update title to not truncate

Addresses #1488

.dir-locals.el

@@ -1,6 +1,12 @@
-;;; Directory Local Variables
-;;; For more information see (info "(emacs) Directory Variables")
-
 ((emacs-lisp-mode
-  (eval . (require 'org-roam-dev))
+  (fill-column . 110)
-  (sentence-end-double-space . nil)))
+  (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)
+                              (org-roam-with-file . 2)))))

.github/workflows/test.yml

@@ -34,36 +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: Initialize sandbox
+      - name: Install Eldev
-      run: |
+        run: curl -fsSL https://raw.github.com/doublep/eldev/master/webinstall/github-eldev | sh
-        SANDBOX_DIR=$(mktemp -d) || exit 1
-        echo ::set-env name=SANDBOX_DIR::$SANDBOX_DIR
-        ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
 
-    # The "all" rule is not used, because it treats compilation warnings
+      - name: Install dependencies
-    # as failures, so linting and testing are run as separate steps.
+        run: make prepare
 
-    # org-roam-compat is excluded from linting because it contains
+      - name: Lint
-    # symbols/aliases from other packages
+        run: make lint
-    - 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

@@ -12,4 +12,5 @@
 /doc/mimetype
 /doc/stats/
 /config.mk
-/doc/manual/
+/doc/manual.html
+/.eldev/

.readthedocs.yml

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

BACKERS.md

@@ -3,3 +3,6 @@
 Many thanks to the following backers, your contributions are greatly appreciated!
 
 - Nathan Tran
+- Burke Libbey
+- forkrul
+- Andreas Stuhlmüller

CHANGELOG.md

@@ -1,5 +1,133 @@
 # 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
+
+### Fixed
+
+- [#1281](https://github.com/org-roam/org-roam/pull/1281) fixed idle-timer not instantiated on `org-roam-mode`
+- [#1308](https://github.com/org-roam/org-roam/pull/1308) fixed file renames corrupting database
+- [#1325](https://github.com/org-roam/org-roam/pull/1325) make titles and tags extracted unique per note
+- [#1327](https://github.com/org-roam/org-roam/pull/1327) preserve existing link description during automatic replacement
+- [#1346](https://github.com/org-roam/org-roam/pull/1346) prevent malformed path to `org-roam-index-file`
+- [#1347](https://github.com/org-roam/org-roam/pull/1347) allow use of `%a` element in regular Org-roam captures
+- [#1352](https://github.com/org-roam/org-roam/pull/1352) fixed org-roam-{tag/alias}-{add/delete} altering the original case of the Org property
+- [#1374](https://github.com/org-roam/org-roam/pull/1374) fix headline completions erroring out
+- [#1375](https://github.com/org-roam/org-roam/pull/1375) fix org-roam-protocol to use existing ref file
+- [#1403](https://github.com/org-roam/org-roam/issues/1403) fixed inconsistency between how we write and read props like alias and tags
+- [#1409](https://github.com/org-roam/org-roam/issues/1398) prevent inclusion of non-org-roam files in `org-roam-dailies--list-files`
+
+## 1.2.3 (13-11-2020)
+
+Primarily a stabilization and bug-fix release.
+
+Org-roam-dailies has also been revamped to include new features, see [this video](https://www.youtube.com/watch?v=1q9x2aZCJJ4) for a quick overview.
+
+### Added
+
+- [#978](https://github.com/org-roam/org-roam/pull/978) Revamp org-roam-dailies
+- [#1183](https://github.com/org-roam/org-roam/pull/1183) Interactive functions for managing aliases and tags in Org-roam file, namely `org-roam-alias-add`, `org-roam-alias-delete`, `org-roam-tag-add`, and `org-roam-tag-delete`.
+- [#1215](https://github.com/org-roam/org-roam/pull/1215) Multiple `ROAM_KEY` keywords can now be specified in one file. This allows bibliographical entries to share the same note file.
+- [#1238](https://github.com/org-roam/org-roam/pull/1238) Add `org-roam-prefer-id-links` variable to select linking method
+- [#1239](https://github.com/org-roam/org-roam/pull/1239) Allow `org-roam-protocol` to capture the webpage's selection, and add a toggle for storing the links to the pages
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) add `org-roam-db-update-method` to control when the cache is rebuilt.
+
+### Changed
+
+- [#1264](https://github.com/org-roam/org-roam/pull/1264) renamed `org-roam-update-db-idle-seconds` to `org-roam-db-idle-idle-seconds`
+
+### Fixed
+
+- [#1074](https://github.com/org-roam/org-roam/issues/1074) fix `org-roam--extract-links` to handle content boundaries.
+- [#1193](https://github.com/org-roam/org-roam/issues/1193) fix `org-roam-db-build-cache` by not killing temporary buffer in `org-roam--extract-links`.
+- [#1195](https://github.com/org-roam/org-roam/issues/1195) fix ID face showing as invalid if within Org ID files, but not Org-roam's.
+- [#1199](https://github.com/org-roam/org-roam/issues/1199) make Org-roam link insertions respect `org-roam-link-title-format` everywhere.
+- [#1201](https://github.com/org-roam/org-roam/issues/1201) fix `org-roam-db-build-cache` failing in scenarios involving duplicate IDs and deleted files.
+- [#1226](https://github.com/org-roam/org-roam/issues/1226) only update relative path of file links
+- [#1232](https://github.com/org-roam/org-roam/issues/1232) fix incorrect title extractions from narrowed buffers
+- [#1233](https://github.com/org-roam/org-roam/issues/1233) fixes bug where descriptive file links become plain links during update for relative paths
+- [#1252](https://github.com/org-roam/org-roam/issues/1252) respect original link type during automatic replacement
+
+## 1.2.2 (06-10-2020)
+
+In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
+
+Org-roam now does not resolve symlinks. This significantly speeds up cache builds, but may result in some workflows breaking. In particular, Org-roam now cannot figure out if two distinct file paths in the Org-roam directory are the same file, and both files will be processed as if they were different files. This error seems to be unavoidable now that symlinks are not resolved, but this workflow is rare and should not affect most users.
+
+This change requires you to set `org-roam-directory` to the resolved path of a folder. That is:
+
+```elisp
+(setq org-roam-directory (file-truename "/path/to/directory/"))
+```
+
+### Breaking Changes
+
+- [#1164](https://github.com/org-roam/org-roam/pull/1164) Org-roam now stores the database in the user's Emacs directory by default
+- [#910](https://github.com/org-roam/org-roam/pull/910) Deprecate `company-org-roam`, using `completion-at-point` instead. To use this with company, add the `company-capf` backend instead.
+- [#1109](https://github.com/org-roam/org-roam/pull/1109) Org-roam now does not resolve symlinks.
+
+### Features
+
+- [#1163](https://github.com/org-roam/org-roam/pull/1163) Support file-level IDs introduced in Org 9.4
+- [#1093](https://github.com/org-roam/org-roam/pull/1093) Add `vanilla` org-roam-tag-source to extract buffer Org tags
+- [#1079](https://github.com/org-roam/org-roam/pull/1079) Add `org-roam-tag-face` to customize appearance of tags in interactive commands
+- [#1073](https://github.com/org-roam/org-roam/pull/1073) Rename file on title change, when `org-roam-rename-file-on-title-change` is non-nil.
+- [#1071](https://github.com/org-roam/org-roam/pull/1071) Update link descriptions on title changes, and clean-up rename file advice
+- [#1061](https://github.com/org-roam/org-roam/pull/1061) Speed up the extraction of file properties, headlines, and titles
+- [#1046](https://github.com/org-roam/org-roam/pull/1046) New user option to exclude files from Org-roam
+- [#1032](https://github.com/org-roam/org-roam/pull/1032) File changes are now propagated to the database on idle timer. This prevents large wait times during file saves.
+- [#974](https://github.com/org-roam/org-roam/pull/974) Protect region targeted by `org-roam-insert`
+- [#994](https://github.com/org-roam/org-roam/pull/994) Simplify org-roam-store-link
+- [#1062](https://github.com/org-roam/org-roam/pull/1062) Variable `org-roam-completions-everywhere` allows for completions everywhere from word at point
+- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`
+
+### Bugfixes
+
+- [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
+- [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
+
+## 1.2.1 (27-07-2020)
+
+This release consisted of a big deal of refactoring and bug fixes. Notably, we fixed several catastrophic failures on db builds with bad setups (#854), and modularized tag and title extractions.
+
+We also added some new features that had been a long time coming:
+
+1. We made the backlinks more outline-friendly by also showing the outline hierarchy for a backlink (#863)
+2. We now support nested captures, which is crucial for `org-roam-protocol` (#966)
+
+### Breaking Changes
+
+- [#908](https://github.com/org-roam/org-roam/pull/908) Normalized titles in database. May break external packages that rely on unnormalized titles.
+
+### Features
+
+- [#814](https://github.com/org-roam/org-roam/pull/814) Implement `org-roam-insert-immediate`
+- [#833](https://github.com/org-roam/org-roam/pull/833) Add customization of file titles with `org-roam-title-to-slug-function`.
+- [#839](https://github.com/org-roam/org-roam/pull/839) Return selected file from `org-roam-insert`
+- [#847](https://github.com/org-roam/org-roam/pull/847) Add GC threshold `org-roam-db-gc-threshold` to temporarily change the threshold on expensive operations.
+- [#847](https://github.com/org-roam/org-roam/pull/847) Use sqlite3 transactions instead of storing the values to be inserted.
+- [#851](https://github.com/org-roam/org-roam/pull/851) Add `'first-directory'` option for `org-roam-tag-sources`
+- [#863](https://github.com/org-roam/org-roam/pull/863) Display outline hierarchy in backlinks buffer
+- [#898](https://github.com/org-roam/org-roam/pull/898) Add `org-roam-random-note` to browse a random note.
+- [#900](https://github.com/org-roam/org-roam/pull/900) Support and index all valid org links
+- [#966](https://github.com/org-roam/org-roam/pull/966) Enable nested captures
+
+### Bugfixes
+
+- [#854](https://github.com/org-roam/org-roam/pull/854) Warn instead of fail when duplicate refs and IDs exist.
+- [#857](https://github.com/org-roam/org-roam/pull/857) Fix tag extraction for symlinked directories.
+- [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
+- [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
+
 ## 1.2.0 (12-06-2020)
 
 In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
@@ -23,6 +151,7 @@ We also add `org-roam-unlinked-references`, which naively finds text that could
 - [#679](https://github.com/org-roam/org-roam/pull/679), [#683](https://github.com/org-roam/org-roam/pull/683) Building of the graph now happens in a separate process
 
 ### Bugfixes
+
 - [#714](https://github.com/org-roam/org-roam/pull/714) No longer print citelinks in backlinks buffer if there is no `ROAM_KEY` property or `org-ref` is not installed
 - [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
 - [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
@@ -32,7 +161,7 @@ We also add `org-roam-unlinked-references`, which naively finds text that could
 In this release, we added two new features:
 
 1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
-2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://org-roam.github.io/org-roam/manual/Tags.html#Tags).
+2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://www.orgroam.com/manual/Tags.html#Tags).
 
 As usual, this release comes with a multitude of bug-fixes and refactorings.
 

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

@@ -1,42 +1,35 @@
-[![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
+# Org-roam [![GitHub Release][release-badge]][release] [![MELPA][melpa-badge]][melpa] [![License GPL 3][gpl3-badge]][gpl3]
-[![GitHub Release](https://img.shields.io/github/v/release/org-roam/org-roam)](https://img.shields.io/github/v/release/org-roam/org-roam)
-[![MELPA](https://melpa.org/packages/org-roam-badge.svg)](https://melpa.org/#/org-roam)
 
-## Synopsis
+<img src="https://www.orgroam.com/img/logo.svg" align="right" alt="Org-roam Logo" width="240">
 
-Org-roam is a [Roam][roamresearch] replica built on top of the
+Org-roam is a plain-text knowledge management system. It brings some of
-all-powerful [Org-mode][org].
+[Roam's][roamresearch] more powerful features into the [Org-mode][org]
+ecosystem.
 
-Org-roam is a solution for effortless non-hierarchical note-taking
+Org-roam borrows principles from the Zettelkasten method, providing a solution
-with Org-mode. With Org-roam, notes flow naturally, making note-taking
+for non-hierarchical note-taking. It should also work as a plug-and-play
-fun and easy. Org-roam should also work as a plug-and-play solution
+solution for anyone already using Org-mode for their personal wiki.
-for anyone already using Org-mode for their personal wiki.
 
-Org-roam aims to implement the core features of Roam, leveraging the
+- **Private and Secure**: Edit your personal wiki completely offline, entirely
-mature ecosystem around Org-mode where possible. Eventually, we hope
+  in your control. Encrypt your notes with GPG. Take lasting notes in
-to further introduce features enabled by the Emacs ecosystem.
+  plain-text.
+- **Networked Thought**: Connect notes and thoughts together with ease using
+  backlinks. Discover surprising and previously unseen connections in your notes
+  with the built-in graph visualization.
+- **Extensible and Powerful**: Leverage Emacs' fantastic text-editing interface,
+  and the mature Emacs and Org-mode ecosystem of packages.
+- **Free and Open Source**: Org-roam is licensed under the GNU General Public
+  License version 3 or later.
 
-[@technovangelist](https://github.com/technovangelist/) has produced a video
+<p align="center">
-describing Org-roam and the concepts behind it:
+  <img src="https://www.orgroam.com/img/screenshot.png" alt="Org-roam Screenshot" width="738">
-
+</p>
-[![Making Connections in your Notes](http://img.youtube.com/vi/Lg61ocfxk3c/0.jpg)](http://www.youtube.com/watch?v=Lg61ocfxk3c "Making Connections in your Notes")
-
-Important links:
 
 - **[Documentation][docs]**
 - **[Discourse][discourse]**
 - **[Slack][slack]**
-
+- **[Frequently Asked Questions][faq]**
-## A Preview
+- **[Changelog](CHANGELOG.md)**
-
-Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
-right) shows backlinks for the active Org-roam buffer (window on the
-left), as well as the surrounding content in the backlink file. The
-database is built once, and updated incrementally. The graph is
-generated from the link structure, and can be used to navigate to the
-respective files.
-
-![img](doc/images/org-roam-graph.gif)
 
 ## Installation
 
@@ -46,10 +39,11 @@ You can install `org-roam` using `package.el`:
 M-x package-install RET org-roam RET
 ```
 
-Here's a sample configuration with using `use-package`:
+Here's a sample configuration with `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
+      :ensure t
       :hook
       (after-init . org-roam-mode)
       :custom
@@ -57,29 +51,35 @@ Here's a sample configuration with using `use-package`:
       :bind (:map org-roam-mode-map
               (("C-c n l" . org-roam)
                ("C-c n f" . org-roam-find-file)
-               ("C-c n g" . org-roam-show-graph))
+               ("C-c n g" . org-roam-graph))
               :map org-mode-map
               (("C-c n i" . org-roam-insert))))
 ```
 
-`org-roam-graph` by default expects to find the `dot` executable
+Org-roam requires sqlite to function. Org-roam optionally uses Graphviz for
-from the `graphviz` package in the `exec-path`.
+graph-related functionality. It is recommended to install PCRE-enabled ripgrep
-Ensure `graphviz` is installed and found if you want to use this
+for better performance and extended functionality.
-feature or customize your configuration for `org-roam-graph` to use a
-different tool.
 
-For more detailed installation and configuration instructions (including for
+## Getting Help
-Doom and Spacemacs users), please see [the
+
-documentation][docs].
+Before creating a new topic/issue, please be mindful of our time and ensure that
+it has not already been addressed on [GitHub][issues] or on
+[Discourse][discourse].
+
+- If you are new to Emacs and have problem setting up Org-roam, please ask your
+  question on [Slack, channel #how-do-i][slack].
+- For quick questions, please ask them on [Slack, channel
+  #troubleshooting][slack].
+- If something is not working as it should, or if you would like to suggest a
+  new feature, please [create a new issue][issues].
+- If you have questions about your workflow with the slip-box method, please
+  find a relevant topic on [Discourse][discourse], or create a new one.
 
 ## Knowledge Bases using Org-roam
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
-
+- [Alexey Shmalko](https://braindump.rasen.dev/)
-## Changelog
-
-A changelog is being maintained [here](CHANGELOG.md)
 
 ## Contributing
 
@@ -90,11 +90,18 @@ request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
 ## License
 
 Copyright © Jethro Kuan and contributors. Distributed under the GNU
-General Public License, Version 3
+General Public License, Version 3.
 
