(release): 1.1.0: update version headers in source (#502)

Use destructive elisp functions to optimize for speed and memory
usage.

Refs #104

.github/CONTRIBUTING.md

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

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug Report
+about: Something's not working.
+title: ''
+labels: ''
+assignees: 'jethrokuan'
+---
+
+### Description
+
+#### Steps to Reproduce
+<!--
+Example:
+
+1. Load Emacs
+2. Run `org-roam--build-cache-async`
+3. Run `org-roam-find-file`
+...
+-->
+
+
+#### Expected Results
+<!-- Example: File A is there -->
+
+#### Actual Results
+<!-- Example: File A is missing -->
+
+### Versions
+- Emacs (`C-h v emacs-version`): vX.X.X
+- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,16 @@
+---
+name: Feature Request
+about: Create a feature request to improve Org-roam
+title: ''
+labels: 'enhancement'
+assignees: 'jethrokuan'
+---
+
+### Brief Abstract
+
+### Long Description
+
+### Proposed Implementation (if any)
+
+### Please check the following:
+- [ ] No similar feature requests

.github/PULL_REQUEST_TEMPLATE.md

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

.github/workflows/test.yml

@@ -0,0 +1,68 @@
+# * test.yml --- Test Emacs packages using makem.sh on GitHub Actions
+
+# https://github.com/alphapapa/makem.sh
+
+# Based on Steve Purcell's examples at
+# <https://github.com/purcell/setup-emacs/blob/master/.github/workflows/test.yml>,
+# <https://github.com/purcell/package-lint/blob/master/.github/workflows/test.yml>.
+
+# * License:
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+# * Code:
+
+name: "CI"
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+      - develop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        emacs_version:
+          - snapshot
+    steps:
+    - uses: purcell/setup-emacs@master
+      with:
+        version: ${{ matrix.emacs_version }}
+
+    - uses: actions/checkout@v2
+
+    - name: Initialize sandbox
+      run: |
+        SANDBOX_DIR=$(mktemp -d) || exit 1
+        echo ::set-env name=SANDBOX_DIR::$SANDBOX_DIR
+        ./makem.sh -vv --sandbox $SANDBOX_DIR --install-deps --install-linters
+
+    # The "all" rule is not used, because it treats compilation warnings
+    # as failures, so linting and testing are run as separate steps.
+
+    - name: Lint
+      continue-on-error: true
+      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
+
+    - name: Test
+      if: always()  # Run test even if linting fails.
+      run: ./makem.sh -vv --sandbox $SANDBOX_DIR test
+
+# Local Variables:
+# eval: (outline-minor-mode)
+# End:

.gitignore

@@ -0,0 +1,2 @@
+/.sandbox/
+**/*.elc

CHANGELOG.md

@@ -0,0 +1,141 @@
+# Changelog
+
+## 1.1.0 (21-04-2020)
+
+To the average user, this release is mainly a bugfix release with additional options to customize. However, the changes made to the source is significant. Most notably, in this release:
+
+1. The codebase has been modularized into separate files, to ease future maintenance and adding of new features (mainly by [@progfolio](https://github.com/progfolio)). Because of these changes, we had to rename many functions and variables: the old names are kept for backwards compatibility, but you are encouraged to use the new function names. You'll receive a warning when you're calling the function with its obsolete name.
+2. [@kljohann](https://github.com/kljohann) did some fantastic work on graph generation: allowing building images for connected components within the graph up to a specified distance
+3. We also started supporting `org-ref` natively: cite links now show up in both the graph and the org-roam buffer.
+
+In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer). 
+ 
+### Breaking Changes
+* [#385](https://github.com/jethrokuan/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
+* [#473](https://github.com/jethrokuan/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.
+
+### New Features
+* [#350](https://github.com/jethrokuan/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
+* [#359](https://github.com/jethrokuan/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
+* [#374](https://github.com/jethrokuan/org-roam/pull/374) Add support for `org-ref` `cite:` links
+* [#380](https://github.com/jethrokuan/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
+* [#385](https://github.com/jethrokuan/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
+* [#398](https://github.com/jethrokuan/org-roam/pull/398), [#418](https://github.com/jethrokuan/org-roam/pull/418) Add graph building for connected components
+* [#435](https://github.com/jethrokuan/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
+* [#439](https://github.com/jethrokuan/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
+* [#465](https://github.com/jethrokuan/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
+* [#488](https://github.com/jethrokuan/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
+* [#491](https://github.com/jethrokuan/org-roam/pull/491) Use TITLE as description when linking before first heading
+
+### Bugfixes
+* [#470](https://github.com/jethrokuan/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.
+
+### Internal Changes
+* [#363](https://github.com/jethrokuan/org-roam/pull/363), [#473](https://github.com/jethrokuan/org-roam/pull/473) Modularize org-roam features.
+* [#497](https://github.com/jethrokuan/org-roam/pull/497) Simplify `org-roam--list-files` implementation
+
+## 1.0.0 (23-03-2020)
+
+Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
+been stable for the most part.
+
+### New Features
+* [#269](https://github.com/jethrokuan/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
+* [#257](https://github.com/jethrokuan/org-roam/pull/257) Add a company-backend `company-org-roam`
+* [#284](https://github.com/jethrokuan/org-roam/pull/284), [#289](https://github.com/jethrokuan/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
+* [#289](https://github.com/jethrokuan/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
+* [#290](https://github.com/jethrokuan/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
+* [#296](https://github.com/jethrokuan/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`
+
+### Bugfixes
+* [#293](https://github.com/jethrokuan/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
+* [#275](https://github.com/jethrokuan/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
+
+## 1.0.0-rc1 (06-03-2020)
+
+This is a pre-release before the push to MELPA. It contains large
+internal changes, with little user-facing changes. Most notably, the
+backing storage has been changed to a SQLite database, and a
+templating system using `org-capture` is introduced.
+
+### Breaking Changes
+* [#200](https://github.com/jethrokuan/org-roam/pull/200) Move Org-roam cache into a SQLite database.
+* [#203](https://github.com/jethrokuan/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.
+
+### New Features
+* [#182](https://github.com/jethrokuan/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
+* [#216](https://github.com/jethrokuan/org-roam/pull/216) Adds templating functionality by extending org-capture.
+* [#232](https://github.com/jethrokuan/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
+* [#233](https://github.com/jethrokuan/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
+* [#247](https://github.com/jethrokuan/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
+* [#259](https://github.com/jethrokuan/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`
+
+### Bugfixes
+* [#207](https://github.com/jethrokuan/org-roam/pull/207), [#221](https://github.com/jethrokuan/org-roam/pull/221) small bugfixes to Org-roam graph generation
+* [#230](https://github.com/jethrokuan/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors
+
+### New Contributors
+* [@acowley][https://github.com/acowley]
+* [@teesloane][https://github.com/teesloane]
+
+## 0.1.2 (2020-02-21)
+
+### Breaking Changes
+* [#143](https://github.com/jethrokuan/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+* [#103](https://github.com/jethrokuan/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+### New Features
+* [#145](https://github.com/jethrokuan/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
+* [#141](https://github.com/jethrokuan/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
+* [#138](https://github.com/jethrokuan/org-roam/pull/138) add `org-roam-switch-to-buffer`
+* [#124](https://github.com/jethrokuan/org-roam/pull/124), [#141](https://github.com/jethrokuan/org-roam/pull/141) Maintain cache consistency on file rename and delete
+* [#87](https://github.com/jethrokuan/org-roam/pull/87), [#90](https://github.com/jethrokuan/org-roam/pull/90) Support encrypted Org files
+* [#110](https://github.com/jethrokuan/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
+* [#99](https://github.com/jethrokuan/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+### Changes
+
+* [#108](https://github.com/jethrokuan/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+
+### Bugfixes
+* [#86](https://github.com/jethrokuan/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+* [#98](https://github.com/jethrokuan/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
+* [#136](https://github.com/jethrokuan/org-roam/pull/136) Misc bugfixes
+
+### Internal
+* [#122](https://github.com/jethrokuan/org-roam/pull/122), [#128](https://github.com/jethrokuan/org-roam/pull/128) Improve performance of post-command-hook
+* [#92](https://github.com/jethrokuan/org-roam/pull/92), [#105](https://github.com/jethrokuan/org-roam/pull/105) Add tests for core functionality
+
+### New Contributors
+* [@frigge](https://github.com/frigge)
+* [@juergenhoetzel](https://github.com/juergenhoetzel)
+* [@chip2n](https://github.com/chip2n)
+* [@l3kn](https://github.com/l3kn)
+* [@jdormit](https://github.com/jdormit)
+* [@herbertjones](https://github.com/herbertjones)
+* [@CeleritasCelery](https://github.com/CeleritasCelery)
+* [@daniel-koudouna](https://github.com/daniel-koudouna)
+
+## 0.1.1 (2020-02-15)
+
+Mostly a documentation/cleanup release.
+
+### New Features
+* [#62](https://github.com/jethrokuan/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
+
+### Breaking Changes
+* [#62](https://github.com/jethrokuan/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
+
+### Changes
+* [#66](https://github.com/jethrokuan/org-roam/pull/66), [#68](https://github.com/jethrokuan/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
+* [#73](https://github.com/jethrokuan/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
+* [#69](https://github.com/jethrokuan/org-roam/pull/69), [#72](https://github.com/jethrokuan/org-roam/pull/72), [#75](https://github.com/jethrokuan/org-roam/pull/75): Major cleanup and de-duplication of code
+
+### Bugfixes
+* [#67](https://github.com/jethrokuan/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
+* [#71](https://github.com/jethrokuan/org-roam/pull/71), [#78](https://github.com/jethrokuan/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
+* [#82](https://github.com/jethrokuan/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
+
+<!-- Local Variables: -->
+<!-- eval: (auto-fill-mode -1) -->
+<!-- End: -->

Makefile

@@ -0,0 +1,56 @@
+# * makem.sh/Makefile --- Script to aid building and testing Emacs Lisp packages
+
+# This Makefile is from the makem.sh repo: <https://github.com/alphapapa/makem.sh>.
+
+# * Arguments
+
+# For consistency, we use only var=val options, not hyphen-prefixed options.
+
+# NOTE: I don't like duplicating the arguments here and in makem.sh,
+# but I haven't been able to find a way to pass arguments which
+# conflict with Make's own arguments through Make to the script.
+# Using -- doesn't seem to do it.
+
+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)

README.md

@@ -1,52 +1,94 @@
+[![License GPL 3][badge-license]](http://www.gnu.org/licenses/gpl-3.0.txt)
 [![Documentation Status](https://readthedocs.org/projects/org-roam/badge/?version=latest)](https://org-roam.readthedocs.io/en/latest/?badge=latest)
+[![GitHub Release](https://img.shields.io/github/v/release/jethrokuan/org-roam)](https://img.shields.io/github/v/release/jethrokuan/org-roam)
+[![MELPA](https://melpa.org/packages/org-roam-badge.svg)](https://melpa.org/#/org-roam)
 
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
+## Synopsis
 
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. 
+Org-roam is a [Roam][roamresearch] replica built on top of the
+all-powerful [Org-mode][org].
 
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem. 
+Org-roam is a solution for effortless non-hierarchical note-taking
+with Org-mode. With Org-roam, notes flow naturally, making note-taking
+fun and easy. Org-roam should also work as a plug-and-play solution
+for anyone already using Org-mode for their personal wiki.
 
-For more documentation, see [the documentation page](https://org-roam.readthedocs.io/en/latest/).
+Org-roam aims to implement the core features of Roam, leveraging the
+mature ecosystem around Org-mode where possible. Eventually, we hope
+to further introduce features enabled by the Emacs ecosystem.
 
