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

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

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

.dir-locals.el

@@ -0,0 +1,6 @@
+;;; Directory Local Variables
+;;; For more information see (info "(emacs) Directory Variables")
+
+((emacs-lisp-mode
+  (eval . (require 'org-roam-dev))
+  (sentence-end-double-space . nil)))

.github/FUNDING.yml

@@ -0,0 +1,12 @@
+# These are supported funding model platforms
+
+github: [jethrokuan, zaeph]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,14 +1,15 @@
 ---
 name: Bug Report
 about: Something's not working.
-title: ''
-labels: ''
-assignees: 'jethrokuan'
+title: ""
+labels: ""
+assignees: ""
 ---
 
 ### Description
 
 #### Steps to Reproduce
+
 <!--
 Example:
 
@@ -18,13 +19,25 @@ Example:
 ...
 -->
 
+#### Backtrace
+<!--
+   Will help us track and understand issues faster.
+   How to provide a backtrace:
+   1. M-x toggle-debug-on-error
+   2. Trigger error. The debugger buffer should pop up.
+   3. Copy the contents of the debugger buffer and paste here
+-->
 
 #### Expected Results
+
 <!-- Example: File A is there -->
 
 #### Actual Results
+
 <!-- Example: File A is missing -->
 
-### Versions
-- Emacs (`C-h v emacs-version`): vX.X.X
+### Environment
+
+<!-- Please M-x org-roam-diagnostics and paste results here -->
+
 - Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,9 +1,9 @@
 ---
 name: Feature Request
 about: Create a feature request to improve Org-roam
-title: ''
-labels: 'enhancement'
-assignees: 'jethrokuan'
+title: ""
+labels: "enhancement"
+assignees: ""
 ---
 
 ### Brief Abstract
@@ -13,4 +13,5 @@ assignees: 'jethrokuan'
 ### Proposed Implementation (if any)
 
 ### Please check the following:
+
 - [ ] No similar feature requests

.github/workflows/docs.yml

@@ -0,0 +1,31 @@
+# * docs.yml --- Build the documentation and publish to Github Pages
+
+name: "Docs"
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install deps
+      run: |
+        sudo apt-get install texinfo
+
+    - name: Build docs
+      continue-on-error: false
+      run: make html
+
+    - name: Deploy 🚀
+      uses: JamesIves/github-pages-deploy-action@releases/v3
+      with:
+        ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
+        BRANCH: gh-pages # The branch the action should deploy to.
+        FOLDER: doc # The folder the action should deploy.
+        CLEAN: true

.github/workflows/test.yml

@@ -29,7 +29,6 @@ on:
   push:
     branches:
       - master
-      - develop
 
 jobs:
   build:
@@ -55,9 +54,11 @@ jobs:
     # The "all" rule is not used, because it treats compilation warnings
     # as failures, so linting and testing are run as separate steps.
 
+    # org-roam-compat is excluded from linting because it contains
+    # symbols/aliases from other packages
     - name: Lint
-      continue-on-error: true
-      run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
+      continue-on-error: false
+      run: ./makem.sh -vv --sandbox $SANDBOX_DIR --exclude org-roam-compat.el lint
 
     - name: Test
       if: always()  # Run test even if linting fails.

.gitignore

@@ -1,2 +1,15 @@
 /.sandbox/
 **/*.elc
+/doc/dir
+/doc/*.info
+/doc/*.pdf
+/doc/*.epub
+/doc/META_INF/
+/doc/OEBPS/
+/doc/dir
+/doc/epub.xml
+/doc/org-roam/
+/doc/mimetype
+/doc/stats/
+/config.mk
+/doc/manual/

BACKERS.md

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

CHANGELOG.md

@@ -1,5 +1,72 @@
 # Changelog
 
+## 1.2.0 (12-06-2020)
+
+In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
+
+This is a major step forward. Supporting the in-file structure of Org-mode files means that we can interface with many of its core-features like TODOs, properties, priorities, etc. UX will have to be figured out, but this release ushers in a new age in terms of functionalities.
+
+We also add `org-roam-unlinked-references`, which naively finds text that could be references to the current Org-roam file.
+
+### Breaking Changes
+
+- [#701](https://github.com/org-roam/org-roam/pull/701) Use `emacsql-sqlite3` instead of `emacsql-sqlite` for better Windows compatibility. This requires the presence of the standard `sqlite3` binary on your machine.
+- [#750](https://github.com/org-roam/org-roam/pull/750) Deprecate `org-roam-buffer-no-delete-other-windows` in favour of `org-roam-buffer-window-parameters`.
+
+### Features
+
+- [#787](https://github.com/org-roam/org-roam/pull/787) Add `org-roam-unlinked-references`
+- [#783](https://github.com/org-roam/org-roam/pull/783) Add support for headlines
+- [#757](https://github.com/org-roam/org-roam/pull/757) Roam global properties are now case-insensitive
+- [#680](https://github.com/org-roam/org-roam/pull/680) , [#703](https://github.com/org-roam/org-roam/pull/703), [#708](https://github.com/org-roam/org-roam/pull/708) Add `org-roam-doctor` checkers for `ROAM_*` properties
+- [#664](https://github.com/org-roam/org-roam/pull/664) Add support for shelling out to `rg` and `find` in `org-roam--list-files`
+- [#679](https://github.com/org-roam/org-roam/pull/679), [#683](https://github.com/org-roam/org-roam/pull/683) Building of the graph now happens in a separate process
+
+### Bugfixes
+- [#714](https://github.com/org-roam/org-roam/pull/714) No longer print citelinks in backlinks buffer if there is no `ROAM_KEY` property or `org-ref` is not installed
+- [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
+- [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
+
+## 1.1.1 (18-05-2020)
+
+In this release, we added two new features:
+
+1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
+2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://org-roam.github.io/org-roam/manual/Tags.html#Tags).
+
+As usual, this release comes with a multitude of bug-fixes and refactorings.
+
+### Breaking Changes
+
+- [#523](https://github.com/org-roam/org-roam/pull/523) remove `org-roam-completion-fuzzy-match` in favor of using completion mechanism's configuration options directly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Deprecate `org-roam-db--maybe-update`, in favour of `org-roam-db--update-maybe`
+- [#604](https://github.com/org-roam/org-roam/pull/604) Deprecate `org-roam-title-include-subdirs`, `org-roam-title-subdir-format` `org-roam-title-subdir-separator`, for a more general tagging system built on subdirectories
+
+### Bugfixes
+
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix backup files being tracked in database
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix external org files being tracked in database
+- [#537](https://github.com/org-roam/org-roam/pull/537) quote graphviz node and edge configuration options to allow multi-word configurations
+- [#545](https://github.com/org-roam/org-roam/pull/545) fix `org-roam--extract-links` to ensure that multiple citations (`cite:key1,key2`) are split correctly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Fix unlinked citations
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix rename-file advice not working for renaming to directories
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix links breaking within file on file movement
+
+### Features
+
+- [#538](https://github.com/org-roam/org-roam/pull/538) Optionally use text in first headline as title
+- [#553](https://github.com/org-roam/org-roam/pull/553) Add prefix argument to `org-roam-db-build-cache` for forcing rebuilds
+- [#560](https://github.com/org-roam/org-roam/pull/560) Apply 'error face to distinguish broken links
+- [#570](https://github.com/org-roam/org-roam/pull/570) Add `org-roam-doctor` to diagnose org-roam files
+- [#625](https://github.com/org-roam/org-roam/pull/625) Add `org-roam-title-sources` to control how titles are retrieved within notes
+- [#604](https://github.com/org-roam/org-roam/pull/604) Add a tagging system. `org-roam-tag-sources` controls how tags are retrieved from notes
+
+### Internal Changes
+
+- [#547](https://github.com/org-roam/org-roam/pull/547) Added `type` column to the `refs` table
+- [#606](https://github.com/org-roam/org-roam/pull/606) Added `org-roam-dev.el` for developer coding standards
+- [#622](https://github.com/org-roam/org-roam/pull/622) Online documentation now points to the Org-based documentation
+
 ## 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:
@@ -8,31 +75,35 @@ To the average user, this release is mainly a bugfix release with additional opt
 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). 
- 
+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`.
+
+- [#385](https://github.com/org-roam/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
+- [#473](https://github.com/org-roam/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
+
+- [#350](https://github.com/org-roam/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
+- [#359](https://github.com/org-roam/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
+- [#374](https://github.com/org-roam/org-roam/pull/374) Add support for `org-ref` `cite:` links
+- [#380](https://github.com/org-roam/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
+- [#385](https://github.com/org-roam/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
+- [#398](https://github.com/org-roam/org-roam/pull/398), [#418](https://github.com/org-roam/org-roam/pull/418) Add graph building for connected components
+- [#435](https://github.com/org-roam/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
+- [#439](https://github.com/org-roam/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/org-roam/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
+- [#488](https://github.com/org-roam/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
+- [#491](https://github.com/org-roam/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`.
+
+- [#470](https://github.com/org-roam/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
+
+- [#363](https://github.com/org-roam/org-roam/pull/363), [#473](https://github.com/org-roam/org-roam/pull/473) Modularize org-roam features.
+- [#497](https://github.com/org-roam/org-roam/pull/497) Simplify `org-roam--list-files` implementation
 
 ## 1.0.0 (23-03-2020)
 
@@ -40,16 +111,18 @@ 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`
+
+- [#269](https://github.com/org-roam/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
+- [#257](https://github.com/org-roam/org-roam/pull/257) Add a company-backend `company-org-roam`
+- [#284](https://github.com/org-roam/org-roam/pull/284), [#289](https://github.com/org-roam/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
+- [#289](https://github.com/org-roam/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
+- [#290](https://github.com/org-roam/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/org-roam/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
+
+- [#293](https://github.com/org-roam/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
+- [#275](https://github.com/org-roam/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
 
