(release): org-roam v0.1.2 (#147)

Thanks @naistran for instructions, and @leothelocust and @seandavi for
discussion and confirmation

.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 +1,69 @@
+# * 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:
+          - 26.3
+          - 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 +1,93 @@
+# Changelog
+
+## 0.1.2 (2020-02-21)
+
+### Breaking Changes
+* [#143][gh-143] `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+* [#103][gh-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][gh-145] `org-roam-show-graph`: Fallback to Emacs SVG viewer
+* [#141][gh-141] add variable `org-roam-new-file-directory` for new Org-roam files
+* [#138][gh-138] add `org-roam-switch-to-buffer`
+* [#124][gh-124], [#141][gh-141] Maintain cache consistency on file rename and delete
+* [#87][gh-87], [#90][gh-90] Support encrypted Org files
+* [#110][gh-110] Add prefix to `org-roam-insert`, for inserting titles down-cased
+* [#99][gh-99] Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+### Changes
+
+* [#108][gh-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][gh-86] Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+* [#98][gh-98] Fix `org-roam--find-file` picking up temporary files
+* [#136][gh-136] Misc bugfixes
+
+### Internal
+* [#122][gh-122], [#128][gh-128] Improve performance of post-command-hook
+* [#92][gh-92], [#105][gh-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][gh-62] Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
+
+### Breaking Changes
+* [#62][gh-62] The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
+
+### Changes
+* [#66][gh-66], [#68][gh-68]: Improved the quality of the package in preparation of submission to MELPA
+* [#73][gh-73]: Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
+* [#69][gh-69], [#72][gh-72], [#75][gh-75]: Major cleanup and de-duplication of code
+
+### Bugfixes
+* [#67][gh-67]: Fixed `org-roam--make-file` not creating files with extensions
+* [#71][gh-71], [#78][gh-78]: Fixed `org-roam-insert` not inserting correct paths
+* [#82][gh-82]: Fixed nested Org-roam files not being detected as part of Org-roam
+
+[gh-62]: https://github.com/jethrokuan/org-roam/pull/66
+[gh-66]: https://github.com/jethrokuan/org-roam/pull/66
+[gh-67]: https://github.com/jethrokuan/org-roam/pull/67
+[gh-68]: https://github.com/jethrokuan/org-roam/pull/68
+[gh-69]: https://github.com/jethrokuan/org-roam/pull/69
+[gh-71]: https://github.com/jethrokuan/org-roam/pull/71
+[gh-72]: https://github.com/jethrokuan/org-roam/pull/72
+[gh-73]: https://github.com/jethrokuan/org-roam/pull/73
+[gh-75]: https://github.com/jethrokuan/org-roam/pull/75
+[gh-78]: https://github.com/jethrokuan/org-roam/pull/78
+[gh-82]: https://github.com/jethrokuan/org-roam/pull/82
+[gh-86]: https://github.com/jethrokuan/org-roam/pull/86
+[gh-87]: https://github.com/jethrokuan/org-roam/pull/87
+[gh-90]: https://github.com/jethrokuan/org-roam/pull/90
+[gh-92]: https://github.com/jethrokuan/org-roam/pull/92
+[gh-98]: https://github.com/jethrokuan/org-roam/pull/98
+[gh-99]: https://github.com/jethrokuan/org-roam/pull/99
+[gh-103]: https://github.com/jethrokuan/org-roam/pull/103
+[gh-105]: https://github.com/jethrokuan/org-roam/pull/105
+[gh-108]: https://github.com/jethrokuan/org-roam/pull/108
+[gh-110]: https://github.com/jethrokuan/org-roam/pull/110
+[gh-122]: https://github.com/jethrokuan/org-roam/pull/122
+[gh-124]: https://github.com/jethrokuan/org-roam/pull/124
+[gh-128]: https://github.com/jethrokuan/org-roam/pull/128
+[gh-136]: https://github.com/jethrokuan/org-roam/pull/136
+[gh-138]: https://github.com/jethrokuan/org-roam/pull/138
+[gh-141]: https://github.com/jethrokuan/org-roam/pull/141
+[gh-142]: https://github.com/jethrokuan/org-roam/pull/142
+[gh-143]: https://github.com/jethrokuan/org-roam/pull/143
+
+ # 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

@@ -1,28 +1,26 @@
+[![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)
+
+## Synopsis
 
 Org-roam is a rudimentary [Roam][roamresearch] replica built around
 the all-powerful [Org-mode][org]. 
 
