defvar org-roam-grep-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map org-roam-mode-map)
+    (define-key map [remap org-roam-visit-thing] 'org-roam-file-visit)
+    map)
+  "Keymap for Org-roam grep result sections.")
+
+(defclass org-roam-grep-section (magit-section)
+  ((keymap :initform 'org-roam-grep-map)
+   (file :initform nil)
+   (row :initform nil)
+   (col :initform nil)))
+
+(defun org-roam-file-at-point (&optional assert)
+  "Return the file at point.
+If ASSERT, throw an error."
+  (if-let ((file (magit-section-case
+                   (org-roam-node-section (org-roam-node-file (oref it node)))
+                   (org-roam-grep-section (oref it file))
+                   (org-roam-preview-section (oref it file)))))
+      file
+    (when assert
+      (user-error "No file at point"))))
+
+(defun org-roam-file-visit (file &optional other-window row col)
+  "Visits FILE.
+With a prefix argument OTHER-WINDOW, display the buffer in
+another window instead.
+If ROW, move to the row, and if COL move to the COL."
+  (interactive (list (org-roam-file-at-point t)
+                     current-prefix-arg
+                     (oref (magit-current-section) row)
+                     (oref (magit-current-section) col)))
+  (let ((buf (find-file-noselect file)))
+    (with-current-buffer buf
+      (widen)
+      (goto-char (point-min))
+      (when row
+        (forward-line (1- row)))
+      (when col
+        (forward-char (1- col))))
+    (funcall (if other-window
+                 #'switch-to-buffer-other-window
+               #'pop-to-buffer-same-window) buf)))
+
+(defvar org-roam-unlinked-references-result-re
+  (rx (group (one-or-more anything))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (one-or-more digit))
+      ":"
+      (group (zero-or-more anything)))
+  "Regex for the return result of a ripgrep query.")
+
+(defun org-roam-unlinked-references-preview-line (file row)
+  "Return the preview line from FILE.
+This is the ROW within FILE."
+  (with-temp-buffer
+    (insert-file-contents-literally file)
+    (forward-line (1- row))
+    (buffer-substring-no-properties
+     (save-excursion
+       (beginning-of-line)
+       (point))
+     (save-excursion
+       (end-of-line)
+       (point)))))
+
+(defun org-roam-unlinked-references-section (node)
+  "The unlinked references section for NODE.
+References from FILE are excluded."
+  (when (and (executable-find "rg")
+             (not (string-match "PCRE2 is not available"
+                                (shell-command-to-string "rg --pcre2-version"))))
+    (let* ((titles (cons (org-roam-node-title node)
+                         (org-roam-node-aliases node)))
+           (rg-command (concat "rg -o --vimgrep -P -i "
+                               (mapconcat (lambda (glob) (concat "-g " glob))
+                                          (org-roam--list-files-search-globs org-roam-file-extensions)
+                                          " ")
+                               (format " '\\[([^[]]++|(?R))*\\]%s' "
+                                       (mapconcat (lambda (title)
+                                                    (format "|(\\b%s\\b)" (shell-quote-argument title)))
+                                                  titles ""))
+                               org-roam-directory))
+           (results (split-string (shell-command-to-string rg-command) "\n"))
+           f row col match)
+      (magit-insert-section (unlinked-references)
+        (magit-insert-heading "Unlinked References:")
+        (dolist (line results)
+          (save-match-data
+            (when (string-match org-roam-unlinked-references-result-re line)
+              (setq f (match-string 1 line)
+                    row (string-to-number (match-string 2 line))
+                    col (string-to-number (match-string 3 line))
+                    match (match-string 4 line))
+              (when (and match
+                         (not (f-equal-p (org-roam-node-file node) f))
+                         (member (downcase match) (mapcar #'downcase titles)))
+                (magit-insert-section section (org-roam-grep-section)
+                  (oset section file f)
+                  (oset section row row)
+                  (oset section col col)
+                  (insert (propertize (format "%s:%s:%s"
+                                              (truncate-string-to-width (file-name-base f) 15 nil nil "...")
+                                              row col) 'font-lock-face 'org-roam-dim)
+                          " "
+                          (org-roam-fontify-like-in-org-mode
+                           (org-roam-unlinked-references-preview-line f row))
+                          "\n"))))))
+        (insert ?\n)))))
+
+(provide 'org-roam-mode)
+;;; org-roam-mode.el ends here