 ## 1.0.0-rc1 (06-03-2020)
 
@@ -59,82 +132,95 @@ 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.
+
+- [#200](https://github.com/org-roam/org-roam/pull/200) Move Org-roam cache into a SQLite database.
+- [#203](https://github.com/org-roam/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`
+
+- [#182](https://github.com/org-roam/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
+- [#216](https://github.com/org-roam/org-roam/pull/216) Adds templating functionality by extending org-capture.
+- [#232](https://github.com/org-roam/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
+- [#233](https://github.com/org-roam/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
+- [#247](https://github.com/org-roam/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
+- [#259](https://github.com/org-roam/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
+
+- [#207](https://github.com/org-roam/org-roam/pull/207), [#221](https://github.com/org-roam/org-roam/pull/221) small bugfixes to Org-roam graph generation
+- [#230](https://github.com/org-roam/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]
+
+- [@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.
+
+- [#143](https://github.com/org-roam/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+- [#103](https://github.com/org-roam/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
+
+- [#145](https://github.com/org-roam/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
+- [#141](https://github.com/org-roam/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
+- [#138](https://github.com/org-roam/org-roam/pull/138) add `org-roam-switch-to-buffer`
+- [#124](https://github.com/org-roam/org-roam/pull/124), [#141](https://github.com/org-roam/org-roam/pull/141) Maintain cache consistency on file rename and delete
+- [#87](https://github.com/org-roam/org-roam/pull/87), [#90](https://github.com/org-roam/org-roam/pull/90) Support encrypted Org files
+- [#110](https://github.com/org-roam/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
+- [#99](https://github.com/org-roam/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
+- [#108](https://github.com/org-roam/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
+
+- [#86](https://github.com/org-roam/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+- [#98](https://github.com/org-roam/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
+- [#136](https://github.com/org-roam/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
+
+- [#122](https://github.com/org-roam/org-roam/pull/122), [#128](https://github.com/org-roam/org-roam/pull/128) Improve performance of post-command-hook
+- [#92](https://github.com/org-roam/org-roam/pull/92), [#105](https://github.com/org-roam/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)
+
+- [@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.
+
+- [#62](https://github.com/org-roam/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.
+
+- [#62](https://github.com/org-roam/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
+
+- [#66](https://github.com/org-roam/org-roam/pull/66), [#68](https://github.com/org-roam/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
+- [#73](https://github.com/org-roam/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/org-roam/org-roam/pull/69), [#72](https://github.com/org-roam/org-roam/pull/72), [#75](https://github.com/org-roam/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
+
+- [#67](https://github.com/org-roam/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
+- [#71](https://github.com/org-roam/org-roam/pull/71), [#78](https://github.com/org-roam/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
+- [#82](https://github.com/org-roam/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
 
 <!-- Local Variables: -->
 <!-- eval: (auto-fill-mode -1) -->

Makefile

@@ -54,3 +54,17 @@ endif
 .DEFAULT: init
 init:
 	@./makem.sh $(DEBUG) $(VERBOSE) $(SANDBOX) $(INSTALL_DEPS) $(INSTALL_LINTERS)
+
+docs:
+	@$(MAKE) -C doc all
+
+html:
+	@$(MAKE) -C doc html-dir
+
+install: install-docs
+
+install-docs: docs
+	@$(MAKE) -C doc install-docs
+
+install-info: info
+	@$(MAKE) -C doc install-info

README.md

@@ -1,6 +1,5 @@
 [![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)
+[![GitHub Release](https://img.shields.io/github/v/release/org-roam/org-roam)](https://img.shields.io/github/v/release/org-roam/org-roam)
 [![MELPA](https://melpa.org/packages/org-roam-badge.svg)](https://melpa.org/#/org-roam)
 
 ## Synopsis
@@ -22,20 +21,20 @@ describing Org-roam and the concepts behind it:
 
 [![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]**
+- **[Discourse][discourse]**
+- **[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 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.
+Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
+right) shows backlinks for the active Org-roam buffer (window on the
+left), as well as the surrounding content in the backlink file. The
+database is built once, and updated incrementally. The graph is
+generated from the link structure, and can be used to navigate to the
+respective files.
 
 ![img](doc/images/org-roam-graph.gif)
 
