(release): v1.1.1 (#668)

Lexically bind org-capture-templates-contexts to nil before calling org-capture
with org-roam-capture-templates. Otherwise, contexts may shadow
org-roam-templates which have same keys as org-capture-templates.

mentioned in #651

.dir-locals.el

@@ -0,0 +1,4 @@
+;;; Directory Local Variables
+;;; For more information see (info "(emacs) Directory Variables")
+
+((emacs-lisp-mode . ((eval . (require 'org-roam-dev)))))

.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/stale.yml

@@ -0,0 +1,19 @@
+name: Mark stale issues and pull requests
+
+on:
+  schedule:
+  - cron: "0 0 * * *"
+
+jobs:
+  stale:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/stale@v1
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-message: 'Stale issue message'
+        stale-pr-message: 'Stale pull request message'
+        stale-issue-label: 'no-issue-activity'
+        stale-pr-label: 'no-pr-activity'

.github/workflows/test.yml

@@ -29,7 +29,6 @@ on:
   push:
     branches:
       - master
-      - develop
 
 jobs:
   build:
@@ -38,7 +37,6 @@ jobs:
       fail-fast: false
       matrix:
         emacs_version:
-          - 26.3
           - snapshot
     steps:
     - uses: purcell/setup-emacs@master
@@ -57,7 +55,7 @@ jobs:
     # as failures, so linting and testing are run as separate steps.
 
     - name: Lint
-      continue-on-error: true
+      continue-on-error: false
       run: ./makem.sh -vv --sandbox $SANDBOX_DIR lint
 
     - name: Test

.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/

CHANGELOG.md

@@ -1,93 +1,200 @@
 # Changelog
 
+## 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_TAG` 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:
+
+1. The codebase has been modularized into separate files, to ease future maintenance and adding of new features (mainly by [@progfolio](https://github.com/progfolio)). Because of these changes, we had to rename many functions and variables: the old names are kept for backwards compatibility, but you are encouraged to use the new function names. You'll receive a warning when you're calling the function with its obsolete name.
+2. [@kljohann](https://github.com/kljohann) did some fantastic work on graph generation: allowing building images for connected components within the graph up to a specified distance
+3. We also started supporting `org-ref` natively: cite links now show up in both the graph and the org-roam buffer.
+
+In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer).
+
+### Breaking Changes
+
+- [#385](https://github.com/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/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/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/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)
+
+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/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/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)
+
+This is a pre-release before the push to MELPA. It contains large
+internal changes, with little user-facing changes. Most notably, the
+backing storage has been changed to a SQLite database, and a
+templating system using `org-capture` is introduced.
+
+### Breaking Changes
+
+- [#200](https://github.com/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/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/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]
+
 ## 0.1.2 (2020-02-21)
 
 ### Breaking Changes
-* [#143][gh-143] `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
-* [#103][gh-103] Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+- [#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][gh-145] `org-roam-show-graph`: Fallback to Emacs SVG viewer
-* [#141][gh-141] add variable `org-roam-new-file-directory` for new Org-roam files
-* [#138][gh-138] add `org-roam-switch-to-buffer`
-* [#124][gh-124], [#141][gh-141] Maintain cache consistency on file rename and delete
-* [#87][gh-87], [#90][gh-90] Support encrypted Org files
-* [#110][gh-110] Add prefix to `org-roam-insert`, for inserting titles down-cased
-* [#99][gh-99] Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+- [#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][gh-108] Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+- [#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][gh-86] Fix `org-roam--parse-content` incorrect `:to` computation for nested files
-* [#98][gh-98] Fix `org-roam--find-file` picking up temporary files
-* [#136][gh-136] Misc bugfixes
+
+- [#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][gh-122], [#128][gh-128] Improve performance of post-command-hook
-* [#92][gh-92], [#105][gh-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][gh-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][gh-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][gh-66], [#68][gh-68]: Improved the quality of the package in preparation of submission to MELPA
-* [#73][gh-73]: Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
-* [#69][gh-69], [#72][gh-72], [#75][gh-75]: Major cleanup and de-duplication of code
+
+- [#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][gh-67]: Fixed `org-roam--make-file` not creating files with extensions
-* [#71][gh-71], [#78][gh-78]: Fixed `org-roam-insert` not inserting correct paths
-* [#82][gh-82]: Fixed nested Org-roam files not being detected as part of Org-roam
 