org-roam-overlay.el

@@ -0,0 +1,98 @@
+;;; org-roam-overlay.el --- Link overlay for Org-roam nodes -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020-2021 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library is an attempt at injecting Roam functionality into Org-mode.
+;; This is achieved primarily through building caches for forward links,
+;; backward links, and file titles.
+;;
+;;
+;;; Code:
+;;;; Dependencies
+
+(defface org-roam-overlay
+  '((((class color) (background light))
+     :background "grey90" :box (:line-width -1 :color "black"))
+    (((class color) (background dark))
+     :background "grey10" :box (:line-width -1 :color "white")))
+  "Face for the Org-roam overlay."
+  :group 'org-roam-faces)
+
+(defun org-roam-overlay--make (l r &rest props)
+  "Make an overlay from L to R with PROPS."
+  (let ((o (make-overlay l (or r l))))
+    (overlay-put o 'category 'org-roam)
+    (while props (overlay-put o (pop props) (pop props)))
+    o))
+
+(defun org-roam-overlay-make-link-overlay (link)
+  "Create overlay for LINK."
+  (save-excursion
+    (save-match-data
+      (let* ((type (org-element-property :type link))
+             (id (org-element-property :path link))
+             (pos (org-element-property :end link))
+             (desc-p (org-element-property :contents-begin link))
+             node)
+        (when (and (string-equal type "id")
+                   (setq node (org-roam-node-from-id id))
+                   (not desc-p))
+          (org-roam-overlay--make
+           pos pos
+           'after-string (format "%s "
+                                 (propertize (org-roam-node-title node)
+                                             'face 'org-roam-overlay))))))))
+
+(defun org-roam-overlay-enable ()
+  "Enable Org-roam overlays."
+  (org-roam-db-map-links
+   (list #'org-roam-overlay-make-link-overlay)))
+
+(defun org-roam-overlay-disable ()
+  "Disable Org-roam overlays."
+  (remove-overlays nil nil 'category 'org-roam))
+
+(defun org-roam-overlay-redisplay ()
+  "Redisplay Org-roam overlays."
+  (org-roam-overlay-disable)
+  (org-roam-overlay-enable))
+
+(define-minor-mode org-roam-overlay-mode
+  "Overlays for Org-roam ID links.
+Org-roam overlay mode is a minor mode.  When enabled,
+overlay displaying the node's title is displayed."
+  :lighter " org-roam-overlay"
+  (if org-roam-overlay-mode
+      (progn
+        (org-roam-overlay-enable)
+        (add-hook 'after-save-hook #'org-roam-overlay-redisplay nil t))
+    (org-roam-overlay-disable)
+    (remove-hook 'after-save-hook #'org-roam-overlay-redisplay t)))
+
+(provide 'org-roam-overlay)
+;;; org-roam-overlay.el ends here

org-roam-protocol.el

@@ -4,8 +4,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.3
+;; Version: 2.0.0
-;; Package-Requires: ((emacs "26.1") (org "9.3"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,12 +31,14 @@
 ;;
 ;; We define 2 protocols:
 ;;
-;; 1. "roam-file": This protocol simply opens the file given by the FILE key
+;; 1. "roam-node": This protocol simply opens the node given by the node ID
 ;; 2. "roam-ref": This protocol creates or opens a note with the given REF
 ;;
 ;;; Code:
 (require 'org-protocol)
 (require 'org-roam)
+(eval-when-compile
+  (require 'org-roam-macs))
 (require 'ol) ;; for org-link-decode
 
 (defcustom org-roam-protocol-store-links nil
@@ -54,40 +56,34 @@ It opens or creates a note with the given ref.
         encodeURIComponent(location.href) + \\='&title=\\=' + \\
         encodeURIComponent(document.title) + \\='&body=\\=' + \\
         encodeURIComponent(window.getSelection())"
-  (when-let* ((alist (org-roam--plist-to-alist info))
+  (unless (plist-get info :ref)
-              (decoded-alist (mapcar (lambda (k.v)
+    (user-error "No ref key provided"))
-                                       (let ((key (car k.v))
+  (org-roam-plist-map! (lambda (k v)
-                                             (val (cdr k.v)))
+                         (org-link-decode
-                                         (cons key (org-link-decode val)))) alist)))
+                          (if (equal k :ref)
-    (unless (assoc 'ref decoded-alist)
+                              (org-protocol-sanitize-uri v)
-      (error "No ref key provided"))
+                            v))) info)
-    (when-let ((title (cdr (assoc 'title decoded-alist))))
+  (when org-roam-protocol-store-links
-      (push (cons 'slug (funcall org-roam-title-to-slug-function title)) decoded-alist))
+    (push (list (plist-get info :ref)
-    (let-alist decoded-alist
+                (plist-get info :title)) org-stored-links))
-      (let* ((ref (org-protocol-sanitize-uri .ref))
+  (org-link-store-props :type (and (string-match org-link-plain-re
-             (type (and (string-match org-link-plain-re ref)
+                                                 (plist-get info :ref))
-                        (match-string 1 ref)))
+                                   (match-string 1 (plist-get info :ref)))
-             (title (or .title ""))
+                        :link (plist-get info :ref)
-             (body (or .body ""))
+                        :annotation (org-link-make-string (plist-get info :ref)
-             (orglink
+                                                          (or (plist-get info :title)
-              (org-link-make-string ref (or (org-string-nw-p title) ref))))
+                                                              (plist-get info :ref)))
-        (when org-roam-protocol-store-links
+                        :initial (or (plist-get info :body) ""))
-          (push (list ref title) org-stored-links))
+  (raise-frame)
-        (org-link-store-props :type type
+  (org-roam-capture-
-                              :link ref
+   :keys (plist-get info :template)
-                              :annotation orglink
+   :node (org-roam-node-create :title (plist-get info :title))
-                              :initial body)))
+   :info (list :ref (plist-get info :ref)
-    (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
+               :body (plist-get info :body))
-           (org-roam-capture--context 'ref)
+   :templates org-roam-capture-ref-templates)
-           (org-roam-capture--info decoded-alist)
-           (org-capture-link-is-already-stored t)
-           (template (cdr (assoc 'template decoded-alist))))
-      (raise-frame)
-      (org-roam-capture--capture nil template)
-      (org-roam-message "Item captured.")))
   nil)
 