@@ -51,7 +50,7 @@ Here's a sample configuration with using `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
-      :hook 
+      :hook
       (after-init . org-roam-mode)
       :custom
       (org-roam-directory "/path/to/org-files/")
@@ -63,9 +62,15 @@ Here's a sample configuration with using `use-package`:
               (("C-c n i" . org-roam-insert))))
 ```
 
+`org-roam-graph` by default expects to find the `dot` executable
+from the `graphviz` package in the `exec-path`.
+Ensure `graphviz` is installed and found if you want to use this
+feature or customize your configuration for `org-roam-graph` to use a
+different tool.
+
 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/).
+documentation][docs].
 
 ## Knowledge Bases using Org-roam
 
@@ -90,5 +95,6 @@ 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/
+[docs]: https://org-roam.github.io/org-roam/manual/
+[discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg

default.mk

@@ -0,0 +1,106 @@
+TOP := $(dir $(lastword $(MAKEFILE_LIST)))
+
+## User options ######################################################
+#
+# You can override these settings in "config.mk" or on the command
+# line.
+#
+# You might also want to set LOAD_PATH.  If you do, then it must
+# contain "-L .".
+#
+# If you don't do so, then the default is set in the "Load-Path"
+# section below.  The default assumes that all dependencies are
+# installed either at "../<DEPENDENCY>", or when using package.el
+# at "ELPA_DIR/<DEPENDENCY>-<HIGHEST-VERSION>".
+
+sharedir ?= $(HOME)/.local/share
+lispdir  ?= $(sharedir)/emacs/site-lisp/org-roam
+infodir  ?= $(sharedir)/info
+docdir   ?= $(sharedir)/doc/org-roam
+statsdir ?= $(TOP)/doc/stats
+
+CP       ?= install -p -m 644
+MKDIR    ?= install -p -m 755 -d
+RMDIR    ?= rm -rf
+TAR      ?= tar
+SED      ?= sed
+
+EMACSBIN ?= emacs
+BATCH     = $(EMACSBIN) -Q --batch $(LOAD_PATH)
+
+INSTALL_INFO     ?= $(shell command -v ginstall-info || printf install-info)
+MAKEINFO         ?= makeinfo
+MANUAL_HTML_ARGS ?= --css-ref /assets/page.css
+
+## Files #############################################################
+
+PKG       = org-roam
+PACKAGES  = org-roam
+
+TEXIPAGES = $(addsuffix .texi,$(PACKAGES))
+INFOPAGES = $(addsuffix .info,$(PACKAGES))
+HTMLFILES = $(addsuffix .html,$(PACKAGES))
+HTMLDIRS  = $(PACKAGES)
+PDFFILES  = $(addsuffix .pdf,$(PACKAGES))
+EPUBFILES = $(addsuffix .epub,$(PACKAGES))
+
+ELS = org-roam-buffer.el
+ELS += org-roam-capture.el
+ELS += org-roam-compat.el
+ELS += org-roam-completion.el
+ELS += org-roam-dailies.el
+ELS += org-roam-db.el
+ELS += org-roam.el
+ELS += org-roam-graph.el
+ELS += org-roam-macs.el
+ELS += org-roam-protocol.el
+ELCS = $(ELS:.el=.elc)
+ELMS = org-roam.el $(filter-out $(addsuffix .el,$(PACKAGES)),$(ELS))
+ELGS = org-roam-autoloads.el org-roam-version.el
+
+## Versions ##########################################################
+
+VERSION ?= $(shell test -e $(TOP).git && git describe --tags --abbrev=0 | cut -c2-)
+
+EMACS_VERSION = 26.1
+
+EMACSOLD := $(shell $(BATCH) --eval \
+  "(and (version< emacs-version \"$(EMACS_VERSION)\") (princ \"true\"))")
+ifeq "$(EMACSOLD)" "true"
+  $(error At least version $(EMACS_VERSION) of Emacs is required)
+endif
+
+## Load-Path #########################################################
+
+ifndef LOAD_PATH
+
+ELPA_DIR ?= $(HOME)/.emacs.d/elpa
+
+SYSTYPE := $(shell $(EMACSBIN) -Q --batch --eval "(princ system-type)")
+ifeq ($(SYSTYPE), windows-nt)
+  CYGPATH := $(shell cygpath --version 2>/dev/null)
+endif
+
+LOAD_PATH = -L $(TOP)
+
+# When making changes here, then don't forget to adjust "Makefile",
+# ".travis.yml", ".github/ISSUE_TEMPLATE/bug_report.md",
+# `magit-emacs-Q-command' and the "Installing from the Git Repository"
+# info node accordingly.  Also don't forget to "rgrep \b<pkg>\b".
+
+endif # ifndef LOAD_PATH
+
+ifndef ORG_LOAD_PATH
+ORG_LOAD_PATH  = $(LOAD_PATH)
+ORG_LOAD_PATH += -L $(TOP)../ox-texinfo-plus
+ORG_LOAD_PATH += -L $(TOP)../org-mode/contrib/lisp
+ORG_LOAD_PATH += -L $(TOP)../org-mode/lisp
+endif
+
+## Publish ###########################################################
+
+PUBLISH_TARGETS ?= html html-dir pdf epub
+
+DOCBOOK_XSL ?= /usr/share/xml/docbook/stylesheet/docbook-xsl/epub/docbook.xsl
+
+EPUBTRASH = epub.xml META-INF OEBPS

doc/AUTHORS.md

@@ -0,0 +1,37 @@
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+- Alexey Shmalko <rasen.dubi@gmail.com>
+- James Ravn <james@r-vn.org>
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Johann Klähn <johann@jklaehn.de>
+- Josh English <josh@joshenglish.com>
+- Jürgen Hötzel <juergen@archlinux.org>
+- Langston Barrett <langston.barrett@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+- Michael Glaesemann <grzm@seespotcode.net>
+- Michael Herold <github@michaeljherold.com>
+- Noboru <noboru.ota@gmail.com>
+- N V <44036031+progfolio@users.noreply.github.com>
+- Rafael Accácio Nogueira <raccacio@poli.ufrj.br>
+- Roland Coeurjoly <rolandcoeurjoly@gmail.com>
+- Sayan <dit7ya@users.noreply.github.com>
+- Tim Quelch <tim@quelch.name>

doc/Makefile

@@ -0,0 +1,130 @@
+-include ../config.mk
+include ../default.mk
+
+###################################################################
+MANUAL_HTML_ARGS = --css-ref assets/page.css
+
+.PHONY: texi install clean AUTHORS.md stats
+
+all: info
+
+## Build #############################################################
+
+info: $(INFOPAGES) dir
+html: $(HTMLFILES)
+pdf:  $(PDFFILES)
+epub: $(EPUBFILES)
+
+%.info: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --no-split $< -o $@
+
+dir: org-roam.info
+	@printf "Generating dir\n"
+	@echo $^ | xargs -n 1 $(INSTALL_INFO) --dir=$@
+
+%.html: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --html --no-split $(MANUAL_HTML_ARGS) $<
+
+html-dir: 
+	@printf "Generating org-roam/*.html\n"
+	@$(MAKEINFO) --html $(MANUAL_HTML_ARGS) org-roam.texi
+	mv org-roam manual
+	cp -r assets manual
+	cp -r images manual
+
+%.pdf: %.texi
+	@printf "Generating $@\n"
+	@texi2pdf --clean $< > /dev/null
+
+%.epub: %.texi
+	@printf "Generating $@\n"
+	@$(MAKEINFO) --docbook $< -o epub.xml
+	@xsltproc $(DOCBOOK_XSL) epub.xml 2> /dev/null
+	@echo "application/epub+zip" > mimetype
+	@zip -X --quiet --recurse-paths -0 $@ mimetype
+	@zip -X --quiet --recurse-paths -9 --no-dir-entries $@ META-INF OEBPS
+	@$(RMDIR) $(EPUBTRASH)
+
+## Install ###########################################################
+
+install: install-info install-docs
+
+install-docs: install-info
+	@$(MKDIR) $(DESTDIR)$(docdir)
+	$(CP) AUTHORS.md $(DESTDIR)$(docdir)
+
+install-info: info
+	@$(MKDIR) $(DESTDIR)$(infodir)
+	$(CP) $(INFOPAGES) $(DESTDIR)$(infodir)
+
+## Clean #############################################################
+
+clean:
+	@printf "Cleaning doc/*...\n"
+	@$(RMDIR) dir $(INFOPAGES) $(HTMLFILES) $(HTMLDIRS) $(PDFFILES)
+	@$(RMDIR) $(EPUBFILES) $(EPUBTRASH)
+
+## Release management ################################################
+
+ORG_ARGS  = --batch -Q $(ORG_LOAD_PATH)
+ORG_ARGS += -l ox-extra -l ox-texinfo+
+ORG_ARGS += --eval "(or (require 'org-man nil t) (require 'ol-man))"
+ORG_EVAL  = --eval "(ox-extras-activate '(ignore-headlines))"
+ORG_EVAL += --eval "(setq indent-tabs-mode nil)"
+ORG_EVAL += --eval "(setq org-src-preserve-indentation nil)"
+ORG_EVAL += --funcall org-texinfo-export-to-texinfo
+
+# This target first bumps version strings in the Org source.  The
+# necessary tools might be missing so other targets do not depend
+# on this target and it has to be run explicitly when appropriate.
+#
+#   AMEND=t make texi    Update manual to be amended to HEAD.
+#   VERSION=N make texi  Update manual for release.
+#
+texi:
+	@$(EMACSBIN) $(ORG_ARGS) $(PKG).org $(ORG_EVAL)
+	@printf "\n" >> $(PKG).texi
+	@rm -f $(PKG).texi~
+
+stats:
+	@printf "Generating statistics\n"
+	@gitstats -c style=/assets/stats.css -c max_authors=999 $(TOP) $(statsdir)
+
+authors: AUTHORS.md
+
+AUTHORS.md:
+	@printf "Generating AUTHORS.md..."
+	@test -e $(TOP).git \
+	&& (printf "$$AUTHORS_HEADER\n" > $@ \
+	&& git log --pretty=format:'- %aN <%aE>' | sort -u >> $@ \
+	&& printf "done\n" ; ) \
+	|| printf "FAILED (non-fatal)\n"
+
+# Templates ##########################################################
+
+define AUTHORS_HEADER
+Authors
+=======
+
+The following people have contributed to Org-Roam.
+
+Names below are sorted alphabetically.
+
+Author
+------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+
+Maintainers
+----------
+
+- Jethro Kuan <jethrokuan95@gmail.com>
+- Leo Vivier <leo.vivier+dev@gmail.com>
+
+Contributors
+------------
+
+endef
+export AUTHORS_HEADER

doc/anatomy.md

@@ -1,41 +0,0 @@
-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/assets/page.css

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

doc/comparison.md

@@ -1,11 +0,0 @@
----
-title: "Comparing Org-roam With Other Packages"
-metaTitle: "Comparing Org-roam With Other Packages"
-metaDescription: "Comparing Org-roam With Other Packages"
----
-
-# Org-brain
-
-# Zetteldeft
-
-# Org-zettelkasten

doc/configuration.md

@@ -1,142 +0,0 @@
-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/css/styles.css

@@ -0,0 +1,85 @@
+body {
+  margin: 20px;
+  background: #303030;
+  color: #f5f5f5;
+  font-size: 1.6rem;
+  font-weight: 300;
+}
+
+.container {
+  max-width: 800px;
+}
+
+.nav {
+  margin-top: 5rem;
+}
+
+.nav-item a {
+  /* color: #797979; */
+  color: #bebebe;
+  text-decoration: none;
+  font-family: "Consolas", "Monaco", "Menlo", monospace;
+}
+
+.nav-item a:hover {
+  cursor: pointer;
+  /* color: #4d4a4a; */
+  color: #dcdcdc;
+  border: none;
+}
+
+.hero {
+  color: #f5f5f5;
+}
+
+.hero div {
+  margin-bottom: 5rem;
+}
+
+.hero h3 {
+  /* font-family: "Edelsans", sans-serif; */
+  font-size: 5rem;
+  margin-bottom: 0;
+}
+
+.hero h5 {
+  margin-top: 1rem;
+  margin-bottom: 0;
+  /* font-weight: 200; */
+  font-weight: 250;
+}
+
+.grid-demo-col {
+  background: #e4e4e4;
+}
+
+a {
+  color: #cd86ff;
+}
+
+a:hover {
+  color: #dbb9f3;
+}
+
+img {
+  max-width: 100%;
+}
+
+.footer-links {
+  font-size: 1.5rem;
+  color: #f5f5f5;
+  text-decoration: none;
+  font-weight: 250;
+}
+
+.header {
+  font-weight: 200;
+}
+
+#footer {
+  margin-bottom: 3rem;
+}
+
+#footer h5 {
+  margin-bottom: 1.5rem;
+}

doc/ecosystem.md

@@ -1,134 +0,0 @@
-A number of packages work well combined with Org-Roam:
-
-## Deft
-
-[Deft][deft] provides a nice interface for browsing and filtering
-org-roam notes.
-
-```emacs-lisp
-(use-package deft
-  :after org
-  :bind
-  ("C-c n d" . deft)
-  :custom
-  (deft-recursive t)
-  (deft-use-filter-string-for-filename t)
-  (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/"))
-```
-
-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)
-  :custom
-  (org-journal-date-prefix "#+TITLE: ")
-  (org-journal-file-format "%Y-%m-%d.org")
-  (org-journal-dir "/path/to/org-roam-files/")
-  (org-journal-date-format "%A, %d %B %Y"))
-```
-
-## 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/htmlxref.cnf

@@ -0,0 +1,15 @@
+# https://www.gnu.org/software/texinfo/manual/texinfo/html_node/HTML-Xref-Configuration.html
+
+EMACS = https://www.gnu.org/software/emacs/manual
+
+auth		mono	${EMACS}/html_mono/auth.html
+auth		node	${EMACS}/html_node/auth/
+
+ediff		mono	${EMACS}/html_mono/ediff.html
+ediff		node	${EMACS}/html_node/ediff/
+
+elisp		mono	${EMACS}/html_mono/elisp.html
+elisp		node	${EMACS}/html_node/elisp/
+
+emacs		mono	${EMACS}/html_mono/emacs.html
+emacs		node	${EMACS}/html_node/emacs/

doc/index.html

@@ -0,0 +1,175 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="description" content="An Effortless PKM System." />
+    <meta name="author" content="Org-roam Contributors" />
+
+    <title>Org-roam</title>
+
+    <link rel="stylesheet" href="https://unpkg.com/wingcss" />
+    <link rel="stylesheet" type="text/css" href="./css/styles.css" />
+
+    <script src="https://code.iconify.design/1/1.0.6/iconify.min.js"></script>
+  </head>
+
+  <body>
+    <section class="hero container center text-center">
+      <div>
+        <img src="./img/logo.png" alt="Org-roam Logo" height="200" />
+        <h3>Org-roam</h3>
+        <h5>A plain-text personal knowledge management system.</h5>
+      </div>
+    </section>
+
+    <section class="container center">
+      <div>
+        <img src="./img/screenshot.png" alt="screenshot" />
+      </div>
+    </section>
+
+    <section id="features" class="container center">
+      <div>
+        <h3 class="header">FEATURES</h3>
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="fxemoji:lock"></iconify-icon> &nbsp;
+              Private and Secure
+            </h5>
+            <p class="content">
+              Edit your personal wiki completely offline, entirely in your
+              control. Encrypt your notes with GPG. Take lasting notes in
+              plain-text.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="flat-color-icons:link"></iconify-icon>
+              &nbsp; Make Connections
+            </h5>
+            <p class="content">
+              Connect notes and thoughts together with ease using backlinks.
+              Discover surprising and previously unseen connections in your
+              notes with the built-in graph visualization.
+            </p>
+          </div>
+        </div>
+
+        <div class="row">
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="twemoji:puzzle-piece"></iconify-icon>
+              &nbsp; Extensible and Powerful
+            </h5>