-[gh-62]: https://github.com/jethrokuan/org-roam/pull/66
-[gh-66]: https://github.com/jethrokuan/org-roam/pull/66
-[gh-67]: https://github.com/jethrokuan/org-roam/pull/67
-[gh-68]: https://github.com/jethrokuan/org-roam/pull/68
-[gh-69]: https://github.com/jethrokuan/org-roam/pull/69
-[gh-71]: https://github.com/jethrokuan/org-roam/pull/71
-[gh-72]: https://github.com/jethrokuan/org-roam/pull/72
-[gh-73]: https://github.com/jethrokuan/org-roam/pull/73
-[gh-75]: https://github.com/jethrokuan/org-roam/pull/75
-[gh-78]: https://github.com/jethrokuan/org-roam/pull/78
-[gh-82]: https://github.com/jethrokuan/org-roam/pull/82
-[gh-86]: https://github.com/jethrokuan/org-roam/pull/86
-[gh-87]: https://github.com/jethrokuan/org-roam/pull/87
-[gh-90]: https://github.com/jethrokuan/org-roam/pull/90
-[gh-92]: https://github.com/jethrokuan/org-roam/pull/92
-[gh-98]: https://github.com/jethrokuan/org-roam/pull/98
-[gh-99]: https://github.com/jethrokuan/org-roam/pull/99
-[gh-103]: https://github.com/jethrokuan/org-roam/pull/103
-[gh-105]: https://github.com/jethrokuan/org-roam/pull/105
-[gh-108]: https://github.com/jethrokuan/org-roam/pull/108
-[gh-110]: https://github.com/jethrokuan/org-roam/pull/110
-[gh-122]: https://github.com/jethrokuan/org-roam/pull/122
-[gh-124]: https://github.com/jethrokuan/org-roam/pull/124
-[gh-128]: https://github.com/jethrokuan/org-roam/pull/128
-[gh-136]: https://github.com/jethrokuan/org-roam/pull/136
-[gh-138]: https://github.com/jethrokuan/org-roam/pull/138
-[gh-141]: https://github.com/jethrokuan/org-roam/pull/141
-[gh-142]: https://github.com/jethrokuan/org-roam/pull/142
-[gh-143]: https://github.com/jethrokuan/org-roam/pull/143
+- [#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)
- # End:
+<!-- Local Variables: -->
+<!-- eval: (auto-fill-mode -1) -->
+<!-- End: -->

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

@@ -1,50 +1,57 @@
 [![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
 
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
+Org-roam is a [Roam][roamresearch] replica built on top of the
+all-powerful [Org-mode][org].
 
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. Org-roam *enables* a note-taking workflow that
-is not fluid with vanilla Org-mode (more in [this blog
-post](https://blog.jethro.dev/posts/how_to_take_smart_notes_org/)).
+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.
 
+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.
 
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem.
+[@technovangelist](https://github.com/technovangelist/) has produced a video
+describing Org-roam and the concepts behind it:
 
-Visit [the documentation
-page](https://org-roam.readthedocs.io/en/latest/) for a tutorial and
-more links.
+[![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]**
+- **[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 backlink database is
-built asynchronously in the background, and is not noticeable to the
-end user. The graph is generated from the link structure, and can be
-used to navigate to the respective files.
+Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
+right) shows backlinks for the active Org-roam buffer (window on the
+left), as well as the surrounding content in the backlink file. The
+database is built once, and updated incrementally. The graph is
+generated from the link structure, and can be used to navigate to the
+respective files.
 
 ![img](doc/images/org-roam-graph.gif)
 