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
-[badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
+[gpl3-badge]: https://img.shields.io/badge/license-GPL_3-green.svg
-[docs]: https://org-roam.github.io/org-roam/manual/
+[gpl3]: http://www.gnu.org/licenses/gpl-3.0.txt
+[melpa-badge]: https://melpa.org/packages/org-roam-badge.svg
+[melpa]: https://melpa.org/#/org-roam
+[release-badge]: https://img.shields.io/github/v/release/org-roam/org-roam
+[release]: https://github.com/org-roam/org-roam/releases
+[docs]: https://www.orgroam.com/manual.html
 [discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
+[issues]: https://github.com/org-roam/org-roam/issues
+[faq]: https://www.orgroam.com/manual.html#FAQ

doc/AUTHORS.md

@@ -34,4 +34,4 @@ Contributors
 - Rafael Accácio Nogueira <raccacio@poli.ufrj.br>
 - Roland Coeurjoly <rolandcoeurjoly@gmail.com>
 - Sayan <dit7ya@users.noreply.github.com>
-- Tim Quelch <tim@quelch.name>
+- Tim Quelch <tim@tquelch.com>

doc/Makefile

@@ -27,12 +27,9 @@ dir: org-roam.info
 	@printf "Generating $@\n"
 	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<
 
-html-dir: 
+html-dir:
-	@printf "Generating org-roam/*.html\n"
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) org-roam.texi
-	@$(MAKEINFO) --html $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam.html manual.html
-	mv org-roam manual
-	cp -r assets manual
-	cp -r images manual
 
 %.pdf: %.texi
 	@printf "Generating $@\n"

doc/assets/page.css

@@ -1,442 +1,68 @@
-/* Import Inter font */
-/* More info at https://github.com/xz/fonts */
-@import url("https://fonts.xz.style/serve/inter.css");
-
 :root {
-  --nc-font-sans: "Inter", -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
+  --border: #526980;
-    Oxygen, Ubuntu, Cantarell, "Open Sans", "Helvetica Neue", sans-serif,
+  --code: #007;
-    "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";
-  --nc-font-mono: "Courier New", Courier, "Ubuntu Mono", "Liberation Mono",
-    monospace;
-  --nc-tx-1: #000000;
-  --nc-tx-2: #1a1a1a;
-  --nc-bg-1: #ffffff;
-  --nc-bg-2: #f6f8fa;
-  --nc-bg-3: #e5e7eb;
-  --nc-lk-1: #0070f3;
-  --nc-lk-2: #0366d6;
-  --nc-lk-tx: #ffffff;
-  --nc-ac-1: #79ffe1;
-  --nc-ac-tx: #0c4047;
-}
-
-@media (prefers-color-scheme: dark) {
-  :root {
-    --nc-tx-1: #ffffff;
-    --nc-tx-2: #eeeeee;
-    --nc-bg-1: #000000;
-    --nc-bg-2: #111111;
-    --nc-bg-3: #222222;
-    --nc-lk-1: #3291ff;
-    --nc-lk-2: #0070f3;
-    --nc-lk-tx: #ffffff;
-    --nc-ac-1: #7928ca;
-    --nc-ac-tx: #ffffff;
-  }
-}
-
-* {
-  /* Reset margins and padding */
-  margin: 0;
-  padding: 0;
-}
-
-address,
-area,
-article,
-aside,
-audio,
-blockquote,
-datalist,
-details,
-dl,
-fieldset,
-figure,
-form,
-input,
-iframe,
-img,
-meter,
-nav,
-ol,
-optgroup,
-option,
-output,
-p,
-pre,
-progress,
-ruby,
-section,
-table,
-textarea,
-ul,
-video {
-  /* Margins for most elements */
-  margin-bottom: 1rem;
-}
-
-html,
-input,
-select,
-button {
-  /* Set body font family and some finicky elements */
-  font-family: var(--nc-font-sans);
 }
 
 body {
-  /* Center body in page */
+    margin: 5ex 10ex;
-  margin: 0 auto;
+    max-width: 80ex;
-  max-width: 750px;
+    line-height: 1.5;
-  padding: 2rem;
+    font-family: sans-serif;
-  border-radius: 6px;
-  overflow-x: hidden;
-  background: var(--nc-bg-1);
-
-  /* Main body text */
-  color: var(--nc-tx-2);
-  font-size: 1.03rem;
-  line-height: 1.5;
 }
 
-::selection {
+h1, h2, h3 {
-  /* Set background color for selected text */
+    font-weight: normal;
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
 }
 
-p {
+pre, code {
-  margin-bottom: 1rem;
+    font-family: x, monospace;
-}
-
-h1,
-h2,
-h3,
-h4,
-h5,
-h6 {
-  line-height: 1;
-  color: var(--nc-tx-1);
-  padding-top: 0.875rem;
-}
-
-h1,
-h2,
-h3 {
-  color: var(--nc-tx-1);
-  padding-bottom: 2px;
-  margin-bottom: 8px;
-  border-bottom: 1px solid var(--nc-bg-2);
-}
-
-h4,
-h5,
-h6 {
-  margin-bottom: 0.3rem;
-}
-
-h1 {
-  font-size: 2.25rem;
-}
-
-h2 {
-  font-size: 1.85rem;
-}
-
-h3 {
-  font-size: 1.55rem;
-}
-
-h4 {
-  font-size: 1.25rem;
-}
-
-h5 {
-  font-size: 1rem;
-}
-
-h6 {
-  font-size: 0.875rem;
-}
-
-a {
-  color: var(--nc-lk-1);
-}
-
-a:hover {
-  color: var(--nc-lk-2);
-}
-
-abbr:hover {
-  /* Set the '?' cursor while hovering an abbreviation */
-  cursor: help;
-}
-
-blockquote {
-  padding: 1.5rem;
-  background: var(--nc-bg-2);
-  border-left: 5px solid var(--nc-bg-3);
-}
-
-abbr {
-  cursor: help;
-}
-
-blockquote *:last-child {
-  padding-bottom: 0;
-  margin-bottom: 0;
-}
-
-header {
-  background: var(--nc-bg-2);
-  border-bottom: 1px solid var(--nc-bg-3);
-  padding: 2rem 1.5rem;
-
-  /* This sets the right and left margins to cancel out the body's margins. It's width is still the same, but the background stretches across the page's width. */
-
-  margin: -2rem calc(0px - (50vw - 50%)) 2rem;
-
-  /* Shorthand for:
-
-	margin-top: -2rem;
-	margin-bottom: 2rem;
-
-	margin-left: calc(0px - (50vw - 50%));
-	margin-right: calc(0px - (50vw - 50%)); */
-
-  padding-left: calc(50vw - 50%);
-  padding-right: calc(50vw - 50%);
-}
-
-header h1,
-header h2,
-header h3 {
-  padding-bottom: 0;
-  border-bottom: 0;
-}
-
-header > *:first-child {
-  margin-top: 0;
-  padding-top: 0;
-}
-
-header > *:last-child {
-  margin-bottom: 0;
-}
-
-.button,
-button,
-input[type="submit"],
-input[type="reset"],
-input[type="button"] {
-  font-size: 1rem;
-  display: inline-block;
-  padding: 6px 12px;
-  text-align: center;
-  text-decoration: none;
-  white-space: nowrap;
-  background: var(--nc-lk-1);
-  color: var(--nc-lk-tx);
-  border: 0;
-  border-radius: 4px;
-  box-sizing: border-box;
-  cursor: pointer;
-  color: var(--nc-lk-tx);
-}
-
-.button[disabled],
-button[disabled],
-input[type="submit"][disabled],
-input[type="reset"][disabled],
-input[type="button"][disabled] {
-  cursor: default;
-  opacity: 0.5;
-
-  /* Set the [X] cursor while hovering a disabled link */
-  cursor: not-allowed;
-}
-
-.button:focus,
-.button:hover,
-button:focus,
-button:hover,
-input[type="submit"]:focus,
-input[type="submit"]:hover,
-input[type="reset"]:focus,
-input[type="reset"]:hover,
-input[type="button"]:focus,
-input[type="button"]:hover {
-  background: var(--nc-lk-2);
-}
-
-code,
-pre,
-kbd,
-samp {
-  /* Set the font family for monospaced elements */
-  font-family: var(--nc-font-mono);
-}
-
-code,
-samp,
-kbd,
-pre {
-  /* The main preformatted style. This is changed slightly across different cases. */
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-  padding: 3px 6px;
-  font-size: 0.9rem;
-}
-
-kbd {
-  /* Makes the kbd element look like a keyboard key */
-  border-bottom: 3px solid var(--nc-bg-3);
 }
 
 pre {
-  padding: 1rem 1.4rem;
+    padding: 1ex;
-  max-width: 100%;
+    background: #eee;
-  overflow: auto;
+    border: solid 1px #ddd;
+    min-width: 0;
+    font-size: 80%;
+    overflow: auto;
 }
 
-pre code {
+code {
-  /* When <code> is in a <pre>, reset it's formatting to blend in */
+    color: var(--code);
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-code pre {
-  /* When <pre> is in a <code>, reset it's formatting to blend in */
-  display: inline;
-  background: inherit;
-  font-size: inherit;
-  color: inherit;
-  border: 0;
-  padding: 0;
-  margin: 0;
-}
-
-details {
-  /* Make the <details> look more "clickable" */
-  padding: 0.6rem 1rem;
-  background: var(--nc-bg-2);
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-summary {
-  /* Makes the <summary> look more like a "clickable" link with the pointer cursor */
-  cursor: pointer;
-  font-weight: bold;
-}
-
-details[open] {
-  /* Adjust the <details> padding while open */
-  padding-bottom: 0.75rem;
-}
-
-details[open] summary {
-  /* Adjust the <details> padding while open */
-  margin-bottom: 6px;
-}
-
-details[open] > *:last-child {
-  /* Resets the bottom margin of the last element in the <details> while <details> is opened. This prevents double margins/paddings. */
-  margin-bottom: 0;
-}
-
-dt {
-  font-weight: bold;
-}
-
-dd::before {
-  /* Add an arrow to data table definitions */
-  content: "→ ";
-}
-
-hr {
-  /* Reset the border of the <hr> separator, then set a better line */
-  border: 0;
-  border-bottom: 1px solid var(--nc-bg-3);
-  margin: 1rem auto;
-}
-
-fieldset {
-  margin-top: 1rem;
-  padding: 2rem;
-  border: 1px solid var(--nc-bg-3);
-  border-radius: 4px;
-}
-
-legend {
-  padding: auto 0.5rem;
-}
-
-textarea {
-  /* Don't let the <textarea> extend off the screen naturally or when dragged by the user */
-  max-width: 100%;
-}
-
-ol,
-ul {
-  /* Replace the browser default padding */
-  padding-left: 2rem;
-}
-
-li {
-  margin-top: 0.4rem;
-}
-
-ul ul,
-ol ul,
-ul ol,
-ol ol {
-  margin-bottom: 0;
-}
-
-mark {
-  padding: 3px 6px;
-  background: var(--nc-ac-1);
-  color: var(--nc-ac-tx);
-}
-
-textarea,
-select,
-input {
-  padding: 6px 12px;
-  margin-bottom: 0.5rem;
-  background: var(--nc-bg-2);
-  color: var(--nc-tx-2);
-
-  /* Set a border of the same color as the main background. It isn't visible on idle, but prevents the cell from growing in size when a darker border is set on focus. */
-  border: 1px solid var(--nc-bg-2);
-  border-radius: 4px;
-  box-shadow: none;
-  box-sizing: border-box;
-}
-
-textarea:focus,
-select:focus,
-input[type]:focus {
-  border: 1px solid var(--nc-bg-3);
-
-  /* Reset any browser default outlines */
-  outline: 0;
 }
 
 img {
-  max-width: 100%;
+    max-width: 100%;
 }
 
-/* Customizations */
+table {
-.menu-comment {
+  border-collapse: collapse;
-  font-weight: bold;
+  width: 100%;
-  border: 0;
+}
-  margin: 0;
+
-  padding: 0;
+pre.menu-comment {
-  font-size: 1.2rem;
+  background: none;
+  border: none;
+  font-family: sans-serif;
+  padding: 0;
+  margin: 0;
+  font-size: 100%;
+}
+
+thead {
+  border-bottom: 1px solid var(--border);
+}
+
+tfoot {
+  border-top: 1px solid var(--border);
+}
+
+blockquote {
+  margin-left: 1rem;
+  font-style: italic;
+  font-family: serif;
+  border-left: 3px solid;
+  border-left-color: currentcolor;
+  border-color: var(--text-color);
+  padding-left: 1em;
 }

doc/index.html

@@ -93,7 +93,7 @@
         You can find us on Discourse and Slack.
         
         <ul>
-            <li>Read our documentation within Emacs, or on the <a href="https://org-roam.github.io/org-roam/manual/">Online Manual</a></li>
+            <li>Read our documentation within Emacs, or on the <a href="https://www.orgroam.com/manual.html">Online Manual</a></li>
             <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
             <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
           </ul>
@@ -120,13 +120,6 @@
             >org-roam-server</a
           >
         </div>
-        <div class="row">
-          <a
-            class="content footer-links"
-            href="https://github.com/org-roam/company-org-roam"
-            >company-org-roam</a
-          >
-        </div>
       </div>
 
       <div class="col">

org-roam-buffer.el

@@ -1,280 +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: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; 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)
-
-(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)
-
-(declare-function org-roam-db--ensure-built   "org-roam-db")
-(declare-function org-roam--extract-ref       "org-roam")
-(declare-function org-roam--get-title-or-slug "org-roam")
-(declare-function org-roam--get-backlinks     "org-roam")
-(declare-function org-roam-backlinks-mode     "org-roam")
-(declare-function org-roam-mode               "org-roam")
-
-(defcustom org-roam-buffer-position 'right
-  "Position of `org-roam' buffer.
-Valid values are
- * left,
- * right,
- * top,
- * bottom."
-  :type '(choice (const left)
-                 (const right)
-                 (const top)
-                 (const bottom))
-  :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-citelinks)
-  "Hook run in the `org-roam-buffer' before it is displayed."
-  :type 'hook
-  :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--insert-title ()
-  "Insert the org-roam-buffer title."
-  (insert (propertize (org-roam--get-title-or-slug
-                       (buffer-file-name org-roam-buffer--current))
-                       'font-lock-face
-                       'org-document-title)))
-
-(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--insert-citelinks ()
-  "Insert citation backlinks for the current buffer."
-  (when-let ((org-ref-p (require 'org-ref nil t)) ;; Ensure that org-ref is present
-             (ref (cdr (with-temp-buffer
-                        (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))))
-    (if-let* ((key-backlinks (org-roam--get-backlinks ref))
-              (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 "Cite backlink" l))))
-          (dolist (group grouped-backlinks)
-            (let ((file-from (car group))
-                  (bls (cdr group)))
-              (insert (format "** [[file:%s][%s]]\n"
-                              file-from
-                              (org-roam--get-title-or-slug file-from)))
-              (dolist (backlink bls)
-                (pcase-let ((`(,file-from _ ,props) backlink))
-                  (insert (propertize
-                           (s-trim (s-replace "\n" " "
-                                              (plist-get props :content)))
-                           'help-echo "mouse-1: visit backlinked note"
-                           'file-from file-from
-                           'file-from-point (plist-get props :point)))
-                  (insert "\n\n"))))))
-      (insert "\n\n* No cite backlinks!"))))
-
-(defun org-roam-buffer--insert-backlinks ()
-  "Insert the org-roam-buffer backlinks string for the current buffer."
-  (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
-            (backlinks (org-roam--get-backlinks file-path))
-            (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)
-          (let ((file-from (car group))
-                (bls (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
-                            file-from
-                            (org-roam--get-title-or-slug file-from)))
-            (dolist (backlink bls)
-              (pcase-let ((`(,file-from _ ,props) backlink))
-                (insert (propertize
-                         (s-trim (s-replace "\n" " "
-                                            (plist-get props :content)))
-                         'help-echo "mouse-1: visit backlinked note"
-                         'file-from file-from
-                         'file-from-point (plist-get props :point)))
-                (insert "\n\n"))))))
-    (insert "\n\n* No backlinks!")))
-
-(defun org-roam-buffer-update ()
-  "Update the `org-roam-buffer'."
-  (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-local-value 'buffer-file-truename 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 (member org-roam-buffer-position '(right left top bottom))
-             org-roam-buffer-position
-           (let ((text-quoting-style 'grave))
-             (lwarn '(org-roam) :error
-                    "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
-                    org-roam-buffer-position))
-           'right)))
-    (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-toggle-display ()
-  "Toggle display of the `org-roam-buffer'."
-  (interactive)
-  (unless org-roam-mode (org-roam-mode))
-  (setq org-roam-last-window (get-buffer-window))
-  (pcase (org-roam-buffer--visibility)
-    ('visible (delete-window (get-buffer-window org-roam-buffer)))
-    ((or 'exists 'none) (org-roam-buffer--get-create))))
-
-(provide 'org-roam-buffer)
-
-;;; org-roam-buffer.el ends here

org-roam-capture.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -29,327 +29,686 @@
 ;;
 ;; This library provides capture functionality for org-roam
 ;;; Code:
+;;;
 ;;;; Library Requires
 (require 'org-capture)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'org-roam-db)
 (require 'dash)
-(require 's)
 (require 'cl-lib)
 
 ;; Declarations
-(defvar org-roam-encrypt-files)
+(declare-function org-roam-ref-add "org-roam" (ref))
+
 (defvar org-roam-directory)
-(defvar org-roam-mode)
-(declare-function  org-roam--get-title-path-completions "org-roam")
-(declare-function  org-roam--get-ref-path-completions   "org-roam")
-(declare-function  org-roam--file-path-from-id          "org-roam")
-(declare-function  org-roam--format-link                "org-roam")
-(declare-function  org-roam--title-to-slug              "org-roam")
-(declare-function  org-roam-mode                        "org-roam")
-(declare-function  org-roam-completion--completing-read "org-roam-completion")
 
-(defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
+(defvar org-roam-capture--node nil
-  "The default file name format for Org-roam templates.")
+  "The node passed during an Org-roam capture.
-
-(defvar org-roam-capture--header-default "#+title: ${title}\n"
-  "The default capture header for Org-roam templates.")
-
-(defvar org-roam-capture--file-path nil
-  "The file path for the Org-roam capture.
-This variable is set during the Org-roam capture process.")
-
-(defvar org-roam-capture--info nil
-  "An alist of additional information passed to the Org-roam template.
 This variable is populated dynamically, and is only non-nil
 during the Org-roam capture process.")
 