+            <p class="content">
+              Leverage Emacs' fantastic text-editing interface, and the mature
+              Emacs and Org-mode ecosystem of packages.
+            </p>
+          </div>
+          <div class="col">
+            <h5 class="left">
+              <iconify-icon data-icon="logos:git-icon"></iconify-icon> &nbsp;
+              Free and Open Source
+            </h5>
+            <p class="content">
+              Org-roam is licensed under the GNU General Public License version
+              3 or later. You are free to extend its functionality and
+              contribute back. Find
+              us <a href="https://github.com/org-roam/org-roam">here</a>.
+            </p>
+          </div>
+        </div>
+      </div>
+    </section>
+    
+    <section id="links" class="container">
+      <div>
+        <h3 class="header">LINKS</h3> New to Emacs and Org-mode, and trying to
+        find your way around? Org-roam has an inclusive community of users
+        passionate about Personal Knowledge Management -- we're happy to help!
+        You can find us on Discourse and Slack.
+        
+        <ul>
+            <li>Read our documentation within Emacs, or on the <a href="https://org-roam.github.io/org-roam/manual/">Online Manual</a></li>
+            <li>Participate in our forum discussions on <a href="https://org-roam.discourse.group">Discourse</a></li>
+            <li>Chat with us on <a href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg">Slack</a></li>
+          </ul>
+      </div>
+    </section>
+
+    <section id="footer" class="row container">
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Ecosystem</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-bibtex"
+            >org-roam-bibtex</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam-server"
+            >org-roam-server</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/company-org-roam"
+            >company-org-roam</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Resources</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc"
+            >Open Issues</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://github.com/org-roam/org-roam/releases"
+            >Releases</a
+          >
+        </div>
+      </div>
+
+      <div class="col">
+        <div class="row">
+          <h5 class="header">Connect</h5>
+        </div>
+
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg"
+            >Slack</a
+          >
+        </div>
+        <div class="row">
+          <a
+            class="content footer-links"
+            href="https://org-roam.discourse.group/"
+            >Discourse</a
+          >
+        </div>
+      </div>
+    </section>
+  </body>
+</html>

doc/index.md

@@ -1,62 +0,0 @@
-![org-roam][org-roam-intro-image]
-
-## What is Org-roam?
-
-Org-roam is a [Roam][roamresearch] replica built around the
-all-powerful [Org-mode][org].
-
-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.
-
-To understand more about Roam, a collection of links are available in
-[the appendix](notetaking_workflow.md).
-
-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 use Org-roam?
-
-##### Private and Secure
-
-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 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/
-[org]: https://orgmode.org/

doc/installation.md

@@ -1,195 +0,0 @@
-## Basic Install and Configuration
-
-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
-      :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 b" . org-roam-switch-to-buffer)
-               ("C-c n g" . org-roam-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-Or without `use-package`:
-
-```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

@@ -1,24 +0,0 @@
-## 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

@@ -1,61 +0,0 @@
-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/requirements.txt

@@ -1,2 +0,0 @@
-mkdocs-material==4.6.2
-pymdown-extensions==6.3

doc/roam_protocol.md

@@ -1,161 +0,0 @@
-## 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

@@ -1,119 +0,0 @@
-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

@@ -1,70 +0,0 @@
-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.
-
-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.
-
-## Activating Org-roam
-
-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)
-
-## 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/

makem.sh

@@ -155,7 +155,8 @@ function elisp-checkdoc-file {
     (when makem-checkdoc-errors-p
       (kill-emacs 1))))
 
-(setq checkdoc-spellcheck-documentation-flag t)
+(setq sentence-end-double-space nil)
+(setq checkdoc-spellcheck-documentation-flag nil)
 (makem-checkdoc-files-and-exit)
 EOF
     echo $file
@@ -325,7 +326,7 @@ function dirnames {
 
 function filter-files-exclude-default {
     # Filter out paths (STDIN) which should be excluded by default.
-    egrep -v "(/\.cask/|-autoloads.el|.dir-locals)"
+    egrep -v "(/\.cask/|-autoloads.el|-macs.el|.dir-locals)"
 }
 
 function filter-files-exclude-args {
@@ -694,7 +695,7 @@ function lint {
     lint-checkdoc
     lint-compile
     lint-declare
-    lint-indent
+    # lint-indent
     lint-package
     lint-regexps
 }

mkdocs.yml

@@ -1,40 +0,0 @@
-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
-- Installation: installation.md
-- Configuration: configuration.md
-- Anatomy of an Org-roam file: anatomy.md
-- The Templating System: templating.md
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.md
-- "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Roam Protocol": roam_protocol.md
-- "Appendix: Org Export": org_export.md
-markdown_extensions:
-  - admonition
-  - pymdownx.betterem:
-      smart_enable: all
-  - pymdownx.caret
-  - pymdownx.critic
-  - pymdownx.details
-  - pymdownx.mark
-  - pymdownx.smartsymbols
-  - pymdownx.superfences
-  - pymdownx.tasklist:
-      custom_checkbox: true
-  - pymdownx.tilde
-
-theme:
-  name: 'material'
-  palette:
-    primary: 'deep purple'
-    accent: 'deep purple'

org-roam-buffer.el

@@ -1,12 +1,12 @@
-;;; org-roam-buffer.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-buffer.el --- Metadata buffer -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -40,11 +40,15 @@
 (defvar org-return-follows-link)
 (defvar org-roam-backlinks-mode)
 (defvar org-roam-last-window)
+(defvar org-ref-cite-types) ;; in org-ref-core.el
+(defvar org-roam-mode)
+
 (declare-function org-roam-db--ensure-built   "org-roam-db")
 (declare-function org-roam--extract-ref       "org-roam")
 (declare-function org-roam--get-title-or-slug "org-roam")
 (declare-function org-roam--get-backlinks     "org-roam")
 (declare-function org-roam-backlinks-mode     "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
 (defcustom org-roam-buffer-position 'right
   "Position of `org-roam' buffer.
@@ -84,10 +88,10 @@ Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
   :type 'hook
   :group 'org-roam)
 
-(defcustom org-roam-buffer-no-delete-other-windows nil
-  "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
+(defcustom org-roam-buffer-window-parameters nil
+  "Additional window parameters for the `org-roam-buffer' side window.
+For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
+  :type '(alist)
   :group 'org-roam)
 
 (defvar org-roam-buffer--current nil
@@ -100,32 +104,44 @@ When non-nil, the window will not be closed when deleting other windows."
                        'font-lock-face
                        'org-document-title)))
 
+(defun org-roam-buffer--pluralize (string number)
+  "Conditionally pluralize STRING if NUMBER is above 1."
+  (let ((l (pcase number
+             ((pred (listp)) (length number))
+             ((pred (integerp)) number)
+             (wrong-type (signal 'wrong-type-argument
+                                 `((listp integerp)
+                                   ,wrong-type))))))
+    (concat string (when (> l 1) "s"))))
+
 (defun org-roam-buffer--insert-citelinks ()
   "Insert citation backlinks for the current buffer."
-  (if-let* ((roam-key (with-temp-buffer
+  (when-let ((org-ref-p (require 'org-ref nil t)) ;; Ensure that org-ref is present
+             (ref (cdr (with-temp-buffer
                         (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))
-            (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!")))
+                        (org-roam--extract-ref)))))
+    (if-let* ((key-backlinks (org-roam--get-backlinks ref))
+              (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
+        (progn
+          (insert (let ((l (length key-backlinks)))
+                    (format "\n\n* %d %s\n"
+                            l (org-roam-buffer--pluralize "Cite backlink" l))))
+          (dolist (group grouped-backlinks)
+            (let ((file-from (car group))
+                  (bls (cdr group)))
+              (insert (format "** [[file:%s][%s]]\n"
+                              file-from
+                              (org-roam--get-title-or-slug file-from)))
+              (dolist (backlink bls)
+                (pcase-let ((`(,file-from _ ,props) backlink))
+                  (insert (propertize
+                           (s-trim (s-replace "\n" " "
+                                              (plist-get props :content)))
+                           'help-echo "mouse-1: visit backlinked note"
+                           'file-from file-from
+                           'file-from-point (plist-get props :point)))
+                  (insert "\n\n"))))))
+      (insert "\n\n* No cite backlinks!"))))
 
 (defun org-roam-buffer--insert-backlinks ()
   "Insert the org-roam-buffer backlinks string for the current buffer."
@@ -133,8 +149,9 @@ When non-nil, the window will not be closed when deleting other windows."
             (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)))
+        (insert (let ((l (length backlinks)))
+                     (format "\n\n* %d %s\n"
+                             l (org-roam-buffer--pluralize "Backlink" l))))
         (dolist (group grouped-backlinks)
           (let ((file-from (car group))
                 (bls (cdr group)))
@@ -178,6 +195,7 @@ When non-nil, the window will not be closed when deleting other windows."
         (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
@@ -226,8 +244,7 @@ Valid states are 'visible, 'exists and 'none."
 
 (defun org-roam-buffer--get-create ()
   "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((window (get-buffer-window))
-        (position
+  (let ((position
          (if (member org-roam-buffer-position '(right left top bottom))
              org-roam-buffer-position
            (let ((text-quoting-style 'grave))
@@ -235,21 +252,24 @@ Valid states are 'visible, 'exists and 'none."
                     "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
                     org-roam-buffer-position))
            'right)))
-    (-> (get-buffer-create org-roam-buffer)
-        (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)))
+    (save-selected-window
+      (-> (get-buffer-create org-roam-buffer)
+          (display-buffer-in-side-window
+           `((side . ,position)
+             (window-parameters . ,org-roam-buffer-window-parameters)))
+          (select-window))
+      (pcase position
+        ((or 'right 'left)
+         (org-roam-buffer--set-width
+          (round (* (frame-width)  org-roam-buffer-width))))
+        ((or 'top  'bottom)
+         (org-roam-buffer--set-height
+          (round (* (frame-height) org-roam-buffer-height))))))))
 
 (defun org-roam-buffer-toggle-display ()
   "Toggle display of the `org-roam-buffer'."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (setq org-roam-last-window (get-buffer-window))
   (pcase (org-roam-buffer--visibility)
     ('visible (delete-window (get-buffer-window org-roam-buffer)))

org-roam-capture.el

@@ -1,12 +1,12 @@
-;;; org-roam-capture.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-capture.el --- Capture functionality -*- 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
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -33,21 +33,24 @@
 (require 'org-capture)
 (require 'dash)
 (require 's)
+(require 'cl-lib)
 
 ;; Declarations
 (defvar org-roam-encrypt-files)
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function  org-roam--get-title-path-completions "org-roam")
 (declare-function  org-roam--get-ref-path-completions   "org-roam")
 (declare-function  org-roam--file-path-from-id          "org-roam")
 (declare-function  org-roam--format-link                "org-roam")
 (declare-function  org-roam--title-to-slug              "org-roam")
+(declare-function  org-roam-mode                        "org-roam")
 (declare-function  org-roam-completion--completing-read "org-roam-completion")
 
 (defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
   "The default file name format for Org-roam templates.")
 
-(defvar org-roam-capture--header-default "#+TITLE: ${title}\n"
+(defvar org-roam-capture--header-default "#+title: ${title}\n"
   "The default capture header for Org-roam templates.")
 
 (defvar org-roam-capture--file-path nil
@@ -82,7 +85,7 @@ note with the given `ref'.")
   '(("d" "default" plain (function org-roam-capture--get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-${slug}"
-     :head "#+TITLE: ${title}\n"
+     :head "#+title: ${title}\n"
      :unnarrowed t))
   "Capture templates for Org-roam.