 ## Installation
 
-The recommended method is using use-package and straight, or a similar package manager.
+You can install `org-roam` using `package.el`:
+
+```
+M-x package-install RET org-roam RET
+```
+
+Here's a sample configuration with using `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
-      :after org
       :hook
       (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
       :custom
       (org-roam-directory "/path/to/org-files/")
       :bind (:map org-roam-mode-map
@@ -55,11 +62,17 @@ The recommended method is using use-package and straight, or a similar package m
               (("C-c n i" . org-roam-insert))))
 ```
 
-For more detailed installation instructions (including instructions for
-Spacemacs users), please see [the installation
-documentation](https://org-roam.readthedocs.io/en/develop/installation/).
+`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.
 
-## Knowledge Bases using Org-Roam
+For more detailed installation and configuration instructions (including for
+Doom and Spacemacs users), please see [the
+documentation][docs].
+
+## Knowledge Bases using Org-roam
 
 - [Jethro Kuan](https://braindump.jethro.dev/)
   ([Source](https://github.com/jethrokuan/braindump/tree/master/org))
@@ -82,3 +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.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/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

@@ -1,121 +0,0 @@
-To ensure that Org-roam remains manageable, the number of
-configuration options is deliberately kept small. However, we have
-attempted to accommodate as many usage styles as possible.
-
-In this section, we'll go over the main customization options
-available to Org-Roam. This section is *crucial*. We need to exploit
-the flexibility of Emacs, and mould our tools exactly to our liking.
-
-All of Org-roam's customization options can be viewed via `M-x
-customize-group org-roam`.
-
-## Setting the Org-roam Directory
-
-Perhaps the single most important variable to set is
-`org-roam-directory`. Set `org-roam-directory` to the folder
-containing all your Org files:
-
-```emacs-lisp
-(setq org-roam-directory "/path/to/org/")
-```
-
-Every Org file, at any level of nesting, within `/path/to/org/` is
-considered part of the Org-roam ecosystem.
-
-## Org-roam Buffer
-
-The Org-roam buffer defaults to popping up from the right. You may
-choose to set it to pop up from the left with `(setq
-org-roam-buffer-position 'left)`.
-
-The Org-roam buffer name can also be renamed: e.g. `(setq
-org-roam-buffer "*my-buffer-name*")`.
-
-The Org-roam buffer width is adjustable via `org-roam-buffer-width`.
-The value of `org-roam-buffer-width` set as a percentage of the total
-frame width. For example:
-
-```emacs-lisp
-(setq org-roam-buffer-width 0.4)
-```
-
-Will result in the Org-roam buffer taking up 40% of the screen width.
-I have found this to be a good number.
-
-## Org-roam Links
-
-By default, links are inserted with the title as the link description.
-This can make them hard to distinguish from external links. If you
-wish, you may choose add special indicators for Org-roam links by
-tweaking `org-roam-link-title-format`, for example:
-
-```emacs-lisp
-(setq org-roam-link-title-format "R:%s")
-```
-
-## Org-roam Files
-
-These customization options revolve around the Org files created and
-managed by Org-roam.
-
-### Automatically Creating Files Using Timestamp
-
-A common hassle is ensuring that files are uniquely named within the
-Org-roam directory. Org-roam's default workflow utilizes the title of
-Org files in all of its main commands (`org-roam-insert`,
-`org-roam-find-file`). Hence, having any unique file name is a decent
-option, and the default workflow uses the timestamp as the filename.
-
-The format of the filename is controlled by the function
-`org-roam-file-name-function`, which defaults to a format like
-`YYYYMMDDHHMMSS_title_here.org`. You may choose to define your own
-function to change this.
-
-If you wish to be prompted to change the file name on creation, set
-`org-roam-filename-noconfirm` to `nil`:
-
-```emacs-lisp
-(setq org-roam-filename-noconfirm nil)
-```
-
-It is then the user's responsibility to ensure that the file names are
-unique.
-
-### Autopopulating Titles
-
-The default workflow uses the title of the Org file in several
-commands. The title is specified via the `#+TITLE:` attribute,
-typically near the top of the file. The option
-`org-roam-autopopulate-title` defaults to `t`. When true, the title
-attribute is automatically inserted into the files created via
-Org-roam commands. Setting it to `nil` will disable this behaviour.
-
-### Encryption
-
-Encryption (via GPG) can be enabled for all new files by setting
-`org-roam-encrypt-files` to `t`. When enabled, new files are created
-with the .org.gpg extension and decryption are handled automatically
-by EasyPG. Note that this causes Emacs to ask for password when the
-cache is built (if you have an encrypted file in `org-roam-directory`)
-as well as each time a new file is created. It might be a good idea to
-cache the password in order to make this more managable.
-
-## Org-roam Graph Viewer
-
-Org-roam generates an SVG image using
-[Graphviz](https://graphviz.org/). To setup graph navigation, see the
-[Graph Setup](graph_setup.md) page.
-
-Org-roam tries its best to locate the Graphviz executable from your
-PATH, but if it fails to do so, you may set it manually:
-
-```
-(setq org-roam-graphviz-executable "/path/to/dot")
-```
-
-Org-roam also attempts to use Firefox (located on PATH) to view the
-SVG, you may choose to set it to any compatible program:
-
-```
-(setq org-roam-graph-viewer "/path/to/image-viewer")
-```

doc/ecosystem.md

@@ -1,126 +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-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.