-## Understanding Roam
+[@technovangelist](https://github.com/technovangelist/) has produced a video
+describing Org-roam and the concepts behind it:
 
-To understand more about Roam, I recommend the following links:
-
--   [Building a second brain in
-    Roam](https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)
--   [Roam: Why I Love It and How I Use
-    It](https://www.nateliason.com/blog/roam)
-
-## Project Status
+[![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")
 
 As of February 2020, it is in a very early stage of development. 
 
+Important links:
+
+- **[Documentation][docs]**
+- **[Org-roam Slack][slack]**
+
 ## A Preview
 
 Here's a screenshot of `org-roam`. The `org-roam` buffer shows
 backlinks for the active org buffer in the left window, as well as the
-surrounding content in the backlink file. The backlink database is
-built asynchronously in the background, and is not noticeable to the
-end user. The graph is generated from the link structure, and can be
-used to navigate to the respective files.
+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)
 
-## Knowledge Bases using Org-Roam
+## Installation
+
+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`:
+
+```emacs-lisp
+(use-package org-roam
+      :hook 
+      (after-init . org-roam-mode)
+      :custom
+      (org-roam-directory "/path/to/org-files/")
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n g" . org-roam-show-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
+```
+
+For more detailed installation and configuration instructions (including for
+Doom and Spacemacs users), please see [the
+documentation](https://org-roam.readthedocs.io/en/master/installation/).
+
+## Knowledge Bases using Org-roam
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
 
+## Changelog
+
+A changelog is being maintained [here](CHANGELOG.md)
+
 ## Contributing
 
 To report bugs and suggest new feature use the issue tracker. If you
 have some code which you would like to be merged, then open a pull
-request. Please also see CONTRIBUTING.md.
+request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).
+
+## License
+
+Copyright © Jethro Kuan and contributors. Distributed under the GNU
+General Public License, Version 3
 
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
+[badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
+[docs]: https://org-roam.readthedocs.io/
+[slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg

doc/anatomy.md

@@ -0,0 +1,41 @@
+The bulk of Org-roam's functionality is built on top of vanilla
+Org-mode. However, to support additional functionality, Org-roam adds
+several Org-roam-specific keywords. These functionality are not
+crucial to effective use of Org-roam.
+
+## File Aliases
+
+Suppose you want a note to be referred to by different names (e.g.
+"World War 2", "WWII"). You may specify such aliases using the
+`#+ROAM_ALIAS` attribute:
+
+```org
+#+TITLE: World War 2
+#+ROAM_ALIAS: "WWII" "World War II"
+```
+
+
+## File Refs
+
+Refs are unique identifiers for files. Each note can only have 1 ref.
+For example, a note for a website may contain a ref:
+
+```org
+#+TITLE: Google
+#+ROAM_KEY: https://www.google.com/
+```
+
+These keys come in useful for when taking website notes, using the
+`roam-ref` protocol (see [Roam Protocol](roam_protocol.md)).
+
+Alternatively, add a ref for notes for a specific paper, using its
+[org-ref](https://github.com/jkitchin/org-ref) citation key:
+
+```org
+#+TITLE: Neural Ordinary Differential Equations
+#+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
+```
+
+The backlinks buffer will show any cites of this key: e.g.
+
+![org-ref-citelink](images/org-ref-citelink.png)

doc/comparison.md

@@ -1,7 +1,7 @@
 ---
-title: "Comparing Org-Roam With Other Packages"
-metaTitle: "Comparing Org-Roam With Other Packages"
-metaDescription: "Comparing Org-Roam With Other Packages"
+title: "Comparing Org-roam With Other Packages"
+metaTitle: "Comparing Org-roam With Other Packages"
+metaDescription: "Comparing Org-roam With Other Packages"
 ---
 
 # Org-brain

doc/configuration.md

@@ -0,0 +1,142 @@
+The number of configuration options is deliberately kept small, to
+keep the Org-roam codebase manageable. However, we attempt to
+accommodate as many usage styles as possible.
+
+All of Org-roam's customization options can be viewed via `M-x
+customize-group org-roam`.
+
+## Setting the Org-roam Directory
+
+Set `org-roam-directory` to the folder containing all your Org files:
+
+```emacs-lisp
+(setq org-roam-directory "/path/to/org/")
+```
+
+Every Org file, at any level of nesting, within `/path/to/org/` is
+considered part of the Org-roam ecosystem.
+
+### Having More Than One Org-roam Directory
+
+Emacs supports directory-local variables, allowing the value of
+`org-roam-directory` to be different in different directories. It does
+this by checking for a file named `.dir-locals.el`. 
+
+To add support for multiple directories, override the
+`org-roam-directory` variable using directory-local variables. This is
+what `.dir-locals.el` may contain:
+
+```emacs-lisp
+((nil . ((org-roam-directory . "/path/to/here/"))))
+```
+
+All files within that directory will be treated as their own separate
+set of Org-roam files. Remember to run `org-roam-db-build-cache` from a
+file within that directory, at least once.
+
+## Org-roam Buffer
+
+The Org-roam buffer defaults to popping up from the right. You may
+choose to set it to pop up from the left with `(setq
+org-roam-buffer-position 'left)`.
+
+The Org-roam buffer name can also be renamed: e.g. `(setq
+org-roam-buffer "*my-buffer-name*")`.
+
+The Org-roam buffer width is adjustable via `org-roam-buffer-width`.
+The value of `org-roam-buffer-width` set as a percentage of the total
+frame width. For example:
+
+```emacs-lisp
+(setq org-roam-buffer-width 0.4)
+```
+
+Will result in the Org-roam buffer taking up 40% of the screen width.
+
+You can change backlinks appearance in the buffer by customizing
+`org-roam-backlink` face (`M-x customize-face org-roam-backlink`).
+
+## Org-roam Links
+
+By default, links are inserted with the title as the link description.
+This can make them hard to distinguish from external links. You may
+choose add special indicators for Org-roam links by tweaking
+`org-roam-link-title-format`, for example:
+
+```emacs-lisp
+(setq org-roam-link-title-format "R:%s")
+```
+
+If your version of Org is at least `9.2`, you may also choose to
+simply style the link differently, by customizing `org-roam-link` face
+(`M-x customize-face org-roam-link`).
+
+## Org-roam Files
+
+Org-roam files are created and prefilled using Org-roam's templating
+system. The templating system is customizable, and the system is
+described in detail in the [Org-roam Template](templating.md) page.
+
+### Encryption
+
+Encryption (via GPG) can be enabled for all new files by setting
+`org-roam-encrypt-files` to `t`. When enabled, new files are created
+with the `.org.gpg` extension and decryption are handled automatically
+by EasyPG. 
+
+Note that Emacs will prompt for a password for encrypted files during
+cache updates if it requires reading the encrypted file. To reduce the
+number of password prompts, you may wish to cache the password.
+
+## Org-roam Graph Viewer
+
+Org-roam generates an SVG image using
+[Graphviz](https://graphviz.org/). To setup graph navigation, see the
+[Graph Setup](graph_setup.md) page.
+
+Org-roam tries its best to locate the Graphviz executable from your
+`PATH`, but if it fails to do so, you may set it manually:
+
+```
+(setq org-roam-graph-executable "/path/to/dot")
+```
+
+You may also choose to use `neato` in place of `dot`, which generates a more compact graph layout.
+
+```
+(setq org-roam-graph-executable "/path/to/neato")
+(setq org-roam-graph-extra-config '(("overlap" . "false")))
+```
+
+Org-roam also attempts to use Firefox (located on `PATH`) to view the
+SVG, you may choose to set it to any compatible program:
+
+```
+(setq org-roam-graph-viewer "/path/to/image-viewer")
+```
+
+### Excluding Nodes and Edges
+One may want to exclude certain files to declutter the graph. You can do so by setting `org-roam-graph-exclude-matcher`.
+
+```
+(setq org-roam-graph-exclude-matcher '("private" "dailies"))
+```
+
+This setting excludes all files whose path contain "private" or "dailies".
+
+## Org-roam Completion System
+
+Org-roam offers completion when choosing note titles etc.
+The completion system is configurable. The default setting,
+
+```
+(setq org-roam-completion-system 'default)
+```
+
+uses Emacs' standard `completing-read`. If you prefer [Helm](https://emacs-helm.github.io/helm/), use
+
+```
+(setq org-roam-completion-system 'helm)
+```
+
+Other options included `'ido`, and `'ivy'`.

doc/ecosystem.md

@@ -1,12 +1,11 @@
-## Ecosystem
-
 A number of packages work well combined with Org-Roam:
 
-### Deft
-[Deft](https://jblevins.org/projects/deft/) provides a nice
-interface for browsing and filtering org-roam notes.
+## Deft
 