 The capture templates are an extension of
@@ -107,8 +110,8 @@ applies.
   '(("r" "ref" plain (function org-roam-capture--get-point)
      ""
      :file-name "${slug}"
-     :head "#+TITLE: ${title}
-#+ROAM_KEY: ${ref}\n"
+     :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'.")
@@ -129,9 +132,11 @@ Details on how to specify for the template is given in `org-roam-capture-templat
 (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)))
+             (and (eq (buffer-local-value 'major-mode buffer)
+                      'org-mode)
+                  (plist-get (buffer-local-value 'org-capture-current-plist buffer)
+                             :org-roam)))
+           (buffer-list)))
 
 (defun org-roam-capture--fill-template (str &optional info)
   "Expands the template STR, returning the string.
@@ -262,8 +267,9 @@ This function is used solely in Org-roam's capture templates: see
                      ('ref
                       (let ((completions (org-roam--get-ref-path-completions))
                             (ref (cdr (assoc 'ref org-roam-capture--info))))
-                        (or (cdr (assoc ref completions))
-                            (org-roam-capture--new-file))))
+                        (if-let ((pl (cdr (assoc ref completions))))
+                            (plist-get pl :path)
+                          (org-roam-capture--new-file))))
                      (_ (error "Invalid org-roam-capture-context")))))
     (org-roam-capture--expand-template)
     (org-roam-capture--put :file-path file-path)
@@ -277,23 +283,21 @@ This function is used solely in Org-roam's capture templates: see
 
 (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))))
+  (pcase template
+    (`(,_key ,_description) template)
+    (`(,key ,description ,type ,target . ,rest)
+     (let ((converted `(,key ,description ,type ,target
+                             ,(unless (keywordp (car rest)) (pop rest))))
+           org-roam-plist
+           options)
+       (while rest
+         (let* ((key (pop rest))
+                (val (pop rest))
+                (custom (member key org-roam-capture--template-keywords)))
+           (push val (if custom org-roam-plist options))
+           (push key (if custom org-roam-plist options))))
+       (append converted options `(:org-roam ,org-roam-plist))))
+    (_ (user-error "Invalid capture template format: %s" template))))
 
 (defun org-roam-capture--find-file-h ()
   "Opens the newly created template file.
@@ -311,12 +315,13 @@ Suitable for moving point."
   :group 'org-roam
   :type 'hook)
 
-(defun org-roam--capture (&optional goto keys)
+(defun org-roam-capture--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)))
+  (let ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates))
+        org-capture-templates-contexts)
     (when (= (length org-capture-templates) 1)
       (setq keys (caar org-capture-templates)))
     (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
@@ -327,17 +332,24 @@ GOTO and KEYS argument have the same functionality as
   "Launches an `org-capture' process for a new or existing note.
 This uses the templates defined at `org-roam-capture-templates'."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (when (org-roam-capture--in-process-p)
     (user-error "Nested Org-roam capture processes not supported"))
   (let* ((completions (org-roam--get-title-path-completions))
-         (title (org-roam-completion--completing-read "File: " completions))
-         (file-path (cdr (assoc title completions))))
+         (title-with-keys (org-roam-completion--completing-read "File: "
+                                                                completions))
+         (res (cdr (assoc title-with-keys completions)))
+         (title (or (plist-get res :title) title-with-keys))
+         (file-path (plist-get res :path)))
     (let ((org-roam-capture--info (list (cons 'title title)
                                         (cons 'slug (org-roam--title-to-slug title))
                                         (cons 'file file-path)))
           (org-roam-capture--context 'capture))
       (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-capture))
-      (org-roam--capture))))
+      (condition-case err
+          (org-roam-capture--capture)
+        (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
+                           (error-message-string err)))))))
 
 (provide 'org-roam-capture)
 

org-roam-compat.el

@@ -1,12 +1,12 @@
-;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t -*-
+;;; 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
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -71,17 +71,25 @@
   "org-roam 1.0.0")
 (define-obsolete-function-alias 'org-roam-graph-build 'org-roam-graph
   "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-find-index 'org-roam-jump-to-index
+  "org-roam 1.1.0")
+(define-obsolete-function-alias 'org-roam--pluralize 'org-roam-buffer--pluralize
+  "org-roam 1.1.0")
+(define-obsolete-function-alias 'org-roam--capture 'org-roam-capture--capture
+  "org-roam 1.1.0")
+(define-obsolete-function-alias 'org-roam-db--maybe-update 'org-roam-db--update-maybe
+  "org-roam 1.1.0")
+
+(when (version< (org-version) "9.3")
+  (defalias 'org-link-make-string 'org-make-link-string))
 
 ;;;; Variables
 (define-obsolete-variable-alias 'org-roam-graphviz-extra-options
   'org-roam-graph-extra-config "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-grapher-extra-options
   'org-roam-graph-extra-config "org-roam 1.0.0")
-(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-graph-node-shape
+  'org-roam-graph-node-extra-config "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam--db-connection
   'org-roam-db--connection "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam--current-buffer
@@ -90,6 +98,8 @@
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-date-filename-format
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
+(make-obsolete-variable 'org-roam-buffer-no-delete-other-windows
+  'org-roam-buffer-window-parameters "org-roam 1.1.1")
 
 (provide 'org-roam-compat)
 

org-roam-completion.el

@@ -1,12 +1,12 @@
-;;; org-roam-completion.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-completion.el --- Completion features -*- 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
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -47,11 +47,6 @@
           (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."
@@ -82,9 +77,7 @@ Return user choice."
                           :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))
+                          :caller 'org-roam--completing-read)
               (user-error "Please install ivy from \
 https://github.com/abo-abo/swiper")))
            ((eq org-roam-completion-system 'helm)
@@ -96,8 +89,7 @@ https://github.com/emacs-helm/helm"))
                             :candidates (mapcar #'car choices)
                             :filtered-candidate-transformer
                             (and (not require-match)
-                                 #'org-roam-completion--helm-candidate-transformer)
-                            :fuzzy-match org-roam-completion-fuzzy-match))
+                                 #'org-roam-completion--helm-candidate-transformer)))
                   (buf (concat "*org-roam "
                                (s-downcase (s-chop-suffix ":" (s-trim prompt)))
                                "*")))

org-roam-dailies.el

@@ -1,12 +1,12 @@
-;;; org-roam-dialies.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-dailies.el --- Daily notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,17 +34,20 @@
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
+(require 'org-roam-macs)
 
 (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>"))
+     :head "#+title: %<%Y-%m-%d>"))
   "Capture templates for daily notes in Org-roam.")
 
 ;; Declarations
+(defvar org-roam-mode)
 (declare-function org-roam--file-path-from-id "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
 (defun org-roam-dailies--file-for-time (time)
   "Create and find file for TIME."
@@ -52,24 +55,28 @@
         (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)))
+    (org-roam--with-template-error 'org-roam-dailies-capture-templates
+      (org-roam-capture--capture))))
 
 (defun org-roam-dailies-today ()
   "Create and find the daily note for today."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (current-time)))
 
 (defun org-roam-dailies-tomorrow (n)
   "Create and find the daily note for tomorrow.
 With numeric argument N, use N days in the future."
   (interactive "p")
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
 
 (defun org-roam-dailies-yesterday (n)
   "Create and find the file for yesterday.
 With numeric argument N, use N days in the past."
   (interactive "p")
-  (org-roam-tomorrow (- n)))
+  (unless org-roam-mode (org-roam-mode))
+  (org-roam-dailies-tomorrow (- n)))
 
 (defun org-roam-dailies-date ()
   "Create the file for any date using the calendar interface."
@@ -78,4 +85,5 @@ With numeric argument N, use N days in the past."
     (org-roam-dailies--file-for-time time)))
 
 (provide 'org-roam-dailies)
+
 ;;; org-roam-dailies.el ends here

org-roam-db.el

@@ -1,12 +1,12 @@
-;;; org-roam-db.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-db.el --- Org-roam database API -*- 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
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -33,21 +33,26 @@
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite)
+(require 'emacsql-sqlite3)
+(require 'seq)
 (require 'org-roam-macs)
 
 (defvar org-roam-directory)
 (defvar org-roam-verbose)
+(defvar org-roam-file-name)
 
-(declare-function org-roam--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")
+(declare-function org-roam--org-roam-file-p                "org-roam")
+(declare-function org-roam--extract-titles                 "org-roam")
+(declare-function org-roam--extract-ref                    "org-roam")
+(declare-function org-roam--extract-tags                   "org-roam")
+(declare-function org-roam--extract-headlines              "org-roam")
+(declare-function org-roam--extract-links                  "org-roam")
+(declare-function org-roam--list-all-files                 "org-roam")
+(declare-function org-roam-buffer--update-maybe            "org-roam-buffer")
 
 ;;;; Options
 (defcustom org-roam-db-location nil
-  "Location of the Org-roam database.
+  "The full path to file where the Org-roam database is stored.
 If this is non-nil, the Org-roam sqlite database is saved here.
 
 It is the user's responsibility to set this correctly, especially
@@ -55,11 +60,7 @@ 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))
+(defconst org-roam-db--version 6)
 
 (defvar org-roam-db--connection (make-hash-table :test #'equal)
   "Database connection to Org-roam database.")
@@ -67,8 +68,7 @@ when used with multiple Org-roam instances."
 ;;;; Core Functions
 (defun org-roam-db--get ()
   "Return the sqlite db file."
-  (interactive "P")
-  (or org-roam-db-location
+    (or org-roam-db-location
       (expand-file-name "org-roam.db" org-roam-directory)))
 
 (defun org-roam-db--get-connection ()
@@ -85,7 +85,7 @@ Performs a database upgrade when required."
     (let* ((db-file (org-roam-db--get))
            (init-db (not (file-exists-p db-file))))
       (make-directory (file-name-directory db-file) t)
-      (let ((conn (emacsql-sqlite db-file)))
+      (let ((conn (emacsql-sqlite3 db-file)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
         (puthash (file-truename org-roam-directory)
                  conn
@@ -93,7 +93,7 @@ Performs a database upgrade when required."
         (when init-db
           (org-roam-db--init conn))
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--maybe-update conn version)))
+               (version (org-roam-db--update-maybe conn version)))
           (cond
            ((> version org-roam-db--version)
             (emacsql-close conn)
@@ -119,7 +119,11 @@ SQL can be either the emacsql vector representation, or a string."
   '((files
      [(file :unique :primary-key)
       (hash :not-null)
-      (last-modified :not-null)])
+      (meta :not-null)])
+
+    (headlines
+     [(id :unique :primary-key)
+      (file :not-null)])
 
     (links
      [(from :not-null)
@@ -127,13 +131,18 @@ SQL can be either the emacsql vector representation, or a string."
       (type :not-null)
       (properties :not-null)])
 
+    (tags
+     [(file :unique :primary-key)
+      (tags)])
+
     (titles
      [(file :not-null)
       titles])
 
     (refs
      [(ref :unique :not-null)
-      (file :not-null)])))
+      (file :not-null)
+      (type :not-null)])))
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
@@ -142,16 +151,16 @@ SQL can be either the emacsql vector representation, or a string."
       (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)
+(defun org-roam-db--update-maybe (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))
+    (if (< version org-roam-db--version)
+        (progn
+          (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
+                                    version org-roam-db--version))
+          (org-roam-db-build-cache t))))
+  version)
 
 (defun org-roam-db--close (&optional db)
   "Closes the database connection for database DB.
@@ -185,32 +194,27 @@ the current `org-roam-directory'."