-(defvar org-roam-capture--context nil
+(defvar org-roam-capture--info nil
-  "A symbol, that reflects the context for obtaining the exact point in a file.
+  "A property-list of additional information passed to the Org-roam template.
-This variable is populated dynamically, and is only active during
+This variable is populated dynamically, and is only non-nil
-an Org-roam capture process.
+during the Org-roam capture process.")
 
-The `title' context is used in `org-roam-insert' and
+(defconst org-roam-capture--template-keywords '(:if-new :id :link-description :call-location)
-`org-roam-find-file', where the capture process is triggered upon
-trying to create a new file without that `title'.
-
-The `ref' context is used by `org-roam-protocol', where the
-capture process is triggered upon trying to find or create a new
-note with the given `ref'.")
-
-(defvar org-roam-capture-additional-template-props nil
-  "Additional props to be added to the Org-roam template.")
-
-(defconst org-roam-capture--template-keywords '(:file-name :head)
   "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
 
-(defvar org-roam-capture-templates
+(defcustom org-roam-capture-templates
-  '(("d" "default" plain (function org-roam-capture--get-point)
+  '(("d" "default" plain "%?"
-     "%?"
+     :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org"
-     :file-name "%<%Y%m%d%H%M%S>-${slug}"
+                        "#+title: ${title}\n")
-     :head "#+title: ${title}\n"
      :unnarrowed t))
-  "Capture templates for Org-roam.
+  "Templates for the creation of new entries within Org-roam.
-The capture templates are an extension of
-`org-capture-templates', and the documentation there also
-applies.
 
-`org-capture-templates' are extended in 3 ways:
+Each entry is a list with the following items:
 
-1. Template expansion capabilities are extended with additional custom syntax.
+keys   The keys that will select the template, as a string, characters only, for
-   See `org-roam-capture--fill-template' for more details.
+       example \"a\" for a template to be selected with a single key, or
+       \"bt\" for selection with two keys. When using several keys, keys
+       using the same prefix must be together in the list and preceded by a
+       2-element entry explaining the prefix key, for example:
 
-2. The `:file-name' key is added, which expands to the file-name
+                   (\"b\" \"Templates for marking stuff to buy\")
-   of the note if it creates a new file.  This file-name is
-   relative to `org-roam-directory', and is without the
-   file-extension.
 
-3. The `:head' key is added, which contains the template that is
+       The \"C\" key is used by default for quick access to the customization of
-   inserted on initial creation (added only once).  This is where
+       the template variable. But if you want to use that key for a template,
-   insertion of any note metadata should go.")
+       you can.
 
-(defvar org-roam-capture-ref-templates
+description   A short string describing the template, which will be shown
-  '(("r" "ref" plain (function org-roam-capture--get-point)
+              during selection.
-     ""
+
-     :file-name "${slug}"
+type       The type of entry. Valid types are:
-     :head "#+title: ${title}
+               entry       an Org node, with a headline.  Will be filed
-#+roam_key: ${ref}\n"
+                           as the child of the target entry or as a
+                           top level entry.  Its default template is:
+                             \"* %?\n %a\"
+               item        a plain list item, will be placed in the
+                           first plain list at the target location.
+                           Its default template is:
+                             \"- %?\"
+               checkitem   a checkbox item.  This differs from the
+                           plain list item only in so far as it uses a
+                           different default template.  Its default
+                           template is:
+                             \"- [ ] %?\"
+               table-line  a new line in the first table at target location.
+                           Its default template is:
+                             \"| %? |\"
+               plain       text to be inserted as it is.
+
+template     The template for creating the capture item.
+             If it is an empty string or nil, a default template based on
+             the entry type will be used (see the \"type\" section above).
+             Instead of a string, this may also be one of:
+
+                 (file \"/path/to/template-file\")
+                 (function function-returning-the-template)
+
+             in order to get a template from a file, or dynamically
+             from a function.
+
+The template contains a compulsory :if-new property. This determines the
+location of the new node. The :if-new property contains a list, supporting
+the following options:
+
+   (file \"path/to/file\")
+       The file will be created, and prescribed an ID.
+
+   (file+head \"path/to/file\" \"head content\")
+       The file will be created, prescribed an ID, and head content will be
+       inserted into the file.
+
+   (file+olp \"path/to/file\" '(\"h1\" \"h2\"))
+       The file will be created, prescribed an ID. The OLP (h1, h2) will be
+       created, and the point placed after.
+
+   (file+head+olp \"path/to/file\" \"head content\" '(\"h1\" \"h2\"))
+       The file will be created, prescribed an ID. Head content will be
+       inserted at the start of the file. The OLP (h1, h2) will be created,
+       and the point placed after.
+
+The rest of the entry is a property list of additional options.  Recognized
+properties are:
+
+ :prepend            Normally newly captured information will be appended at
+                     the target location (last child, last table line,
+                     last list item...).  Setting this property will
+                     change that.
+
+ :immediate-finish   When set, do not offer to edit the information, just
+                     file it away immediately.  This makes sense if the
+                     template only needs information that can be added
+                     automatically.
+
+ :jump-to-captured   When set, jump to the captured entry when finished.
+
+ :empty-lines        Set this to the number of lines that should be inserted
+                     before and after the new item.  Default 0, only common
+                     other value is 1.
+
+ :empty-lines-before Set this to the number of lines that should be inserted
+                     before the new item.  Overrides :empty-lines for the
+                     number lines inserted before.
+
+ :empty-lines-after  Set this to the number of lines that should be inserted
+                     after the new item.  Overrides :empty-lines for the
+                     number of lines inserted after.
+
+ :clock-in           Start the clock in this item.
+
+ :clock-keep         Keep the clock running when filing the captured entry.
+
+ :clock-resume       Start the interrupted clock when finishing the capture.
+                     Note that :clock-keep has precedence over :clock-resume.
+                     When setting both to t, the current clock will run and
+                     the previous one will not be resumed.
+
+ :time-prompt        Prompt for a date/time to be used for date/week trees
+                     and when filling the template.
+
+ :tree-type          When `week', make a week tree instead of the month-day
+                     tree.  When `month', make a month tree instead of the
+                     month-day tree.
+
+ :unnarrowed         Do not narrow the target buffer, simply show the
+                     full buffer.  Default is to narrow it so that you
+                     only see the new stuff.
+
+ :table-line-pos     Specification of the location in the table where the
+                     new line should be inserted.  It should be a string like
+                     \"II-3\", meaning that the new line should become the
+                     third line before the second horizontal separator line.
+
+ :kill-buffer        If the target file was not yet visited by a buffer when
+                     capture was invoked, kill the buffer again after capture
+                     is finalized.
+
+ :no-save            Do not save the target file after finishing the capture.
+
+The template defines the text to be inserted.  Often this is an
+Org mode entry (so the first line should start with a star) that
+will be filed as a child of the target headline.  It can also be
+freely formatted text.  Furthermore, the following %-escapes will
+be replaced with content and expanded:
+
+  %[pathname] Insert the contents of the file given by
+              `pathname'.  These placeholders are expanded at the very
+              beginning of the process so they can be used to extend the
+              current template.
+  %(sexp)     Evaluate elisp `(sexp)' and replace it with the results.
+              Only placeholders pre-existing within the template, or
+              introduced with %[pathname] are expanded this way.  Since this
+              happens after expanding non-interactive %-escapes, those can
+              be used to fill the expression.
+  %<...>      The result of `format-time-string' on the ... format specification.
+  %t          Time stamp, date only.  The time stamp is the current time,
+              except when called from agendas with `\\[org-agenda-capture]' or
+              with `org-capture-use-agenda-date' set.
+  %T          Time stamp as above, with date and time.
+  %u, %U      Like the above, but inactive time stamps.
+  %i          Initial content, copied from the active region.  If
+              there is text before %i on the same line, such as
+              indentation, and %i is not inside a %(sexp), that prefix
+              will be added before every line in the inserted text.
+  %a          Annotation, normally the link created with `org-store-link'.
+  %A          Like %a, but prompt for the description part.
+  %l          Like %a, but only insert the literal link.
+  %L          Like %l, but without brackets (the link content itself).
+  %c          Current kill ring head.
+  %x          Content of the X clipboard.
+  %k          Title of currently clocked task.
+  %K          Link to currently clocked task.
+  %n          User name (taken from the variable `user-full-name').
+  %f          File visited by current buffer when `org-capture' was called.
+  %F          Full path of the file or directory visited by current buffer.
+  %:keyword   Specific information for certain link types, see below.
+  %^g         Prompt for tags, with completion on tags in target file.
+  %^G         Prompt for tags, with completion on all tags in all agenda files.
+  %^t         Like %t, but prompt for date.  Similarly %^T, %^u, %^U.
+              You may define a prompt like: %^{Please specify birthday}t.
+              The default date is that of %t, see above.
+  %^C         Interactive selection of which kill or clip to use.
+  %^L         Like %^C, but insert as link.
+  %^{prop}p   Prompt the user for a value for property `prop'.
+              A default value can be specified like this:
+              %^{prop|default}p.
+  %^{prompt}  Prompt the user for a string and replace this sequence with it.
+              A default value and a completion table can be specified like this:
+              %^{prompt|default|completion2|completion3|...}.
+  %?          After completing the template, position cursor here.
+  %\\1 ... %\\N Insert the text entered at the nth %^{prompt}, where N
+              is a number, starting from 1.
+
+Apart from these general escapes, you can access information specific to
+the link type that is created.  For example, calling `org-capture' in emails
+or in Gnus will record the author and the subject of the message, which you
+can access with \"%:from\" and \"%:subject\", respectively.  Here is a
+complete list of what is recorded for each link type.
+
+Link type               |  Available information
+------------------------+------------------------------------------------------
+bbdb                    |  %:type %:name %:company
+vm, wl, mh, mew, rmail, |  %:type %:subject %:message-id
+gnus                    |  %:from %:fromname %:fromaddress
+                        |  %:to   %:toname   %:toaddress
+                        |  %:fromto (either \"to NAME\" or \"from NAME\")
+                        |  %:date %:date-timestamp (as active timestamp)
+                        |  %:date-timestamp-inactive (as inactive timestamp)
+gnus                    |  %:group, for messages also all email fields
+eww, w3, w3m            |  %:type %:url
+info                    |  %:type %:file %:node
+calendar                |  %:type %:date
+
+When you need to insert a literal percent sign in the template,
+you can escape ambiguous cases with a backward slash, e.g., \\%i.
+
+In addition to all of the above, Org-roam supports additional
+substitutions within its templates. \"${foo}\" will look for the
+foo property in the Org-roam node (see the `org-roam-node'). If
+the property does not exist, the user will be prompted to fill in
+the string value.
+
+Org-roam templates are NOT compatible with regular Org capture:
+they rely on additional hacks and hooks to achieve the
+streamlined user experience in Org-roam."
+  :group 'org-roam
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+(defvar org-roam-capture-new-node-hook (list #'org-roam-capture--insert-ref)
+  "Normal-mode hooks run when a new Org-roam node is created.
+The current point is the point of the new node.
+The hooks must not move the point.")
+
+(defcustom org-roam-capture-ref-templates
+  '(("r" "ref" plain "%?"
+     :if-new (file+head "${slug}.org"
+                        "#+title: ${title}")
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
-Details on how to specify for the template is given in `org-roam-capture-templates'.")
+See `org-roam-capture-templates' for the template documentation."
+  :group 'org-roam
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+(defun org-roam-capture-p ()
+  "Return t if the current capture process is an Org-roam capture.
+This function is to only be called when `org-capture-plist' is
+valid for the capture (i.e. initialization, and finalization of
+the capture)."
+  (plist-get org-capture-plist :org-roam))
 
 (defun org-roam-capture--get (keyword)
-  "Gets the value for KEYWORD from the `org-roam-capture-template'."
+  "Get the value for KEYWORD from the `org-roam-capture-template'."
   (plist-get (plist-get org-capture-plist :org-roam) keyword))
 
 (defun org-roam-capture--put (&rest stuff)
-  "Puts properties from STUFF into the `org-roam-capture-template'."
+  "Put properties from STUFF into the `org-roam-capture-template'."
   (let ((p (plist-get org-capture-plist :org-roam)))
     (while stuff
-      (setq p (plist-put p
+      (setq p (plist-put p (pop stuff) (pop stuff))))
-                         (pop stuff) (pop stuff))))
     (setq org-capture-plist
           (plist-put org-capture-plist :org-roam p))))
 
-(defun org-roam-capture--in-process-p ()
+;; FIXME: Pending upstream patch
-  "Return non-nil if a `org-roam-capture' buffer exists."
+;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
-  (cl-some (lambda (buffer)
+;;
-             (and (eq (buffer-local-value 'major-mode buffer)
+;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
-                      'org-mode)
+;; during the initialization of the Org-capture buffer. The value of
-                  (plist-get (buffer-local-value 'org-capture-current-plist buffer)
+;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
-                             :org-roam)))
+;; However, the value for that particular capture is no longer accessible for
-           (buffer-list)))
+;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
+;; cleaned up.
+;;
+;; This advice restores the global `org-capture-plist' during finalization, so
+;; the plist is valid during both initialization and finalization of the
+;; capture.
+(defun org-roam-capture--update-plist (&optional _)
+  "Update global plist from local var."
+  (setq org-capture-plist org-capture-current-plist))
 
-(defun org-roam-capture--fill-template (str &optional info)
+(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
-  "Expands the template STR, returning the string.
-This is an extension of org-capture's template expansion.
 