-```
+[Deft][deft] provides a nice interface for browsing and filtering
+org-roam notes.
+
+```emacs-lisp
 (use-package deft
   :after org
   :bind
@@ -15,17 +14,50 @@ interface for browsing and filtering org-roam notes.
   (deft-recursive t)
   (deft-use-filter-string-for-filename t)
   (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/")
-  (deft-use-filename-as-title t))
+  (deft-directory "/path/to/org-roam-files/"))
 ```
 
-### Org-journal
-[Org-journal](https://github.com/bastibe/org-journal) is a more
-powerful alternative to the simple function `org-roam-today`. It
-provides better journaling capabilities, and a nice calendar interface
-to see all dated entries.
+If the title of the Org file is not the first line, you might not get
+nice titles. You may choose to patch this to use `org-roam`'s
+functionality. Here I'm using [el-patch](https://github.com/raxod502/el-patch):
 
+```emacs-lisp
+(use-package el-patch
+  :straight (:host github
+                   :repo "raxod502/el-patch"
+                   :branch "develop"))
+
+(eval-when-compile
+  (require 'el-patch))
+
+(use-package deft
+  ;; same as above...
+  :config/el-patch
+  (defun deft-parse-title (file contents)
+    "Parse the given FILE and CONTENTS and determine the title.
+If `deft-use-filename-as-title' is nil, the title is taken to
+be the first non-empty line of the FILE.  Else the base name of the FILE is
+used as title."
+    (el-patch-swap (if deft-use-filename-as-title
+                       (deft-base-filename file)
+                     (let ((begin (string-match "^.+$" contents)))
+                       (if begin
+                           (funcall deft-parse-title-function
+                                    (substring contents begin (match-end 0))))))
+                   (org-roam--get-title-or-slug file))))
 ```
+
+The Deft interface can slow down quickly when the number of files get
+huge. [Notdeft][notdeft] is a fork of Deft that uses an external
+search engine and indexer.
+
+## Org-journal
+
+[Org-journal](https://github.com/bastibe/org-journal) is a more powerful
+alternative to the simple function `org-roam-dailies-today`. It provides better
+journaling capabilities, and a nice calendar interface to see all dated entries.
+
+```emacs-lisp
 (use-package org-journal
   :bind
   ("C-c n j" . org-journal-new-entry)
@@ -35,3 +67,68 @@ to see all dated entries.
   (org-journal-dir "/path/to/org-roam-files/")
   (org-journal-date-format "%A, %d %B %Y"))
 ```
+
+## Note-taking Add-ons
+
+These are some plugins that make note-taking in Org-mode more
+enjoyable.
+
+### Org-download
+
+[Org-download][org-download] lets you screenshot and yank images from
+the web into your notes:
+
+![org-download](images/org-download.gif)
+
+```emacs-lisp
+(use-package org-download
+  :after org
+  :bind
+  (:map org-mode-map
+        (("s-Y" . org-download-screenshot)
+         ("s-y" . org-download-yank))))
+```
+
+### mathpix.el
+
+[mathpix.el][mathpix-el] uses [Mathpix's](https://mathpix.com/) API to convert clips into
+latex equations:
+
+![mathpix](images/mathpix.gif)
+
+```emacs-lisp
+(use-package mathpix.el
+  :straight (:host github :repo "jethrokuan/mathpix.el")
+  :custom ((mathpix-app-id "app-id")
+           (mathpix-app-key "app-key"))
+  :bind
+  ("C-x m" . mathpix-screenshot))
+```
+
+### Org-noter / Interleave
+
+[Org-noter][org-noter] and [Interleave][interleave] are both projects
+that allow synchronised annotation of documents (PDF, EPUB etc.)
+within Org-mode.
+
+### Org-ref
+
+[Org-ref][org-ref] does citation and bibliography management in
+Org-mode, and a great tool for scientific notes.
+
+### Spaced Repetition
+
+[Org-fc][org-fc] is a spaced repetition system that scales well with a
+large number of files. Other alternatives include
+[org-drill][org-drill], and [pamparam][pamparam].
+
+[deft]: https://jblevins.org/projects/deft/
+[notdeft]: https://github.com/hasu/notdeft
+[org-download]: https://github.com/abo-abo/org-download
+[mathpix-el]: https://github.com/jethrokuan/mathpix.el
+[org-noter]: https://github.com/weirdNox/org-noter
+[interleave]: https://github.com/rudolfochrist/interleave
+[org-ref]: https://github.com/jkitchin/org-ref
+[org-fc]: https://github.com/l3kn/org-fc/
+[org-drill]: https://orgmode.org/worg/org-contrib/org-drill.html
+[pamparam]: https://github.com/abo-abo/pamparam

doc/index.md

@@ -1,40 +1,61 @@
 ![org-roam][org-roam-intro-image]
 
-## What is Org-Roam?
+## What is Org-roam?
 
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
+Org-roam is a [Roam][roamresearch] replica built around the
+all-powerful [Org-mode][org].
 
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. To understand more about Roam, I recommend
-the following links:
+Org-roam is a solution for effortless non-hierarchical note-taking
+with Org-mode. With Org-roam, notes flow naturally, making note-taking
+fun and easy. Org-roam should also work as a plug-and-play solution
+for anyone already using Org-mode for their personal wiki.
 
--   [Building a second brain in
-    Roam](https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)
--   [Roam: Why I Love It and How I Use
-    It](https://www.nateliason.com/blog/roam)
+To understand more about Roam, a collection of links are available in
+[the appendix](notetaking_workflow.md).
 
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem. 
+Org-roam aims to implement the core features of Roam, leveraging the
+mature ecosystem around Org-mode where possible. Eventually, we hope
+to further introduce features enabled by the Emacs ecosystem.
 
-## Why build Org-Roam?
+## Why use Org-roam?
 
-With Org-roam, you:
+##### Private and Secure
 
-1. Never have to leave Emacs.
-2. Can leverage all the powerful features of Org-mode: LaTeX, tables,
-   and the whole to-do ecosystem (org-agenda etc.)
-3. Be in full control your second brain, and access it offline. Never
-   share your data with anyone
+Edit your personal wiki completely offline, entirely in your control.
+Encrypt your notes with GPG.
+
+##### Longevity
+
+Unlike web solutions like Roam research, the notes are first and
+foremost plain Org-mode files -- Org-roam simply builds up an
+auxilliary database to give the personal wiki superpowers. Having your
+notes in plain-text is crucial for the longevity of your wiki. Never
+have to worry about proprietary web solutions being taken down. Edit
+your plain-text notes in notepad if all other editors cease to exist.
+
+##### Free and Open-source
+
+Org-roam is free and open-source, which means that if you feel unhappy
+with any part of Org-roam, you may choose to extend Org-roam, or open
+a PR.
+
+##### Leverage the Org-mode Ecosystem
+
+Over the years, Emacs and Org-mode has developed into a mature system
+for plain-text organization. Building upon Org-mode already puts
+Org-roam light-years ahead of many other solutions.
+
+Emacs is also a fantastic interface for editing text, and we can
+inherit many of the powerful text-navigation and editing packages
+available to Emacs.
 
 There are several packages that are similar to Org-roam, see the
 [Comparison](comparison.md) page for a detailed comparison.
 
 ## Project Status
 
-As of February 2020, it is in a very early stage of development. 
+As of March 2020, most of the core functionality and interfaces have
+stabilized, and a stable release is near.
 
 [org-roam-intro-image]: images/org-roam-intro.png
 [roamresearch]: https://www.roamresearch.com/

doc/installation.md

@@ -1,35 +1,195 @@
-## Installation
+## Basic Install and Configuration
 
-The recommended method is using [use-package][use-package] and
-[straight][straight], or a similar package manager.
+Org-roam is now available on MELPA, so you can install it via the following
+command:
 
 ```
+M-x package-install RET org-roam RET
+```
+
+Alternatively, you may use package managers such as [straight][straight] or
+[quelpa][quelpa] to install the package.
+
+The recommended method of configuration is to use [use-package][use-package].
+
+```emacs-lisp
 (use-package org-roam
-      :after org
-      :hook (org-mode . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam")
+      :hook
+      (after-init . org-roam-mode)
       :custom
       (org-roam-directory "/path/to/org-files/")
-      (org-roam-link-representation 'title) ;; or keep it as 'id
-      :bind
-      ("C-c n l" . org-roam)      
-      ("C-c n t" . org-roam-today)
-      ("C-c n f" . org-roam-find-file)
-      ("C-c n i" . org-roam-insert)
-      ("C-c n g" . org-roam-show-graph))
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n b" . org-roam-switch-to-buffer)
+               ("C-c n g" . org-roam-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
 ```
 
-If not using package.el, you can also clone it into your Emacs
-directory and add it to your load path:
+Or without `use-package`:
 
-```
-git clone https://github.com/jethrokuan/org-roam/ ~/.emacs.d/elisp/org-roam
-```
-
-```
-(add-to-list 'load-path "./elisp")
+```emacs-lisp
 (require 'org-roam)
+(define-key org-roam-mode-map (kbd "C-c n l") #'org-roam)
+(define-key org-roam-mode-map (kbd "C-c n f") #'org-roam-find-file)
+(define-key org-roam-mode-map (kbd "C-c n b") #'org-roam-switch-to-buffer)
+(define-key org-roam-mode-map (kbd "C-c n g") #'org-roam-graph)
+(define-key org-mode-map (kbd "C-c n i") #'org-roam-insert)
+(org-roam-mode +1)
 ```
 
+The [Configuration](configuration.md) page details some of the common
+configuration options available.
+
+### Completion
+
+Link auto-completion is offered via
+[company-org-roam](https://github.com/jethrokuan/company-org-roam/), refer to
+the documentation there for further details.
+
+## Spacemacs
+
+If you are using Spacemacs, install org-roam by creating a simple layer that
+wraps Org-roam. Paste the following into a new file
+`~/.emacs.d/private/org-roam/packages.el`.
+
+```emacs-lisp
+(defconst org-roam-packages
+  '(org-roam))
+
+(defun org-roam/init-org-roam ()
+  (use-package org-roam
+    :hook
+    (after-init . org-roam-mode)
+    :custom
+    (org-roam-directory "/path/to/org-files/")
+    :init
+    (progn
+      (spacemacs/declare-prefix "ar" "org-roam")
+      (spacemacs/set-leader-keys
+       "arl" 'org-roam
+       "art" 'org-roam-dailies-today
+       "arf" 'org-roam-find-file
+       "arg" 'org-roam-graph)
+
+      (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
+      (spacemacs/set-leader-keys-for-major-mode 'org-mode
+                                                "rl" 'org-roam
+                                                "rt" 'org-roam-dailies-today
+                                                "rb" 'org-roam-switch-to-buffer
+                                                "rf" 'org-roam-find-file
+                                                "ri" 'org-roam-insert
+                                                "rg" 'org-roam-graph))))
+```
+
+Next, append `org-roam` to the `dotspacemacs-configuration-layers`
+list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or
+restart Emacs to load `org-roam`. It's functions are available under
+the prefix `SPC a r` and `, r` when visiting an org-mode buffer.
+
+If you also have the ranger layer installed, the prefix 'ar' conflict
+with that of the ranger layer. You might want to change it to 'aor'
+(also change the 'ar' to 'aor' in the other key-binding declarations)
+
+## Doom Emacs
+
+[Doom Emacs][doom] has a `+roam` flag on its `org` module for easy
+installation and configuration. Simply add the flag to the `org` section
+of your `~/.doom.d/init.el` and run `~/.emacs.d/bin/doom sync`.
+
 [use-package]: https://github.com/jwiegley/use-package
 [straight]: https://github.com/raxod502/straight.el
+[quelpa]: https://github.com/quelpa/quelpa
+[doom]: https://github.com/hlissner/doom-emacs
+[doom-getting-started]: https://github.com/hlissner/doom-emacs/blob/develop/docs/getting_started.org#configuring-packages
+
+## Windows
+
+On Windows, if you follow the installation instructions above, you will likely get the error message: **"No EmacSQL SQLite binary available, aborting"**, and `org-roam` won't start properly.
+
+You need to do some additional steps to get `org-roam` to work.
+
+Essentially, you will need to have a binary file for `emacsql-sqlite` so that your Emacs can work with `sqlite` database -- `org-roam` uses it to track backlinks. The following options have been reported to work by Windows users in the community.
+
+Option 1. **Windows Subsystem for Linux (WSL)**
+: This option lets you use Linux on your Windows machine. It's Linux, so you don't need to do anything specific for Windows.
+
+Option 2. **mingw-x64**
+: Use mingw-x64. You would spend a bit of time to download it, and get familiar with how it works. You should be able to use Linux tools within your Windows [more contribution welcome].
+
+Option 3. **scoop**
+: Use [scoop](https://scoop.sh/) to install a couple of software tools (make and gcc) and manually compile a binary (`.exe`) file yourself. Find a short step-by-step guide below.
+
+Option 4. **emacsql-sqlite3**
+: Use another Emacs package called [`emacsql-sqlite3`](https://github.com/cireu/emacsql-sqlite3). You can download an [official binary](https://sqlite.org/download.html) for `sqlite3`. `emacsql-sqlite3` lets you use it. For this option to work, you need to adjust the `org-roam` source code, and get your modified version to work in your Emacs environment. Find a suggestion below.
+
+### scoop
+**Step 1.** In PowerShell, install `scoop` ([instruction here](https://scoop.sh/)).
+
+```powershell
+iwr -useb get.scoop.sh | iex
+```
+
+**Step 2.** In PowerShell, install `make` and `gcc` via scoop
+
+```powershell
+scoop install make gcc
+```
+
+**Step 3.** In Emacs, install the `emacsql-sqlite` package for your Emacs if it is not done yet.
+
+**Step 4.** In PowerShell, move to the directory where `emacsql.c` is stored.
+
+With MELPA, it is likely to be under your ELPA folder:
+
+```
+~\AppData\Roaming\.emacs.d\elpa\emacsql-sqlite-20190727.1710\sqlite
+```
+
+With Doom Emacs, it should be under your `.emacs\.local`:
+
+```
+~\.emacs.d\.local\straight\build\emacsql-sqlite\sqlite
+```
+
+Check the files via `dir` command. You should see these files:
+
+```powershell
+Mode                LastWriteTime         Length Name
+----                -------------         ------ ----
+-a----       22/03/2020  12:10 PM           5170 emacsql.c
+-a----       22/03/2020  12:10 PM            439 Makefile
+-a----       22/03/2020  12:10 PM        7516138 sqlite3.c
+-a----       22/03/2020  12:10 PM         526684 sqlite3.h
+```
+
+**Step 5.** Compile the `.exe` file with `make`
+
+```powershell
+make emacsql-sqlite CC=gcc LDLIBS=
+```
+
+You will see the process triggered with lots of text automatically scrolling down; it may take a couple of minutes for compilation to finish.
+
+Once compilation is done, check that `emacsql-sqlite.exe` has been added to the directory.
+
+**Step 6.** Relaunch Emacs, use `org-roam`
+
+When you start `org-roam` (e.g. via `org-roam-mode`), now you should no longer see the "No EmacSQL SQLite binary available, aborting" error. You are good to go.
+
+
+### emacsql-sqlite3
+
+1. In Emacs, install the `emacsql-sqlite3` package
+
+2. Using your text editor, etc. modify `org-roam-db.el`:
+
+    1. Replace `(require 'emacsql-sqlite)` with `(require 'emacsql-sqlite3)`
+
+    2. Comment/deactivate the complete `(defconst org-roam-db--sqlite-available-p ... )`
+
+    3. In `(defun org-roam-db ...`, replace `emacsql-sqlite`
+with `emacsql-sqlite3`
+
+3. If you compile `.el` files, ensure to replace `org-roam-db.elc` with the new source you modified.