-
-[deft]: https://jblevins.org/projects/deft/
-[notdeft]: https://github.com/hasu/notdeft
-[org-download]: https://github.com/abo-abo/org-download
-[mathpix-el]: https://github.com/jethrokuan/mathpix.el
-[org-noter]: https://github.com/weirdNox/org-noter
-[interleave]: https://github.com/rudolfochrist/interleave
-[org-ref]: https://github.com/jkitchin/org-ref

doc/graph_setup.md

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

doc/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 +1,3 @@
+<html>
+  <h1>--> <a href="manual/index.html">MANUAL HERE</a> <--</h1>
+</html>

doc/index.md

@@ -1,41 +0,0 @@
-![org-roam][org-roam-intro-image]
-
-## What is Org-Roam?
-
-Org-roam is a rudimentary [Roam][roamresearch] replica built around
-the all-powerful [Org-mode][org]. 
-
-Like Roam, Org-roam offers a powerful and effortless non-hierarchical
-note-taking approach. With Org-roam, notes flow naturally, making
-note-taking fun and easy. To understand more about Roam, I recommend
-the following links:
-
--   [Building a second brain in
-    Roam](https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might)
--   [Roam: Why I Love It and How I Use
-    It](https://www.nateliason.com/blog/roam)
-
-The goal of the project is to implement core features of Roam around
-Org-mode, and eventually introduce features enabled by the Emacs
-ecosystem. 
-
-## Why build Org-Roam?
-
-With Org-roam, you:
-
-1. Never have to leave Emacs.
-2. Can leverage all the powerful features of Org-mode: LaTeX, tables,
-   and the whole to-do ecosystem (org-agenda etc.)
-3. Be in full control your second brain, and access it offline. Never
-   share your data with anyone
-
-There are several packages that are similar to Org-roam, see the
-[Comparison](comparison.md) page for a detailed comparison.
-
-## Project Status
-
-As of February 2020, it is in a very early stage of development. 
-
-[org-roam-intro-image]: images/org-roam-intro.png
-[roamresearch]: https://www.roamresearch.com/
-[org]: https://orgmode.org/

doc/installation.md

@@ -1,93 +0,0 @@
-## Installation
-
-The recommended method is using [use-package][use-package] and
-[straight][straight], or a similar package manager.
-
-```
-(use-package org-roam
-      :after org
-      :hook 
-      (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
-      :custom
-      (org-roam-directory "/path/to/org-files/")
-      :bind (:map org-roam-mode-map
-              (("C-c n l" . org-roam)
-               ("C-c n f" . org-roam-find-file)
-               ("C-c n g" . org-roam-show-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-If not using package.el, you can also clone it into your Emacs
-directory and add it to your load path:
-
-```
-git clone https://github.com/jethrokuan/org-roam/ ~/.emacs.d/elisp/org-roam
-```
-
-```
-(use-package org-roam
-      :after org
-      :load-path "elisp/"
-      :hook 
-      (after-init . org-roam-mode)
-      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
-      :custom
-      (org-roam-directory "/path/to/org-files/")
-      :bind (:map org-roam-mode-map
-              (("C-c n l" . org-roam)
-               ("C-c n f" . org-roam-find-file)
-               ("C-c n g" . org-roam-show-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-Or without use-package:
-
-```
-(add-to-list 'load-path "./elisp")
-(require 'org-roam)
-```
-
-There are a number of important configuration options, that greatly
-affect the Roam workflow. Do look through them at the
-[Configuration](configuration.md) page.
-
-[use-package]: https://github.com/jwiegley/use-package
-[straight]: https://github.com/raxod502/straight.el
-
-## Spacemacs
-If you are using Spacemacs, you can easily install org-roam by creating a simple layer that wraps org-roam. Paste the following into a new file `/.emacs.d/private/org-roam/packages.el`.
-```
-(defconst org-roam-packages
-  '((org-roam :location
-        (recipe :fetcher github :repo "jethrokuan/org-roam" :branch "develop"))))
-
-(defun org-roam/init-org-roam ()
-    (use-package org-roam
-        :after org
-        :hook
-        (after-init . org-roam-mode)
-        :custom
-        (org-roam-directory "/path/to/org-files/")
-        :init
-        (progn
-          (spacemacs/declare-prefix "ar" "org-roam")
-          (spacemacs/set-leader-keys
-            "arl" 'org-roam
-            "art" 'org-roam-today
-            "arf" 'org-roam-find-file
-            "arg" 'org-roam-show-graph)
-
-          (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
-          (spacemacs/set-leader-keys-for-major-mode 'org-mode
-            "rl" 'org-roam
-            "rt" 'org-roam-today
-            "rb" 'org-roam-switch-to-buffer
-            "rf" 'org-roam-find-file
-            "ri" 'org-roam-insert
-            "rg" 'org-roam-show-graph))))
-```
-
-Next, append `org-roam` to the `dotspacemacs-configuration-layers` list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or restart Emacs to load `org-roam`. It's functions are available under the prefix `SPC a r` and `, r` when visiting an org-mode buffer. 

doc/notetaking_workflow.md

@@ -1,20 +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]
-
-## What to Do With Your Notes
-- [How to Use Roam to Outline a New Article in Under 20 Minutes][2]
-
-[1]: https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes?ac=1&from_search=true&qid=6L8iEE1FIA&rank=1
-[2]: https://www.youtube.com/watch?v=RvWic15iXjk
-[3]: https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1
-[4]: https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might
-[5]: https://www.nateliason.com/blog/roam
-[6]: https://twitter.com/adam_keesling/status/1196864424725774336?s=20
-[7]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