-First, it expands ${var} occurrences in STR, using the INFO alist.
+(defun org-roam-capture--finalize-find-file ()
-If there is a ${var} with no matching var in the alist, the value
+  "Visit the buffer after Org-capture is done.
-of var is prompted for via `completing-read'.
+This function is to be called in the Org-capture finalization process.
+ID is unused."
+  (switch-to-buffer (org-capture-get :buffer)))
 
-Next, it expands the remaining template string using
+(defun org-roam-capture--finalize-insert-link ()
-`org-capture-fill-template'."
+  "Insert a link to ID into the buffer where Org-capture was called.
-  (-> str
+ID is the Org id of the newly captured content.
-      (s-format (lambda (key)
+This function is to be called in the Org-capture finalization process."
-                  (or (s--aget info key)
+  (when-let* ((mkr (org-roam-capture--get :call-location))
-                      (completing-read (format "%s: " key ) nil))) nil)
+              (buf (marker-buffer mkr)))
-      (org-capture-fill-template)))
+    (with-current-buffer buf
+      (when-let ((region (org-roam-capture--get :region)))
+        (org-roam-unshield-region (car region) (cdr region))
+        (delete-region (car region) (cdr region))
+        (set-marker (car region) nil)
+        (set-marker (cdr region) nil))
+      (org-with-point-at mkr
+        (insert (org-link-make-string (concat "id:" (org-roam-capture--get :id))
+                                      (org-roam-capture--get :link-description)))))))
 
-(defun org-roam-capture--insert-link-h ()
+(defun org-roam-capture--finalize ()
-  "Insert the link into the original buffer, after the capture process is done.
+  "Finalize the `org-roam-capture' process."
-This is added as a hook to `org-capture-after-finalize-hook'."
+  (when-let ((region (org-roam-capture--get :region)))
-  (when (and (not org-note-abort)
+    (org-roam-unshield-region (car region) (cdr region)))
-             (eq (org-roam-capture--get :capture-fn)
+  (unless org-note-abort
-                 'org-roam-insert))
+    (when-let ((finalize (org-roam-capture--get :finalize)))
-    (when-let ((region (org-roam-capture--get :region))) ;; Remove previously selected text.
+      (funcall (intern (concat "org-roam-capture--finalize-"
-      (delete-region (car region) (cdr region)))
+                               (symbol-name (org-roam-capture--get :finalize)))))))
-    (insert (org-roam--format-link (org-roam-capture--get :file-path)
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize))
-                                   (org-roam-capture--get :link-description))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--insert-link-h))
 
-(defun org-roam-capture--save-file-maybe-h ()
+(defun org-roam-capture--install-finalize ()
-  "Save the file conditionally.
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
-The file is saved if the original value of :no-save is not t and
+  (when (org-roam-capture-p)
-`org-note-abort' is not t. It is added to
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
-`org-capture-after-finalize-hook'."
-  (cond
-   ((and (org-roam-capture--get :new-file)
-         org-note-abort)
-    (with-current-buffer (org-capture-get :buffer)
-      (set-buffer-modified-p nil)
-      (kill-buffer)))
-   ((and (not (org-roam-capture--get :orig-no-save))
-         (not org-note-abort))
-    (with-current-buffer (org-capture-get :buffer)
-      (save-buffer))))
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h))
 
-(defun org-roam-capture--new-file ()
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
-  "Return the path to the new file during an Org-roam capture.
 
-This function reads the file-name attribute of the currently
+(defun org-roam-capture--fill-template (template &optional org-capture-p)
-active Org-roam template.
+  "Expand TEMPLATE and return it.
+It expands ${var} occurrences in TEMPLATE. When ORG-CAPTURE-P,
+also run Org-capture's template expansion."
+  (funcall (if org-capture-p #'org-capture-fill-template #'identity)
+           (org-roam-format
+            template
+            (lambda (key)
+              (let ((fn (intern (concat "org-roam-node-" key)))
+                    (ksym (intern (concat ":" key))))
+                (cond
+                 ((fboundp fn)
+                  (funcall fn org-roam-capture--node))
+                 ((plist-get org-roam-capture--info ksym)
+                  (plist-get org-roam-capture--info ksym))
+                 (t (let ((r (completing-read (format "%s: " key) nil)))
+                      (plist-put org-roam-capture--info ksym r)
+                      r))))))))
 
-If the file path already exists, it throw an error.
+(defun org-roam-capture--insert-ref ()
+  "Insert the ref if any."
+  (when-let ((ref (plist-get org-roam-capture--info :ref)))
+    (org-roam-ref-add ref)))
 
-Else, to insert the header content in the file, `org-capture'
+(defun org-roam-capture--goto-location ()
-prepends the `:head' property of the Org-roam capture template.
+  "Initialize the buffer, and goto the location of the new capture.
+Return the ID of the location."
+  (let (p)
+    (pcase (or (org-roam-capture--get :if-new)
+               (user-error "Template needs to specify `:if-new'"))
+      (`(file ,path)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (set-buffer (org-capture-target-buffer path))
+       (widen)
+       (setq p (point)))
+      (`(file+olp ,path ,olp)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (set-buffer (org-capture-target-buffer path))
+       (setq p (point-min))
+       (let ((m (org-roam-capture-find-or-create-olp olp)))
+         (goto-char m))
+       (widen))
+      (`(file+head ,path ,head)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (let ((exists-p (file-exists-p path)))
+         (set-buffer (org-capture-target-buffer path))
+         (unless exists-p
+           (insert (org-roam-capture--fill-template head t))))
+       (widen)
+       (setq p (point-min)))
+      (`(file+head+olp ,path ,head ,olp)
+       (setq path (expand-file-name
+                   (string-trim (org-roam-capture--fill-template path t))
+                   org-roam-directory))
+       (widen)
+       (let ((exists-p (file-exists-p path)))
+         (set-buffer (org-capture-target-buffer path))
+         (unless exists-p
+           (insert (org-roam-capture--fill-template head t))))
+       (setq p (point-min))
+       (let ((m (org-roam-capture-find-or-create-olp olp)))
+         (goto-char m)))
+      (`(node ,title-or-id)
+       ;; first try to get ID, then try to get title/alias
+       (let ((node (or (org-roam-node-from-id title-or-id)
+                       (org-roam-node-from-title-or-alias title-or-id)
+                       (user-error "No node with title or id \"%s\" title-or-id"))))
+         (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
+         (goto-char (org-roam-node-point node))
+         (setq p (org-roam-node-point node))
+         (org-end-of-subtree t t))))
+    (save-excursion
+      (goto-char p)
+      (run-hooks 'org-roam-capture-new-node-hook)
+      (org-id-get-create))))
 
-To prevent the creation of a new file if the capture process is
+(defun org-roam-capture-find-or-create-olp (olp)
-aborted, we do the following:
+  "Return a marker pointing to the entry at OLP in the current buffer.
+If OLP does not exist, create it. If anything goes wrong, throw
+an error, and if you need to do something based on this error,
+you can catch it with `condition-case'."
+  (let* ((level 1)
+         (lmin 1)
+         (lmax 1)
+         (start (point-min))
+         (end (point-max))
+         found flevel)
+    (unless (derived-mode-p 'org-mode)
+      (error "Buffer %s needs to be in Org mode" (current-buffer)))
+    (org-with-wide-buffer
+     (goto-char start)
+     (dolist (heading olp)
+       (let ((re (format org-complex-heading-regexp-format
+                         (regexp-quote heading)))
+             (cnt 0))
+         (while (re-search-forward re end t)
+           (setq level (- (match-end 1) (match-beginning 1)))
+           (when (and (>= level lmin) (<= level lmax))
+             (setq found (match-beginning 0) flevel level cnt (1+ cnt))))
+         (when (> cnt 1)
+           (error "Heading not unique on level %d: %s" lmax heading))
+         (when (= cnt 0)
+           ;; Create heading if it doesn't exist
+           (goto-char end)
+           (unless (bolp) (newline))
+           (org-insert-heading nil nil t)
+           (unless (= lmax 1) (org-do-demote))
+           (insert heading)
+           (setq end (point))
+           (goto-char start)
+           (while (re-search-forward re end t)
+             (setq level (- (match-end 1) (match-beginning 1)))
+             (when (and (>= level lmin) (<= level lmax))
+               (setq found (match-beginning 0) flevel level cnt (1+ cnt))))))
+       (goto-char found)
+       (setq lmin (1+ flevel) lmax (+ lmin (if org-odd-levels-only 1 0)))
+       (setq start found
+             end (save-excursion (org-end-of-subtree t t))))
+     (copy-marker end))))
 
-1. Save the original value of the capture template's :no-save.
+(defun org-roam-capture--get-node-from-ref (ref)
-
+  "Return the node from reference REF."
-2. Set the capture template's :no-save to t.
+  (save-match-data
-
+    (when (string-match org-link-plain-re ref)
-3. Add a function on `org-capture-after-finalize-hook' that saves
+      (let ((type (match-string 1 ref))
-the file if the original value of :no-save is not t and
+            (path (match-string 2 ref)))
-`org-note-abort' is not t."
+        (when-let ((id (caar (org-roam-db-query
-  (let* ((name-templ (or (org-roam-capture--get :file-name)
+                              [:select [nodes:id]
-                         org-roam-capture--file-name-default))
+                               :from refs
-         (new-id (s-trim (org-roam-capture--fill-template
+                               :left-join nodes
-                          name-templ
+                               :on (= refs:node-id nodes:id)
-                          org-roam-capture--info)))
+                               :where (= refs:type $s1)
-         (file-path (org-roam--file-path-from-id new-id))
+                               :and (= refs:ref $s2)
-         (roam-head (or (org-roam-capture--get :head)
+                               :limit 1]
-                        org-roam-capture--header-default))
+                              type path))))
-         (org-template (org-capture-get :template))
+          (org-roam-populate (org-roam-node-create :id id)))))))
-         (roam-template (concat roam-head org-template)))
-    (unless (file-exists-p file-path)
-      (make-directory (file-name-directory file-path) t)
-      (org-roam-capture--put :orig-no-save (org-capture-get :no-save)
-                             :new-file t)
-      (org-capture-put :template
-                       ;; Fixes org-capture-place-plain-text throwing 'invalid search bound'
-                       ;; when both :unnarowed t and "%?" is missing from the template string;
-                       ;; may become unnecessary when the upstream bug is fixed
-                       (if (s-contains-p "%?" roam-template)
-                           roam-template
-                         (concat roam-template "%?"))
-                       :type 'plain
-                       :no-save t))
-    file-path))
-
-(defun org-roam-capture--expand-template ()
-  "Expand capture template with information from `org-roam-capture--info'."
-  (org-capture-put :template
-                   (s-format (org-capture-get :template)
-                             (lambda (key)
-                               (or (s--aget org-roam-capture--info key)
-                                   (when-let ((v (completing-read (format "%s: " key ) nil)))
-                                     (push (cons key v) org-roam-capture--info)
-                                     v))) nil)))
 
 (defun org-roam-capture--get-point ()
   "Return exact point to file for org-capture-template.
-The file to use is dependent on the context:
-
-If the search is via title, it is assumed that the file does not
-yet exist, and Org-roam will attempt to create new file.
-
-If the search is via daily notes, 'time will be passed via
-`org-roam-capture--info'. This is used to alter the default time
-in `org-capture-templates'.
-
-If the search is via ref, it is matched against the Org-roam database.
-If there is no file with that ref, a file with that ref is created.
-
 This function is used solely in Org-roam's capture templates: see
 `org-roam-capture-templates'."
-  (let ((file-path (pcase org-roam-capture--context
+  (let ((id (cond ((plist-get org-roam-capture--info :ref)
-                     ('capture
+                   (if-let ((node (org-roam-capture--get-node-from-ref
-                      (or (cdr (assoc 'file org-roam-capture--info))
+                                   (plist-get org-roam-capture--info :ref))))
-                          (org-roam-capture--new-file)))
+                       (progn
-                     ('title
+                         (set-buffer (org-capture-target-buffer (org-roam-node-file node)))
-                      (org-roam-capture--new-file))
+                         (goto-char (org-roam-node-point node))
-                     ('dailies
+                         (widen)
-                      (org-capture-put :default-time (cdr (assoc 'time org-roam-capture--info)))
+                         (org-end-of-subtree t t))
-                      (org-roam-capture--new-file))
+                     (org-roam-capture--goto-location)))
-                     ('ref
+                  ((and (org-roam-node-file org-roam-capture--node)
-                      (let ((completions (org-roam--get-ref-path-completions))
+                        (org-roam-node-point org-roam-capture--node))
-                            (ref (cdr (assoc 'ref org-roam-capture--info))))
+                   (set-buffer (org-capture-target-buffer (org-roam-node-file org-roam-capture--node)))
-                        (if-let ((pl (cdr (assoc ref completions))))
+                   (goto-char (org-roam-node-point org-roam-capture--node))
-                            (plist-get pl :path)
+                   (widen)
-                          (org-roam-capture--new-file))))
+                   (org-end-of-subtree t t)
-                     (_ (error "Invalid org-roam-capture-context")))))
+                   (org-roam-node-id org-roam-capture--node))
-    (org-roam-capture--expand-template)
+                  (t
-    (org-roam-capture--put :file-path file-path)
+                   (org-roam-capture--goto-location)))))
-    (while org-roam-capture-additional-template-props
+    (org-capture-put :template
-      (let ((prop (pop org-roam-capture-additional-template-props))
+                     (org-roam-capture--fill-template (org-capture-get :template)))
-            (val (pop org-roam-capture-additional-template-props)))
+    (org-roam-capture--put :id id)
-        (org-roam-capture--put prop val)))
+    (org-roam-capture--put :finalize (or (org-capture-get :finalize)
-    (set-buffer (org-capture-target-buffer file-path))
+                                         (org-roam-capture--get :finalize)))))
-    (widen)
-    (goto-char (point-max))))
 
-(defun org-roam-capture--convert-template (template)
+(defun org-roam-capture--convert-template (template &optional props)
-  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
+  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax.
+PROPS is a plist containing additional Org-roam specific
+properties to be added to the template."
   (pcase template
-    (`(,_key ,_description) template)
+    (`(,key ,desc)
-    (`(,key ,description ,type ,target . ,rest)
+     template)
-     (let ((converted `(,key ,description ,type ,target
+    (`(,key ,desc ,type ,body . ,rest)
-                             ,(unless (keywordp (car rest)) (pop rest))))
+     (setq rest (append rest props))
-           org-roam-plist
+     (let (org-roam-plist options)
-           options)
        (while rest
          (let* ((key (pop rest))
                 (val (pop rest))
                 (custom (member key org-roam-capture--template-keywords)))
-           (push val (if custom org-roam-plist options))
+           (when (and custom
-           (push key (if custom org-roam-plist options))))
+                      (not val))
-       (append converted options `(:org-roam ,org-roam-plist))))
+             (user-error "Invalid capture template format: %s\nkey %s cannot be nil" template key))
-    (_ (user-error "Invalid capture template format: %s" template))))
+           (if custom
+               (setq org-roam-plist (plist-put org-roam-plist key val))
+             (setq options (plist-put options key val)))))
+       (append `(,key ,desc ,type #'org-roam-capture--get-point ,body)
+               options
+               (list :org-roam org-roam-plist))))
+    (_
+     (signal 'invalid-template template))))
 
-(defun org-roam-capture--find-file-h ()
+;;;###autoload
-  "Opens the newly created template file.
+(cl-defun org-roam-capture- (&key goto keys node info props templates)
-This is added as a hook to `org-capture-after-finalize-hook'.
+  "Main entry point.
-Run the hooks defined in `org-roam-capture-after-find-file-hook'."
+GOTO and KEYS correspond to `org-capture' arguments.
-  (unless org-note-abort
+INFO is an alist for filling up Org-roam's capture templates.
-    (when-let ((file-path (org-roam-capture--get :file-path)))
+NODE is an `org-roam-node' construct containing information about the node.
-      (find-file file-path))
+PROPS is a plist containing additional Org-roam properties for each template.
-    (run-hooks 'org-roam-capture-after-find-file-hook))
+TEMPLATES is a list of org-roam templates."
-  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h))
+  (let* ((props (plist-put props :call-location (point-marker)))
-
+         (org-capture-templates
-(defcustom org-roam-capture-after-find-file-hook nil
+          (mapcar (lambda (template)
-  "Hook that is run right after an Org-roam capture process is finalized.
+                    (org-roam-capture--convert-template template props))
-Suitable for moving point."
+                  (or templates org-roam-capture-templates)))
-  :group 'org-roam
+         (org-roam-capture--node node)
-  :type 'hook)
+         (org-roam-capture--info info))
-
+    (when (and (not keys)
-(defun org-roam-capture--capture (&optional goto keys)
+               (= (length org-capture-templates) 1))
-  "Create a new file, and return the path to the edited file.
-The templates are defined at `org-roam-capture-templates'.  The
-GOTO and KEYS argument have the same functionality as
-`org-capture'."
-  (let ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates))
-        org-capture-templates-contexts)
-    (when (= (length org-capture-templates) 1)
       (setq keys (caar org-capture-templates)))
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
     (org-capture goto keys)))
 
 ;;;###autoload
-(defun org-roam-capture ()
+(defun org-roam-capture (&optional goto keys)
   "Launches an `org-capture' process for a new or existing note.
-This uses the templates defined at `org-roam-capture-templates'."
+This uses the templates defined at `org-roam-capture-templates'.
-  (interactive)
+Arguments GOTO and KEYS see `org-capture'."
-  (unless org-roam-mode (org-roam-mode))
+  (interactive "P")
-  (when (org-roam-capture--in-process-p)
+  (let ((node (org-roam-node-read)))
-    (user-error "Nested Org-roam capture processes not supported"))
+    (org-roam-capture- :goto goto
-  (let* ((completions (org-roam--get-title-path-completions))
+                       :keys keys
-         (title-with-keys (org-roam-completion--completing-read "File: "
+                       :node node
-                                                                completions))
+                       :props '(:immediate-finish nil))))
-         (res (cdr (assoc title-with-keys completions)))
-         (title (or (plist-get res :title) title-with-keys))
-         (file-path (plist-get res :path)))
-    (let ((org-roam-capture--info (list (cons 'title title)
-                                        (cons 'slug (org-roam--title-to-slug title))
-                                        (cons 'file file-path)))
-          (org-roam-capture--context 'capture))
-      (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-capture))
-      (condition-case err
-          (org-roam-capture--capture)
-        (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
-                           (error-message-string err)))))))
 
 (provide 'org-roam-capture)
 

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: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,72 +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--get-db     'org-roam-db--get
-  "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--maybe-update 'org-roam-db--update-maybe
-  "org-roam 1.1.0")
-
-(when (version< (org-version) "9.3")
-  (defalias 'org-link-make-string 'org-make-link-string))
-
-;;;; Variables
-(define-obsolete-variable-alias 'org-roam-graphviz-extra-options
-  'org-roam-graph-extra-config "org-roam 1.0.0")
-(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")
-(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: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
-
 ;; This file is NOT part of GNU Emacs.
 