doc/notetaking_workflow.md

@@ -0,0 +1,24 @@
+## Recommended Books
+- [How to Take Smart Notes][1]
+
+## Articles
+- [How to Take Smart Notes in Org-mode - Jethro Kuan][7]
+- [The Zettelkasten Method - LessWrong 2.0][3]
+- [Building a second brain in Roam][4]
+- [Roam: Why I Love It and How I Use It][5]
+- [Adam Keesling's Twitter Thread][6]
+
+## Threads
+- [Ask HN: How to Take Good Notes][8]
+
+## What to Do With Your Notes
+- [How to Use Roam to Outline a New Article in Under 20 Minutes][2]
+
+[1]: https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes?ac=1&from_search=true&qid=6L8iEE1FIA&rank=1
+[2]: https://www.youtube.com/watch?v=RvWic15iXjk
+[3]: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1
+[4]: https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might
+[5]: https://www.nateliason.com/blog/roam
+[6]: https://twitter.com/adam_keesling/status/1196864424725774336?s=20
+[7]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/
+[8]: https://news.ycombinator.com/item?id=22473209

doc/org_export.md

@@ -0,0 +1,61 @@
+While exporting your documents to another format such as HTML -- whether using Org's in-built export or ox-hugo -- you can add a backlinks section which would display the backlinks to the current file. This is done via org-export's preprocessing hooks. See more at [Advanced Export Configuration (The Org Manual)](https://orgmode.org/manual/Advanced-Export-Configuration.html#Advanced-Export-Configuration).
+
+Following are two different configs that might be suitable for different use-cases. Add one of these snippets in your Emacs init file.
+
+### Only Backlinks
+
+This will display only the backlinks and not the contents.
+
+```emacs-lisp
+(defun my/org-roam--backlinks-list (file)
+  (if (org-roam--org-roam-file-p file)
+      (--reduce-from
+       (concat acc (format "- [[file:%s][%s]]\n"
+                           (file-relative-name (car it) org-roam-directory)
+			                     (org-roam--get-title-or-slug (car it))))
+       "" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
+    ""))
+
+(defun my/org-export-preprocessor (backend)
+  (let ((links (my/org-roam--backlinks-list (buffer-file-name))))
+    (unless (string= links "")
+      (save-excursion
+      	(goto-char (point-max))
+      	(insert (concat "\n* Backlinks\n") links)))))
+
+(add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
+```
+
+### Backlinks and Contents
+
+This would insert both backlinks and the contents, just like the org-roam buffer. This might be especially useful if you host a web version of your personal knowledgebase and want to browse the files along with the backlinks from mobile devices.
+
+```emacs-lisp
+(defun my/org-roam--backlinks-list-with-content (file)
+  (with-temp-buffer
+    (if-let* ((backlinks (org-roam--get-backlinks file))
+              (grouped-backlinks (--group-by (nth 0 it) backlinks)))
+        (progn
+          (insert (format "\n\n* %d Backlinks\n"
+                          (length backlinks)))
+          (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 (s-trim (s-replace "\n" " " (plist-get props :content))))
+                  (insert "\n\n")))))))
+    (buffer-string)))
+
+  (defun my/org-export-preprocessor (backend)
+    (let ((links (my/org-roam--backlinks-list-with-content (buffer-file-name))))
+      (unless (string= links "")
+        (save-excursion
+          (goto-char (point-max))
+          (insert (concat "\n* Backlinks\n") links)))))
+
+  (add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
+```

doc/roam_protocol.md

@@ -0,0 +1,161 @@
+## What is Roam protocol?
+
+Org-roam extending `org-protocol` with 2 protocols: the `roam-file`
+and `roam-ref` protocol.
+
+## The `roam-file` protocol
+
+This is a simple protocol that opens the path specified by the `file`
+key (e.g. `org-protocol://roam-file?file=/tmp/file.org`). This is used
+in the generated graph.
+
+## The `roam-ref` Protocol
+
+This protocol finds or creates a new note with a given `ROAM_KEY` (see
+[Anatomy](anatomy.md)):
+
+![roam-ref](images/roam-ref.gif)
+
+To use this, create a Firefox bookmarklet as follows:
+
+```javascript
+javascript:location.href =
+'org-protocol:/roam-ref?template=r&ref='
++ encodeURIComponent(location.href)
++ '&title='
++ encodeURIComponent(document.title)
+```
+
+where `template` is the template key for a template in
+`org-roam-capture-ref-templates`. More documentation on the templating
+system can be found [here](templating.md).
+
+These templates should contain a `#+ROAM_KEY: ${ref}` in it.
+
+## Setting up Org-roam protocol
+
+To enable org-roam's protocol extensions, you have to add the
+following to your init file:
+
+```emacs-lisp
+(require 'org-roam-protocol)
+```
+
+The instructions for setting up `org-protocol` can be found
+[here][org-protocol-inst], but they are reproduced below.
+
+We will also need to create a desktop application for `emacsclient`.
+The instructions for various platforms are shown below:
+
+## Linux
+
+Create a desktop application. I place mine in
+`~/.local/share/applications/org-protocol.desktop`:
+
+```
+[Desktop Entry]
+Name=Org-Protocol
+Exec=emacsclient %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/org-protocol
+```
+
+Associate `org-protocol://` links with the desktop application by
+running in your shell:
+
+```bash
+xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
+```
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the `Org-Protocol Client` app will be used
+without confirmation. To do this, run in a shell:
+
+```sh
+sudo mkdir -p /etc/opt/chrome/policies/managed/
+sudo tee /etc/opt/chrome/policies/managed/external_protocol_dialog.json >/dev/null <<'EOF'
+{
+  "ExternalProtocolDialogShowAlwaysOpenCheckbox": true
+}
+EOF
+sudo chmod 644 /etc/opt/chrome/policies/managed/external_protocol_dialog.json
+```
+
+and then restart Chrome (for example, by navigating to <chrome://restart>) to
+make the new policy take effect.
+
+See [here](https://www.chromium.org/administrators/linux-quick-start)
+for more info on the `/etc/opt/chrome/policies/managed` directory and
+[here](https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox)
+for information on the `ExternalProtocolDialogShowAlwaysOpenCheckbox`
+policy.
+
+
+## Mac OS
+
+One solution is to use
+[Platypus](https://github.com/sveinbjornt/Platypus). Here are the
+instructions for setting up with Platypus and Chrome:
+
+1. Install and launch Platypus (with [Homebrew](https://brew.sh/)):
+
+```sh
+brew cask install platypus
+```
+2. Create a script `launch_emacs.sh`:
+
+```
+#!/usr/bin/env bash
+/usr/local/bin/emacsclient --no-wait $1
+```
+
+3. Create a Platypus app with the following settings:
+
+```
+| Setting                        | Value                     |
+|--------------------------------+---------------------------|
+| App Name                       | "OrgProtocol"             |
+| Script Type                    | "env" · "/usr/bin/env"    |
+| Script Path                    | "path/to/launch-emacs.sh" |
+| Interface                      | None                      |
+| Accept dropped items           | true                      |
+| Remain running after execution | false                     |
+```
+
+Inside `Settings`:
+
+```
+| Setting                        | Value          |
+|--------------------------------+----------------|
+| Accept dropped files           | true           |
+| Register as URI scheme handler | true           |
+| Protocol                       | "org-protocol" |
+```
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the `OrgProtocol` app will be used
+without confirmation. To do this, run in a shell:
+
+```sh
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+```
+
+
+##### Note for Emacs Mac Port
+
+If you're using [Emacs Mac Port](https://github.com/railwaycat/homebrew-emacsmacport), it
+registered its `Emacs.app` as the default handler for the URL scheme
+`org-protocol`. We have to make our `OrgProtocol.app` the default
+handler instead (replace `org.yourusername.OrgProtocol` with your app
+identifier):
+
+```
+$ defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
+'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
+```
+
+Then restart your computer.
+
+[org-protocol-inst]: https://orgmode.org/worg/org-contrib/org-protocol.html