-(defun org-roam-protocol-open-file (info)
+(defun org-roam-protocol-open-node (info)
   "This handler simply opens the file with emacsclient.
 
 INFO is an alist containing additional information passed by the protocol URL.
@@ -95,15 +91,15 @@ It should contain the FILE key, pointing to the path of the file to open.
 
   Example protocol string:
 
-org-protocol://roam-file?file=/path/to/file.org"
+org-protocol://roam-node?node=uuid"
-  (when-let ((file (plist-get info :file)))
+  (when-let ((node (plist-get info :node)))
     (raise-frame)
-    (org-roam--find-file file))
+    (org-roam-node-visit (org-roam-populate (org-roam-node-create :id node))))
   nil)
 
 (push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
       org-protocol-protocol-alist)
-(push '("org-roam-file"  :protocol "roam-file"   :function org-roam-protocol-open-file)
+(push '("org-roam-node"  :protocol "roam-node"   :function org-roam-protocol-open-node)
       org-protocol-protocol-alist)
 
 (provide 'org-roam-protocol)

org-roam-utils.el

@@ -0,0 +1,296 @@
+;;; org-roam-utils.el --- Utilities for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite "1.0.0") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements utility functions used throughout
+;; Org-roam.
+;;
+;;
+;;; Code:
+;;;; Library Requires
+(require 'dash)
+
+(eval-when-compile
+  (require 'org-roam-macs)
+  (require 'org-macs))
+
+(defvar org-roam-verbose)
+
+;; This is necessary to ensure all dependents on this module see
+;; `org-mode-hook' and `org-inhibit-startup' as dynamic variables,
+;; regardless of whether Org is loaded before their compilation.
+(require 'org)
+
+;;;; String Utilities
+(defun org-roam-truncate (len s &optional ellipsis)
+  "If S is longer than LEN, cut it down and add ELLIPSIS to the end.
+
+The resulting string, including ellipsis, will be LEN characters
+long.
+
+When not specified, ELLIPSIS defaults to ‘...’."
+  (declare (pure t) (side-effect-free t))
+  (unless ellipsis
+    (setq ellipsis "..."))
+  (if (> (length s) len)
+      (format "%s%s" (substring s 0 (- len (length ellipsis))) ellipsis)
+    s))
+
+(defun org-roam-replace (old new s)
+  "Replace OLD with NEW in S."
+  (declare (pure t) (side-effect-free t))
+  (replace-regexp-in-string (regexp-quote old) new s t t))
+
+(defun org-roam-quote-string (s)
+  "Quotes string S."
+  (->> s
+    (org-roam-replace "\\" "\\\\")
+    (org-roam-replace "\"" "\\\"")))
+
+;;;; Utility Functions
+(defun org-roam--list-interleave (lst separator)
+  "Interleaves elements in LST with SEPARATOR."
+  (when lst
+    (let ((new-lst (list (pop lst))))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
+
+(defun org-roam-up-heading-or-point-min ()
+  "Fixed version of Org's `org-up-heading-or-point-min'."
+  (ignore-errors (org-back-to-heading t))
+  (let ((p (point)))
+    (if (< 1 (funcall outline-level))
+        (progn
+          (org-up-heading-safe)
+          (when (= (point) p)
+            (goto-char (point-min))))
+      (unless (bobp) (goto-char (point-min))))))
+
+(defun org-roam-message (format-string &rest args)
+  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
+  (when org-roam-verbose
+    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
+
+(defvar org-ref-buffer-hacked)
+
+(defun org-roam-fontify-like-in-org-mode (s)
+  "Fontify string S like in Org mode.
+Like `org-fontify-like-in-org-mode', but supports `org-ref'."
+  ;; NOTE: pretend that the temporary buffer created by `org-fontify-like-in-org-mode' to
+  ;; fontify a `cite:' reference has been hacked by org-ref, whatever that means;
+  ;;
+  ;; `org-ref-cite-link-face-fn', which is used to supply a face for `cite:' links, calls
+  ;; `hack-dir-local-variables' rationalizing that `bibtex-completion' would throw some warnings
+  ;; otherwise.  This doesn't seem to be the case and calling this function just before
+  ;; `org-font-lock-ensure' (alias of `font-lock-ensure') actually instead of fixing the alleged
+  ;; warnings messes the things so badly that `font-lock-ensure' crashes with error and doesn't let
+  ;; org-roam to proceed further. I don't know what's happening there exactly but disabling this hackery
+  ;; fixes the crashing.  Fortunately, org-ref provides the `org-ref-buffer-hacked' switch, which we use
+  ;; here to make it believe that the buffer was hacked.
+  ;;
+  ;; This is a workaround for `cite:' links and does not have any effect on other ref types.
+  ;;
+  ;; `org-ref-buffer-hacked' is a buffer-local variable, therefore we inline
+  ;; `org-fontify-like-in-org-mode' here
+  (with-temp-buffer
+    (insert s)
+    (let ((org-ref-buffer-hacked t))
+      (org-mode)
+      (org-font-lock-ensure)
+      (buffer-string))))
+
+(defun org-roam-set-header-line-format (string)
+  "Set the header-line using STRING.
+If the `face' property of any part of STRING is already set, then
+that takes precedence. Also pad the left side of STRING so that
+it aligns with the text area."
+  (setq-local header-line-format
+              (concat (propertize " " 'display '(space :align-to 0))
+                      string)))
+
+;;; Keywords
+(defun org-roam--get-keyword (name &optional bound)
+  "Return keyword property NAME in current buffer.
+If BOUND, scan up to BOUND bytes of the buffer."
+  (save-excursion
+    (let ((re (format "^#\\+%s:[ \t]*\\([^\n]+\\)" (upcase name))))
+      (goto-char (point-min))
+      (when (re-search-forward re bound t)
+        (buffer-substring-no-properties (match-beginning 1) (match-end 1))))))
+
+(defun org-roam-get-keyword (name &optional file bound)
+  "Return keyword property NAME from an org FILE.
+FILE defaults to current file.
+Only scans up to BOUND bytes of the document."
+  (unless bound