   "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])))
-
+    (dolist (table (mapcar #'car org-roam-db--table-schemata))
+      (org-roam-db-query `[:delete :from ,table]))))
 
 (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)))
+  (let ((file (file-truename (or filepath
+                                 (buffer-file-name (buffer-base-buffer))))))
+    (dolist (table (mapcar #'car org-roam-db--table-schemata))
+      (org-roam-db-query `[:delete :from ,table
+                           :where (= ,(if (eq table 'links) 'from 'file) $s1)]
+                         file))))
 
 ;;;;; Insertion
+(defun org-roam-db--insert-meta (file hash meta)
+  "Insert HASH and META for a FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into files
+    :values $v1]
+   (list (vector file hash meta))))
+
 (defun org-roam-db--insert-links (links)
   "Insert LINKS into the Org-roam cache."
   (org-roam-db-query
@@ -225,12 +229,27 @@ This is equivalent to removing the node from the graph."
     :values $v1]
    (list (vector file titles))))
 
+(defun org-roam-db--insert-headlines (headlines)
+  "Insert HEADLINES into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into headlines
+    :values $v1]
+   headlines))
+
+(defun org-roam-db--insert-tags (file tags)
+  "Insert TAGS for a FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into tags
+    :values $v1]
+   (list (vector file tags))))
+
 (defun org-roam-db--insert-ref (file ref)
   "Insert REF for FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into refs
-    :values $v1]
-   (list (vector ref file))))
+  (let ((key (cdr ref))
+        (type (car ref)))
+    (org-roam-db-query
+     [:insert :into refs :values $v1]
+     (list (vector key file type)))))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
@@ -253,12 +272,12 @@ This is equivalent to removing the node from the graph."
 If the file does not have any connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    connected_component(file) AS
@@ -270,16 +289,17 @@ If the file does not have any connections, nil is returned."
     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."
+  "Return all files connected to FILE in at most MAX-DISTANCE steps.
+This includes the file itself. If the file does not have any
+connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE \"type\" = '\"file\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    -- Links are traversed in a breadth-first search.  In order to calculate the
@@ -302,13 +322,36 @@ including the file itself.  If the file does not have any connections, nil is re
     files))
 
 ;;;;; Updating
+(defun org-roam-db--update-meta ()
+  "Update the metadata of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name)))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (secure-hash 'sha1 (current-buffer))))
+    (org-roam-db-query [:delete :from files
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-meta file hash (list :atime atime :mtime mtime))))
+
 (defun org-roam-db--update-titles ()
   "Update the title of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name))))
+  (let* ((file (file-truename (buffer-file-name)))
+         (title (org-roam--extract-titles)))
     (org-roam-db-query [:delete :from titles
                         :where (= file $s1)]
                        file)
-    (org-roam-db--insert-titles file (org-roam--extract-titles))))
+    (org-roam-db--insert-titles file title)))
+
+(defun org-roam-db--update-tags ()
+  "Update the tags of the current buffer into the cache."
+  (let ((file (file-truename (buffer-file-name)))
+        (tags (org-roam--extract-tags)))
+    (org-roam-db-query [:delete :from tags
+                        :where (= file $s1)]
+                       file)
+    (when tags
+      (org-roam-db--insert-tags file tags))))
 
 (defun org-roam-db--update-refs ()
   "Update the ref of the current buffer into the cache."
@@ -319,7 +362,7 @@ including the file itself.  If the file does not have any connections, nil is re
     (when-let ((ref (org-roam--extract-ref)))
       (org-roam-db--insert-ref file ref))))
 
-(defun org-roam-db--update-cache-links ()
+(defun org-roam-db--update-links ()
   "Update the file links of the current buffer in the cache."
   (let ((file (file-truename (buffer-file-name))))
     (org-roam-db-query [:delete :from links
@@ -328,53 +371,87 @@ including the file itself.  If the file does not have any connections, nil is re
     (when-let ((links (org-roam--extract-links)))
       (org-roam-db--insert-links links))))
 
+(defun org-roam-db--update-headlines ()
+  "Update the file headlines of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name))))
+    (org-roam-db-query [:delete :from headlines
+                        :where (= file $s1)]
+                       file)
+    (when-let ((headlines (org-roam--extract-headlines)))
+      (org-roam-db--insert-headlines headlines))))
+
 (defun org-roam-db--update-file (&optional file-path)
   "Update Org-roam cache for FILE-PATH."
-  (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)))))
+  (when (org-roam--org-roam-file-p file-path)
+    (let ((buf (or (and file-path
+                        (find-file-noselect file-path t))
+                   (current-buffer))))
+      (with-current-buffer buf
+        (save-excursion
+          (org-roam-db--update-meta)
+          (org-roam-db--update-tags)
+          (org-roam-db--update-titles)
+          (org-roam-db--update-refs)
+          (org-roam-db--update-headlines)
+          (org-roam-db--update-links)
+          (org-roam-buffer--update-maybe :redisplay t))))))
 
-;;;;; org-roam-db-build-cache
-(defun org-roam-db-build-cache ()
-  "Build the cache for `org-roam-directory'."
-  (interactive)
+(defun org-roam-db-build-cache (&optional force)
+  "Build the cache for `org-roam-directory'.
+If FORCE, force a rebuild of the cache from scratch."
+  (interactive "P")
+  (when force (delete-file (org-roam-db--get)))
   (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))
+  (let* ((org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         (time (current-time))
-         all-files all-links all-titles all-refs)
+         all-files all-headlines all-links all-titles all-refs all-tags)
+    ;; Two-step building
+    ;; First step: Rebuild files and headlines
     (dolist (file org-roam-files)
-      (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))
+      (let* ((attr (file-attributes file))
+             (atime (file-attribute-access-time attr))
+             (mtime (file-attribute-modification-time attr)))
+        (org-roam--with-temp-buffer file
+          (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+            (unless (string= (gethash file current-files)
+                             contents-hash)
+              (org-roam-db--clear-file file)
+              (push (vector file contents-hash (list :atime atime :mtime mtime))
+                    all-files)
+              (when-let (headlines (org-roam--extract-headlines file))
+                (push headlines all-headlines)))))))
     (when all-files
       (org-roam-db-query
        [:insert :into files
         :values $v1]
        all-files))
+    (when all-headlines
+      (org-roam-db-query
+       [:insert :into headlines
+        :values $v1]
+       all-headlines))
+    ;; Second step: Rebuild the rest
+    (dolist (file org-roam-files)
+      (org-roam--with-temp-buffer file
+        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
+          (unless (string= (gethash file current-files)
+                           contents-hash)
+            (when-let (links (org-roam--extract-links file))
+              (push links all-links))
+            (when-let (tags (org-roam--extract-tags file))
+              (push (vector file tags) all-tags))
+            (let ((titles (org-roam--extract-titles)))
+              (push (vector file titles)
+                    all-titles))
+            (when-let* ((ref (org-roam--extract-ref))
+                        (type (car ref))
+                        (key (cdr ref)))
+              (setq all-refs (cons (vector key file type) all-refs))))
+          (remhash file current-files))))
+    (dolist (file (hash-table-keys current-files))
+      ;; These files are no longer around, remove from cache...
+      (org-roam-db--clear-file file))
     (when all-links
       (org-roam-db-query
        [:insert :into links
@@ -385,23 +462,31 @@ including the file itself.  If the file does not have any connections, nil is re
        [:insert :into titles
         :values $v1]
        all-titles))
+    (when all-tags
+      (org-roam-db-query
+       [:insert :into tags
+        :values $v1]
+       all-tags))
     (when all-refs
       (org-roam-db-query
        [:insert :into refs
         :values $v1]
        all-refs))
     (let ((stats (list :files (length all-files)
+                       :headlines (length all-headlines)
                        :links (length all-links)
+                       :tags (length all-tags)
                        :titles (length all-titles)
                        :refs (length all-refs)
                        :deleted (length (hash-table-keys current-files)))))
-      (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)))
+      (org-roam-message "files: %s, headlines: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
+                        (plist-get stats :files)
+                        (plist-get stats :headlines)
+                        (plist-get stats :links)
+                        (plist-get stats :tags)
+                        (plist-get stats :titles)
+                        (plist-get stats :refs)
+                        (plist-get stats :deleted))
       stats)))
 
 (provide 'org-roam-db)

org-roam-dev.el

@@ -0,0 +1,39 @@
+;;; org-roam-dev.el --- Org-roam development code -mode -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides code for org-roam developers.
+;; It is intended to be loaded before editing org-roam source files.
+;; It ensures consistent application of various developer settings.
+;;
+;;; Code:
+(require 'emacsql)
+(emacsql-fix-vector-indentation)
+(provide 'org-roam-dev)
+
+;;; org-roam-dev.el ends here

org-roam-doctor.el

@@ -0,0 +1,308 @@
+;;; org-roam-doctor.el --- Linter for Org-roam files -*- coding: utf-8; lexical-binding: t; -*-
+;;
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+
+;;; Commentary:
+;;
+;; This library provides `org-roam-doctor', a utility for diagnosing and fixing
+;; Org-roam files. Running `org-roam-doctor' launches a list of checks defined
+;; by `org-roam-doctor--checkers'. Every checker is an instance of
+;; `org-roam-doctor-checker'.
+;;
+;; Each checker is given the Org parse tree (AST), and is expected to return a
+;; list of errors. The checker can also provide "actions" for auto-fixing errors
+;; (see `org-roam-doctor--remove-link' for an example).
+;;
+;; The UX experience is inspired by both org-lint and checkdoc, and their code
+;; is heavily referenced.
+;;
+;;; Code:
+;; Library Requires
+(require 'cl-lib)
+(require 'org)
+(require 'org-element)
+(require 's)
+(require 'dash)
+(require 'org-roam-macs)
+
+(declare-function org-roam-insert "org-roam")
+(declare-function org-roam--get-roam-buffers "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam--org-roam-file-p "org-roam")
+(declare-function org-roam--str-to-list "org-roam")
+(declare-function org-roam-mode "org-roam")
+
+(defvar org-roam-verbose)
+(defvar org-roam-mode)
+
+(cl-defstruct (org-roam-doctor-checker (:copier nil))
+  (name 'missing-checker-name)
+  (description "")
+  (actions nil))
+
+(defconst org-roam-doctor--checkers
+  (list
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-broken-links
+    :description "Fix broken links."
+    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
+               ("r" . ("Replace link" . org-roam-doctor--replace-link))
+               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-roam-props
+    :description "Check #+roam_* properties.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-tags
+    :description "Check #+roam_tags.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-alias
+    :description "Check #+roam_alias.")))
+
+(defconst org-roam-doctor--supported-roam-properties
+  '("roam_tags" "roam_alias" "roam_key")
+  "List of supported Org-roam properties.")
+
+(defun org-roam-doctor-check-roam-props (ast)
+  "Checker for detecting invalid #+roam_* properties.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (let ((key (org-element-property :key kw)))
+          (when (and (string-prefix-p "ROAM_" key t)
+                     (not (member (downcase key) org-roam-doctor--supported-roam-properties)))
+            (push
+             `(,(org-element-property :begin kw)
+               ,(concat "Possible mispelled key: "
+                        (prin1-to-string key)
+                        "\nOrg-roam supports the following keys: "
+                        (s-join ", " org-roam-doctor--supported-roam-properties)))
+             reports)))))
+    reports))
+
+(defun org-roam-doctor-check-tags (ast)
+  "Checker for detecting invalid #+roam_tags.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_tags" nil t)
+          (let ((tags (org-element-property :value kw)))
+            (condition-case nil
+                (org-roam--str-to-list tags)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse tags: "