 ;; This program is free software; you can redistribute it and/or modify
@@ -27,84 +26,107 @@
 
 ;;; 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-ignore-case t
-  "The completion system to be used by `org-roam'."
+  "Whether to ignore case in Org-roam `completion-at-point' completions."
-  :type '(radio
+  :group 'org-roam
-          (const :tag "Default" default)
+  :type 'boolean)
-          (const :tag "Ido" ido)
-          (const :tag "Ivy" ivy)
-          (const :tag "Helm" helm)
-          (function :tag "Custom function"))
-  :group 'org-roam)
 
-(defun org-roam-completion--helm-candidate-transformer (candidates _source)
+(defcustom org-roam-completion-everywhere nil
-  "Transforms CANDIDATES for Helm-based completing read.
+  "When non-nil, provide link completion matching outside of Org links."
-SOURCE is not used."
+  :group 'org-roam
-  (let ((prefix (propertize "[?] "
+  :type 'boolean)
-                            'face 'helm-ff-prefix)))
-    (cons (propertize helm-pattern
-                      'display (concat prefix helm-pattern))
-          candidates)))
 
-(cl-defun org-roam-completion--completing-read (prompt choices &key
+(defvar org-roam-completion-functions (list #'org-roam-complete-link-at-point
-                                                       require-match initial-input
+                                            #'org-roam-complete-everywhere)
-                                                       action)
+  "List of functions to be used with `completion-at-point' for Org-roam.")
-  "Present a PROMPT with CHOICES and optional INITIAL-INPUT.
+
-If REQUIRE-MATCH is t, the user must select one of the CHOICES.
+(defun org-roam-complete-everywhere ()
-Return user choice."
+  "Provides completions for links for any word at point.
-  (let (res)
+This is a `completion-at-point' function, and is active when
-    (setq res
+`org-roam-completion-everywhere' is non-nil."
-          (cond
+  (let ((end (point))
-           ((eq org-roam-completion-system 'ido)
+        (start (point))
-            (let ((candidates (mapcar #'car choices)))
+        (exit-fn (lambda (&rest _) nil))
-              (ido-completing-read prompt candidates nil require-match initial-input)))
+        collection)
-           ((eq org-roam-completion-system 'default)
+    (when (and org-roam-completion-everywhere
-            (completing-read prompt choices nil require-match initial-input))
+               (thing-at-point 'word)
-           ((eq org-roam-completion-system 'ivy)
+               (not (save-match-data (org-in-regexp org-link-any-re))))
-            (if (fboundp 'ivy-read)
+      (let ((bounds (bounds-of-thing-at-point 'word)))
-                (ivy-read prompt choices
+        (setq start (car bounds)
-                          :initial-input initial-input
+              end (cdr bounds)
-                          :require-match require-match
+              collection #'org-roam--get-titles
-                          :action (prog1 action
+              exit-fn (lambda (str _status)
-                                    (setq action nil))
+                        (delete-char (- (length str)))
-                          :caller 'org-roam--completing-read)
+                        (insert "[[roam:" str "]]")))))
-              (user-error "Please install ivy from \
+    (when collection
-https://github.com/abo-abo/swiper")))
+      (let ((prefix (buffer-substring-no-properties start end)))
-           ((eq org-roam-completion-system 'helm)
+        (list start end
-            (unless (and (fboundp 'helm)
+              (if (functionp collection)
-                         (fboundp 'helm-make-source))
+                  (completion-table-case-fold
-              (user-error "Please install helm from \
+                   (completion-table-dynamic
-https://github.com/emacs-helm/helm"))
+                    (lambda (_)
-            (let ((source (helm-make-source prompt 'helm-source-sync
+                      (cl-remove-if (apply-partially #'string= prefix)
-                            :candidates (mapcar #'car choices)
+                                    (funcall collection))))
-                            :filtered-candidate-transformer
+                   (not org-roam-completion-ignore-case))
-                            (and (not require-match)
+                collection)
-                                 #'org-roam-completion--helm-candidate-transformer)))
+              :exit-function exit-fn)))))
-                  (buf (concat "*org-roam "
+
-                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
+(defun org-roam-complete-link-at-point ()
-                               "*")))
+  "Do appropriate completion for the link at point."
-              (or (helm :sources source
+  (let ((end (point))
-                        :action (if action
+        (start (point))
-                                    (prog1 action
+        collection link-type)
-                                      (setq action nil))
+    (when (org-in-regexp org-link-bracket-re 1)
-                                  #'identity)
+      (setq start (match-beginning 1)
-                        :prompt prompt
+            end (match-end 1))
-                        :input initial-input
+      (let ((context (org-element-context)))
-                        :buffer buf)
+        (pcase (org-element-lineage context '(link) t)
-                  (keyboard-quit))))))
+          (`nil nil)
-    (if action
+          (link
-        (funcall action res)
+           (setq link-type (org-element-property :type link))
-      res)))
+           (when (member link-type '("roam" "fuzzy"))
+             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
+             (setq collection #'org-roam--get-titles))))))
+    (when collection
+      (let ((prefix (buffer-substring-no-properties start end)))
+        (list start end
+              (if (functionp collection)
+                  (completion-table-case-fold
+                   (completion-table-dynamic
+                    (lambda (_)
+                      (cl-remove-if (apply-partially #'string= prefix)
+                                    (funcall collection))))
+                   (not org-roam-completion-ignore-case))
+                collection)
+              :exit-function
+              (lambda (str &rest _)
+                (delete-char (- 0 (length str)))
+                (insert (concat (unless (string= link-type "roam") "roam:")
+                                str))
+                (forward-char 2)))))))
+
+(defun org-roam--register-completion-functions ()
+  "."
+  (dolist (fn org-roam-completion-functions)
+    (add-hook 'completion-at-point-functions fn nil t)))
+
+(add-hook 'org-roam-find-file-hook #'org-roam--register-completion-functions)
 
 (provide 'org-roam-completion)
 

org-roam-dailies.el

@@ -1,12 +1,14 @@
-;;; org-roam-dailies.el --- Daily notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+;;; org-roam-dailies.el --- Daily-notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Copyright © 2020 Leo Vivier <leo.vivier+dev@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;;      Leo Vivier <leo.vivier+dev@gmail.com>
 ;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,62 +29,318 @@
 
 ;;; Commentary:
 ;;
-;; This library provides functionality for creating daily notes. This is a
+;; This library provides functionality for creating daily-notes. This is a
 ;; concept borrowed from Roam Research.
 ;;
 ;;; Code:
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
-(require 'org-roam-macs)
+(require 'f)
 
-(defvar org-roam-dailies-capture-templates
+;;;; Declarations
-  '(("d" "daily" plain (function org-roam-capture--get-point)
+(defvar org-roam-directory)
-     ""
+(defvar org-roam-file-extensions)
-     :immediate-finish t
+(declare-function org-roam--org-file-p        "org-roam")
-     :file-name "%<%Y-%m-%d>"
-     :head "#+title: %<%Y-%m-%d>"))
-  "Capture templates for daily notes in Org-roam.")
 
-;; Declarations
+;;;; Faces
-(defvar org-roam-mode)
+(defface org-roam-dailies-calendar-note
-(declare-function org-roam--file-path-from-id "org-roam")
+  '((t :inherit (org-link) :underline nil))
-(declare-function org-roam-mode               "org-roam")
+  "Face for dates with a daily-note in the calendar."
+  :group 'org-roam-faces)
 
-(defun org-roam-dailies--file-for-time (time)
+;;;; Customizable variables
-  "Create and find file for TIME."
+(defcustom org-roam-dailies-directory "daily/"
-  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
+  "Path to daily-notes."
-        (org-roam-capture--info (list (cons 'time time)))
+  :group 'org-roam
-        (org-roam-capture--context 'dailies))
+  :type 'string)
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
-    (org-roam--with-template-error 'org-roam-dailies-capture-templates
-      (org-roam-capture--capture))))
 
-(defun org-roam-dailies-today ()
+(defcustom org-roam-dailies-find-file-hook nil
-  "Create and find the daily note for today."
+  "Hook that is run right after navigating to a daily-note."
+  :group 'org-roam
+  :type 'hook)
+
+(defcustom org-roam-dailies-capture-templates
+  '(("d" "default" entry
+     "* %?"
+     :if-new `(file+head ,(concat org-roam-dailies-directory "%<%Y-%m-%d>.org")
+                         "#+title: %<%Y-%m-%d>\n")))
+  "Capture templates for daily-notes in Org-roam.
+See `org-roam-capture-templates' for the template documentation."
+  :group 'org-roam
+  :type '(repeat
+          (choice (list :tag "Multikey description"
+                        (string :tag "Keys       ")
+                        (string :tag "Description"))
+                  (list :tag "Template entry"
+                        (string :tag "Keys           ")
+                        (string :tag "Description    ")
+                        (choice :tag "Capture Type   " :value entry
+                                (const :tag "Org entry" entry)
+                                (const :tag "Plain list item" item)
+                                (const :tag "Checkbox item" checkitem)
+                                (const :tag "Plain text" plain)
+                                (const :tag "Table line" table-line))
+                        (choice :tag "Template       "
+                                (string)
+                                (list :tag "File"
+                                      (const :format "" file)
+                                      (file :tag "Template file"))
+                                (list :tag "Function"
+                                      (const :format "" function)
+                                      (function :tag "Template function")))
+                        (plist :inline t
+                               ;; Give the most common options as checkboxes
+                               :options (((const :format "%v " :if-new)
+                                          (choice :tag "Node location"
+                                                  (list :tag "File"
+                                                        (const :format "" file)
+                                                        (string :tag "  File"))
+                                                  (list :tag "File & Head Content"
+                                                        (const :format "" file+head)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content"))
+                                                  (list :tag "File & Outline path"
+                                                        (const :format "" file+olp)
+                                                        (string :tag "  File")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))
+                                                  (list :tag "File & Head Content & Outline path"
+                                                        (const :format "" file+head+olp)
+                                                        (string :tag "  File")
+                                                        (string :tag "  Head Content")
+                                                        (list :tag "Outline path"
+                                                              (repeat string :tag "Headline")))))
+                                         ((const :format "%v " :prepend) (const t))
+                                         ((const :format "%v " :immediate-finish) (const t))
+                                         ((const :format "%v " :jump-to-captured) (const t))
+                                         ((const :format "%v " :empty-lines) (const 1))
+                                         ((const :format "%v " :empty-lines-before) (const 1))
+                                         ((const :format "%v " :empty-lines-after) (const 1))
+                                         ((const :format "%v " :clock-in) (const t))
+                                         ((const :format "%v " :clock-keep) (const t))
+                                         ((const :format "%v " :clock-resume) (const t))
+                                         ((const :format "%v " :time-prompt) (const t))
+                                         ((const :format "%v " :tree-type) (const week))
+                                         ((const :format "%v " :unnarrowed) (const t))
+                                         ((const :format "%v " :table-line-pos) (string))
+                                         ((const :format "%v " :kill-buffer) (const t))))))))
+
+;;;; Utilities
+(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))
+
+(defun org-roam-dailies-find-directory ()
+  "Find and open `org-roam-dailies-directory'."
   (interactive)
-  (unless org-roam-mode (org-roam-mode))
+  (find-file (org-roam-dailies-directory--get-absolute-path)))
-  (org-roam-dailies--file-for-time (current-time)))
 
-(defun org-roam-dailies-tomorrow (n)
+(defun org-roam-dailies--daily-note-p (&optional file)
-  "Create and find the daily note for tomorrow.
+  "Return t if FILE is an Org-roam daily-note, nil otherwise.
-With numeric argument N, use N days in the future."
-  (interactive "p")
-  (unless org-roam-mode (org-roam-mode))
-  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
 
-(defun org-roam-dailies-yesterday (n)
+If FILE is not specified, use the current buffer's file-path."
-  "Create and find the file for yesterday.
+  (when-let ((path (or file
-With numeric argument N, use N days in the past."
+                       (buffer-base-buffer (buffer-file-name))))
-  (interactive "p")
+             (directory (org-roam-dailies-directory--get-absolute-path)))
-  (unless org-roam-mode (org-roam-mode))
+    (setq path (expand-file-name path))
-  (org-roam-dailies-tomorrow (- n)))
+    (save-match-data
+      (and
+       (org-roam--org-file-p path)
+       (f-descendant-of-p path directory)))))
 