+    (setq bound 1024))
+  (if file
+      (with-temp-buffer
+        (insert-file-contents-literally file nil 0 bound)
+        (org-roam--get-keyword name))
+    (org-roam--get-keyword name bound)))
+
+;;; Shielding regions
+(defface org-roam-shielded
+  '((t :inherit (warning)))
+  "Face for regions that are shielded (marked as read-only).
+This face is used on the region target by org-roam-insertion
+during an `org-roam-capture'."
+  :group 'org-roam-faces)
+
+(defun org-roam-shield-region (beg end)
+  "Shield region against modifications.
+BEG and END are markers for the beginning and end regions.
+REGION must be a cons-cell containing the marker to the region
+beginning and maximum values."
+  (add-text-properties beg end
+                       '(font-lock-face org-roam-shielded
+                                        read-only t)
+                       (marker-buffer beg)))
+
+(defun org-roam-unshield-region (beg end)
+  "Unshield the shielded REGION.
+BEG and END are markers for the beginning and end regions."
+  (let ((inhibit-read-only t))
+    (remove-text-properties beg end
+                            '(font-lock-face org-roam-shielded
+                                             read-only t)
+                            (marker-buffer beg))))
+
+;;; Formatting
+(defun org-roam-format (template replacer)
+  "Format TEMPLATE with the function REPLACER.
+REPLACER takes an argument of the format variable and optionally
+an extra argument which is the EXTRA value from the call to
+`org-roam-format'.
+Adapted from `s-format'."
+  (let ((saved-match-data (match-data)))
+    (unwind-protect
+        (replace-regexp-in-string
+         "\\${\\([^}]+\\)}"
+         (lambda (md)
+           (let ((var (match-string 1 md))
+                 (replacer-match-data (match-data)))
+             (unwind-protect
+                 (let ((v (progn
+                            (set-match-data saved-match-data)
+                            (funcall replacer var))))
+                   (if v (format "%s" v) (signal 'org-roam-format-resolve md)))
+               (set-match-data replacer-match-data)))) template
+         ;; Need literal to make sure it works
+         t t)
+      (set-match-data saved-match-data))))
+
+(defvar org-roam--cached-display-format nil)
+
+(defun org-roam--process-display-format (format)
+  "Pre-calculate minimal widths needed by the FORMAT string."
+  (or org-roam--cached-display-format
+      (setq org-roam--cached-display-format
+            (let* ((fields-width 0)
+                   (string-width
+                    (string-width
+                     (org-roam-format
+                      format
+                      (lambda (field)
+                        (setq fields-width
+                              (+ fields-width
+                                 (string-to-number
+                                  (or (cadr (split-string field ":"))
+                                      "")))))))))
+              (cons format (+ fields-width string-width))))))
+
+;;; for org-roam-demote-entire-buffer in org-roam-refile.el
+(defun org-roam--file-keyword-get (keyword)
+  "Pull a KEYWORD setting from the top of the file.
+
+Keyword must be specified in ALL CAPS."
+  (cadr (assoc keyword
+               (org-collect-keywords (list keyword)))))
+
+(defun org-roam--file-keyword-kill (keyword)
+  "Erase KEYWORD setting line from the top of the file."
+  (let ((case-fold-search t))
+    (org-with-point-at 1
+      (when (re-search-forward (concat "^#\\+" keyword ":") nil t)
+        (beginning-of-line)
+        (delete-region (point) (line-end-position))
+        (delete-char 1)))))
+
+(defun org-roam--kill-empty-buffer ()
+  "If the source buffer has been emptied, kill it.
+
+If the buffer is associated with a file, delete the file.
+
+If the buffer is associated with an in-process capture operation, abort the operation."
+  (when (eq (buffer-size) 0)
+    (if (buffer-file-name)
+        (delete-file (buffer-file-name)))
+    (set-buffer-modified-p nil)
+    (when (and org-capture-mode
+               (buffer-base-buffer (current-buffer)))
+      (org-capture-kill))
+    (kill-buffer (current-buffer))))
+
+;;; Diagnostics
+;;;###autoload
+(defun org-roam-version (&optional message)
+  "Return `org-roam' version.
+Interactively, or when MESSAGE is non-nil, show in the echo area."
+  (interactive)
+  (let* ((version
+          (with-temp-buffer
+            (insert-file-contents-literally (locate-library "org-roam.el"))
+            (goto-char (point-min))
+            (save-match-data
+              (if (re-search-forward "\\(?:;; Version: \\([^z-a]*?$\\)\\)" nil nil)
+                  (substring-no-properties (match-string 1))
+                "N/A")))))
+    (if (or message (called-interactively-p 'interactive))
+        (message "%s" version)
+      version)))
+
+;;;###autoload
+(defun org-roam-diagnostics ()
+  "Collect and print info for `org-roam' issues."
+  (interactive)
+  (with-current-buffer (switch-to-buffer-other-window (get-buffer-create "*org-roam diagnostics*"))
+    (erase-buffer)
+    (insert (propertize "Copy info below this line into issue:\n" 'face '(:weight bold)))
+    (insert (format "- Emacs: %s\n" (emacs-version)))
+    (insert (format "- Framework: %s\n"
+                    (condition-case _
+                        (completing-read "I'm using the following Emacs framework:"
+                                         '("Doom" "Spacemacs" "N/A" "I don't know"))
+                      (quit "N/A"))))
+    (insert (format "- Org: %s\n" (org-version nil 'full)))
+    (insert (format "- Org-roam: %s" (org-roam-version)))))
+
+(provide 'org-roam-utils)
+;;; org-roam-utils.el ends here