+                           tags
+                           (when (s-contains? "," tags)
+                             "\nCheck that your tags are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-check-alias (ast)
+  "Checker for detecting invalid #+roam_alias.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
+          (let ((aliases (org-element-property :value kw)))
+            (condition-case nil
+              (org-roam--str-to-list aliases)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse aliases: "
+                           aliases
+                           (when (s-contains? "," aliases)
+                             "\nCheck that your aliases are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-broken-links (ast)
+  "Checker for detecting broken links.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'link
+      (lambda (l)
+        (when (equal "file" (org-element-property :type l))
+          (let ((file (org-element-property :path l)))
+            (or (file-exists-p file)
+                (file-remote-p file)
+                (push
+                 `(,(org-element-property :begin l)
+                   ,(format (if (org-element-lineage l '(link))
+                                "Link to non-existent image file \"%s\"\
+ in link description"
+                              "Link to non-existent local file \"%s\"")
+                            file))
+                 reports))))))
+    reports))
+
+(defun org-roam-doctor--check (buffer checkers)
+  "Check BUFFER for errors.
+CHECKERS is the list of checkers used."
+  (with-current-buffer buffer
+    (save-excursion
+      (goto-char (point-min))
+      (let* ((ast (org-element-parse-buffer))
+             (errors (sort (cl-mapcan
+                            (lambda (c)
+                              (mapcar
+                               (lambda (report)
+                                 (list (set-marker (make-marker) (car report))
+                                       (nth 1 report) c))
+                               (save-excursion
+                                 (funcall
+                                  (org-roam-doctor-checker-name c)
+                                  ast))))
+                            checkers)
+                           #'car-less-than-car)))
+        (dolist (e errors)
+          (pcase-let ((`(,m ,msg ,checker) e))
+            (switch-to-buffer buffer)
+            (goto-char m)
+            (org-reveal)
+            (undo-boundary)
+            (org-roam-doctor--resolve msg checker)
+            (set-marker m nil)))
+        errors))))
+
+;;; Actions
+(defun org-roam-doctor--recursive-edit ()
+  "Launch into a recursive edit."
+  (message "When you're done editing press C-M-c to continue.")
+  (recursive-edit))
+
+(defun org-roam-doctor--skip ()
+  "Skip the current error."
+  (org-roam-message "Skipping..."))
+
+(defun org-roam-doctor--replace-link ()
+  "Replace the current link with a new link."
+  (save-match-data
+    (unless (org-in-regexp org-link-bracket-re 1)
+      (user-error "No link at point"))
+    (let ((orig (buffer-string))
+          (p (point)))
+      (condition-case nil
+          (save-excursion
+            (replace-match "")
+            (org-roam-insert))
+        (quit (progn
+                (replace-buffer-contents orig)
+                (goto-char p)))))))
+
+(defun org-roam-doctor--replace-link-keep-label ()
+  "Replace the current link with a new link, keeping the current link's label."
+  (save-match-data
+    (unless (org-in-regexp org-link-bracket-re 1)
+      (user-error "No link at point"))
+    (let ((orig (buffer-string))
+          (p (point)))
+      (condition-case nil
+          (save-excursion
+            (let ((label (if (match-end 2)
+                             (match-string-no-properties 2)
+                           (org-link-unescape (match-string-no-properties 1)))))
+              (replace-match "")
+              (org-roam-insert nil nil label)))
+        (quit (progn
+                (replace-buffer-contents orig)
+                (goto-char p)))))))
+
+(defun org-roam-doctor--remove-link ()
+  "Unlink the text at point."
+  (unless (org-in-regexp org-link-bracket-re 1)
+    (user-error "No link at point"))
+  (save-excursion
+    (let ((label (if (match-end 2)
+                     (match-string-no-properties 2)
+                   (org-link-unescape (match-string-no-properties 1)))))
+      (delete-region (match-beginning 0) (match-end 0))
+      (insert label))))
+
+(defun org-roam-doctor--resolve (msg checker)
+  "Resolve an error.
+MSG is the error that was found, which is displayed in a help buffer.
+CHECKER is a org-roam-doctor checker instance."
+  (let ((actions (org-roam-doctor-checker-actions checker))
+        c)
+    (push '("e" . ("Edit" . org-roam-doctor--recursive-edit)) actions)
+    (push '("s" . ("Skip" . org-roam-doctor--skip)) actions)
+    (with-output-to-temp-buffer "*Org-roam-doctor Help*"
+      (mapc #'princ
+            (list "Error message:\n   " msg "\n\n"))
+      (dolist (action actions)
+        (princ (format "[%s]: %s\n"
+                       (car action)
+                       (cadr action))))
+      (princ "\n\n"))
+    (shrink-window-if-larger-than-buffer
+     (get-buffer-window "*Org-roam-doctor Help*"))
+    (message "Press key for command:")
+    (unwind-protect
+        (progn
+          (cl-loop
+           do (setq c (char-to-string (read-char-exclusive)))
+           until (assoc c actions)
+           do (message "Please enter a valid key for command:"))
+          (funcall (cddr (assoc c actions)))
+          (redisplay))
+      (when (get-buffer-window "*Org-roam-doctor Help*")
+        (delete-window (get-buffer-window "*Org-roam-doctor Help*"))
+        (kill-buffer "*Org-roam-doctor Help*")))))
+
+;;;###autoload
+(defun org-roam-doctor (&optional checkall)
+  "Perform a check on the current buffer to ensure cleanliness.
+If CHECKALL, run the check for all Org-roam files."
+  (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
+  (let ((files (if checkall
+                  (org-roam--list-all-files)
+                (unless (org-roam--org-roam-file-p)
+                  (user-error "Not in an org-roam file"))
+                `(,(buffer-file-name)))))
+    (org-roam-doctor-start files org-roam-doctor--checkers)))
+
+(defun org-roam-doctor-start (files checkers)
+  "Lint FILES using CHECKERS."
+  (save-window-excursion
+    (let ((existing-buffers (org-roam--get-roam-buffers)))
+      (dolist (f files)
+        (let ((buf (find-file-noselect f)))
+          (org-roam-doctor--check buf checkers)
+          (unless (memq buf existing-buffers)
+            (save-buffer buf)
+            (kill-buffer buf))))))
+  (org-roam-message "Linting completed."))
+
+(provide 'org-roam-doctor)
+
+;;; org-roam-doctor.el ends here

org-roam-graph.el

@@ -1,12 +1,12 @@
-;;; org-roam-graph.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -37,8 +37,10 @@
 
 ;;;; Declarations
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function org-roam--org-roam-file-p  "org-roam")
 (declare-function org-roam--path-to-slug     "org-roam")
+(declare-function org-roam-mode              "org-roam")
 
 ;;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
@@ -53,8 +55,8 @@ It may be one of the following:
           (const    :tag "view-file"))
   :group 'org-roam)
 
-(defcustom org-roam-graph-executable (executable-find "dot")
-  "Path to graphing executable."
+(defcustom org-roam-graph-executable "dot"
+  "Path to graphing executable, or its name."
   :type 'string
   :group 'org-roam)
 
@@ -65,14 +67,20 @@ Example:
   :type '(alist)
   :group 'org-roam)
 
-(defcustom org-roam-graph-node-extra-config nil
+(defcustom org-roam-graph-node-extra-config
+  '(("shape"      . "underline")
+    ("style"      . "rounded,filled")
+    ("fillcolor"  . "#EEEEEE")
+    ("color"      . "#C9C9C9")
+    ("fontcolor"  . "#111111"))
   "Extra options for graphviz nodes.
 Example:
  '((\"color\" . \"skyblue\"))"
   :type '(alist)
   :group 'org-roam)
 
-(defcustom org-roam-graph-edge-extra-config nil
+(defcustom org-roam-graph-edge-extra-config
+  '(("color" . "#333333"))
   "Extra options for graphviz edges.
 Example:
  '((\"dir\" . \"back\"))"
@@ -91,6 +99,19 @@ Example:
   :type 'number
   :group 'org-roam)
 
+(defcustom org-roam-graph-shorten-titles 'truncate
+  "Determines how long titles appear in graph nodes.
+Recognized values are the symbols `truncate' and `wrap', in which
+cases the title will be truncated or wrapped, respectively, if it
+is longer than `org-roam-graph-max-title-length'.
+
+All other values including nil will have no effect."
+  :type '(choice
+          (const :tag "truncate" truncate)
+          (const :tag "wrap" wrap)
+          (const :tag "no" nil))
+  :group 'org-roam)
+
 (defcustom org-roam-graph-exclude-matcher nil
   "Matcher for excluding nodes from the generated graph.
 Any nodes and links for file paths matching this string is
@@ -144,7 +165,7 @@ The Org-roam database titles table is read, to obtain the list of titles.
 The links table is then read to obtain all directed links, and formatted
 into a digraph."
   (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer
+  (org-roam--with-temp-buffer nil
     (let* ((nodes (org-roam-db-query node-query))
            (edges-query
             `[:with selected :as [:select [file] :from ,node-query]
@@ -154,7 +175,8 @@ into a digraph."
             `[: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"))
+                                                     (= links:type "cite")
+                                                     (= refs:type "cite"))
               :where (and (in file selected) (in from selected))])
            (edges       (org-roam-db-query edges-query))
            (edges-cites (org-roam-db-query edges-cites-query)))
@@ -163,7 +185,8 @@ into a digraph."
         (insert (org-roam-graph--dot-option option) ";\n"))
       (dolist (attribute '("node" "edge"))
         (insert (format " %s [%s];\n" attribute
-                        (mapconcat #'org-roam-graph--dot-option
+                        (mapconcat (lambda (var)
+                                     (org-roam-graph--dot-option var nil "\""))
                                    (symbol-value
                                     (intern (concat "org-roam-graph-" attribute "-extra-config")))
                                    ","))))
@@ -171,7 +194,10 @@ into a digraph."
         (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))
+               (shortened-title (pcase org-roam-graph-shorten-titles
+                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
+                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                  (_ title)))
                (node-properties
                 `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
                   ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
@@ -193,21 +219,31 @@ into a digraph."
       (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"
+(defun org-roam-graph--build (&optional node-query callback)
+  "Generate a graph showing the relations between nodes in NODE-QUERY.
+Execute CALLBACK when process exits successfully.
+CALLBACK is passed the graph file as its sole argument."
+  (unless (stringp org-roam-graph-executable)
+    (user-error "`org-roam-graph-executable' is not a string"))
+  (unless (executable-find org-roam-graph-executable)
+    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+                        "Please adjust `org-roam-graph-executable'")
                 org-roam-graph-executable))
   (let* ((node-query (or node-query
-                         `[:select [file titles]
-                           :from titles
+                         `[: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))
+    (org-roam-message "building graph")
+    (make-process
+     :name "*org-roam-graph--build-process*"
+     :buffer "*org-roam-graph--build-process*"
+     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-o" ,temp-graph)
+     :sentinel (when callback
+                 (lambda (process _event)
+                   (when (= 0 (process-exit-status process))
+                     (funcall callback temp-graph)))))))
 
 (defun org-roam-graph--open (file)
   "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
@@ -216,15 +252,16 @@ into a digraph."
      (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))))
+           (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)
+(defun org-roam-graph--build-connected-component (file &optional max-distance callback)
   "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
+CALLBACK is passed to `org-roam-graph--build'."
   (let* ((file (file-truename file))
          (files (or (if (and max-distance (>= max-distance 0))
                         (org-roam-db--links-with-max-distance file max-distance)
@@ -233,7 +270,7 @@ If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
          (query `[:select [file titles]
                   :from titles
                   :where (in file [,@files])]))
-    (org-roam-graph--build query)))
+    (org-roam-graph--build query callback)))
 
 ;;;; Commands
 ;;;###autoload
@@ -248,17 +285,17 @@ ARG may be any of the following values:
   - `\\[universal-argument]' -   build the graph for FILE.
   - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