-(defun org-roam-dailies-date ()
+(defun org-roam-dailies--capture (time &optional goto)
-  "Create the file for any date using the calendar interface."
+  "Capture an entry in a daily-note for TIME, creating it if necessary.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (org-roam-capture- :goto (when goto '(4))
+                     :node (org-roam-node-create)
+                     :templates org-roam-dailies-capture-templates
+                     :props (list :default-time time)))
+
+;;;; Commands
+;;; Today
+(defun org-roam-dailies-capture-today (&optional goto)
+  "Create an entry in the daily-note for today.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "P")
+  (org-roam-dailies--capture (current-time) goto)
+  (when goto
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-find-today ()
+  "Find the daily-note for today, creating it if necessary."
   (interactive)
-  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
+  (org-roam-dailies-capture-today t))
-    (org-roam-dailies--file-for-time time)))
+
+;;; Tomorrow
+(defun org-roam-dailies-capture-tomorrow (n &optional goto)
+  "Create an entry in the daily-note for tomorrow.
+
+With numeric argument N, use the daily-note N days in the future.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "p")
+  (org-roam-dailies--capture (time-add (* n 86400) (current-time)) goto))
+
+(defun org-roam-dailies-find-tomorrow (n)
+  "Find the daily-note for tomorrow, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow n t))
+
+;;; Yesterday
+(defun org-roam-dailies-capture-yesterday (n &optional goto)
+  "Create an entry in the daily-note for yesteday.
+
+With numeric argument N, use the daily-note N days in the past.
+
+When GOTO is non-nil, go the note without creating an entry."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) goto))
+
+(defun org-roam-dailies-find-yesterday (n)
+  "Find the daily-note for yesterday, creating it if necessary.
+
+With numeric argument N, use the daily-note N days in the
+future."
+  (interactive "p")
+  (org-roam-dailies-capture-tomorrow (- n) t))
+
+;;; Calendar
+(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-file-name)))))
+    (cl-destructuring-bind (_ _ _ d m y _ _ _)
+        (org-parse-time-string
+         (file-name-sans-extension
+          (file-name-nondirectory file)))
+      (list m d y))))
+
+(defun org-roam-dailies-calendar--date-to-time (date)
+  "Convert DATE as returned from the calendar (MONTH DAY YEAR) to a time."
+  (encode-time 0 0 0 (nth 1 date) (nth 0 date) (nth 2 date)))
+
+(defun org-roam-dailies-calendar-mark-entries ()
+  "Mark days in the calendar for which a daily-note is present."
+  (when (file-exists-p (org-roam-dailies-directory--get-absolute-path))
+    (dolist (date (mapcar #'org-roam-dailies-calendar--file-to-date
+                          (org-roam-dailies--list-files)))
+      (when (calendar-date-is-visible-p date)
+        (calendar-mark-visible-date date 'org-roam-dailies-calendar-note)))))
+
+;;; Date
+(defun org-roam-dailies-capture-date (&optional goto prefer-future)
+  "Create an entry in the daily-note for a date using the calendar.
+
+Prefer past dates, unless PREFER-FUTURE is non-nil.
+
+With a `C-u' prefix or when GOTO is non-nil, go the note without
+creating an entry."
+  (interactive "P")
+  (org-roam-dailies-calendar--install-hook)
+  (let* ((time-str (let ((org-read-date-prefer-future prefer-future))
+                     (org-read-date nil nil nil (if goto
+                                                    "Find daily-note: "
+                                                  "Capture to daily-note: "))))
+         (time (org-read-date nil t time-str)))
+    (org-roam-dailies--capture time goto)
+    (when goto
+      (run-hooks 'org-roam-dailies-find-file-hook))))
+
+(defun org-roam-dailies-find-date (&optional prefer-future)
+  "Find the daily-note for a date using the calendar, creating it if necessary.
+Prefer past dates, unless PREFER-FUTURE is non-nil."
+  (interactive)
+  (org-roam-dailies-capture-date t prefer-future))
+
+;;; Navigation
+(defun org-roam-dailies--list-files (&rest extra-files)
+  "List all files in `org-roam-dailies-directory'.
+EXTRA-FILES can be used to append extra files to the list."
+  (let ((dir (org-roam-dailies-directory--get-absolute-path))
+        (regexp (rx-to-string `(and "." (or ,@org-roam-file-extensions)))))
+    (append (--remove (let ((file (file-name-nondirectory it)))
+                        (when (or (auto-save-file-name-p file)
+                                  (backup-file-name-p file)
+                                  (string-match "^\\." file))
+                          it))
+                      (directory-files-recursively dir regexp))
+            extra-files)))
+
+(defun org-roam-dailies-find-next-note (&optional n)
+  "Find next daily-note.
+
+With numeric argument N, find note N days in the future. If N is
+negative, find note N days in the past."
+  (interactive "p")
+  (unless (org-roam-dailies--daily-note-p)
+    (user-error "Not in a daily-note"))
+  (setq n (or n 1))
+  (let* ((dailies (org-roam-dailies--list-files))
+         (position
+          (cl-position-if (lambda (candidate)
+                            (string= (buffer-file-name (buffer-base-buffer)) candidate))
+                          dailies))
+         note)
+    (unless position
+      (user-error "Can't find current note file - have you saved it yet?"))
+    (pcase n
+      ((pred (natnump))
+       (when (eq position (- (length dailies) 1))
+         (user-error "Already at newest note")))
+      ((pred (integerp))
+       (when (eq position 0)
+         (user-error "Already at oldest note"))))
+    (setq note (nth (+ position n) dailies))
+    (find-file note)
+    (run-hooks 'org-roam-dailies-find-file-hook)))
+
+(defun org-roam-dailies-find-previous-note (&optional n)
+  "Find previous daily-note.
+
+With numeric argument N, find note N days in the past. If N is
+negative, find note N days in the future."
+  (interactive "p")
+  (let ((n (if n (- n) -1)))
+    (org-roam-dailies-find-next-note n)))
+
+;;;; Bindings
+(defvar org-roam-dailies-map (make-sparse-keymap)
+  "Keymap for `org-roam-dailies'.")
+
+(define-prefix-command 'org-roam-dailies-map)
+
+(define-key org-roam-dailies-map (kbd "d") #'org-roam-dailies-find-today)
+(define-key org-roam-dailies-map (kbd "y") #'org-roam-dailies-find-yesterday)
+(define-key org-roam-dailies-map (kbd "t") #'org-roam-dailies-find-tomorrow)
+(define-key org-roam-dailies-map (kbd "n") #'org-roam-dailies-capture-today)
+(define-key org-roam-dailies-map (kbd "f") #'org-roam-dailies-find-next-note)
+(define-key org-roam-dailies-map (kbd "b") #'org-roam-dailies-find-previous-note)
+(define-key org-roam-dailies-map (kbd "c") #'org-roam-dailies-find-date)
+(define-key org-roam-dailies-map (kbd "v") #'org-roam-dailies-capture-date)
+(define-key org-roam-dailies-map (kbd ".") #'org-roam-dailies-find-directory)
 
 (provide 'org-roam-dailies)
 

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: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,7 +27,7 @@
 
 ;;; 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
@@ -35,23 +35,27 @@
 (require 'emacsql)
 (require 'emacsql-sqlite3)
 (require 'seq)
-(require 'org-roam-macs)
 
+(eval-and-compile
+  (require 'org-roam-macs)
+  ;; For `org-with-wide-buffer'
+  (require 'org-macs))
+(require 'org)
+(require 'ol)
+(require 'org-roam-utils)
+
+(defvar org-roam-find-file-hook)
 (defvar org-roam-directory)
 (defvar org-roam-verbose)
-(defvar org-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--org-roam-file-p "org-roam")
-(declare-function org-roam--extract-ref                    "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
-(declare-function org-roam--extract-tags                   "org-roam")
+(declare-function org-roam-node-at-point "org-roam")
-(declare-function org-roam--extract-headlines              "org-roam")
-(declare-function org-roam--extract-links                  "org-roam")
-(declare-function org-roam--list-all-files                 "org-roam")
-(declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
-(defcustom org-roam-db-location nil
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
   "The full path to file where the Org-roam database is stored.
 If this is non-nil, the Org-roam sqlite database is saved here.
 
@@ -60,20 +64,31 @@ when used with multiple Org-roam instances."
   :type 'string
   :group 'org-roam)
 
-(defconst org-roam-db--version 6)
+(defcustom org-roam-db-gc-threshold gc-cons-threshold
+  "The value to temporarily set the `gc-cons-threshold' threshold to.
+During large, heavy operations like `org-roam-db-sync',
+many GC operations happen because of the large number of
+temporary structures generated (e.g. parsed ASTs). Temporarily
+increasing `gc-cons-threshold' will help reduce the number of GC
+operations, at the cost of temporary memory usage.
+
+This defaults to the original value of `gc-cons-threshold', but
+tweaking this number may lead to better overall performance. For
+example, to reduce the number of GCs, one may set it to a large
+value like `most-positive-fixnum'."
+  :type 'int
+  :group 'org-roam)
+
+(defconst org-roam-db--version 12)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
 
 ;;;; Core Functions
-(defun org-roam-db--get ()
-  "Return the sqlite db file."
-    (or org-roam-db-location
-      (expand-file-name "org-roam.db" org-roam-directory)))
 
 (defun org-roam-db--get-connection ()
   "Return the database connection, if any."
-  (gethash (file-truename org-roam-directory)
+  (gethash (expand-file-name org-roam-directory)
            org-roam-db--connection))
 
 (defun org-roam-db ()
@@ -82,18 +97,17 @@ Initializes and stores the database, and the database connection.
 Performs a database upgrade when required."
   (unless (and (org-roam-db--get-connection)
                (emacsql-live-p (org-roam-db--get-connection)))
-    (let* ((db-file (org-roam-db--get))
+    (let ((init-db (not (file-exists-p org-roam-db-location))))
-           (init-db (not (file-exists-p db-file))))
+      (make-directory (file-name-directory org-roam-db-location) t)
-      (make-directory (file-name-directory db-file) t)
+      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
-      (let ((conn (emacsql-sqlite3 db-file)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
-        (puthash (file-truename org-roam-directory)
+        (puthash (expand-file-name org-roam-directory)
                  conn
                  org-roam-db--connection)
         (when init-db
           (org-roam-db--init conn))
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--update-maybe conn version)))
+               (version (org-roam-db--upgrade-maybe conn version)))
           (cond
            ((> version org-roam-db--version)
             (emacsql-close conn)
@@ -115,43 +129,61 @@ SQL can be either the emacsql vector representation, or a string."
     (apply #'emacsql (org-roam-db) sql args)))
 
 ;;;; Schemata
+;; NOTE: Foreign key somehow doesn't work! Adding a file column to every table as a workaround.
 (defconst org-roam-db--table-schemata
   '((files
      [(file :unique :primary-key)
-      (hash :not-null)
+      (hash :not-null)])
-      (meta :not-null)])
 
-    (headlines
+    (nodes
-     [(id :unique :primary-key)
+     [(id :primary-key :not-null)
-      (file :not-null)])
+      (file :not-null)
+      (level :not-null)
+      (pos :not-null)
+      todo
+      priority
+      (scheduled text)
+      (deadline text)
+      title]
+     (:foreign-key [file] :references files [file] :on-delete :cascade))
 
-    (links
+    (aliases
-     [(from :not-null)
-      (to :not-null)
-      (type :not-null)
-      (properties :not-null)])
-
-    (tags
-     [(file :unique :primary-key)
-      (tags)])
-
-    (titles
      [(file :not-null)
-      titles])
+      (node-id :not-null)
+      alias]
+     (:foreign-key [node-id] :references nodes [id] :on-delete :cascade))
 
     (refs
-     [(ref :unique :not-null)
+     ([(file :not-null)
-      (file :not-null)
+       (node-id :not-null)
-      (type :not-null)])))
+       (ref :not-null)
+       (type :not-null)]
+      (:foreign-key [node-id] :references nodes [id] :on-delete :cascade)))
+
+    (tags
+     [(file :not-null)
+      (node-id :not-null)
+      tag]
+     (:foreign-key [node-id] :references nodes [id] :on-delete :cascade))
+
+    (links
+     [(file :not-null)
+      (pos :not-null)
+      (source :not-null)
+      (dest :not-null)
+      (type :not-null)
+      (properties :not-null)]
+     (:foreign-key [file] :references files [file] :on-delete :cascade))))
 
 (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))))
 
-(defun org-roam-db--update-maybe (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
@@ -159,7 +191,7 @@ SQL can be either the emacsql vector representation, or a string."
         (progn
           (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
                                     version org-roam-db--version))
-          (org-roam-db-build-cache t))))
+          (org-roam-db-sync t))))
   version)
 
 (defun org-roam-db--close (&optional db)
@@ -177,317 +209,280 @@ the current `org-roam-directory'."
     (org-roam-db--close conn)))
 
 ;;;; Database API
-;;;;; Initialization
-(defun org-roam-db--initialized-p ()
-  "Whether the cache has been initialized."
-  (and (file-exists-p (org-roam-db--get))
-       (> (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 caches."
+  "Clears all entries in the Org-roam cache."
   (interactive)
-  (when (file-exists-p (org-roam-db--get))
+  (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 filepath)
+(defun org-roam-db-clear-file (&optional file)
-  "Remove any related links to the file at FILEPATH.
+  "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.
-  (let ((file (file-truename (or filepath
+If FILE is nil, clear the current buffer."
-                                 (buffer-file-name (buffer-base-buffer))))))
+  (setq file (or file (buffer-file-name (buffer-base-buffer))))
-    (dolist (table (mapcar #'car org-roam-db--table-schemata))
+  (dolist (table (mapcar #'car org-roam-db--table-schemata))
-      (org-roam-db-query `[:delete :from ,table
+    (org-roam-db-query `[:delete :from ,table
-                           :where (= ,(if (eq table 'links) 'from 'file) $s1)]
+                         :where (= file $s1)]
-                         file))))
+                       file)))
 
-;;;;; Insertion
+;;;;; Updating tables
-(defun org-roam-db--insert-meta (file hash meta)
+(defun org-roam-db-insert-file ()
-  "Insert HASH and META for a FILE into the Org-roam cache."
+  "Update the files table for the current buffer.
-  (org-roam-db-query
+If UPDATE-P is non-nil, first remove the file in the database."
-   [:insert :into files
+  (let* ((file (buffer-file-name))
-    :values $v1]
+         (hash (org-roam-db--file-hash)))
-   (list (vector file hash meta))))
-
-(defun org-roam-db--insert-links (links)
-  "Insert LINKS into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into links
-    :values $v1]
-   links))
-
-(defun org-roam-db--insert-titles (file titles)
-  "Insert TITLES for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into titles
-    :values $v1]
-   (list (vector file titles))))
-
-(defun org-roam-db--insert-headlines (headlines)
-  "Insert HEADLINES into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into headlines
-    :values $v1]
-   headlines))
-
-(defun org-roam-db--insert-tags (file tags)
-  "Insert TAGS for a FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into tags
-    :values $v1]
-   (list (vector file tags))))
-
-(defun org-roam-db--insert-ref (file ref)
-  "Insert REF for FILE into the Org-roam cache."
-  (let ((key (cdr ref))
-        (type (car ref)))
     (org-roam-db-query
-     [:insert :into refs :values $v1]
+     [:insert :into files
-     (list (vector key file type)))))
+      :values $v1]
+     (list (vector file hash)))))
+
+(defun org-roam-db-get-scheduled-time ()
+  "Return the scheduled time at point in ISO8601 format."
+  (when-let ((time (org-get-scheduled-time (point))))
+    (org-format-time-string "%FT%T%z" time)))
+
+(defun org-roam-db-get-deadline-time ()
+  "Return the deadline time at point in ISO8601 format."
+  (when-let ((time (org-get-deadline-time (point))))
+    (org-format-time-string "%FT%T%z" time)))
+
+(defun org-roam-db-map-headlines (fns)
+  "Run FNS over all headlines in the current buffer."
+  (org-with-point-at 1
+    (org-map-entries
+     (lambda ()
+       (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 (= (org-outline-level) 0)
+      (when-let ((id (org-id-get)))
+        (let* ((file (buffer-file-name (buffer-base-buffer)))
+               (title (or (cadr (assoc "TITLE" (org-collect-keywords '("title"))
+                                       #'string-equal))
+                          (file-relative-name file org-roam-directory)))
+               (pos (point))
+               (todo nil)
+               (priority nil)
+               (scheduled nil)
+               (deadline nil)
+               (level 0)
+               (aliases (org-entry-get (point) "ROAM_ALIASES"))
+               (tags org-file-tags)
+               (refs (org-entry-get (point) "ROAM_REFS")))
+          (condition-case nil
+              (progn
+                (org-roam-db-query
+                 [:insert :into nodes
+                  :values $v1]
+                 (vector id file level pos todo priority
+                         scheduled deadline title))
+                (when tags
+                  (org-roam-db-query
+                   [:insert :into tags
+                    :values $v1]
+                   (mapcar (lambda (tag)
+                             (vector file id (substring-no-properties tag)))
+                           tags)))
+                (when aliases
+                  (org-roam-db-query
+                   [:insert :into aliases
+                    :values $v1]
+                   (mapcar (lambda (alias)
+                             (vector file id alias))
+                           (split-string-and-unquote aliases))))
+                (when refs
+                  (setq refs (split-string-and-unquote refs))
+                  (let (rows)
+                    (dolist (ref refs)
+                      (if (string-match org-link-plain-re ref)
+                          (progn
+                            (push (vector file id (match-string 2 ref)
+                                          (match-string 1 ref)) rows))
+                        (lwarn '(org-roam) :warning
+                               "%s:%s\tInvalid ref %s, skipping..."
+                               (buffer-file-name) (point) ref)))
+                    (when rows
+                      (org-roam-db-query
+                       [:insert :into refs
+                        :values $v1]
+                       rows)))))
+            (t
+             (lwarn '(org-roam) :error "Duplicate ID %s, skipping..." id))))))))
+
+(defun org-roam-db-insert-node-data ()
+  "Insert node data for headline at point into the Org-roam cache."
+  (when-let ((id (org-id-get)))
+    (let* ((file (buffer-file-name (buffer-base-buffer)))
+           (heading-components (org-heading-components))
+           (pos (point))
+           (todo (nth 2 heading-components))
+           (priority (nth 3 heading-components))
+           (level (nth 1 heading-components))
+           (scheduled (org-roam-db-get-scheduled-time))
+           (deadline (org-roam-db-get-deadline-time))
+           (title (nth 4 heading-components)))
+      (condition-case nil
+          (org-roam-db-query
+           [:insert :into nodes
+            :values $v1]
+           (vector id file level pos todo priority
+                   scheduled deadline title))
+        (t
+         (lwarn '(org-roam) :error
+                "Duplicate ID %s, skipping..." id))))))
+
+(defun org-roam-db-insert-aliases ()
+  "Insert aliases for node at point into Org-roam cache."
+  (when-let ((file (buffer-file-name (buffer-base-buffer)))
+             (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 file 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 ((file (buffer-file-name (buffer-base-buffer)))
+             (node-id (org-id-get))
+             (tags (org-get-tags)))
+    (org-roam-db-query [:insert :into tags
+                        :values $v1]
+                       (mapcar (lambda (tag)
+                                 (vector file node-id tag)) tags))))
+
+(defun org-roam-db-insert-refs ()
+  "Insert refs for node at point into Org-roam cache."
+  (when-let* ((file (buffer-file-name (buffer-base-buffer)))
+              (node-id (org-id-get))
+              (refs (org-entry-get (point) "ROAM_REFS"))
+              (refs (split-string-and-unquote refs)))
+    (let (rows)
+      (dolist (ref refs)
+        (save-match-data
+          (if (string-match org-link-plain-re ref)
+              (progn
+                (push (vector file 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 ((file (buffer-file-name (buffer-base-buffer)))
+          (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 file (point) source dest type properties))))))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
   "Return a hash-table of file to the hash of its file contents."
-  (let* ((current-files (org-roam-db-query [:select * :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-titles (file)
+(defun org-roam-db--file-hash (&optional file-path)
-  "Return the titles of FILE from the cache."
+  "Compute the hash of FILE-PATH, a file or current buffer."
-  (caar (org-roam-db-query [:select [titles] :from titles
+  (if file-path
-                            :where (= file $s1)]
+      (with-temp-buffer
-                           file
+        (set-buffer-multibyte nil)
-                           :limit 1)))
+        (insert-file-contents-literally file-path)
-
+        (secure-hash 'sha1 (current-buffer)))
-(defun org-roam-db--connected-component (file)
+    (org-with-wide-buffer
-  "Return all files reachable from/connected to FILE, including the file itself.
+     (secure-hash 'sha1 (current-buffer)))))
-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 \"type\" = '\"file\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
-                   connected_component(file) AS
-                     (SELECT link FROM links_of WHERE file = $s1
-                      UNION
-                      SELECT link FROM links_of JOIN connected_component USING(file))
-                   SELECT * FROM connected_component;")
-         (files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
-    files))
-
-(defun org-roam-db--links-with-max-distance (file max-distance)
-  "Return all files connected to FILE in at most MAX-DISTANCE steps.
-This includes the file itself. If the file does not have any
-connections, nil is returned."
-  (let* ((query "WITH RECURSIVE
-                   links_of(file, link) AS
-                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
-                           citelinks AS (SELECT * FROM links
-                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
-                                                            AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM filelinks UNION
-                      SELECT \"to\", \"from\" FROM filelinks UNION
-                      SELECT \"file\", \"from\" FROM citelinks UNION
-                      SELECT \"from\", \"file\" FROM citelinks),
-                   -- Links are traversed in a breadth-first search.  In order to calculate the
-                   -- distance of nodes and to avoid following cyclic links, the visited nodes
-                   -- are tracked in 'trace'.
-                   connected_component(file, trace) AS
-                     (VALUES($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))
 