 Like Roam, Org-roam offers a powerful and effortless non-hierarchical
 note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. 
+note-taking fun and easy. Org-roam *enables* a note-taking workflow that
+is not fluid with vanilla Org-mode (more in [this blog
+post](https://blog.jethro.dev/posts/how_to_take_smart_notes_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. 
+ecosystem.
 
-For more documentation, see [the documentation page](https://org-roam.readthedocs.io/en/latest/).
-
-## Understanding Roam
-
-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
+Visit [the documentation
+page](https://org-roam.readthedocs.io/en/latest/) for a tutorial and
+more links.
 
 As of February 2020, it is in a very early stage of development. 
 
@@ -37,16 +35,50 @@ used to navigate to the respective files.
 
 ![img](doc/images/org-roam-graph.gif)
 
+## Installation
+
+The recommended method is using use-package and straight, or a similar package manager.
+
+```emacs-lisp
+(use-package org-roam
+      :after org
+      :hook 
+      (after-init . org-roam-mode)
+      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
+      :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 instructions (including instructions for
+Spacemacs users), please see [the installation
+documentation](https://org-roam.readthedocs.io/en/develop/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

doc/configuration.md

@@ -0,0 +1,121 @@
+To ensure that Org-roam remains manageable, the number of
+configuration options is deliberately kept small. However, we have
+attempted to accommodate as many usage styles as possible.
+
+In this section, we'll go over the main customization options
+available to Org-Roam. This section is *crucial*. We need to exploit
+the flexibility of Emacs, and mould our tools exactly to our liking.
+
+All of Org-roam's customization options can be viewed via `M-x
+customize-group org-roam`.
+
+## Setting the Org-roam Directory
+
+Perhaps the single most important variable to set is
+`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.
+
+## 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.
+I have found this to be a good number.
+
+## 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. If you
+wish, 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")
+```
+
+## Org-roam Files
+
+These customization options revolve around the Org files created and
+managed by Org-roam.
+
+### Automatically Creating Files Using Timestamp
+
+A common hassle is ensuring that files are uniquely named within the
+Org-roam directory. Org-roam's default workflow utilizes the title of
+Org files in all of its main commands (`org-roam-insert`,
+`org-roam-find-file`). Hence, having any unique file name is a decent
+option, and the default workflow uses the timestamp as the filename.
+
+The format of the filename is controlled by the function
+`org-roam-file-name-function`, which defaults to a format like
+`YYYYMMDDHHMMSS_title_here.org`. You may choose to define your own
+function to change this.
+
+If you wish to be prompted to change the file name on creation, set
+`org-roam-filename-noconfirm` to `nil`:
+
+```emacs-lisp
+(setq org-roam-filename-noconfirm nil)
+```
+
+It is then the user's responsibility to ensure that the file names are
+unique.
+
+### Autopopulating Titles
+
+The default workflow uses the title of the Org file in several
+commands. The title is specified via the `#+TITLE:` attribute,
+typically near the top of the file. The option
+`org-roam-autopopulate-title` defaults to `t`. When true, the title
+attribute is automatically inserted into the files created via
+Org-roam commands. Setting it to `nil` will disable this behaviour.
+
+### 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 this causes Emacs to ask for password when the
+cache is built (if you have an encrypted file in `org-roam-directory`)
+as well as each time a new file is created. It might be a good idea to
+cache the password in order to make this more managable.
+
+## 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-graphviz-executable "/path/to/dot")
+```
+
+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")
+```