tests/roam-files/alias.org

@@ -1,2 +0,0 @@
-#+roam_alias: "a1" "a 2"
-#+title: t1

tests/roam-files/bar.org

@@ -1,3 +1,6 @@
+:PROPERTIES:
+:ID:       440795d0-70c1-4165-993d-aebd5eef7a24
+:END:
 #+title: Bar
 
-This is file bar. Bar links to [[file:nested/bar.org][Nested Bar]].
+[[id:884b2341-b7fe-434d-848c-5282c0727861][Foo]]

tests/roam-files/base.org

@@ -1 +0,0 @@
-#+title: Base

tests/roam-files/cite_ref.org

@@ -1 +0,0 @@
-#+roam_key: cite:mitsuha2007

tests/roam-files/foo.org

@@ -1,8 +1,4 @@
+:PROPERTIES:
+:ID:       884b2341-b7fe-434d-848c-5282c0727861
+:END:
 #+title: Foo
-
-This is the foo file. It contains a link to [[file:bar.org][Bar]].
-
-To make the tests more robust, here are some arbitrary links:
-
-- [[https:google.com][Google]]
-- [[mailto:foo@john.com][mail to foo]]

tests/roam-files/headlines/headline.org

@@ -1,14 +0,0 @@
-#+TITLE: Headline
-
-* Headline 1
-:PROPERTIES:
-:ID:       e84d0630-efad-4017-9059-5ef917908823
-:END:
-
-* No headline here
-Oops.
-
-* Headline 2
-:PROPERTIES:
-:ID:       801b58eb-97e2-435f-a33e-ff59a2f0c213
-:END:

tests/roam-files/multiple-refs.org

@@ -1,2 +0,0 @@
-#+roam_key: https://www.orgroam.com/
-#+roam_key: cite:orgroam2020

tests/roam-files/nested/bar.org

@@ -1,3 +0,0 @@
-#+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 +0,0 @@
-#+title: Deeply Nested File

tests/roam-files/nested/foo.org

@@ -1,3 +0,0 @@
-#+title: Nested Foo
-
-This file has no links.

tests/roam-files/no-title.org

@@ -1,5 +0,0 @@
-no title in this file :O
-
-links to itself, with no title: [[file:no-title.org][no-title]]
-
-* Headline title

tests/roam-files/tags/no_tag.org

@@ -1,3 +0,0 @@
-#+title: Tagless File
-
-This file has no tags, and should not yield any tags on extracting via ~#+roam_tags~.

tests/roam-files/tags/tag.org

@@ -1,5 +0,0 @@
-#+roam_tags: "t1" "t2 with space" t3
-#+roam_tags: "t4 second-line"
-#+title: Tags
-
-This file is used to test functionality for =(org-roam--extract-tags)=

tests/roam-files/titles/aliases.org

@@ -1,2 +0,0 @@
-#+roam_alias: "roam" "alias"
-#+roam_alias: "second" "line"

tests/roam-files/titles/combination.org

@@ -1,4 +0,0 @@
-#+title: TITLE PROP
-#+roam_alias: "roam" "alias"
-
-* Headline

tests/roam-files/titles/headline.org

@@ -1 +0,0 @@
-* Headline

tests/roam-files/titles/title.org

@@ -1 +0,0 @@
-#+title: Title

tests/roam-files/unlinked.org

@@ -1,3 +0,0 @@
-#+title: Unlinked
-
-Nothing links here :(

tests/roam-files/web_ref.org

@@ -1 +0,0 @@
-#+roam_key: https://google.com/

tests/test-org-roam-perf.el

@@ -1,53 +0,0 @@
-;;; test-org-roam-perf.el --- Performance Tests for Org-roam -*- lexical-binding: t; -*-
-
-;; Copyright (C) 2020 Jethro Kuan
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation, either version 3 of the License, or
-;; (at your option) any later version.
-
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-
-;; You should have received a copy of the GNU General Public License
-;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-;;; Commentary:
-;;; Code:
-
-(require 'buttercup)
-(require 'org-roam)
-
-(defconst test-org-roam-perf-zip-url "https://github.com/org-roam/test-org-files/archive/master.zip"
-  "Path to zip for test org-roam files.")
-
-(defun test-org-roam-perf--abs-path (file-path)
-  "Get absolute FILE-PATH from `org-roam-directory'."
-  (expand-file-name file-path org-roam-directory))
-
-(defun test-org-roam-perf--init ()
-  "."
-  (let* ((temp-loc (expand-file-name (make-temp-name "test-org-files-") temporary-file-directory))
-         (zip-file-loc (concat temp-loc ".zip"))
-         (_ (url-copy-file test-org-roam-perf-zip-url zip-file-loc))
-         (_ (shell-command (format "mkdir -p %s && unzip -j -qq %s -d %s" temp-loc zip-file-loc temp-loc))))
-    (setq org-roam-directory temp-loc)))
-
-(describe "Cache Build"
-  (it "cache build from scratch time to be acceptable"
-    (test-org-roam-perf--init)
-    (pcase (benchmark-run 1 (org-roam-db-build-cache t))
-      (`(,time ,gcs ,time-in-gc)
-       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
-       (expect time :to-be-less-than 110))))
-  (it "builds quickly without change"
-    (pcase (benchmark-run 1 (org-roam-db-build-cache))
-      (`(,time ,gcs ,time-in-gc)
-       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
-       (expect time :to-be-less-than 5)))))

tests/test-org-roam.el

@@ -23,341 +23,31 @@
 
 (require 'buttercup)
 (require 'org-roam)
-(require 'dash)
 