doc/templating.md

@@ -0,0 +1,119 @@
+Rather than creating blank files on `org-roam-insert` and
+`org-roam-find-file`, it is may be desirable to prefill the file with
+content. This may include:
+
+- Time of creation
+- File it was created from
+- Clipboard content
+- Any other data you may want to input manually
+
+This requires a complex template insertion system, but fortunately,
+Org ships with a powerful one: `org-capture`. However, org-capture was
+not designed for such use. Org-roam abuses `org-capture` to some
+extent, extending its syntax. To first understand how org-roam's
+templating system works, it may be useful to look into org-capture.
+
+## Org-roam Templates
+
+The org-roam capture template extends org-capture's template with 2
+additional properties:
+
+1. `:file-name`: This is the file name template used when a new note
+   is created.
+2. `:head`: This is the template that is inserted on initial note
+   creation.
+
+### Org-roam Template Expansion
+
+Org-roam's template definitions also extend org-capture's template
+syntax, to allow prefilling of strings. In many scenarios,
+`org-roam--capture` is passed a mapping between variables and strings.
+For example, during `org-roam-insert`, a title is prompted for. If the
+title doesn't already exist, we would like to create a new file,
+without prompting for the title again.
+
+Variables passed are expanded with the `${var}` syntax. For example,
+during `org-roam-insert`, `${title}` is prefilled for expansion. Any
+variables that do not contain strings, are prompted for values using
+`completing-read`.
+
+After doing this expansion, the org-capture's template expansion
+system is used to fill up the rest of the template. You may read up
+more on this on [org-capture's documentation
+page](https://orgmode.org/manual/Template-expansion.html#Template-expansion).
+
+For example, take the template: `"%<%Y%m%d%H%M%S>-${title}"`, with the title
+`"Foo"`. The template is first expanded into `%<%Y%m%d%H%M%S>-Foo`. Then
+org-capture expands `%<%Y%m%d%H%M%S>` with timestamp: e.g.
+`20200213032037-Foo`.
+
+All of the flexibility afforded by emacs and org-mode are
+available. For example, if you want to encode a UTC timestamp in the
+filename, you can take advantage of org-mode's `%(EXP)` template
+expansion to call `format-time-string` directly to provide its third
+argument to specify UTC.
+
+``` emacs-lisp
+("d" "default" plain (function org-roam--capture-get-point)
+     "%?"
+     :file-name "%(format-time-string \"%Y-%m-%d--%H-%M-%SZ--${slug}\" (current-time) t)"
+     :head "#+TITLE: ${title}\n"
+     :unnarrowed t)
+```
+
+Similarly, if you want to change how titles are transformed into
+slugs, you can override `org-roam--title-to-slug`. For example, to use
+hyphens instead of underscores:
+
+
+``` emacs-lisp
+  (defun org-roam--title-to-slug (title)
+    "Convert TITLE to a filename-suitable slug. Uses hyphens rather than underscores."
+    (cl-flet* ((nonspacing-mark-p (char)
+                                  (eq 'Mn (get-char-code-property char 'general-category)))
+               (strip-nonspacing-marks (s)
+                                       (apply #'string (seq-remove #'nonspacing-mark-p
+                                                                   (ucs-normalize-NFD-string s))))
+               (cl-replace (title pair)
+                           (replace-regexp-in-string (car pair) (cdr pair) title)))
+      (let* ((pairs `(("[^[:alnum:][:digit:]]" . "-")  ;; convert anything not alphanumeric
+                      ("--*" . "-")  ;; remove sequential underscores
+                      ("^-" . "")  ;; remove starting underscore
+                      ("-$" . "")))  ;; remove ending underscore
+             (slug (-reduce-from #'cl-replace (strip-nonspacing-marks title) pairs)))
+        (s-downcase slug))))
+```
+
+This templating system is used throughout org-roam templates.
+
+### Template examples
+
+Here I walkthrough the default template, reproduced below.
+
+```
+("d" "default" plain (function org-roam--capture-get-point)
+     "%?"
+     :file-name "%<%Y%m%d%H%M%S>-${slug}"
+     :head "#+TITLE: ${title}\n"
+     :unnarrowed t)
+```
+
+1. The template has short key `"d"`. If you have only one template,
+   org-roam automatically chooses this template for you.
+2. The template is given a description of `"default"`.
+3. `plain` text is inserted. Other options include Org headings via
+   `entry`.
+4. `(function org-roam--capture-get-point)` should not be changed.
+5. `"%?"` is the template inserted on each call to `org-roam--capture`.
+   This template means don't insert any content, but place the cursor
+   here.
+6. `:file-name` is the file-name template for a new note, if it
+doesn't yet exist. This creates a file at path that looks like
+   `/path/to/org-roam-directory/20200213032037-foo.org`.
+7. `:head` contains the initial template to be inserted (once only),
+   at the beginning of the file. Here, the title global attribute is
+   inserted.
+8. `:unnarrowed t` tells org-capture to show the contents for the
+   whole file, rather than narrowing to just the entry.
+
+Other options you may want to learn about include `:immediate-finish`.

doc/tour.md

@@ -1,20 +1,70 @@
-### A Tour of Org-Roam
+Org-roam was built to support a workflow that was not possible with
+vanilla Org-mode. This flow is modelled after the [Zettelkasten
+method][zettelkasten], and many of [Roam Research][roam]'s workflows.
+It is crucial to understand that Org-roam does not auto-magically make
+note-taking better -- it's changing the note-taking workflow that
+does.
 
-All of this starts from the note. A note is just a simple `.org` file
-in the directory. Any org file in the directory is considered part of
-the org-roam ecosystem. Notes are quickly linked together (and created
-if necessary) using `org-roam-insert`.
+To understand more about the methods and madness, the [Note-Taking
+Workflow][appendix:ntw] page contains a page of useful references. The
+author has also written [a post][jethro-blog-post] about how he uses
+Org-roam.
 
-![org-roam-insert](images/org-roam-insert.gif)
+## Activating Org-roam
 
-Org-roam tracks all of these file links, and builds a cache
-asynchronously in the background. This cache is used to populate the
-backlinks buffer, which shows files that link to the current file, as
-well as some preview contents:
+Org-roam's entry point is the global minor `org-roam-mode`. This sets
+up Emacs with several hooks, for keeping the org-roam cache
+consistently updated, as well as showing the backlinks buffer. 
+
+The cache is a sqlite database named `org-roam.db`, which resides at
+the root of the `org-roam-directory`. Activating `org-roam-mode`
+builds the cache, which may take a while the first time, but is
+generally instantaneous in subsequent runs. To build the cache
+manually again, run `M-x org-roam-db-build-cache`.
+
+## Finding a Note
+
+`org-roam-find-file` shows the list of titles for notes that reside in
+`org-roam-directory`. Selecting a note title will bring you to the
+corresponding note. Entering a title of a note that does not yet exist
+will create a new note with that title.
+
+![org-roam-find-file](images/org-roam-find-file.gif)
+
+Note that in the above image, the [ivy](https://github.com/abo-abo/swiper)
+completion frontend is used. The default frontend has some usability issues with
+non-matching candidates (e.g. when you want to enter a title of a new note,
+there is no completion candidate), so either `ivy` or `helm` is recommended.
+
+## Inserting Links
+
+`org-roam-insert` insert links to existing (or new) notes. Entering a
+non-existent title will also create a new note with that title.
+
+![org-roam-insert](images/org-roam-insert-filetag.gif)
+
+Good usage of Org-roam requires liberally linking files. This allows
+the build-up of a dense knowledge graph.
+
+## The Org-roam Buffer
+
+The Org-roam buffer is often displayed in the side window. It shows
+backlinks for the currently active Org-roam note, along with some
+surrounding context.
 
 ![org-roam-buffer](images/org-roam-buffer.gif)
 
-These file links also form a graph. The generated graph is navigable
-in Emacs.
+## Exporting the Graph
+
+Org-roam also uses Graphviz to generate a graph, with notes as nodes,
+and links between them as edges. The generated graph can be used to
+navigate to the files, but this requires some additional setup
+described in the [Roam Protocol][appendix:roam-protocol] page.
 
 ![org-roam-graph](images/org-roam-graph.gif)
+
+[zettelkasten]: https://zettelkasten.de/
+[appendix:ntw]: notetaking_workflow.md
+[appendix:roam-protocol]: roam_protocol.md
+[roam]: https://www.roamresearch.com/
+[jethro-blog-post]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

mkdocs.yml

@@ -1,14 +1,24 @@
-site_name: "Org-Roam: Roam + Org-Mode = ♥"
+site_name: "Org-roam"
 repo_url: https://github.com/jethrokuan/org-roam/
 edit_uri: edit/master/doc/
 copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
 docs_dir: doc
+extra:
+  social:
+    - type: 'slack'
+      link: 'https://join.slack.com/t/orgroam/shared_invite/zt-clh0g0tx-j8xg1kVxnrWdKt16gmSGPQ'
 nav:
 - Home: index.md
-- A Tour of Org-Roam: tour.md
+- A Tour of Org-roam: tour.md
 - Installation: installation.md
+- Configuration: configuration.md
+- Anatomy of an Org-roam file: anatomy.md
+- The Templating System: templating.md
 - Ecosystem: ecosystem.md
 - Similar Packages: comparison.md
+- "Appendix: Note-taking Workflow": notetaking_workflow.md
+- "Appendix: Roam Protocol": roam_protocol.md
+- "Appendix: Org Export": org_export.md
 markdown_extensions:
   - admonition
   - pymdownx.betterem:

org-roam-buffer.el

@@ -0,0 +1,260 @@
+;;; org-roam-buffer.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; 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)
+(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")
+
+(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-no-delete-other-windows nil
+  "The `no-delete-other-windows' parameter of the `org-roam-buffer' window.
+When non-nil, the window will not be closed when deleting other windows."
+  :type 'boolean
+  :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--insert-citelinks ()
+  "Insert citation backlinks for the current buffer."
+  (if-let* ((roam-key (with-temp-buffer
+                        (insert-buffer-substring org-roam-buffer--current)
+                        (org-roam--extract-ref)))
+            (key-backlinks (org-roam--get-backlinks (s-chop-prefix "cite:" roam-key)))
+            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
+      (progn
+        (insert (format "\n\n* %d Cite backlinks\n"
+                        (length key-backlinks)))
+        (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 (format "\n\n* %d Backlinks\n"
+                        (length backlinks)))
+        (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 ((window (get-buffer-window))
+        (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)))
+    (-> (get-buffer-create org-roam-buffer)
+        (display-buffer-in-side-window
+         `((side . ,position)
+           (window-parameters . ((no-delete-other-windows . ,org-roam-buffer-no-delete-other-windows)))))
+        (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)))))
+    (select-window window)))
+
+(defun org-roam-buffer-toggle-display ()
+  "Toggle display of the `org-roam-buffer'."
+  (interactive)
+  (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