doc/org-roam.org

@@ -0,0 +1,974 @@
+#+TITLE: Org-roam User Manual
+:PREAMBLE:
+#+AUTHOR: Jethro Kuan
+#+EMAIL: jethrokuan95@gmail.com
+#+DATE: 2020-2020
+#+LANGUAGE: en
+
+#+TEXINFO_DIR_CATEGORY: Emacs
+#+TEXINFO_DIR_TITLE: Org-roam: (org-roam).
+#+TEXINFO_DIR_DESC: Rudimentary Roam Replica for Emacs.
+#+SUBTITLE: for version 1.1.1
+
+#+OPTIONS: H:4 num:3 toc:2 creator:t
+#+PROPERTY: header-args :eval never
+#+TEXINFO: @noindent
+
+This manual is for Org-roam version 1.1.1.
+
+#+BEGIN_QUOTE
+Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+You can redistribute this document and/or modify it under the terms of the GNU
+General Public License as published by the Free Software Foundation, either
+version 3 of the License, or (at your option) any later version.
+
+This document 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.
+#+END_QUOTE
+
+:END:
+
+* Introduction
+
+Org-roam is a [[https://roamresearch.com/][Roam Research]] replica built around the
+all-powerful [[https://orgmode.org/][Org-mode]].
+
+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
+[[*Note-taking Workflows][Note-taking Workflows]].
+
+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.
+
+Org-roam provides several benefits over other tooling:
+
+- Privacy and Security :: Edit your personal wiki completely offline, entirely in your control. Encrypt your notes with GPG.
+- Longevity of Plain Text :: 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.
+- Leverages 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.
+- Built on Emacs :: 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.
+* Installation
+** _ :ignore:
+Org-roam can be installed using Emacs' package manager or manually from its development repository.
+
+** Installing from MELPA
+
+Org-roam is available from Melpa and Melpa-Stable. If you haven't used Emacs' package manager before, you may familiarize yourself with it by reading the documentation in the Emacs manual, see info:emacs#Packages. Then, add one of the archives to =package-archives=:
+
+- To use Melpa:
+
+#+BEGIN_SRC emacs-lisp
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa" . "http://melpa.org/packages/") t)
+#+END_SRC
+
+- To use Melpa-Stable:
+
+#+BEGIN_SRC emacs-lisp
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa-stable" . "http://stable.melpa.org/packages/") t)
+#+END_SRC
+
+Once you have added your preferred archive, you need to update the
+local package list using:
+
+#+BEGIN_EXAMPLE
+  M-x package-refresh-contents RET
+#+END_EXAMPLE
+
+Once you have done that, you can install Org-roam and its dependencies
+using:
+
+#+BEGIN_EXAMPLE
+  M-x package-install RET org-roam RET
+#+END_EXAMPLE
+
+Now see [[*Post-Installation Tasks][Post-Installation Tasks]].
+
+** TODO Installing from the Git Repository
+
+** TODO Post-Installation Tasks
+
+* Getting Started
+
+This short tutorial describes the essential commands used in Org-roam, to help
+you get started.
+
+First, it is important to understand how Org-roam was designed. Org-roam was
+built to support a workflow that was not possible with vanilla Org-mode. This
+flow is modelled after the [[https://zettelkasten.de/][Zettelkasten Method]], and many of [[https://roamresearch.com][Roam Research's]]
+workflows. Org-roam does not magically make note-taking better -- this often
+requires a radical change in your current note-taking workflow. To understand
+more about the methods and madness, see [[*Note-taking Workflows][Note-taking Workflows]].
+
+To begin using Org-roam, one should set the =org-roam-directory= to the directory
+containing your notes. For this tutorial, create an empty directory, and set the
+=org-roam-directory=:
+
+#+BEGIN_SRC emacs-lisp
+(make-directory "~/org-roam")
+(setq org-roam-directory "~/org-roam")
+#+END_SRC
+
+We encourage using a flat hierarchy for storing notes, but some prefer using
+folders for storing specific kinds of notes (e.g. websites, papers). This is
+fine; Org-roam searches recursively within =org-roam-directory= for any notes.
+Instead of relying on the file hierarchy for any form of categorization, we
+solely rely on links between files to establish connections between notes.
+
+Next, we need to enable the global minor mode =org-roam-mode=. This sets up Emacs
+with several hooks, builds a cache and keeps it consistent. We recommend
+starting =org-roam-mode= on startup:
+
+#+BEGIN_SRC emacs-lisp
+(add-hook 'after-init-hook 'org-roam-mode)
+#+END_SRC
+
+To build the cache manually, one can run =M-x org-roam-db-build-cache=. The cache
+is a sqlite database named =org-roam.db=, which defaults to residing in the root
+=org-roam-directory=. Cache builds may take a while the first time, but is often
+instantaneous in subsequent runs.
+
+Let us now create our first note. Call =M-x org-roam-find-file=. This shows a list
+of titles for notes that reside in =org-roam-directory=. It should show nothing
+right now, since there are no notes in the directory. Entering the title of the
+note you wish to create, and pressing =RET= should begin the note creation
+process. This process uses =org-capture='s templating system, and can be freely
+customized (see [[*The Templating System][The Templating System]]). Using the default template, pressing =C-c
+C-c= finishes the note capture. Running =M-x org-roam-find-file= again should show
+the note you have created, and selecting that entry will bring you to that note.
+
+The crux of Org-roam is making it easy to create notes, and link them together.
+To link notes together, we call =M-x org-roam-insert=. This brings up a prompt
+with a list of title for existing notes. Selecting an existing entry will create
+and insert a link to the current file. Entering a non-existent title will create
+a new note with that title. Good usage of Org-roam requires liberally linking