-(defun test-org-roam--abs-path (file-path)
+(describe "org-roam-db-sync"
-  "Get absolute FILE-PATH from `org-roam-directory'."
-  (expand-file-name file-path org-roam-directory))
-
-(defun test-org-roam--find-file (path)
-  "PATH."
-  (let ((path (test-org-roam--abs-path path)))
-    (make-directory (file-name-directory path) t)
-    (find-file path)))
-
-(defvar test-org-roam-directory (expand-file-name "tests/roam-files")
-  "Directory containing org-roam test org files.")
-
-(defun test-org-roam--init ()
-  "."
-  (let ((original-dir test-org-roam-directory)
-        (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
-    (copy-directory original-dir new-dir)
-    (setq org-roam-directory new-dir)
-    (org-roam-mode +1)
-    (sleep-for 2)))
-
-(defun test-org-roam--teardown ()
-  (org-roam-mode -1)
-  (delete-file org-roam-db-location)
-  (org-roam-db--close))
-
-(describe "Ref extraction"
   (before-all
-    (test-org-roam--init))
+    (setq org-roam-directory (expand-file-name "tests/roam-files")
+          org-roam-db-location (expand-file-name "org-roam.db" temporary-file-directory))
+    (org-roam-setup))
 
   (after-all
-    (test-org-roam--teardown))
+    (org-roam-teardown)
+    (delete-file org-roam-db-location))
 