@@ -0,0 +1,344 @@
+;;; org-roam-capture.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides capture functionality for org-roam
+;;; Code:
+;;;; Library Requires
+(require 'org-capture)
+(require 'dash)
+(require 's)
+
+;; Declarations
+(defvar org-roam-encrypt-files)
+(defvar org-roam-directory)
+(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-completion--completing-read "org-roam-completion")
+
+(defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
+  "The default file name format for Org-roam templates.")
+
+(defvar org-roam-capture--header-default "#+TITLE: ${title}\n"
+  "The default capture header for Org-roam templates.")
+
+(defvar org-roam-capture--file-path nil
+  "The file path for the Org-roam capture.
+This variable is set during the Org-roam capture process.")
+
+(defvar org-roam-capture--info nil
+  "An alist of additional information passed to the Org-roam template.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defvar org-roam-capture--context nil
+  "A symbol, that reflects the context for obtaining the exact point in a file.
+This variable is populated dynamically, and is only active during
+an Org-roam capture process.
+
+The `title' context is used in `org-roam-insert' and
+`org-roam-find-file', where the capture process is triggered upon
+trying to create a new file without that `title'.
+
+The `ref' context is used by `org-roam-protocol', where the
+capture process is triggered upon trying to find or create a new
+note with the given `ref'.")
+
+(defvar org-roam-capture-additional-template-props nil
+  "Additional props to be added to the Org-roam template.")
+
+(defconst org-roam-capture--template-keywords '(:file-name :head)
+  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
+
+(defvar org-roam-capture-templates
+  '(("d" "default" plain (function org-roam-capture--get-point)
+     "%?"
+     :file-name "%<%Y%m%d%H%M%S>-${slug}"
+     :head "#+TITLE: ${title}\n"
+     :unnarrowed t))
+  "Capture templates for Org-roam.
+The capture templates are an extension of
+`org-capture-templates', and the documentation there also
+applies.
+
+`org-capture-templates' are extended in 3 ways:
+
+1. Template expansion capabilities are extended with additional custom syntax.
+   See `org-roam-capture--fill-template' for more details.
+
+2. The `:file-name' key is added, which expands to the file-name
+   of the note if it creates a new file.  This file-name is
+   relative to `org-roam-directory', and is without the
+   file-extension.
+
+3. The `:head' key is added, which contains the template that is
+   inserted on initial creation (added only once).  This is where
+   insertion of any note metadata should go.")
+
+(defvar org-roam-capture-ref-templates
+  '(("r" "ref" plain (function org-roam-capture--get-point)
+     ""
+     :file-name "${slug}"
+     :head "#+TITLE: ${title}
+#+ROAM_KEY: ${ref}\n"
+     :unnarrowed t))
+  "The Org-roam templates used during a capture from the roam-ref protocol.
+Details on how to specify for the template is given in `org-roam-capture-templates'.")
+
+(defun org-roam-capture--get (keyword)
+  "Gets 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'."
+  (let ((p (plist-get org-capture-plist :org-roam)))
+    (while stuff
+      (setq p (plist-put p
+                         (pop stuff) (pop stuff))))
+    (setq org-capture-plist
+          (plist-put org-capture-plist :org-roam p))))
+
+(defun org-roam-capture--in-process-p ()
+  "Return non-nil if a `org-roam-capture' buffer exists."
+  (cl-some (lambda (buffer)
+	     (and (eq (buffer-local-value 'major-mode (current-buffer)) 'org-mode)
+		  (plist-get (buffer-local-value 'org-capture-current-plist (current-buffer)) :org-roam)))
+	   (buffer-list)))
+
+(defun org-roam-capture--fill-template (str &optional info)
+  "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.
+If there is a ${var} with no matching var in the alist, the value
+of var is prompted for via `completing-read'.
+
+Next, it expands the remaining template string using
+`org-capture-fill-template'."
+  (-> str
+      (s-format (lambda (key)
+                  (or (s--aget info key)
+                      (completing-read (format "%s: " key ) nil))) nil)
+      (org-capture-fill-template)))
+
+(defun org-roam-capture--insert-link-h ()
+  "Insert the link into the original buffer, after the capture process is done.
+This is added as a hook to `org-capture-after-finalize-hook'."
+  (when (and (not org-note-abort)
+             (eq (org-roam-capture--get :capture-fn)
+                 'org-roam-insert))
+    (when-let ((region (org-roam-capture--get :region))) ;; Remove previously selected text.
+      (delete-region (car region) (cdr region)))
+    (insert (org-roam--format-link (org-roam-capture--get :file-path)
+                                   (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 ()
+  "Save the file conditionally.
+The file is saved if the original value of :no-save is not t and
+`org-note-abort' is not t. It is added to
+`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 ()
+  "Return the path to the new file during an Org-roam capture.
+
+This function reads the file-name attribute of the currently
+active Org-roam template.
+
+If the file path already exists, it throw an error.
+
+Else, to insert the header content in the file, `org-capture'
+prepends the `:head' property of the Org-roam capture template.
+
+To prevent the creation of a new file if the capture process is
+aborted, we do the following:
+
+1. Save the original value of the capture template's :no-save.
+
+2. Set the capture template's :no-save to t.
+
+3. Add a function on `org-capture-after-finalize-hook' that saves
+the file if the original value of :no-save is not t and
+`org-note-abort' is not t."
+  (let* ((name-templ (or (org-roam-capture--get :file-name)
+                         org-roam-capture--file-name-default))
+         (new-id (s-trim (org-roam-capture--fill-template
+                          name-templ
+                          org-roam-capture--info)))
+         (file-path (org-roam--file-path-from-id new-id))
+         (roam-head (or (org-roam-capture--get :head)
+                        org-roam-capture--header-default))
+         (org-template (org-capture-get :template))
+         (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
+                     ('capture
+                      (or (cdr (assoc 'file org-roam-capture--info))
+                          (org-roam-capture--new-file)))
+                     ('title
+                      (org-roam-capture--new-file))
+                     ('dailies
+                      (org-capture-put :default-time (cdr (assoc 'time org-roam-capture--info)))
+                      (org-roam-capture--new-file))
+                     ('ref
+                      (let ((completions (org-roam--get-ref-path-completions))
+                            (ref (cdr (assoc 'ref org-roam-capture--info))))
+                        (or (cdr (assoc ref completions))
+                            (org-roam-capture--new-file))))
+                     (_ (error "Invalid org-roam-capture-context")))))
+    (org-roam-capture--expand-template)
+    (org-roam-capture--put :file-path file-path)
+    (while org-roam-capture-additional-template-props
+      (let ((prop (pop org-roam-capture-additional-template-props))
+            (val (pop org-roam-capture-additional-template-props)))
+        (org-roam-capture--put prop val)))
+    (set-buffer (org-capture-target-buffer file-path))
+    (widen)
+    (goto-char (point-max))))
+
+(defun org-roam-capture--convert-template (template)
+  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
+  (let* ((copy (copy-tree template))
+         converted
+         org-roam-plist
+         key
+         val)
+    ;;put positional args on converted template
+    (dotimes (_ 5)
+      (push (pop copy) converted))
+    (while (setq key (pop copy)
+                 val (pop copy))
+      (if (member key org-roam-capture--template-keywords)
+          (progn
+            (push val org-roam-plist)
+            (push key org-roam-plist))
+        (push key converted)
+        (push val converted)))
+    (append (nreverse converted) `(:org-roam ,org-roam-plist))))
+
+(defun org-roam-capture--find-file-h ()
+  "Opens the newly created template file.
+This is added as a hook to `org-capture-after-finalize-hook'.
+Run the hooks defined in `org-roam-capture-after-find-file-hook'."
+  (unless org-note-abort
+    (when-let ((file-path (org-roam-capture--get :file-path)))
+      (find-file file-path))
+    (run-hooks 'org-roam-capture-after-find-file-hook))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h))
+
+(defcustom org-roam-capture-after-find-file-hook nil
+  "Hook that is run right after an Org-roam capture process is finalized.
+Suitable for moving point."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam--capture (&optional goto keys)
+  "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)))
+    (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 ()
+  "Launches an `org-capture' process for a new or existing note.
+This uses the templates defined at `org-roam-capture-templates'."
+  (interactive)
+  (when (org-roam-capture--in-process-p)
+    (user-error "Nested Org-roam capture processes not supported"))
+  (let* ((completions (org-roam--get-title-path-completions))
+         (title (org-roam-completion--completing-read "File: " completions))
+         (file-path (cdr (assoc title completions))))
+    (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))
+      (org-roam--capture))))
+
+(provide 'org-roam-capture)
+
+;;; org-roam-capture.el ends here

org-roam-compat.el

@@ -0,0 +1,96 @@
+;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This file contains code needed for backward compatibility with older Emacsen
+;; and previous versions of org-roam.
+;;
+;;; Code:
+;;;; Library Requires
+
+;;; Obsolete aliases (remove after next major release)
+;;;; 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")
+
+;;;; 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")
+(make-obsolete-variable 'org-roam-graph-node-shape  'org-roam-graph-node-extra-config "org-roam 1.0.0")
+(defcustom org-roam-graph-node-shape "ellipse"
+  "Shape of graph nodes."
+  :type 'string
+  :group 'org-roam)
+(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")
+
+(provide 'org-roam-compat)
+
+;;; org-roam-compat.el ends here

org-roam-completion.el

@@ -0,0 +1,119 @@
+;;; org-roam-completion.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides completion for org-roam.
+;;; Code:
+;;;; Library Requires
+(require 'cl-lib)
+(require 's)
+
+(defvar helm-pattern)
+(declare-function helm "ext:helm")
+(declare-function helm-make-source "ext:helm-source" (name class &rest args) t)
+
+(defcustom org-roam-completion-system 'default
+  "The completion system to be used by `org-roam'."
+  :type '(radio
+          (const :tag "Default" default)
+          (const :tag "Ido" ido)
+          (const :tag "Ivy" ivy)
+          (const :tag "Helm" helm)
+          (function :tag "Custom function"))
+  :group 'org-roam)
+
+(defcustom org-roam-completion-fuzzy-match nil
+  "Whether to fuzzy match Org-roam's completion candidates."
+  :type 'boolean
+  :group 'org-roam)
+
+(defun org-roam-completion--helm-candidate-transformer (candidates _source)
+  "Transforms CANDIDATES for Helm-based completing read.
+SOURCE is not used."
+  (let ((prefix (propertize "[?] "
+                            'face 'helm-ff-prefix)))
+    (cons (propertize helm-pattern
+                      'display (concat prefix helm-pattern))
+          candidates)))
+
+(cl-defun org-roam-completion--completing-read (prompt choices &key
+                                                       require-match initial-input
+                                                       action)
+  "Present a PROMPT with CHOICES and optional INITIAL-INPUT.
+If REQUIRE-MATCH is t, the user must select one of the CHOICES.
+Return user choice."
+  (let (res)
+    (setq res
+          (cond
+           ((eq org-roam-completion-system 'ido)
+            (let ((candidates (mapcar #'car choices)))
+              (ido-completing-read prompt candidates nil require-match initial-input)))
+           ((eq org-roam-completion-system 'default)
+            (completing-read prompt choices nil require-match initial-input))
+           ((eq org-roam-completion-system 'ivy)
+            (if (fboundp 'ivy-read)
+                (ivy-read prompt choices
+                          :initial-input initial-input
+                          :require-match require-match
+                          :action (prog1 action
+                                    (setq action nil))
+                          :caller 'org-roam--completing-read
+                          :re-builder (if org-roam-completion-fuzzy-match 'ivy--regex-fuzzy
+                                        'regexp-quote))
+              (user-error "Please install ivy from \
+https://github.com/abo-abo/swiper")))
+           ((eq org-roam-completion-system 'helm)
+            (unless (and (fboundp 'helm)
+                         (fboundp 'helm-make-source))
+              (user-error "Please install helm from \
+https://github.com/emacs-helm/helm"))
+            (let ((source (helm-make-source prompt 'helm-source-sync
+                            :candidates (mapcar #'car choices)
+                            :filtered-candidate-transformer
+                            (and (not require-match)
+                                 #'org-roam-completion--helm-candidate-transformer)
+                            :fuzzy-match org-roam-completion-fuzzy-match))
+                  (buf (concat "*org-roam "
+                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
+                               "*")))
+              (or (helm :sources source
+                        :action (if action
+                                    (prog1 action
+                                      (setq action nil))
+                                  #'identity)
+                        :prompt prompt
+                        :input initial-input
+                        :buffer buf)
+                  (keyboard-quit))))))
+    (if action
+        (funcall action res)
+      res)))
+
+(provide 'org-roam-completion)
+
+;;; org-roam-completion.el ends here

org-roam-dailies.el

@@ -0,0 +1,81 @@
+;;; org-roam-dialies.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;;
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides functionality for creating daily notes. This is a
+;; concept borrowed from Roam Research.
+;;
+;;; Code:
+;;; Library Requires
+(require 'org-capture)
+(require 'org-roam-capture)
+
+(defvar org-roam-dailies-capture-templates
+  '(("d" "daily" plain (function org-roam-capture--get-point)
+     ""
+     :immediate-finish t
+     :file-name "%<%Y-%m-%d>"
+     :head "#+TITLE: %<%Y-%m-%d>"))
+  "Capture templates for daily notes in Org-roam.")
+
+;; Declarations
+(declare-function org-roam--file-path-from-id "org-roam")
+
+(defun org-roam-dailies--file-for-time (time)
+  "Create and find file for TIME."
+  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
+        (org-roam-capture--info (list (cons 'time time)))
+        (org-roam-capture--context 'dailies))
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
+    (org-roam--capture)))
+
+(defun org-roam-dailies-today ()
+  "Create and find the daily note for today."
+  (interactive)
+  (org-roam-dailies--file-for-time (current-time)))
+
+(defun org-roam-dailies-tomorrow (n)
+  "Create and find the daily note for tomorrow.
+With numeric argument N, use N days in the future."
+  (interactive "p")
+  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
+
+(defun org-roam-dailies-yesterday (n)
+  "Create and find the file for yesterday.
+With numeric argument N, use N days in the past."
+  (interactive "p")
+  (org-roam-tomorrow (- n)))
+
+(defun org-roam-dailies-date ()
+  "Create the file for any date using the calendar interface."
+  (interactive)
+  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
+    (org-roam-dailies--file-for-time time)))
+
+(provide 'org-roam-dailies)
+;;; org-roam-dailies.el ends here