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 +14,51 @@ 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
+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-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 +68,59 @@ 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.
+
+[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

doc/graph_setup.md

@@ -0,0 +1,78 @@
+The setup is similar to that of org-protocol. Here `roam://` links are
+defined, and need to be associated with an application. 
+
+The gist of the setup is setting up a Bash script to trim off the
+`roam://` prefix from the link, causing the desktop application to
+call `emacsclient path/to/org-roam-file.org`.
+
+## Linux
+
+Create a desktop application. I place mine in
+`~/.local/share/applications/roam.desktop`:
+
+```
+[Desktop Entry]
+Name=Org-Roam Client
+Exec=/home/jethro/.local/bin/launch_emacs %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/roam
+```
+
+Note the `Exec` key is set to a bash script poorly named
+`launch_emacs`. You can set it to whatever you want.
+
+Create the corresponding bash script, and make it executable. Here's
+how it looks like:
+
+```bash
+#!/usr/bin/env bash
+emacsclient "${1#*:}"
+```
+
+Finally, associate `roam://` links with the desktop application by
+running in your shell:
+
+```bash
+xdg-mime default roam.desktop x-scheme-handler/roam
+```
+
+## Mac OS
+
+One solution to this, recommended in [Issue
+#115](https://github.com/jethrokuan/org-roam/issues/115), is to use
+[Platypus](https://github.com/sveinbjornt/Platypus). Here are the
+instructions for setting up with Platypus and Chrome:
+
+1. Create an executable `launch-emacs.sh` script:
+
+```sh
+#!/usr/bin/env bash
+/usr/local/bin/emacsclient --no-wait "${1#*:}"
+```
+
+2. Install and launch Platypus (with [Homebrew](https://brew.sh/)):
+
+```sh
+brew cask install playtpus
+```
+
+3. Playtpus settings:
+
+- App Name: `OrgRoam`
+- Script Type: `env` and `/usr/bin/env`
+- Script Path: `/path/to/your/launch-emacs.sh`
+- Tick Accept dropped items and click Settings
+- Tick Accept dropped files
+- Tick Register as URI scheme handler
+- Add `roam` as a protocol
+- Create the app
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the `OrgRoam` app will be used
+without confirmation. To do this, run in a shell:
+
+```sh
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+```

doc/installation.md

@@ -6,17 +6,17 @@ The recommended method is using [use-package][use-package] and
 ```
 (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)
+      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
       :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 g" . org-roam-show-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
@@ -26,10 +26,68 @@ directory and add it to your load path:
 git clone https://github.com/jethrokuan/org-roam/ ~/.emacs.d/elisp/org-roam
 ```
 
+```
+(use-package org-roam
+      :after org
+      :load-path "elisp/"
+      :hook 
+      (after-init . org-roam-mode)
+      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
+      :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))))
+```
+
+Or without use-package:
+
 ```
 (add-to-list 'load-path "./elisp")
 (require 'org-roam)
 ```
 
+There are a number of important configuration options, that greatly
+affect the Roam workflow. Do look through them at the
+[Configuration](configuration.md) page.
+
 [use-package]: https://github.com/jwiegley/use-package
 [straight]: https://github.com/raxod502/straight.el
+
+## Spacemacs
+If you are using Spacemacs, you can easily 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`.
+```
+(defconst org-roam-packages
+  '((org-roam :location
+        (recipe :fetcher github :repo "jethrokuan/org-roam" :branch "develop"))))
+
+(defun org-roam/init-org-roam ()
+    (use-package org-roam
+        :after org
+        :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-today
+            "arf" 'org-roam-find-file
+            "arg" 'org-roam-show-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-today
+            "rb" 'org-roam-switch-to-buffer
+            "rf" 'org-roam-find-file
+            "ri" 'org-roam-insert
+            "rg" 'org-roam-show-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. 

doc/notetaking_workflow.md

@@ -0,0 +1,20 @@
+## 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]
+
+## 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/

doc/tour.md

@@ -1,20 +1,69 @@
-### 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.
+Understanding this flow is crucial! Org-roam doesn't auto-magically
+make your 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 the methods and madness, the [Note-Taking
+Workflow][appendix:ntw] page contains a page of useful references.
+I've also written [a post][jethro-blog-post] about how I use Org-roam.
 