-  (cl-flet
+  (it "has the correct number of files"
-      ((test (fn file)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files]))
-             (let* ((fname (test-org-roam--abs-path file))
-                    (buf (find-file-noselect fname)))
-               (with-current-buffer buf
-                 ;; Unlike tag extraction, it doesn't make sense to
-                 ;; pass a filename.
-                 (funcall fn)))))
-    ;; Enable "cite:" link parsing
-    (org-link-set-parameters "cite")
-    (it "extracts web keys"
-      (expect (test #'org-roam--extract-ref
-                    "web_ref.org")
-              :to-equal
-              '("website" . "//google.com/")))
-    (it "extracts cite keys"
-      (expect (test #'org-roam--extract-ref
-                    "cite_ref.org")
-              :to-equal
-              '("cite" . "mitsuha2007")))
-    (it "extracts all keys"
-      (expect (test #'org-roam--extract-refs
-                    "multiple-refs.org")
-              :to-have-same-items-as
-              '(("cite" . "orgroam2020")
-                ("website" . "//www.orgroam.com/"))))))
-
-(describe "Title extraction"
-  :var (org-roam-title-sources)
-  (before-all
-    (test-org-roam--init))
-
-  (after-all
-    (test-org-roam--teardown))
-
-  (cl-flet
-      ((test (fn file)
-             (let ((buf (find-file-noselect
-                         (test-org-roam--abs-path file))))
-               (with-current-buffer buf
-                 (funcall fn)))))
-    (it "extracts title from title property"
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/title.org")
-              :to-equal
-              '("Title"))
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/aliases.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/headline.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-title
-                    "titles/combination.org")
-              :to-equal
-              '("TITLE PROP")))
-
-    (it "extracts alias"
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/title.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/aliases.org")
-              :to-equal
-              '("roam" "alias" "second" "line"))
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/headline.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/combination.org")
-              :to-equal
-              '("roam" "alias")))
-
-    (it "extracts headlines"
-      (expect (test #'org-roam--extract-titles-alias
-                    "titles/title.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/aliases.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/headline.org")
-              :to-equal
-              '("Headline"))
-      (expect (test #'org-roam--extract-titles-headline
-                    "titles/combination.org")
-              :to-equal
-              '("Headline")))
-
-    (describe "uses org-roam-title-sources correctly"
-      (it "'((title headline) alias)"
-        (expect (let ((org-roam-title-sources '((title headline) alias)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("TITLE PROP" "roam" "alias")))
-      (it "'((headline title) alias)"
-        (expect (let ((org-roam-title-sources '((headline title) alias)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("Headline" "roam" "alias")))
-      (it "'(headline alias title)"
-        (expect (let ((org-roam-title-sources '(headline alias title)))
-                  (test #'org-roam--extract-titles
-                        "titles/combination.org"))
-                :to-equal
-                '("Headline" "roam" "alias" "TITLE PROP"))))))
-
-(describe "Tag extraction"
-  :var (org-roam-tag-sources)
-  (before-all
-    (test-org-roam--init))
-
-  (after-all
-    (test-org-roam--teardown))
-
-  (cl-flet
-      ((test (fn file)
-             (let* ((fname (test-org-roam--abs-path file))
-                    (buf (find-file-noselect fname)))
-               (with-current-buffer buf
-                 (funcall fn fname)))))
-    (it "extracts from prop"
-      (expect (test #'org-roam--extract-tags-prop
-                    "tags/tag.org")
-              :to-equal
-              '("t1" "t2 with space" "t3" "t4 second-line"))
-      (expect (test #'org-roam--extract-tags-prop
-                    "tags/no_tag.org")
-              :to-equal
-              nil))
-
-    (it "extracts from all directories"
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-all-directories
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("nested" "deeply")))
-
-    (it "extracts from last directory"
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-last-directory
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("deeply")))
-
-    (it "extracts from first directory"
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "base.org")
-              :to-equal
-              nil)
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "tags/tag.org")