org-roam-db.el

@@ -0,0 +1,409 @@
+;;; org-roam-db.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library is provides the underlying database api to org-roam
+;;
+;;; Code:
+;;;; Library Requires
+(eval-when-compile (require 'subr-x))
+(require 'emacsql)
+(require 'emacsql-sqlite)
+(require 'org-roam-macs)
+
+(defvar org-roam-directory)
+(defvar org-roam-verbose)
+
+(declare-function org-roam--extract-titles      "org-roam")
+(declare-function org-roam--extract-ref         "org-roam")
+(declare-function org-roam--extract-links       "org-roam")
+(declare-function org-roam--list-files          "org-roam")
+(declare-function org-roam-buffer--update-maybe "org-roam-buffer")
+
+;;;; Options
+(defcustom org-roam-db-location nil
+  "Location of the Org-roam database.
+If this is non-nil, the Org-roam sqlite database is saved here.
+
+It is the user's responsibility to set this correctly, especially
+when used with multiple Org-roam instances."
+  :type 'string
+  :group 'org-roam)
+
+(defconst org-roam-db--version 2)
+(defconst org-roam-db--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))
+
+(defvar org-roam-db--connection (make-hash-table :test #'equal)
+  "Database connection to Org-roam database.")
+
+;;;; Core Functions
+(defun org-roam-db--get ()
+  "Return the sqlite db file."
+  (interactive "P")
+  (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)
+           org-roam-db--connection))
+
+(defun org-roam-db ()
+  "Entrypoint to the Org-roam sqlite database.
+Initializes and stores the database, and the database connection.
+Performs a database upgrade when required."
+  (unless (and (org-roam-db--get-connection)
+               (emacsql-live-p (org-roam-db--get-connection)))
+    (let* ((db-file (org-roam-db--get))
+           (init-db (not (file-exists-p db-file))))
+      (make-directory (file-name-directory db-file) t)
+      (let ((conn (emacsql-sqlite db-file)))
+        (set-process-query-on-exit-flag (emacsql-process conn) nil)
+        (puthash (file-truename 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--maybe-update conn version)))
+          (cond
+           ((> version org-roam-db--version)
+            (emacsql-close conn)
+            (user-error
+             "The Org-roam database was created with a newer Org-roam version.  "
+             "You need to update the Org-roam package"))
+           ((< version org-roam-db--version)
+            (emacsql-close conn)
+            (error "BUG: The Org-roam database scheme changed %s"
+                   "and there is no upgrade path")))))))
+  (org-roam-db--get-connection))
+
+;;;; Entrypoint: (org-roam-db-query)
+(defun org-roam-db-query (sql &rest args)
+  "Run SQL query on Org-roam database with ARGS.
+SQL can be either the emacsql vector representation, or a string."
+  (if  (stringp sql)
+      (emacsql (org-roam-db) (apply #'format sql args))
+    (apply #'emacsql (org-roam-db) sql args)))
+
+;;;; Schemata
+(defconst org-roam-db--table-schemata
+  '((files
+     [(file :unique :primary-key)
+      (hash :not-null)
+      (last-modified :not-null)])
+
+    (links
+     [(from :not-null)
+      (to :not-null)
+      (type :not-null)
+      (properties :not-null)])
+
+    (titles
+     [(file :not-null)
+      titles])
+
+    (refs
+     [(ref :unique :not-null)
+      (file :not-null)])))
+
+(defun org-roam-db--init (db)
+  "Initialize database DB with the correct schema and user version."
+  (emacsql-with-transaction db
+    (pcase-dolist (`(,table . ,schema) org-roam-db--table-schemata)
+      (emacsql db [:create-table $i1 $S2] table schema))
+    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
+
+(defun org-roam-db--maybe-update (db version)
+  "Upgrades the database schema for DB, if VERSION is old."
+  (emacsql-with-transaction db
+    'ignore
+    (when (= version 1)
+      (progn
+        (warn "No good way to perform a DB upgrade, rebuilding from scratch...")
+        (delete-file (org-roam-db--get))
+        (org-roam-db-build-cache)))
+    version))
+
+(defun org-roam-db--close (&optional db)
+  "Closes the database connection for database DB.
+If DB is nil, closes the database connection for the database in
+the current `org-roam-directory'."
+  (unless db
+    (setq db (org-roam-db--get-connection)))
+  (when (and db (emacsql-live-p db))
+    (emacsql-close db)))
+
+(defun org-roam-db--close-all ()
+  "Closes all database connections made by Org-roam."
+  (dolist (conn (hash-table-values org-roam-db--connection))
+    (org-roam-db--close conn)))
+
+;;;; Database API
+;;;;; 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 ()
+  "Clears all entries in the caches."
+  (interactive)
+  (when (file-exists-p (org-roam-db--get))
+    (org-roam-db-query [:delete :from files])
+    (org-roam-db-query [:delete :from titles])
+    (org-roam-db-query [:delete :from links])
+    (org-roam-db-query [:delete :from refs])))
+
+
+(defun org-roam-db--clear-file (&optional filepath)
+  "Remove any related links to the file at FILEPATH.
+This is equivalent to removing the node from the graph."
+  (let* ((path (or filepath
+                   (buffer-file-name)))
+         (file (file-truename path)))
+    (org-roam-db-query [:delete :from files
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db-query [:delete :from links
+                        :where (= from $s1)]
+                       file)
+    (org-roam-db-query [:delete :from titles
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db-query [:delete :from refs
+                        :where (= file $s1)]
+                       file)))
+
+;;;;; Insertion
+(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-ref (file ref)
+  "Insert REF for FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into refs
+    :values $v1]
+   (list (vector ref file))))
+
+;;;;; 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]))
+         (ht (make-hash-table :test #'equal)))
+    (dolist (row current-files)
+      (puthash (car row) (cadr row) ht))
+    ht))
+
+(defun org-roam-db--get-titles (file)
+  "Return the titles of FILE from the cache."
+  (caar (org-roam-db-query [:select [titles] :from titles
+                            :where (= file $s1)]
+                           file
+                           :limit 1)))
+
+(defun org-roam-db--connected-component (file)
+  "Return all files reachable from/connected to FILE, including the file itself.
+If the file does not have any connections, nil is returned."
+  (let* ((query "WITH RECURSIVE
+                   links_of(file, link) AS
+                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                           citelinks AS (SELECT * FROM links
+                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                            AND links.\"type\" = '\"cite\"')
+                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"from\", \"file\" FROM citelinks),
+                   connected_component(file) AS
+                     (SELECT link FROM links_of WHERE file = $s1
+                      UNION
+                      SELECT link FROM links_of JOIN connected_component USING(file))
+                   SELECT * FROM connected_component;")
+         (files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
+    files))
+
+(defun org-roam-db--links-with-max-distance (file max-distance)
+  "Return all files reachable from/connected to FILE in at most MAX-DISTANCE steps,
+including the file itself.  If the file does not have any connections, nil is returned."
+  (let* ((query "WITH RECURSIVE
+                   links_of(file, link) AS
+                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                           citelinks AS (SELECT * FROM links
+                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                            AND links.\"type\" = '\"cite\"')
+                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"from\", \"file\" FROM citelinks),
+                   -- Links are traversed in a breadth-first search.  In order to calculate the
+                   -- distance of nodes and to avoid following cyclic links, the visited nodes
+                   -- are tracked in 'trace'.
+                   connected_component(file, trace) AS
+                     (VALUES($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-titles ()
+  "Update the title of the current buffer into the cache."
+  (let ((file (file-truename (buffer-file-name))))
+    (org-roam-db-query [:delete :from titles
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-titles file (org-roam--extract-titles))))
+
+(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-cache-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-file (&optional file-path)
+  "Update Org-roam cache for FILE-PATH."
+  (let (buf)
+    (if file-path
+        (setq buf (find-file-noselect file-path))
+      (setq buf (current-buffer)))
+    (with-current-buffer buf
+      (save-excursion
+        (org-roam-db--update-titles)
+        (org-roam-db--update-refs)
+        (org-roam-db--update-cache-links)
+        (org-roam-buffer--update-maybe :redisplay t)))))
+
+;;;;; org-roam-db-build-cache
+(defun org-roam-db-build-cache ()
+  "Build the cache for `org-roam-directory'."
+  (interactive)
+  (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-files org-roam-directory))
+         (current-files (org-roam-db--get-current-files))
+         (time (current-time))
+         all-files all-links all-titles all-refs)
+    (dolist (file org-roam-files)
+      (org-roam--with-temp-buffer
+        (insert-file-contents file)
+        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+          (unless (string= (gethash file current-files)
+                           contents-hash)
+            (org-roam-db--clear-file file)
+            (setq all-files
+                  (cons (vector file contents-hash time) all-files))
+            (when-let (links (org-roam--extract-links file))
+              (setq all-links (append links all-links)))
+            (let ((titles (org-roam--extract-titles)))
+              (setq all-titles (cons (vector file titles) all-titles)))
+            (when-let ((ref (org-roam--extract-ref)))
+              (setq all-refs (cons (vector ref file) all-refs))))
+          (remhash file current-files))))
+    (dolist (file (hash-table-keys current-files))
+      ;; These files are no longer around, remove from cache...
+      (org-roam-db--clear-file file))
+    (when all-files
+      (org-roam-db-query
+       [:insert :into files
+        :values $v1]
+       all-files))
+    (when all-links
+      (org-roam-db-query
+       [:insert :into links
+        :values $v1]
+       all-links))
+    (when all-titles
+      (org-roam-db-query
+       [:insert :into titles
+        :values $v1]
+       all-titles))
+    (when all-refs
+      (org-roam-db-query
+       [:insert :into refs
+        :values $v1]
+       all-refs))
+    (let ((stats (list :files (length all-files)
+                       :links (length all-links)
+                       :titles (length all-titles)
+                       :refs (length all-refs)
+                       :deleted (length (hash-table-keys current-files)))))
+      (when org-roam-verbose
+        (message "files: %s, links: %s, titles: %s, refs: %s, deleted: %s"
+                 (plist-get stats :files)
+                 (plist-get stats :links)
+                 (plist-get stats :titles)
+                 (plist-get stats :refs)
+                 (plist-get stats :deleted)))
+      stats)))
+
+(provide 'org-roam-db)
+
+;;; org-roam-db.el ends here

org-roam-graph.el

@@ -0,0 +1,268 @@
+;;; org-roam-graph.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; 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)
+(declare-function org-roam--org-roam-file-p  "org-roam")
+(declare-function org-roam--path-to-slug     "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 (executable-find "dot")
+  "Path to graphing executable."
+  :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 nil
+  "Extra options for graphviz nodes.
+Example:
+ '((\"color\" . \"skyblue\"))"
+  :type '(alist)
+  :group 'org-roam)
+
+(defcustom org-roam-graph-edge-extra-config nil
+  "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-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
+    (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"))
+              :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 #'org-roam-graph--dot-option
+                                   (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 (s-truncate org-roam-graph-max-title-length 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)
+  "Generate a graph showing the relations between nodes in NODE-QUERY."
+  (unless org-roam-graph-executable
+    (user-error "Can't find %s executable.  Please check if it is in your path"
+                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")))
+    (call-process org-roam-graph-executable nil 0 nil
+                  temp-dot "-Tsvg" "-o" temp-graph)
+    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)
+  "Build a graph of nodes connected to FILE.
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
+  (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)))
+
+;;;; 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")
+  (let ((file (or file (buffer-file-name))))
+    (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--open (org-roam-graph--build node-query)))
+      ('(4)            (org-roam-graph--open (org-roam-graph--build-connected-component file)))
+      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component (buffer-file-name) (abs arg))))
+                         (when (>= arg 0)
+                           (org-roam-graph--open graph))))
+      ('(16)           (org-roam-graph--build node-query))
+      ('-              (org-roam-graph--build-connected-component file))
+      (_ (user-error "Unrecognized ARG: %s" arg)))))
+
+(provide 'org-roam-graph)
+
+;;; org-roam-graph.el ends here