-![org-roam-insert](images/org-roam-insert.gif)
+Without further ado, let's begin!
 
-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:
+## Building the Cache
+
+Assuming you've set `org-roam-directory` appropriately, running `M-x
+org-roam--build-cache-async` should build up the caches that will
+allow you to begin using Org-roam. I do this on startup:
+
+```emacs-lisp
+(add-hook 'after-init-hook 'org-roam--build-cache-async)
+```
+
+## Finding a Note
+
+`org-roam-find-file` shows you the list of notes you currently have in
+Org-roam. Selecting the 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)
+
+## Inserting Links
+
+Within your Org-roam notes, you are encouraged to liberally insert
+links to existing (or new) Org-roam notes with `org-roam-insert`.
+Entering a non-existent title will also create a new note with that
+title.
+
+![org-roam-insert](images/org-roam-insert-filetag.gif)
+
+It is crucial for good usage of Org-roam to insert links liberally,
+where you want them the notes to resurface!
+
+## The Org-roam Buffer
+
+All of Org-roam's operations are designed such that the built cache is
+a consistent view of the inter-connectivity between your notes. The
+Org-roam buffer shows backlinks: i.e. the files that link to the
+currently viewed file, along with some surrounding context. The
+Org-roam buffer will always show the backlinks for the current
+Org-roam file in view.
 
 ![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
+
+It's also possible to export the links as a graph, using graphviz. The
+generated graph is navigable in Emacs, but requires some additional
+setup, which I describe in the [Graph Appendix][appendix:graph-setup]
+page.
 
 ![org-roam-graph](images/org-roam-graph.gif)
+
+[zettelkasten]: https://zettelkasten.de/
+[appendix:ntw]: notetaking_workflow.md
+[appendix:graph-setup]: graph_setup.md
+[roam]: https://www.roamresearch.com/
+[jethro-blog-post]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

mkdocs.yml

@@ -7,8 +7,11 @@ nav:
 - Home: index.md
 - A Tour of Org-Roam: tour.md
 - Installation: installation.md
+- Configuration: configuration.md
 - Ecosystem: ecosystem.md
 - Similar Packages: comparison.md
+- "Appendix: Note-taking Workflow": notetaking_workflow.md
+- "Appendix: Graph Setup": graph_setup.md
 markdown_extensions:
   - admonition
   - pymdownx.betterem:

org-roam-utils.el

@@ -0,0 +1,169 @@
+;;; org-roam-utils.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: 0.1.2
+;; Package-Requires: ((emacs "26.1"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library is an attempt at injecting Roam functionality into Org-mode.
+;; This is achieved primarily through building caches for forward links,
+;; backward links, and file titles.
+;;
+;;; Code:
+
+(require 'org)
+(require 'org-element)
+(require 'subr-x)
+(require 'cl-lib)
+
+(defun org-roam--file-name-extension (filename)
+  "Return file name extension for FILENAME.
+
+Like file-name-extension, but does not strip version number."
+  (save-match-data
+    (let ((file (file-name-nondirectory filename)))
+      (if (and (string-match "\\.[^.]*\\'" file)
+                     (not (eq 0 (match-beginning 0))))
+          (substring file (+ (match-beginning 0) 1))))))
+
+(defun org-roam--org-file-p (path)
+  "Check if PATH is pointing to an org file."
+  (let ((ext (org-roam--file-name-extension path)))
+    (or (string= ext "org")
+        (and
+         (string= ext "gpg")
+         (string= (org-roam--file-name-extension (file-name-sans-extension path)) "org")))))
+
+(defun org-roam--find-files (dir)
+  "Return all `org-roam' files in `DIR'."
+  (if (file-exists-p dir)
+      (let ((files (directory-files dir t "." t))
+            (dir-ignore-regexp (concat "\\(?:"
+                                       "\\."
+                                       "\\|\\.\\."
+                                       "\\)$"))
+            result)
+        (dolist (file files)
+          (cond
+           ((file-directory-p file)
+            (when (not (string-match dir-ignore-regexp file))
+              (setq result (append (org-roam--find-files file) result))))
+           ((and (file-readable-p file)
+                 (org-roam--org-file-p file))
+            (setq result (cons (file-truename file) result)))))
+        result)))
+
+(defun org-roam--parse-content (&optional file-path)
+  "Parse the current buffer, and return a list of items for processing."
+  (org-element-map (org-element-parse-buffer) 'link
+    (lambda (link)
+      (let ((type (org-element-property :type link))
+            (path (org-element-property :path link))
+            (start (org-element-property :begin link)))
+        (when (and (string= type "file")
+                   (org-roam--org-file-p path))
+          (goto-char start)
+          (let* ((element (org-element-at-point))
+                 (begin (or (org-element-property :content-begin element)
+                            (org-element-property :begin element)))
+                 (content (or (org-element-property :raw-value element)
+                              (buffer-substring
+                               begin
+                               (or (org-element-property :content-end element)
+                                   (org-element-property :end element)))))
+                 (content (string-trim content))
+                 (file-path (or file-path
+                                (file-truename (buffer-file-name (current-buffer))))))
+            (list :from file-path
+                  :to (file-truename (expand-file-name path (file-name-directory file-path)))
+                  :properties (list :content content :point begin))))))))
+
+(cl-defun org-roam--insert-item (item &key forward backward)
+  "Insert ITEM into FORWARD and BACKWARD cache.
+
+ITEM is of the form: (:from from-path :to to-path :properties (:content preview-content :point point))."
+  (pcase-let ((`(:from ,p-from :to ,p-to :properties ,props) item))
+    ;; Build forward-links
+    (let ((links (gethash p-from forward)))
+      (if links
+          (puthash p-from
+                   (if (member p-to links)
+                       links
+                     (cons p-to links)) forward)
+        (puthash p-from (list p-to) forward)))
+    ;; Build backward-links
+    (let ((contents-hash (gethash p-to backward)))
+      (if contents-hash
+          (if-let ((contents-list (gethash p-from contents-hash)))
+              (let ((updated (cons props contents-list)))
+                (puthash p-from updated contents-hash)
+                (puthash p-to contents-hash backward))
+            (progn
+              (puthash p-from (list props) contents-hash)
+              (puthash p-to contents-hash backward)))
+        (let ((contents-hash (make-hash-table :test #'equal)))
+          (puthash p-from (list props) contents-hash)
+          (puthash p-to contents-hash backward))))))
+
+(defun org-roam--extract-title ()
+  "Extract the title from `BUFFER'."
+  (org-element-map
+      (org-element-parse-buffer)
+      'keyword
+    (lambda (kw)
+      (when (string= (org-element-property :key kw) "TITLE")
+        (org-element-property :value kw)))
+    :first-match t))
+
+(defun org-roam--build-cache (dir)
+  "Build the org-roam caches in DIR."
+  (let ((backward-links (make-hash-table :test #'equal))
+        (forward-links (make-hash-table :test #'equal))
+        (file-titles (make-hash-table :test #'equal)))
+    (let* ((org-roam-files (org-roam--find-files dir))
+           (file-items (mapcar (lambda (file)
+                                 (with-temp-buffer
+                                   (insert-file-contents file)
+                                   (org-roam--parse-content file))) org-roam-files)))
+      (dolist (items file-items)
+        (dolist (item items)
+          (org-roam--insert-item
+           item
+           :forward forward-links
+           :backward backward-links)))
+      (dolist (file org-roam-files)
+        (with-temp-buffer
+          (insert-file-contents file)
+          (when-let ((title (org-roam--extract-title)))
+            (puthash file title file-titles)))
+        org-roam-files))
+    (list
+     :forward forward-links
+     :backward backward-links
+     :titles file-titles)))
+
+(provide 'org-roam-utils)
+
+;;; org-roam-utils.el ends here