   (interactive "P")
-  (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))
+  (unless org-roam-mode (org-roam-mode))
+  (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
+    (unless (or (not arg) (equal arg '(16)))
+      (unless file
+        (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
+      (unless (org-roam--org-roam-file-p file)
+        (user-error "\"%s\" is not an org-roam file" file)))
     (pcase arg
-      ('nil            (org-roam-graph--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))))
+      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
+      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
+      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
       ('(16)           (org-roam-graph--build node-query))
       ('-              (org-roam-graph--build-connected-component file))
       (_ (user-error "Unrecognized ARG: %s" arg)))))

org-roam-macs.el

@@ -1,12 +1,12 @@
-;;; org-roam-macs.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-macs.el --- Macros/utility functions -*- 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
+;; URL: https://github.com/org-roam/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"))
+;; Version: 1.2.0
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.0"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,22 +27,47 @@
 
 ;;; Commentary:
 ;;
-;; This library implements macros used throughout org-roam
+;; This library implements macros and utility functions used throughout
+;; org-roam.
 ;;
 ;;
 ;;; Code:
 ;;;; Library Requires
 
-(defmacro org-roam--with-temp-buffer (&rest body)
+(defvar org-roam-verbose)
+
+(defmacro org-roam--with-temp-buffer (file &rest body)
   "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'."
-  (declare (indent 0) (debug t))
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `org-roam-temp-file-name' to file and insert its contents."
+  (declare (indent 1) (debug t))
   (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
          (let ((org-roam-directory ,current-org-roam-directory))
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local org-roam-file-name ,file))
            ,@body)))))
 
+(defmacro org-roam--with-template-error (templates &rest body)
+  "Eval BODY, and point to TEMPLATES on error.
+Provides more informative error messages so that users know where
+to look.
+
+\(fn TEMPLATES BODY...)"
+  (declare (debug (form body)) (indent 1))
+  `(condition-case err
+       ,@body
+     (error (user-error "%s.  Please adjust `%s'"
+                        (error-message-string err)
+                        ,templates))))
+
+(defun org-roam-message (format-string &rest args)
+  "Pass FORMAT-STRING and ARGS to `message' when `org-roam-verbose' is t."
+  (when org-roam-verbose
+    (apply #'message `(,(concat "(org-roam) " format-string) ,@args))))
+
 (provide 'org-roam-macs)
 
 ;;; org-roam-macs.el ends here

org-roam-protocol.el

@@ -1,10 +1,10 @@
-;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t -*-
+;;; 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
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.2.0
 ;; Package-Requires: ((emacs "26.1") (org "9.3"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -62,8 +62,9 @@ It opens or creates a note with the given ref.
            (org-roam-capture--info decoded-alist)
            (template (cdr (assoc 'template decoded-alist))))
       (raise-frame)
-      (org-roam--capture nil template)
-      (message "Item captured.")))
+      (org-roam--with-template-error 'org-roam-capture-ref-templates
+        (org-roam-capture--capture nil template))
+      (org-roam-message "Item captured.")))
   nil)
 
 (defun org-roam-protocol-open-file (info)

tests/roam-files/alias.org

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

tests/roam-files/bar.org

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

tests/roam-files/base.org

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

tests/roam-files/foo.org

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

tests/roam-files/nested/bar.org

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

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

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

tests/roam-files/nested/foo.org

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

tests/roam-files/no-title.org

@@ -1,3 +1,5 @@
 no title in this file :O
 
 links to itself, with no title: [[file:no-title.org][no-title]]
+
+* Headline title

tests/roam-files/tags/no_tag.org

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

tests/roam-files/tags/tag.org

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

tests/roam-files/titles/aliases.org

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

tests/roam-files/titles/combination.org

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

tests/roam-files/titles/headline.org

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

tests/roam-files/titles/title.org

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

tests/roam-files/unlinked.org

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

tests/roam-files/web_ref.org

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

tests/test-org-roam.el

@@ -1,4 +1,4 @@
-;;; test-org-roam.el --- Tests for org-roam -*- lexical-binding: t; -*-
+;;; test-org-roam.el --- Tests for Org-roam -*- lexical-binding: t; -*-
 
 ;; Copyright (C) 2020 Jethro Kuan
 
@@ -19,291 +19,274 @@
 ;; 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)
+(defun test-org-roam--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)
+(defun test-org-roam--find-file (path)
   "PATH."
-  (let ((path (org-roam-test-abs-path path)))
+  (let ((path (test-org-roam--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"))
+(defvar test-org-roam-directory (file-truename (concat default-directory "tests/roam-files"))
   "Directory containing org-roam test org files.")
 
-(defun org-roam-test-init ()
+(defun test-org-roam--init ()
   "."
-  (org-roam-db--close)
-  (let ((original-dir org-roam-test-directory)
+  (let ((original-dir test-org-roam-directory)
         (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
     (copy-directory original-dir new-dir)
     (setq org-roam-directory new-dir)
-    (org-roam-mode +1)))
+    (org-roam-mode +1)
+    (sleep-for 2)))
+
+(defun test-org-roam--teardown ()
+  (org-roam-mode -1)
+  (delete-file (org-roam-db--get))
+  (org-roam-db--close))
+
+(describe "org-roam--str-to-list"
+  (it "nil"
+    (expect (org-roam--str-to-list nil)
+            :to-be
+            nil))
+  (it "\"multi word\" prop 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "prop \"multi word\" 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "errors on bad input"
+    (expect (org-roam--str-to-list 1)
+            :to-throw)
+    (expect (org-roam--str-to-list "\"hello")
+            :to-throw)))
+
+(describe "Title extraction"
+  :var (org-roam-title-sources)
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (cl-flet
+      ((test (fn file)
+             (let ((buf (find-file-noselect
+                         (test-org-roam--abs-path file))))
+               (with-current-buffer buf
+                 (funcall fn)))))
+    (it "extracts title from title property"
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/title.org")
+              :to-equal
+              '("Title"))
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/aliases.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/headline.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/combination.org")
+              :to-equal
+              '("TITLE PROP")))
+
+    (it "extracts alias"
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/title.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/aliases.org")
+              :to-equal
+              '("roam" "alias"))
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/headline.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/combination.org")
+              :to-equal
+              '("roam" "alias")))
+
+    (it "extracts headlines"
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/title.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/aliases.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/headline.org")
+              :to-equal
+              '("Headline"))
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/combination.org")
+              :to-equal
+              '("Headline")))
+
+    (describe "uses org-roam-title-sources correctly"
+      (it "'((title headline) alias)"
+        (expect (let ((org-roam-title-sources '((title headline) alias)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("TITLE PROP" "roam" "alias")))
+      (it "'((headline title) alias)"
+        (expect (let ((org-roam-title-sources '((headline title) alias)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("Headline" "roam" "alias")))
+      (it "'(headline alias title)"
+        (expect (let ((org-roam-title-sources '(headline alias title)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("Headline" "roam" "alias" "TITLE PROP"))))))
+
+(describe "Tag extraction"
+  :var (org-roam-tag-sources)
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (cl-flet
+      ((test (fn file)
+             (let* ((fname (test-org-roam--abs-path file))
+                    (buf (find-file-noselect fname)))
+               (with-current-buffer buf
+                 (funcall fn fname)))))
+    (it "extracts from prop"
+      (expect (test #'org-roam--extract-tags-prop
+                    "tags/tag.org")
+              :to-equal
+              '("t1" "t2 with space" "t3"))
+      (expect (test #'org-roam--extract-tags-prop
+                    "tags/no_tag.org")
+              :to-equal
+              nil))
+
+    (it "extracts from all directories"
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("nested" "deeply")))
+
+    (it "extracts from last directory"
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("deeply")))
+
+    (describe "uses org-roam-tag-sources correctly"
+      (it "'(prop)"
+        (expect (let ((org-roam-tag-sources '(prop)))
+                  (test #'org-roam--extract-tags
+                        "tags/tag.org"))
+                :to-equal
+                '("t1" "t2 with space" "t3")))
+      (it "'(prop all-directories)"
+        (expect (let ((org-roam-tag-sources '(prop all-directories)))
+                  (test #'org-roam--extract-tags
+                        "tags/tag.org"))
+                :to-equal
+                '("t1" "t2 with space" "t3" "tags"))))))
 
 ;;; Tests
-(describe "org-roam-db-build-cache"
-  (it "initializes correctly"
-    (org-roam-test-init)
-    (org-roam-db-build-cache)
+(xdescribe "org-roam-db-build-cache"
+  (before-each
+    (test-org-roam--init))
 
+  (after-each
+    (test-org-roam--teardown))
+
+  (it "initializes correctly"
     ;; Cache
     (expect (caar (org-roam-db-query [:select (funcall count) :from files])) :to-be 8)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links])) :to-be 5)
     (expect (caar (org-roam-db-query [:select (funcall count) :from titles])) :to-be 8)
     (expect (caar (org-roam-db-query [:select (funcall count) :from titles
-                                      :where titles :is-null])) :to-be 2)
+                                      :where titles :is-null])) :to-be 1)
     (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)
+                                     (test-org-roam--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)
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
 
     ;; Links -- File-to
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "nested/foo.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "unlinked.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
     ;; TODO Test titles
     (expect (org-roam-db-query [:select * :from titles])
             :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "alias.org")
+            (list (list (test-org-roam--abs-path "alias.org")
                         (list "t1" "a1" "a 2"))
-                  (list (org-roam-test-abs-path "bar.org")
+                  (list (test-org-roam--abs-path "bar.org")
                         (list "Bar"))
-                  (list (org-roam-test-abs-path "foo.org")
+                  (list (test-org-roam--abs-path "foo.org")
                         (list "Foo"))
-                  (list (org-roam-test-abs-path "nested/bar.org")
+                  (list (test-org-roam--abs-path "nested/bar.org")
                         (list "Nested Bar"))
-                  (list (org-roam-test-abs-path "nested/foo.org")
+                  (list (test-org-roam--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 (test-org-roam--abs-path "no-title.org")
+                        (list "Headline title"))
+                  (list (test-org-roam--abs-path "web_ref.org") nil)
+                  (list (test-org-roam--abs-path "unlinked.org")
                         (list "Unlinked"))))
 
     (expect (org-roam-db-query [:select * :from refs])
             :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
 
     ;; Expect rebuilds to be really quick (nothing changed)
     (expect (org-roam-db-build-cache)
             :to-equal
-            (list :files 0 :links 0 :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))))
+            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
 (provide 'test-org-roam)