+files: this facilitates building up a dense knowledge graph of inter-connected
+notes.
+
+Org-roam provides an interface to view backlinks. It shows backlinks for the
+currently active Org-roam note, along with some surrounding context. To toggle
+the visibility of this buffer, call =M-x org-roam=.
+
+For a visual representation of the notes and their connections, Org-roam also
+provides graphing capabilities, using Graphviz. It generates graphs with notes
+as nodes, and links between them as edges. The generated graph can be used to
+navigate to the files, but this requires some additional setup (see [[*Roam Protocol][Roam
+Protocol]]).
+
+* Anatomy of an Org-roam File
+
+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.
+
+** Titles
+
+To easily find a note, a title needs to be prescribed to a note. A note can have
+many titles: this allows a note to be referred to by different names, which is
+especially useful for topics or concepts with acronyms. For example, for a note
+like "World War 2", it may be desirable to also refer to it using the acronym
+"WWII".
+
+Org-roam calls =org-roam--extract-titles= to extract titles. It uses the
+variable =org-roam-title-sources=, to control how the titles are extracted. The
+title extraction methods supported are:
+
+1. ='title=: This extracts the title using the file =#+TITLE= property
+2. ='headline=: This extracts the title from the first headline in the Org file
+3. ='alias=: This extracts a list of titles using the =#ROAM_ALIAS= property.
+   The aliases are space-delimited, and can be multi-worded using quotes
+
+Take for example the following org file:
+
+#+BEGIN_SRC org
+  #+TITLE: World War 2
+  #+ROAM_ALIAS: "WWII" "World War II"
+
+  * Headline
+#+END_SRC
+
+| Method      | Titles                   |
+|-------------+--------------------------|
+| ='title=    | '("World War 2")         |
+| ='headline= | '("Headline")            |
+| ='alias=    | '("WWII" "World War II") |
+
+One can freely control which extraction methods to use by customizing
+=org-roam-title-sources=: see the doc-string for the variable for more
+information. If all methods of title extraction return no results, the file-name
+is used in place of the titles for completions.
+
+If you wish to add your own title extraction method, you may push a symbol
+='foo= into =org-roam-title-sources=, and define a
+=org-roam--extract-titles-foo= which accepts no arguments. See
+=org-roam--extract-titles-title= for an example.
+
+** Tags
+
+Tags are used as meta-data for files: they facilitate interactions with notes
+where titles are insufficient. For example, tags allow for categorization of
+notes: differentiating between bibliographical and structure notes during interactive commands.
+
+Org-roam calls =org-roam--extract-tags= to extract tags from files. It uses the
+variable =org-roam-tag-sources=, to control how tags are extracted. The tag
+extraction methods supported are:
+
+1. ='prop=: This extracts tags from the =#+ROAM_TAGS= property. Tags are space delimited, and can be multi-word using double quotes.
+2. ='all-directories=: All sub-directories relative to =org-roam-directory= are
+   extracted as tags. That is, if a file is located at relative path
+   =foo/bar/file.org=, the file will have tags =foo= and =bar=.
+3. ='last-directory=: Extracts the last directory relative to
+   =org-roam-directory= as the tag. That is, if a file is located at relative
+   path =foo/bar/file.org=, the file will have tag =bar=.
+
+By default, only the ='prop= extraction method is enabled. To enable the other
+extraction methods, you may modify =org-roam-tag-sources=:
+
+#+BEGIN_SRC emacs-lisp
+(setq org-roam-tag-sources '(prop last-directory))
+#+END_SRC
+
+If you wish to add your own tag extraction method, you may push a symbol ='foo=
+into =org-roam-tag-sources=, and define a =org-roam--extract-tags-foo= which
+accepts the absolute file path as its argument. See
+=org-roam--extract-tags-prop= for an example.
+
+** 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:
+
+#+BEGIN_SRC org
+  #+TITLE: Google
+  #+ROAM_KEY: https://www.google.com/
+#+END_SRC
+
+These keys come in useful for when taking website notes, using the
+=roam-ref= protocol (see [[*Roam Protocol][Roam Protocol]]).
+
+Alternatively, add a ref for notes for a specific paper, using its
+[[https://github.com/jkitchin/org-ref][org-ref]] citation key:
+
+#+BEGIN_SRC org
+  #+TITLE: Neural Ordinary Differential Equations
+  #+ROAM_KEY: cite:chen18_neural_ordin_differ_equat
+#+END_SRC
+
+The backlinks buffer will show any cites of this key: e.g.
+
+#+CAPTION: org-ref-citelink
+[[file:images/org-ref-citelink.png]]
+* The Templating System
+
+Rather than creating blank files on =org-roam-insert= and =org-roam-find-file=, it
+may be desirable to prefill the file with templated 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. Fortunately, Org ships with a
+powerful one: =org-capture=. However, org-capture was not designed for such use.
+Org-roam abuses =org-capture=, extending its syntax. To first understand how
+org-roam's templating system works, it may be useful to look into basic usage of
+=org-capture=.
+
+Org-roam's templates can be customized by modifying the variable
+=org-roam-capture-templates=.
+
+** Template Walkthrough
+
+To demonstrate the additions made to org-capture templates. Here, we walkthrough
+the default template, reproduced below.
+
+#+BEGIN_SRC emacs-lisp
+  ("d" "default" plain (function org-roam--capture-get-point)
+       "%?"
+       :file-name "%<%Y%m%d%H%M%S>-${slug}"
+       :head "#+TITLE: ${title}\n"
+       :unnarrowed t)
+#+END_SRC
+
+1. The template has short key ="d"=. If you have only one template,
+   org-roam automatically chooses this template for you.