org-roam-macs.el

@@ -0,0 +1,48 @@
+;;; org-roam-macs.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements macros used throughout org-roam
+;;
+;;
+;;; Code:
+;;;; Library Requires
+
+(defmacro org-roam--with-temp-buffer (&rest body)
+  "Execute BODY within a temp buffer.
+Like `with-temp-buffer', but propagates `org-roam-directory'."
+  (declare (indent 0) (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))
+           ,@body)))))
+
+(provide 'org-roam-macs)
+
+;;; org-roam-macs.el ends here

org-roam-protocol.el

@@ -0,0 +1,90 @@
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.0
+;; Package-Requires: ((emacs "26.1") (org "9.3"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; We extend org-protocol, adding custom Org-roam handlers. The setup
+;; instructions for `org-protocol' can be found in org-protocol.el.
+;;
+;; We define 2 protocols:
+;;
+;; 1. "roam-file": This protocol simply opens the file given by the FILE key
+;; 2. "roam-ref": This protocol creates or opens a note with the given REF
+;;
+;;; Code:
+(require 'org-protocol)
+(require 'org-roam)
+
+;;;; Functions
+(defun org-roam-protocol-open-ref (info)
+  "Process an org-protocol://roam-ref?ref= style url with INFO.
+
+It opens or creates a note with the given ref.
+
+  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
+        encodeURIComponent(location.href) + \\='&title=\\=' \\
+        encodeURIComponent(document.title) + \\='&body=\\=' + \\
+        encodeURIComponent(window.getSelection())"
+  (when-let* ((alist (org-roam--plist-to-alist info))
+              (decoded-alist (mapcar (lambda (k.v)
+                                       (let ((key (car k.v))
+                                             (val (cdr k.v)))
+                                         (cons key (org-link-decode val)))) alist)))
+    (unless (assoc 'ref decoded-alist)
+      (error "No ref key provided"))
+    (when-let ((title (cdr (assoc 'title decoded-alist))))
+      (push (cons 'slug (org-roam--title-to-slug title)) decoded-alist))
+    (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
+           (org-roam-capture--context 'ref)
+           (org-roam-capture--info decoded-alist)
+           (template (cdr (assoc 'template decoded-alist))))
+      (raise-frame)
+      (org-roam--capture nil template)
+      (message "Item captured.")))
+  nil)
+
+(defun org-roam-protocol-open-file (info)
+  "This handler simply opens the file with emacsclient.
+
+INFO is an alist containing additional information passed by the protocol URL.
+It should contain the FILE key, pointing to the path of the file to open.
+
+  Example protocol string:
+
+org-protocol://roam-file?file=/path/to/file.org"
+  (when-let ((file (plist-get info :file)))
+    (raise-frame)
+    (find-file file))
+  nil)
+
+(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
+      org-protocol-protocol-alist)
+(push '("org-roam-file"  :protocol "roam-file"   :function org-roam-protocol-open-file)
+      org-protocol-protocol-alist)
+
+(provide 'org-roam-protocol)
+
+;;; org-roam-protocol.el ends here

shell.nix

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

tests/roam-files/alias.org

@@ -0,0 +1,2 @@
+#+ROAM_ALIAS: "a1" "a 2"
+#+TITLE: t1

tests/roam-files/bar.org

@@ -0,0 +1,3 @@
+#+TITLE: Bar
+
+This is file bar. Bar links to [[file:nested/bar.org][Nested Bar]].

tests/roam-files/foo.org

@@ -0,0 +1,8 @@
+#+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

@@ -0,0 +1,3 @@
+#+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/foo.org

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

tests/roam-files/no-title.org

@@ -0,0 +1,3 @@
+no title in this file :O
+
+links to itself, with no title: [[file:no-title.org][no-title]]

tests/roam-files/unlinked.org

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

tests/roam-files/web_ref.org

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

tests/test-org-roam.el

@@ -0,0 +1,310 @@
+;;; test-org-roam.el --- Tests for org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup) (with-simulated-input))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;;
+
+;;; Code:
+
+;;;; Requirements
+
+(require 'buttercup)
+(require 'with-simulated-input)
+(require 'org-roam)
+(require 'dash)
+
+(defun org-roam-test-abs-path (file-path)
+  "Get absolute FILE-PATH from `org-roam-directory'."
+  (file-truename (expand-file-name file-path org-roam-directory)))
+
+(defun org-roam-test-find-new-file (path)
+  "PATH."
+  (let ((path (org-roam-test-abs-path path)))
+    (make-directory (file-name-directory path) t)
+    (find-file path)))
+
+(defvar org-roam-test-directory (file-truename (concat default-directory "tests/roam-files"))
+  "Directory containing org-roam test org files.")
+
+(defun org-roam-test-init ()
+  "."
+  (org-roam-db--close)
+  (let ((original-dir org-roam-test-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)))
+
+;;; Tests
+(describe "org-roam-db-build-cache"
+  (it "initializes correctly"
+    (org-roam-test-init)
+    (org-roam-db-build-cache)
+
+    ;; 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 2)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)
+
+    ;; TODO Test files
+
+    ;; Links
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-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)]
+                                     (org-roam-test-abs-path "nested/foo.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= to $s1)]
+                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= to $s1)]
+                                     (org-roam-test-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 (org-roam-test-abs-path "alias.org")
+                        (list "t1" "a1" "a 2"))
+                  (list (org-roam-test-abs-path "bar.org")
+                        (list "Bar"))
+                  (list (org-roam-test-abs-path "foo.org")
+                        (list "Foo"))
+                  (list (org-roam-test-abs-path "nested/bar.org")
+                        (list "Nested Bar"))
+                  (list (org-roam-test-abs-path "nested/foo.org")
+                        (list "Nested Foo"))
+                  (list (org-roam-test-abs-path "no-title.org") nil)
+                  (list (org-roam-test-abs-path "web_ref.org") nil)
+                  (list (org-roam-test-abs-path "unlinked.org")
+                        (list "Unlinked"))))
+
+    (expect (org-roam-db-query [:select * :from refs])
+            :to-have-same-items-as
+            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+
+    ;; Expect rebuilds to be really quick (nothing changed)
+    (expect (org-roam-db-build-cache)
+            :to-equal
+            (list :files 0 :links 0 :titles 0 :refs 0 :deleted 0))))
+
+(describe "org-roam-insert"
+  (before-each
+    (org-roam-test-init)
+    (org-roam-db--clear)
+    (org-roam-db-build-cache))
+
+  (it "temp1 -> foo"
+    (let ((buf (org-roam-test-find-new-file "temp1.org")))
+      (with-current-buffer buf
+        (with-simulated-input
+         "Foo RET"
+         (org-roam-insert nil))))
+    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))
+
+  (it "temp2 -> nested/foo"
+    (let ((buf (org-roam-test-find-new-file "temp2.org")))
+      (with-current-buffer buf
+        (with-simulated-input
+         "Nested SPC Foo RET"
+         (org-roam-insert nil))))
+    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))
+
+  (it "nested/temp3 -> foo"
+    (let ((buf (org-roam-test-find-new-file "nested/temp3.org")))
+      (with-current-buffer buf
+        (with-simulated-input
+         "Foo RET"
+         (org-roam-insert nil))))
+    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))
+
+  (it "a/b/temp4 -> nested/foo"
+    (let ((buf (org-roam-test-find-new-file "a/b/temp4.org")))
+      (with-current-buffer buf
+        (with-simulated-input
+         "Nested SPC Foo RET"
+         (org-roam-insert nil))))
+    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))
+
+(describe "rename file updates cache"
+  (before-each
+    (org-roam-test-init)
+    (org-roam-db--clear)
+    (org-roam-db-build-cache))
+
+  (it "foo -> new_foo"
+    (rename-file (org-roam-test-abs-path "foo.org")
+                 (org-roam-test-abs-path "new_foo.org"))
+    ;; Cache should be cleared of old file
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+
+    ;; Cache should be updated
+    (expect (org-roam-db-query [:select [to]
+                                :from links
+                                :where (= from $s1)]
+                               (org-roam-test-abs-path "new_foo.org"))
+            :to-have-same-items-as
+            (list (list (org-roam-test-abs-path "bar.org"))))
+    (expect (org-roam-db-query [:select [from]
+                                :from links
+                                :where (= to $s1)]
+                               (org-roam-test-abs-path "new_foo.org"))
+            :to-have-same-items-as
+            (list (list (org-roam-test-abs-path "nested/bar.org"))))
+
+    ;; Links are updated
+    (expect (with-temp-buffer
+              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:../new_foo.org][Foo]]")))
+
+  (it "foo -> foo with spaces"
+    (rename-file (org-roam-test-abs-path "foo.org")
+                 (org-roam-test-abs-path "foo with spaces.org"))
+    ;; Cache should be cleared of old file
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+
+    ;; Cache should be updated
+    (expect (org-roam-db-query [:select [to]
+                                :from links
+                                :where (= from $s1)]
+                               (org-roam-test-abs-path "foo with spaces.org"))
+            :to-have-same-items-as
+            (list (list (org-roam-test-abs-path "bar.org"))))
+    (expect (org-roam-db-query [:select [from]
+                                :from links
+                                :where (= to $s1)]
+                               (org-roam-test-abs-path "foo with spaces.org"))
+            :to-have-same-items-as
+            (list (list (org-roam-test-abs-path "nested/bar.org"))))
+
+    ;; Links are updated
+    (expect (with-temp-buffer
+              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))
+
+  (it "no-title -> meaningful-title"
+    (rename-file (org-roam-test-abs-path "no-title.org")
+                 (org-roam-test-abs-path "meaningful-title.org"))
+    ;; File has no forward links
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "no-title.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "meaningful-title.org"))) :to-be 1)
+
+    ;; Links are updated with the appropriate name
+    (expect (with-temp-buffer
+              (insert-file-contents (org-roam-test-abs-path "meaningful-title.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
+
+  (it "web_ref -> hello"
+    (expect (org-roam-db-query
+             [:select [file] :from refs
+              :where (= ref $s1)]
+             "https://google.com/")
+            :to-equal
+            (list (list (org-roam-test-abs-path "web_ref.org"))))
+    (rename-file (org-roam-test-abs-path "web_ref.org")
+                 (org-roam-test-abs-path "hello.org"))
+    (expect (org-roam-db-query
+             [:select [file] :from refs
+              :where (= ref $s1)]
+             "https://google.com/")
+            :to-equal (list (list (org-roam-test-abs-path "hello.org"))))
+    (expect (caar (org-roam-db-query
+                   [:select [ref] :from refs
+                    :where (= file $s1)]
+                   (org-roam-test-abs-path "web_ref.org")))
+            :to-equal nil)))
+
+(describe "delete file updates cache"
+  (before-each
+    (org-roam-test-init)
+    (org-roam-db--clear)
+    (org-roam-db-build-cache)
+    (sleep-for 1))
+
+  (it "delete foo"
+    (delete-file (org-roam-test-abs-path "foo.org"))
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (org-roam-test-abs-path "foo.org"))) :to-be 0))
+
+  (it "delete web_ref"
+    (expect (org-roam-db-query [:select * :from refs])
+            :to-have-same-items-as
+            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+    (delete-file (org-roam-test-abs-path "web_ref.org"))
+    (expect (org-roam-db-query [:select * :from refs])
+            :to-have-same-items-as
+            (list))))
+
+(provide 'test-org-roam)
+
+;;; test-org-roam.el ends here