 ;;;;; Updating
-(defun org-roam-db--update-meta ()
+(defun org-roam-db-sync (&optional force)
-  "Update the metadata of the current buffer into the cache."
+  "Synchronize the cache state with the current Org files on-disk.
-  (let* ((file (file-truename (buffer-file-name)))
-         (attr (file-attributes file))
-         (atime (file-attribute-access-time attr))
-         (mtime (file-attribute-modification-time attr))
-         (hash (secure-hash 'sha1 (current-buffer))))
-    (org-roam-db-query [:delete :from files
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-meta file hash (list :atime atime :mtime mtime))))
-
-(defun org-roam-db--update-titles ()
-  "Update the title of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name)))
-         (title (org-roam--extract-titles)))
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db--insert-titles file title)))
-
-(defun org-roam-db--update-tags ()
-  "Update the tags of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name)))
-        (tags (org-roam--extract-tags)))
-    (org-roam-db-query [:delete :from tags
-                        :where (= file $s1)]
-                       file)
-    (when tags
-      (org-roam-db--insert-tags file tags))))
-
-(defun org-roam-db--update-refs ()
-  "Update the ref of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from refs
-                        :where (= file $s1)]
-                       file)
-    (when-let ((ref (org-roam--extract-ref)))
-      (org-roam-db--insert-ref file ref))))
-
-(defun org-roam-db--update-links ()
-  "Update the file links of the current buffer in the cache."
-  (let ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from links
-                        :where (= from $s1)]
-                       file)
-    (when-let ((links (org-roam--extract-links)))
-      (org-roam-db--insert-links links))))
-
-(defun org-roam-db--update-headlines ()
-  "Update the file headlines of the current buffer into the cache."
-  (let* ((file (file-truename (buffer-file-name))))
-    (org-roam-db-query [:delete :from headlines
-                        :where (= file $s1)]
-                       file)
-    (when-let ((headlines (org-roam--extract-headlines)))
-      (org-roam-db--insert-headlines headlines))))
-
-(defun org-roam-db--update-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH."
-  (when (org-roam--org-roam-file-p file-path)
-    (let ((buf (or (and file-path
-                        (find-file-noselect file-path t))
-                   (current-buffer))))
-      (with-current-buffer buf
-        (save-excursion
-          (org-roam-db--update-meta)
-          (org-roam-db--update-tags)
-          (org-roam-db--update-titles)
-          (org-roam-db--update-refs)
-          (org-roam-db--update-headlines)
-          (org-roam-db--update-links)
-          (org-roam-buffer--update-maybe :redisplay t))))))
-
-(defun org-roam-db-build-cache (&optional force)
-  "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--get)))
+  (when force (delete-file org-roam-db-location))
   (org-roam-db--close) ;; Force a reconnect
   (org-roam-db) ;; To initialize the database, no-op if already initialized
-  (let* ((org-roam-files (org-roam--list-all-files))
+  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
+         (org-agenda-files nil)
+         (org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         all-files all-headlines all-links all-titles all-refs all-tags)
+         (modified-files nil))
-    ;; Two-step building
-    ;; First step: Rebuild files and headlines
     (dolist (file org-roam-files)
-      (let* ((attr (file-attributes file))
+      (let ((contents-hash (org-roam-db--file-hash file)))
-             (atime (file-attribute-access-time attr))
+        (unless (string= (gethash file current-files)
-             (mtime (file-attribute-modification-time attr)))
+                         contents-hash)
-        (org-roam--with-temp-buffer file
+          (push file modified-files)))
-          (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+      (remhash file current-files))
-            (unless (string= (gethash file current-files)
+    (if (fboundp 'dolist-with-progress-reporter)
-                             contents-hash)
+        (dolist-with-progress-reporter (file (hash-table-keys current-files))
-              (org-roam-db--clear-file file)
+            "Clearing removed files..."
-              (push (vector file contents-hash (list :atime atime :mtime mtime))
+          (org-roam-db-clear-file file))
-                    all-files)
+      (dolist (file (hash-table-keys current-files))
-              (when-let (headlines (org-roam--extract-headlines file))
+        (org-roam-db-clear-file file)))
-                (push headlines all-headlines)))))))
+    (if (fboundp 'dolist-with-progress-reporter)
-    (when all-files
+        (dolist-with-progress-reporter (file modified-files)
-      (org-roam-db-query
+            "Processing modified files..."
-       [:insert :into files
+          (org-roam-db-update-file file))
-        :values $v1]
+      (dolist (file modified-files)
-       all-files))
+        (org-roam-db-update-file file)))))
-    (when all-headlines
+
-      (org-roam-db-query
+(defun org-roam-db-update-file (&optional file-path)
-       [:insert :into headlines
+  "Update Org-roam cache for FILE-PATH.
-        :values $v1]
+If the file does not exist anymore, remove it from the cache.
-       all-headlines))
+If the file exists, update the cache with information."
-    ;; Second step: Rebuild the rest
+  (setq file-path (or file-path (buffer-file-name (buffer-base-buffer))))
-    (dolist (file org-roam-files)
+  (let ((content-hash (org-roam-db--file-hash file-path))
-      (org-roam--with-temp-buffer file
+        (db-hash (caar (org-roam-db-query [:select hash :from files
-        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+                                           :where (= file $s1)] file-path))))
-          (unless (string= (gethash file current-files)
+    (unless (string= content-hash db-hash)
-                           contents-hash)
+      (org-roam-with-file file-path nil
-            (when-let (links (org-roam--extract-links file))
+        (save-excursion
-              (push links all-links))
+          (org-set-regexps-and-options 'tags-only)
-            (when-let (tags (org-roam--extract-tags file))
+          (org-roam-db-clear-file)
-              (push (vector file tags) all-tags))
+          (org-roam-db-insert-file)
-            (let ((titles (org-roam--extract-titles)))
+          (org-roam-db-insert-file-node)
-              (push (vector file titles)
+          (org-roam-db-map-headlines
-                    all-titles))
+           (list #'org-roam-db-insert-node-data
-            (when-let* ((ref (org-roam--extract-ref))
+                 #'org-roam-db-insert-aliases
-                        (type (car ref))
+                 #'org-roam-db-insert-tags
-                        (key (cdr ref)))
+                 #'org-roam-db-insert-refs))
-              (setq all-refs (cons (vector key file type) all-refs))))
+          (org-roam-db-map-links
-          (remhash file current-files))))
+           (list #'org-roam-db-insert-link)))))))
-    (dolist (file (hash-table-keys current-files))
+
-      ;; These files are no longer around, remove from cache...
+(defun org-roam-db--update-on-save-h ()
-      (org-roam-db--clear-file file))
+  "."
-    (when all-links
+  (add-hook 'after-save-hook #'org-roam-db-update-file nil t))
-      (org-roam-db-query
+
-       [:insert :into links
+(add-to-list 'org-roam-find-file-hook #'org-roam-db--update-on-save-h)
-        :values $v1]
+
-       all-links))
+;; Diagnostic Interactives
-    (when all-titles
+(defun org-roam-db-diagnose-node ()
-      (org-roam-db-query
+  "Print information about node at point."
-       [:insert :into titles
+  (interactive)
-        :values $v1]
+  (prin1 (org-roam-node-at-point)))
-       all-titles))
-    (when all-tags
-      (org-roam-db-query
-       [:insert :into tags
-        :values $v1]
-       all-tags))
-    (when all-refs
-      (org-roam-db-query
-       [:insert :into refs
-        :values $v1]
-       all-refs))
-    (let ((stats (list :files (length all-files)
-                       :headlines (length all-headlines)
-                       :links (length all-links)
-                       :tags (length all-tags)
-                       :titles (length all-titles)
-                       :refs (length all-refs)
-                       :deleted (length (hash-table-keys current-files)))))
-      (org-roam-message "files: %s, headlines: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
-                        (plist-get stats :files)
-                        (plist-get stats :headlines)
-                        (plist-get stats :links)
-                        (plist-get stats :tags)
-                        (plist-get stats :titles)
-                        (plist-get stats :refs)
-                        (plist-get stats :deleted))
-      stats)))
 
 (provide 'org-roam-db)
 

org-roam-dev.el

@@ -1,39 +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: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; 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)
-(emacsql-fix-vector-indentation)
-(provide 'org-roam-dev)
-
-;;; org-roam-dev.el ends here

org-roam-doctor.el

@@ -5,8 +5,8 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -45,19 +45,27 @@
 (require 'cl-lib)
 (require 'org)
 (require 'org-element)
-(require 's)
 (require 'dash)
-(require 'org-roam-macs)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'org-roam)
+
+(defvar org-roam-mode-map)
 
-(declare-function org-roam-insert "org-roam")
 (declare-function org-roam--get-roam-buffers "org-roam")
 (declare-function org-roam--list-all-files "org-roam")
 (declare-function org-roam--org-roam-file-p "org-roam")
-(declare-function org-roam--str-to-list "org-roam")
-(declare-function org-roam-mode "org-roam")
 
 (defvar org-roam-verbose)
-(defvar org-roam-mode)
+
+(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)
@@ -70,79 +78,7 @@
     :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" . 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
-                (org-roam--str-to-list tags)
-              (error
-               (push
-                `(,(org-element-property :begin kw)
-                  ,(concat "Unable to parse tags: "
-                           tags
-                           (when (s-contains? "," tags)
-                             "\nCheck that your tags are not comma-separated.")))
-                reports)))))))
-    reports))
-
-(defun org-roam-doctor-check-alias (ast)
-  "Checker for detecting invalid #+roam_alias.
-AST is the org-element parse tree."
-  (let (reports)
-    (org-element-map ast 'keyword
-      (lambda (kw)
-        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
-          (let ((aliases (org-element-property :value kw)))
-            (condition-case nil
-              (org-roam--str-to-list aliases)
-              (error
-               (push
-                `(,(org-element-property :begin kw)
-                  ,(concat "Unable to parse aliases: "
-                           aliases
-                           (when (s-contains? "," aliases)
-                             "\nCheck that your aliases are not comma-separated.")))
-                reports)))))))
-    reports))
 
 (defun org-roam-doctor-broken-links (ast)
   "Checker for detecting broken links.
@@ -150,18 +86,12 @@ AST is the org-element parse tree."
   (let (reports)
     (org-element-map ast 'link
       (lambda (l)
-        (when (equal "file" (org-element-property :type l))
+        (when (equal "id" (org-element-property :type l))
-          (let ((file (org-element-property :path l)))
+          (let ((id (org-element-property :path l)))
-            (or (file-exists-p file)
+            (unless (org-id-find id)
-                (file-remote-p file)
+              (push `(,(org-element-property :begin l)
-                (push
+                      ,(format "Broken id link \"%s\"" id))
-                 `(,(org-element-property :begin l)
+                    reports))))))
-                   ,(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)
@@ -213,25 +143,7 @@ CHECKERS is the list of checkers used."
       (condition-case nil
           (save-excursion
             (replace-match "")
-            (org-roam-insert))
+            (org-roam-node-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)))))))
@@ -250,7 +162,7 @@ CHECKERS is the list of checkers used."
 (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."
+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)
@@ -283,18 +195,19 @@ CHECKER is a org-roam-doctor checker instance."
   "Perform a check on the current buffer to ensure cleanliness.
 If CHECKALL, run the check for all Org-roam files."
   (interactive "P")
-  (unless org-roam-mode (org-roam-mode))
   (let ((files (if checkall
-                  (org-roam--list-all-files)
+                   (org-roam--list-all-files)
-                (unless (org-roam--org-roam-file-p)
+                 (unless (org-roam--org-roam-file-p)
-                  (user-error "Not in an org-roam file"))
+                   (user-error "Not in an org-roam file"))
-                `(,(buffer-file-name)))))
+                 `(,(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)))
+    (let ((existing-buffers (org-roam--get-roam-buffers))
+          (org-inhibit-startup org-roam-doctor-inhibit-startup))
+      (org-id-update-id-locations)
       (dolist (f files)
         (let ((buf (find-file-noselect f)))
           (org-roam-doctor--check buf checkers)