+2. The template is given a description of ="default"=.
+3. =plain= text is inserted. Other options include Org headings via
+   =entry=.
+4. =(function org-roam--capture-get-point)= should not be changed.
+5. ="%?"= is the template inserted on each call to =org-roam-capture--capture=.
+   This template means don't insert any content, but place the cursor
+   here.
+6. =:file-name= is the file-name template for a new note, if it doesn't
+   yet exist. This creates a file at path that looks like
+   =/path/to/org-roam-directory/20200213032037-foo.org=.
+7. =:head= contains the initial template to be inserted (once only), at
+   the beginning of the file. Here, the title global attribute is
+   inserted.
+8. =:unnarrowed t= tells org-capture to show the contents for the whole
+   file, rather than narrowing to just the entry.
+
+Other options you may want to learn about include =:immediate-finish=.
+
+** Org-roam Template Expansion
+
+Org-roam's template definitions also extend org-capture's template syntax, to
+allow prefilling of strings. We have seen a glimpse of this in [[*Template Walkthrough][Template
+Walkthrough]].
+
+In org-roam templates, the =${var}= syntax allows for the expansion of
+variables, stored in =org-roam-capture--info=. For example, during
+=org-roam-insert=, the user is prompted for a title. Upon entering a
+non-existent title, the =title= key in =org-roam-capture--info= is set to the
+provided title. =${title}= is then expanded into the provided title during the
+org-capture process. Any variables that do not contain strings, are prompted for
+values using =completing-read=.
+
+After doing this expansion, the org-capture's template expansion system
+is used to fill up the rest of the template. You may read up more on
+this on [[https://orgmode.org/manual/Template-expansion.html#Template-expansion][org-capture's documentation page]].
+
+To illustrate this dual expansion process, take for example the template string:
+="%<%Y%m%d%H%M%S>-${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.
+
+#+BEGIN_SRC 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)
+#+END_SRC
+
+* Concepts and Configuration
+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=.
+
+** Directories and Files
+
+This section concerns the placement and creation of files.
+
+- Variable: org-roam-directory
+
+  This is the default path to Org-roam files. All Org files, at any level of
+  nesting, are considered part of the Org-roam.
+
+- Variable: org-roam-db-location
+
+  Location of the Org-roam database. If this is non-nil, the Org-roam sqlite
+  database is saved here.
+
+  It is the user’s responsibility to set this correctly, especially when used
+  with multiple Org-roam instances.
+
+** The Org-roam Buffer
+
+The Org-roam buffer displays backlinks for the currently active Org-roam note.
+
+- User Option: org-roam-buffer
+
+  The name of the org-roam buffer. Defaults to =*org-roam*=.
+
+- User Option: org-roam-buffer-position
+
+  The position of the Org-roam buffer side window. Valid values are ='left=,
+  ='right=, ='top=, ='bottom=.
+
+- User Option: org-roam-buffer-width
+
+  Width of =org-roam-buffer=. Has an effect only if =org-roam-buffer-position= is
+  ='left= or ='right=.
+
+- User Option: org-roam-buffer-height
+
+  Height of =org-roam-buffer=. Has an effect only if =org-roam-buffer-position= is
+  ='top= or ='bottom=.
+
+- User Option: org-roam-buffer-no-delete-other-windows
+
+  The =no-delete-window= parameter for the org-roam buffer. Setting it to ='t= prevents the window from being deleted when calling =delete-other-windows=.
+
+** Org-roam Links
+
+Org-roam links are regular =file:= links in Org-mode. By default, links are
+inserted with the title as the link description with =org-roam-insert=.
+
+- User Option: org-roam-link-title-format
+
+  To distinguish between org-roam links and regular links, one may choose to use
+  special indicators for Org-roam links. Defaults to ="%s"=.
+
+  If your version of Org is at least =9.2=, consider styling the link differently,
+  by customizing the =org-roam-link=, and =org-roam-link-current= faces.
+
+** Org-roam Files
+
+Org-roam files are created and prefilled using Org-roam's templating
+system. The templating system is customizable (see [[*The Templating System][The Templating System]]).
+
+* Navigating Around
+
+** Index File
+
+As your collection grows, you might want to create an index where you keep links
+to your main files.
+
+In Org-roam, you can define the path to your index file by setting
+=org-roam-index-file=.
+
+- Variable: org-roam-index-file
+
+  Path to the Org-roam index file.
+
+  The path can be a string or a function. If it is a string, it should be the
+  path (absolute or relative to =org-roam-directory=) to the index file. If it
+  is is a function, the function should return the path to the index file.
+  Otherwise, the index is assumed to be a note in =org-roam-index= whose
+  title is ="Index"=.
+
+- Function: org-roam-find-index
+
+  Opens the Index file in the current =org-roam-directory=.
+
+* Encryption
+
+One may wish to keep private, encrypted files. Org-roam supports encryption (via
+GPG), which 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.
+
+- Variable: org-roam-encrypt-files
+
+  Whether to encrypt new files.  If true, create files with .org.gpg extension.
+
+* Graphing
+
+Org-roam provides graphing capabilities to explore interconnections between
+notes. This is done by performing SQL queries and generating images using
+[[https://graphviz.org/][Graphviz]]. The graph can also be navigated: see [[*Roam Protocol][Roam Protocol]].
+
+The entry point to graph creation is =org-roam-graph=.
+
+- Function: org-roam-graph & optional arg file node-query
+
+  Build and possibly display a graph for FILE from NODE-QUERY.