-              :to-equal
-              '("tags"))
-      (expect (test #'org-roam--extract-tags-first-directory
-                    "nested/deeply/deeply_nested_file.org")
-              :to-equal
-              '("nested")))
-
-    (describe "uses org-roam-tag-sources correctly"
-      (it "'(prop)"
-        (expect (let ((org-roam-tag-sources '(prop)))
-                  (test #'org-roam--extract-tags
-                        "tags/tag.org"))
-                :to-equal
-                '("t1" "t2 with space" "t3" "t4 second-line")))
-      (it "'(prop all-directories)"
-        (expect (let ((org-roam-tag-sources '(prop all-directories)))
-                  (test #'org-roam--extract-tags
-                        "tags/tag.org"))
-                :to-equal
-                '("t1" "t2 with space" "t3" "t4 second-line" "tags"))))))
-
-(describe "ID extraction"
-  (before-all
-    (test-org-roam--init))
-
-  (after-all
-    (test-org-roam--teardown))
-
-  (cl-flet
-      ((test (fn file)
-             (let* ((fname (test-org-roam--abs-path file))
-                    (buf (find-file-noselect fname)))
-               (with-current-buffer buf
-                 (funcall fn fname)))))
-    (it "extracts ids"
-      (expect (test #'org-roam--extract-ids
-                    "headlines/headline.org")
-              :to-have-same-items-as
-              `(["e84d0630-efad-4017-9059-5ef917908823" ,(test-org-roam--abs-path "headlines/headline.org") 1]
-                ["801b58eb-97e2-435f-a33e-ff59a2f0c213" ,(test-org-roam--abs-path "headlines/headline.org") 1])))))
-
-(describe "Test roam links"
-  (it ""
-    (expect (org-roam-link--split-path "")
             :to-equal
-            '(title "" "" nil)))
+            2))
-  (it "title"
+
-    (expect (org-roam-link--split-path "title")
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
             :to-equal
-            '(title "title" "" nil)))
+            2))
-  (it "title*"
+
-    (expect (org-roam-link--split-path "title*")
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
             :to-equal
-            '(title+headline "title" "" 5)))
+            1)))
-  (it "title*headline"
-    (expect (org-roam-link--split-path "title*headline")
-            :to-equal
-            '(title+headline "title" "headline" 5)))
-  (it "*headline"
-    (expect (org-roam-link--split-path "*headline")
-            :to-equal
-            '(headline "" "headline" 0))))
-
-;;; Tests
-(xdescribe "org-roam-db-build-cache"
-  (before-each
-    (test-org-roam--init))
-
-  (after-each
-    (test-org-roam--teardown))
-
-  (it "initializes correctly"
-    ;; Cache
-    (expect (caar (org-roam-db-query [:select (funcall count) :from files])) :to-be 8)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links])) :to-be 5)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from titles])) :to-be 8)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from titles
-                                      :where titles :is-null])) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)
-
-    ;; Links
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= source $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= source $s1)]
-                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
-
-    ;; Links -- File-to
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= dest $s1)]
-                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= dest $s1)]
-                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= dest $s1)]
-                                     (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
-    ;; TODO Test titles
-    (expect (org-roam-db-query [:select * :from titles])
-            :to-have-same-items-as
-            (list (list (test-org-roam--abs-path "alias.org")
-                        (list "t1" "a1" "a 2"))
-                  (list (test-org-roam--abs-path "bar.org")
-                        (list "Bar"))
-                  (list (test-org-roam--abs-path "foo.org")
-                        (list "Foo"))
-                  (list (test-org-roam--abs-path "nested/bar.org")
-                        (list "Nested Bar"))
-                  (list (test-org-roam--abs-path "nested/foo.org")
-                        (list "Nested Foo"))
-                  (list (test-org-roam--abs-path "no-title.org")
-                        (list "Headline title"))
-                  (list (test-org-roam--abs-path "web_ref.org") nil)
-                  (list (test-org-roam--abs-path "unlinked.org")
-                        (list "Unlinked"))))
-
-    (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")))
-
-    ;; Expect rebuilds to be really quick (nothing changed)
-    (expect (org-roam-db-build-cache)
-            :to-equal
-            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
 (provide 'test-org-roam)