shell.nix

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

tests/roam-files/f1.org

@@ -0,0 +1,7 @@
+#+TITLE: File 1
+
+link to [[file:nested/f1.org][Nested File 1]] 
+link to [[file:f2.org][File 2]]
+
+Arbitrary [[https://google.com][HTML]] link
+Arbitrary text

tests/roam-files/f2.org

@@ -0,0 +1,3 @@
+#+TITLE: File 2
+
+This file has no links.

tests/roam-files/f3.org

@@ -0,0 +1,5 @@
+#+TITLE: File 3
+
+This file has a link to an file with no title.
+
+[[file:no-title.org][no-title]]

tests/roam-files/nested/f1.org

@@ -0,0 +1,4 @@
+#+TITLE: Nested File 1
+
+Link to [[file:f2.org][Nested File 2]]
+Link to [[file:../f1.org][File 1]]

tests/roam-files/nested/f2.org

@@ -0,0 +1,3 @@
+#+TITLE: Nested File 2
+
+Link to [[file:f1.org][Nested File 1]]

tests/roam-files/no-title.org

@@ -0,0 +1 @@
+no title in this file :O

tests/test-org-roam.el

@@ -0,0 +1,230 @@
+;;; 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 abs-path (file-path)
+  (file-truename (expand-file-name file-path org-roam-directory)))
+
+(defun org-roam--test-find-new-file (path)
+  (let ((path (abs-path path)))
+    (make-directory (file-name-directory path) t)
+    (find-file path)))
+
+(defvar org-roam--tests-directory (file-truename (concat default-directory "tests/roam-files"))
+  "Directory containing org-roam test org files.")
+
+(defun org-roam--test-init ()
+  (let ((original-dir org-roam--tests-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))
+
+(defun org-roam--test-build-cache ()
+  "Builds the caches synchronously."
+  (let ((cache (org-roam--build-cache org-roam-directory)))
+    (setq org-roam-forward-links-cache (plist-get cache :forward))
+    (setq org-roam-backward-links-cache (plist-get cache :backward))
+    (setq org-roam-titles-cache (plist-get cache :titles))
+    (setq org-roam-cache-initialized t)))
+
+;;; Tests
+(describe "org-roam--build-cache-async"
+          (it "initializes correctly"
+              (org-roam--test-init)
+              (expect org-roam-cache-initialized :to-be nil)
+              (expect (hash-table-count org-roam-forward-links-cache) :to-be 0)
+              (expect (hash-table-count org-roam-backward-links-cache) :to-be 0)
+              (expect (hash-table-count org-roam-titles-cache) :to-be 0)
+
+              (org-roam--build-cache-async)
+              (sleep-for 3) ;; Because it's async
+
+              ;; Caches should be populated
+              (expect org-roam-cache-initialized :to-be t)
+              (expect (hash-table-count org-roam-forward-links-cache) :to-be 4)
+              (expect (hash-table-count org-roam-backward-links-cache) :to-be 5)
+              (expect (hash-table-count org-roam-titles-cache) :to-be 5)
+
+              ;; Forward cache
+              (let ((f1 (gethash (abs-path "f1.org") org-roam-forward-links-cache))
+                    (f2 (gethash (abs-path "f2.org") org-roam-forward-links-cache))
+                    (nested-f1 (gethash (abs-path "nested/f1.org") org-roam-forward-links-cache))
+                    (nested-f2 (gethash (abs-path "nested/f2.org") org-roam-forward-links-cache))
+                    (expected-f1 (list (abs-path "nested/f1.org")
+                                       (abs-path "f2.org")))
+                    (expected-nested-f1 (list (abs-path "nested/f2.org")
+                                              (abs-path "f1.org")))
+                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+
+                (expect f1 :to-have-same-items-as expected-f1)
+                (expect f2 :to-be nil)
+                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
+                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+
+              ;; Backward cache
+              (let ((f1 (hash-table-keys (gethash (abs-path "f1.org") org-roam-backward-links-cache)))
+                    (f2 (hash-table-keys (gethash (abs-path "f2.org") org-roam-backward-links-cache)))
+                    (nested-f1 (hash-table-keys(gethash (abs-path "nested/f1.org") org-roam-backward-links-cache)))
+                    (nested-f2 (hash-table-keys (gethash (abs-path "nested/f2.org") org-roam-backward-links-cache)))
+                    (expected-f1 (list (abs-path "nested/f1.org")))
+                    (expected-f2 (list (abs-path "f1.org")))
+                    (expected-nested-f1 (list (abs-path "nested/f2.org")
+                                              (abs-path "f1.org")))