org-roam-graph.el

@@ -1,305 +0,0 @@
-;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/org-roam/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 1.2.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library provides graphing functionality for org-roam.
-;;
-;;; Code:
-(require 'xml) ;xml-escape-string
-(require 's)   ;s-truncate, s-replace
-(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")
-  "Method to view the org-roam graph.
-It may be one of the following:
-  - a string representing the path to the executable for viewing the graph.
-  - a function accepting a single argument: the graph file path.
-  - nil uses `view-file' to view the graph."
-  :type '(choice
-          (string   :tag "Path to executable")
-          (function :tag "Function to display graph" eww-open-file)
-          (const    :tag "view-file"))
-  :group 'org-roam)
-
-(defcustom org-roam-graph-executable "dot"
-  "Path to graphing executable, or its name."
-  :type 'string
-  :group 'org-roam)
-
-(defcustom org-roam-graph-extra-config nil
-  "Extra options passed to graphviz.
-Example:
- '((\"rankdir\" . \"LR\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-node-extra-config
-  '(("shape"      . "underline")
-    ("style"      . "rounded,filled")
-    ("fillcolor"  . "#EEEEEE")
-    ("color"      . "#C9C9C9")
-    ("fontcolor"  . "#111111"))
-  "Extra options for graphviz nodes.
-Example:
- '((\"color\" . \"skyblue\"))"
-  :type '(alist)
-  :group 'org-roam)
-
-(defcustom org-roam-graph-edge-extra-config
-  '(("color" . "#333333"))
-  "Extra options for graphviz edges.
-Example:
- '((\"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
-  "Maximum length of titles in graph nodes."
-  :type 'number
-  :group 'org-roam)
-
-(defcustom org-roam-graph-shorten-titles 'truncate
-  "Determines how long titles appear in graph nodes.
-Recognized values are the symbols `truncate' and `wrap', in which
-cases the title will be truncated or wrapped, respectively, if it
-is longer than `org-roam-graph-max-title-length'.
-
-All other values including nil will have no effect."
-  :type '(choice
-          (const :tag "truncate" truncate)
-          (const :tag "wrap" wrap)
-          (const :tag "no" nil))
-  :group 'org-roam)
-
-(defcustom org-roam-graph-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.
-If WRAP-VAL is non-nil it wraps the VAL."
-  (concat wrap-key (car option) wrap-key
-          "="
-          wrap-val (cdr option) wrap-val))
-
-(defun org-roam-graph--dot (node-query)
-  "Build the graphviz dot string for NODE-QUERY.
-The Org-roam database titles table is read, to obtain the list of titles.
-The links table is then read to obtain all directed links, and formatted
-into a digraph."
-  (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer nil
-    (let* ((nodes (org-roam-db-query node-query))
-           (edges-query
-            `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [to from] :from links
-              :where (and (in to selected) (in from selected))])
-           (edges-cites-query
-            `[:with selected :as [:select [file] :from ,node-query]
-              :select :distinct [file from]
-              :from links :inner :join refs :on (and (= links:to refs:ref)
-                                                     (= links:type "cite")
-                                                     (= refs:type "cite"))
-              :where (and (in file selected) (in from selected))])
-           (edges       (org-roam-db-query edges-query))
-           (edges-cites (org-roam-db-query edges-cites-query)))
-      (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 " %s [%s];\n" attribute
-                        (mapconcat (lambda (var)
-                                     (org-roam-graph--dot-option var nil "\""))
-                                   (symbol-value
-                                    (intern (concat "org-roam-graph-" attribute "-extra-config")))
-                                   ","))))
-      (dolist (node nodes)
-        (let* ((file (xml-escape-string (car node)))
-               (title (or (caadr node)
-                          (org-roam--path-to-slug file)))
-               (shortened-title (pcase org-roam-graph-shorten-titles
-                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
-                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
-                                  (_ title)))
-               (node-properties
-                `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
-                  ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
-                  ("tooltip" . ,(xml-escape-string title)))))
-          (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)
-  "Generate a graph showing the relations between nodes in NODE-QUERY.
-Execute CALLBACK when process exits successfully.
-CALLBACK is passed the graph file as its sole argument."
-  (unless (stringp org-roam-graph-executable)
-    (user-error "`org-roam-graph-executable' is not a string"))
-  (unless (executable-find org-roam-graph-executable)
-    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
-                        "Please adjust `org-roam-graph-executable'")
-                org-roam-graph-executable))
-  (let* ((node-query (or node-query
-                         `[:select [file titles] :from titles
-                           ,@(org-roam-graph--expand-matcher 'file t)]))
-         (graph      (org-roam-graph--dot node-query))
-         (temp-dot   (make-temp-file "graph." nil ".dot" graph))
-         (temp-graph (make-temp-file "graph." nil ".svg")))
-    (org-roam-message "building graph")
-    (make-process
-     :name "*org-roam-graph--build-process*"
-     :buffer "*org-roam-graph--build-process*"
-     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-o" ,temp-graph)
-     :sentinel (when callback
-                 (lambda (process _event)
-                   (when (= 0 (process-exit-status process))
-                     (funcall callback temp-graph)))))))
-
-(defun org-roam-graph--open (file)
-  "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
-  (pcase org-roam-graph-viewer
-    ((pred stringp)
-     (if (executable-find org-roam-graph-viewer)
-         (condition-case err
-             (call-process org-roam-graph-viewer nil 0 nil file)
-           (error (user-error "Failed to open org-roam graph: %s" err)))
-       (user-error "Executable not found: \"%s\"" org-roam-graph-viewer)))
-    ((pred functionp) (funcall org-roam-graph-viewer file))
-    ('nil (view-file file))
-    (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
-
-(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 (file-truename 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 titles]
-                  :from titles
-                  :where (in file [,@files])]))
-    (org-roam-graph--build query callback)))
-
-;;;; Commands
-;;;###autoload
-(defun org-roam-graph (&optional arg file node-query)
-  "Build and possibly display a graph for FILE from NODE-QUERY.
-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]' N   show the graph for FILE limiting nodes to N steps.
-  - `\\[universal-argument] \\[universal-argument]' build the graph.
-  - `\\[universal-argument]' -   build the graph for FILE.
-  - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
-  (interactive "P")
-  (unless org-roam-mode (org-roam-mode))
-  (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
-    (unless (or (not arg) (equal arg '(16)))
-      (unless file
-        (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
-      (unless (org-roam--org-roam-file-p file)
-        (user-error "\"%s\" is not an org-roam file" file)))
-    (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-graph.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: 1.2.0
+;; 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 "1.0.0"))
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,47 +27,60 @@
 
 ;;; 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)
+  "Map FN over PLIST, modifying it in-place."
+  (declare (indent 1))
+  (let ((plist-var (make-symbol "plist"))
+        (k (make-symbol "k"))
+        (v (make-symbol "v")))
+    `(let ((,plist-var (copy-sequence ,plist)))
+       (while ,plist-var
+         (setq ,k (pop ,plist-var))
+         (setq ,v (pop ,plist-var))
+         (setq ,plist (plist-put ,plist ,k (funcall ,fn ,k ,v)))))))
 
-(defvar org-roam-verbose)
+(defmacro org-roam-with-file (file keep-buf-p &rest body)
+  "Execute BODY within FILE.
+If FILE is nil, execute BODY in the current buffer.
+Kills the buffer if KEEP-BUF-P is nil, and FILE is not yet visited."
+  (declare (indent 2) (debug t))
+  `(let* (new-buf
+          (buf (or (and (not ,file)
+                        (current-buffer)) ;If FILE is nil, use current buffer
+                   (find-buffer-visiting ,file) ; If FILE is already visited, find buffer
+                   (progn
+                     (setq new-buf t)
+                     (find-file-noselect ,file)))) ; Else, visit FILE and return buffer
+          res)
+     (with-current-buffer buf
+       (unless (equal major-mode 'org-mode)
+         (delay-mode-hooks (org-mode)))
+       (setq res (progn ,@body))
+       (unless (and new-buf (not ,keep-buf-p))
+         (save-buffer)))
+     (if (and new-buf (not ,keep-buf-p))
+       (when (find-buffer-visiting ,file)
+         (kill-buffer (find-buffer-visiting ,file))))
+     res))
 
-(defmacro org-roam--with-temp-buffer (file &rest body)
+(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))
+           (delay-mode-hooks (org-mode))
            (when ,file
              (insert-file-contents ,file)
-             (setq-local org-roam-file-name ,file))
+             (setq-local default-directory (file-name-directory ,file)))
            ,@body)))))
 
-(defmacro org-roam--with-template-error (templates &rest body)
-  "Eval BODY, and point to TEMPLATES on error.
-Provides more informative error messages so that users know where
-to look.
-
-\(fn TEMPLATES BODY...)"
-  (declare (debug (form body)) (indent 1))
-  `(condition-case err
-       ,@body
-     (error (user-error "%s.  Please adjust `%s'"
-                        (error-message-string err)
-                        ,templates))))
-
-(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))))
-
 (provide 'org-roam-macs)
 
 ;;; org-roam-macs.el ends here

org-roam-mode.el

@@ -0,0 +1,458 @@
+;;; 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-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements 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--org-file-p "org-roam")
+(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.")
+
+(defcustom org-roam-mode-sections (list #'org-roam-backlinks-section
+                                        #'org-roam-reflinks-section)
+  "List of functions that insert sections for Org-roam."
+  :group 'org-roam
+  :type '(repeat function))
+
+;;; The mode
+(defvar org-roam-mode-map
+  (let ((map (make-sparse-keymap)))
+    (set-keymap-parent map magit-section-mode-map)
+    (define-key map [C-return]  'org-roam-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)
+      (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+      (magit-insert-section (org-roam)
+        (magit-insert-heading)
+        (dolist (fn org-roam-mode-sections)
+          (funcall fn org-roam-current-node))))))
+
+(defun org-roam-buffer ()
+  "Launch an Org-roam buffer for the current node at point."
+  (interactive)
+  (if-let ((node (org-roam-node-at-point)))
+      (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)
+            (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)
+        (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
+       (display-buffer (get-buffer-create org-roam-buffer))
+       (setq org-roam-current-node (org-roam-node-at-point))
+       (org-roam-buffer-persistent-redisplay)))))
+
+(defun org-roam-buffer-persistent-redisplay ()
+  "Recompute contents of the persistent Org-roam buffer.
+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)
+        (org-roam-set-header-line-format (org-roam-node-title org-roam-current-node))
+        (magit-insert-section (org-roam)
+          (magit-insert-heading)
+          (dolist (fn org-roam-mode-sections)
+            (funcall fn org-roam-current-node)))))))
+
+(defun org-roam-buffer--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 "
+                               (string-join (mapcar (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-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: 1.2.0
+;; 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-sqlite3 "1.0.2") (magit-section "2.90.1"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -37,6 +37,14 @@
 ;;; Code:
 (require 'org-protocol)
 (require 'org-roam)
+(eval-when-compile
+  (require 'org-roam-macs))
+(require 'ol) ;; for org-link-decode
+
+(defcustom org-roam-protocol-store-links nil
+  "Whether to store links when capturing websites with `org-roam-protocol'."
+  :type 'boolean
+  :group 'org-roam)
 
 ;;;; Functions
 (defun org-roam-protocol-open-ref (info)
@@ -45,26 +53,34 @@
 It opens or creates a note with the given ref.
 
   javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
-        encodeURIComponent(location.href) + \\='&title=\\=' \\
+        encodeURIComponent(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 (org-roam--title-to-slug title)) decoded-alist))
+    (push (list (plist-get info :ref)
-    (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
+                (plist-get info :title)) org-stored-links))
-           (org-roam-capture--context 'ref)
+  (org-link-store-props :type (and (string-match org-link-plain-re
-           (org-roam-capture--info decoded-alist)
+                                                 (plist-get info :ref))
-           (template (cdr (assoc 'template decoded-alist))))
+                                   (match-string 1 (plist-get info :ref)))
-      (raise-frame)
+                        :link (plist-get info :ref)
-      (org-roam--with-template-error 'org-roam-capture-ref-templates
+                        :annotation (org-link-make-string (plist-get info :ref)
-        (org-roam-capture--capture nil template))
+                                                          (or (plist-get info :title)
-      (org-roam-message "Item captured.")))
+                                                              (plist-get info :ref)))
+                        :initial (or (plist-get info :body) ""))
+  (raise-frame)
+  (org-roam-capture-
+   :keys (plist-get info :template)
+   :node (org-roam-node-create :title (plist-get info :title))
+   :info (list :ref (plist-get info :ref)
+               :body (plist-get info :body))
+   :templates org-roam-capture-ref-templates)
   nil)
 
 (defun org-roam-protocol-open-file (info)

org-roam-refile.el

@@ -0,0 +1,77 @@
+;;; org-roam-refile.el --- Refile Org-roam Notes             -*- lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 2.0.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (org "9.4") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; Org-roam refile allows you to refile notes to your nodes.
+;;
+;;; Code:
+(defvar org-auto-align-tags)
+(defvar org-loop-over-headlines-in-active-region)
+
+(defun org-roam-refile ()
+  "Refile to node."
+  (interactive)
+  (let* ((regionp (org-region-active-p))
+         (region-start (and regionp (region-beginning)))
+         (region-end (and regionp (region-end)))
+         (node (org-roam-node-read nil nil 'require-match))
+         (file (org-roam-node-file node))
+         (nbuf (or (find-buffer-visiting file)
+                   (find-file-noselect file)))
+         level reversed)
+    (if regionp
+        (progn
+          (org-kill-new (buffer-substring region-start region-end))
+          (org-save-markers-in-region region-start region-end))
+      (org-copy-subtree 1 nil t))
+    (with-current-buffer nbuf
+      (org-with-wide-buffer
+       (goto-char (org-roam-node-point node))
+       (setq level (org-get-valid-level (funcall outline-level) 1)
+             reversed (org-notes-order-reversed-p))
+       (goto-char
+        (if reversed
+            (or (outline-next-heading) (point-max))
+          (or (save-excursion (org-get-next-sibling))
+              (org-end-of-subtree t t)
+              (point-max))))
+       (unless (bolp) (newline))
+       (org-paste-subtree level nil nil t)
+       (and org-auto-align-tags
+            (let ((org-loop-over-headlines-in-active-region nil))
+              (org-align-tags)))
+       (when (fboundp 'deactivate-mark) (deactivate-mark))))
+    (if regionp
+        (delete-region (point) (+ (point) (- region-end region-start)))
+      (org-preserve-local-variables
+       (delete-region
+        (and (org-back-to-heading t) (point))
+        (min (1+ (buffer-size)) (org-end-of-subtree t t) (point)))))))
+
+(provide 'org-roam-refile)
+;;; org-roam-refile.el ends here

org-roam-utils.el

@@ -0,0 +1,209 @@
+;;; 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-sqlite3 "1.0.2") (magit-section "2.90.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements utility functions used throughout
+;; Org-roam.
+;;
+;;
+;;; Code:
+;;;; Library Requires
+(require 'dash)
+(require 's)
+
+(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)
+
+;;;; 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)))
+
+;;; 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))))
+
+(defun org-roam--process-display-format (format)
+  "Pre-calculate minimal widths needed by the FORMAT string."
+  (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))))
+
+;;; 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/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/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

@@ -1,4 +0,0 @@
-#+roam_tags: "t1" "t2 with space" t3
-#+title: Tags
-
-This file is used to test functionality for =(org-roam--extract-tags)=

tests/roam-files/titles/aliases.org

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

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.el

@@ -3,7 +3,7 @@
 ;; Copyright (C) 2020 Jethro Kuan
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup) (with-simulated-input))
+;; Package-Requires: ((buttercup))
 
 ;; This program is free software; you can redistribute it and/or modify
 ;; it under the terms of the GNU General Public License as published by
@@ -23,270 +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'."
-  (file-truename (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 (file-truename (concat default-directory "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--get))
-  (org-roam-db--close))
-
-(describe "org-roam--str-to-list"
-  (it "nil"
-    (expect (org-roam--str-to-list nil)
-            :to-be
-            nil))
-  (it "\"multi word\" prop 123"
-    (expect (org-roam--str-to-list "\"multi word\" prop 123")
-            :to-equal
-            '("multi word" "prop" "123")))
-  (it "prop \"multi word\" 123"
-    (expect (org-roam--str-to-list "\"multi word\" prop 123")
-            :to-equal
-            '("multi word" "prop" "123")))
-  (it "errors on bad input"
-    (expect (org-roam--str-to-list 1)
-            :to-throw)
-    (expect (org-roam--str-to-list "\"hello")
-            :to-throw)))
-
-(describe "Title extraction"
-  :var (org-roam-title-sources)
   (before-all
-    (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 ((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"))
-      (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"))
-      (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")))
-
-    (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")))
-      (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" "tags"))))))
-
-;;; 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 (= from $s1)]
-                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= from $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 (= to $s1)]
-                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $s1)]
-                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
-    (expect (caar (org-roam-db-query [:select (funcall count) :from links
-                                      :where (= to $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))))
+            2))
+
+  (it "has the correct number of nodes"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from nodes]))
+            :to-equal
+            2))
+
+  (it "has the correct number of links"
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links]))
+            :to-equal
+            1)))
 
 (provide 'test-org-roam)