+                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+                (expect f1 :to-have-same-items-as expected-f1)
+                (expect f2 :to-have-same-items-as expected-f2)
+                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
+                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+
+              ;; Titles Cache
+              (expect (gethash (abs-path "f1.org") org-roam-titles-cache) :to-equal "File 1")
+              (expect (gethash (abs-path "f2.org") org-roam-titles-cache) :to-equal "File 2")
+              (expect (gethash (abs-path "nested/f1.org") org-roam-titles-cache) :to-equal "Nested File 1")
+              (expect (gethash (abs-path "nested/f2.org") org-roam-titles-cache) :to-equal "Nested File 2")
+              (expect (gethash (abs-path "no-title.org") org-roam-titles-cache) :to-be nil)))
+
+(describe "org-roam-insert"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+
+          (it "temp1 -> f1"
+              (let ((buf (org-roam--test-find-new-file "temp1.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:f1.org")))
+
+          (it "temp2 -> nested/f1"
+              (let ((buf (org-roam--test-find-new-file "temp2.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "Nested SPC File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:nested/f1.org")))
+
+          (it "nested/temp3 -> f1"
+              (let ((buf (org-roam--test-find-new-file "nested/temp3.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:../f1.org")))
+
+          (it "a/b/temp4 -> nested/f1"
+              (let ((buf (org-roam--test-find-new-file "a/b/temp4.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "Nested SPC File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:../../nested/f1.org"))))
+
+(describe "rename file updates cache"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+
+          (it "f1 -> new_f1"
+              (rename-file (abs-path "f1.org")
+                           (abs-path "new_f1.org"))
+              ;; Cache should be cleared of old file
+              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (hash-table-keys)
+                           (member (abs-path "f1.org"))) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "new_f1.org"))) :not :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "new_f1.org"))
+                           (member (abs-path "nested/f1.org"))) :not :to-be nil)
+              ;; Links are updated
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "nested/f1.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:../new_f1.org][File 1]]")))
+
+
+          (it "f1 -> f1 with spaces"
+              (rename-file (abs-path "f1.org")
+                           (abs-path "f1 with spaces.org"))
+              ;; Cache should be cleared of old file
+              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (hash-table-keys)
+                           (member (abs-path "f1.org"))) :to-be nil)
+              ;; Links are updated
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "nested/f1.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:../f1 with spaces.org][File 1]]")))
+
+          (it "no-title -> meaningful-title"
+              (rename-file (abs-path "no-title.org")
+                           (abs-path "meaningful-title.org"))
+              ;; File has no forward links
+              (expect (gethash (abs-path "no-title.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (gethash (abs-path "meaningful-title.org")  org-roam-forward-links-cache) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f3.org"))
+                           (member (abs-path "no-title.org"))) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f3.org"))
+                           (member (abs-path "meaningful-title.org"))) :not :to-be nil)
+
+              ;; Links are updated with the appropriate name
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "f3.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:meaningful-title.org][meaningful-title]]"))))
+
+(describe "delete file updates cache"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+          (it "delete f1"
+              (delete-file (abs-path "f1.org"))
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f1.org"))) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (gethash (abs-path "f1.org"))) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (gethash (abs-path "nested/f2.org"))) :not :to-be nil)))