+  If FILE is nil, default to current buffer’s file name.
+  ARG may be any of the following values:
+
+  - =nil=       show the graph.
+  - =C-u=       show the graph for FILE.
+  - =C-u N=     show the graph for FILE limiting nodes to N steps.
+  - =C-u C-u=   build the graph.
+  - =C-u -=     build the graph for FILE.
+  - =C-u -N=    build the graph for FILE limiting nodes to N steps.
+
+- User Option: org-roam-graph-executable
+
+  Path to the graphing executable (in this case, Graphviz). Set this if Org-roam is unable to find the Graphviz executable on your system.
+
+  You may also choose to use =neato= in place of =dot=, which generates a more
+  compact graph layout.
+
+- User Option: org-roam-graph-viewer
+
+  Org-roam defaults to using Firefox (located on PATH) to view the SVG, but you may choose to set it to:
+
+  1. A string, which is a path to the program used
+  2. a function accepting a single argument: the graph file path.
+
+  =nil= uses =view-file= to view the graph.
+
+** Graph Options
+
+Graphviz provides many options for customizing the graph output, and Org-roam supports some of them. See https://graphviz.gitlab.io/_pages/doc/info/attrs.html for customizable options.
+
+- User Option: org-roam-graph-extra-config
+
+  Extra options passed to graphviz for the digraph (The "G" attributes).
+  Example: ='=(("rankdir" . "LR"))=
+
+- User Option: org-roam-graph-node-extra-config
+
+  Extra options for nodes in the graphviz output (The "N" attributes).
+  Example: ='(("color" . "skyblue"))=
+
+- User Option: org-roam-graph-edge-extra-config
+
+  Extra options for edges in the graphviz output (The "E" attributes).
+  Example: ='(("dir" . "back"))=
+
+- User Option: org-roam-graph-edge-cites-extra-config
+
+  Extra options for citation edges in the graphviz output.
+  Example: ='(("color" . "red"))=
+
+** Excluding Nodes and Edges
+
+One may want to exclude certain files to declutter the graph.
+
+- User Option: org-roam-graph-exclude-matcher
+
+  Matcher for excluding nodes from the generated graph. Any nodes and links for
+  file paths matching this string is excluded from the graph.
+
+  If value is a string, the string is the only matcher.
+
+  If value is a list, all file paths matching any of the strings
+  are excluded.
+
+#+BEGIN_EXAMPLE
+    (setq org-roam-graph-exclude-matcher '("private" "dailies"))
+#+END_EXAMPLE
+
+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,
+
+#+BEGIN_SRC emacs-lisp
+  (setq org-roam-completion-system 'default)
+#+END_SRC
+
+uses Emacs' standard =completing-read=. If you prefer
+[[https://emacs-helm.github.io/helm/][Helm]], use
+
+#+BEGIN_SRC emacs-lisp
+  (setq org-roam-completion-system 'helm)
+#+END_SRC
+
+Other options include ='ido=, and ='ivy=.
+
+* Roam Protocol
+** _ :ignore:
+Org-roam extending =org-protocol= with 2 protocols: the =roam-file=
+and =roam-ref= protocol.
+
+** Installation
+
+To enable Org-roam's protocol extensions, you have to add the following to your init file:
+
+#+BEGIN_SRC emacs-lisp
+(require 'org-roam-protocol)
+#+END_SRC
+
+The instructions for setting up =org-protocol== are reproduced below.
+
+We will also need to create a desktop application for =emacsclient=. The
+instructions for various platforms are shown below.
+
+For Linux users, create a desktop application in =~/.local/share/applications/org-protocol.desktop=:
+
+#+begin_example
+[Desktop Entry]
+Name=Org-Protocol
+Exec=emacsclient %u
+Icon=emacs-icon
+Type=Application
+Terminal=false
+MimeType=x-scheme-handler/org-protocol
+#+end_example
+
+Associate =org-protocol://= links with the desktop application by
+running in your shell:
+
+#+BEGIN_SRC bash
+xdg-mime default org-protocol.desktop x-scheme-handler/org-protocol
+#+END_SRC
+
+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:
+
+#+BEGIN_SRC bash
+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
+#+END_SRC
+
+and then restart Chrome (for example, by navigating to <chrome://restart>) to
+make the new policy take effect.
+
+See [[https://www.chromium.org/administrators/linux-quick-start][here]] for more info on the =/etc/opt/chrome/policies/managed= directory and
+[[https://cloud.google.com/docs/chrome-enterprise/policies/?policy=ExternalProtocolDialogShowAlwaysOpenCheckbox][here]] for information on the =ExternalProtocolDialogShowAlwaysOpenCheckbox= policy.
+
+For MacOS, one solution is to use [[https://github.com/sveinbjornt/Platypus][Platypus]]. Here are the instructions for
+setting up with Platypus and Chrome:
+
+1. Install and launch Platypus (with [[https://brew.sh/][Homebrew]]):
+
+#+BEGIN_SRC bash
+brew cask install platypus
+#+END_SRC
+
+2. Create a script =launch_emacs.sh=:
+
+#+BEGIN_SRC bash
+#!/usr/bin/env bash
+/usr/local/bin/emacsclient --no-wait $1
+#+END_SRC
+
+3. Create a Platypus app with the following settings:
+
+#+begin_example
+| 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                     |
+#+end_example
+
+
+Inside =Settings=:
+
+#+begin_example
+| Setting                        | Value          |
+|--------------------------------+----------------|
+| Accept dropped files           | true           |
+| Register as URI scheme handler | true           |
+| Protocol                       | "org-protocol" |
+#+end_example
+
+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:
+
+#+BEGIN_SRC bash
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+#+END_SRC
+
+
+If you're using [[https://github.com/railwaycat/homebrew-emacsmacport][Emacs Mac Port]], it registered its `Emacs.app` as the default
+handler for the URL scheme `org-protocol`. To make =OrgProtocol.app=
+the default handler instead, run:
+
+#+BEGIN_SRC bash
+defaults write com.apple.LaunchServices/com.apple.launchservices.secure LSHandlers -array-add \
+'{"LSHandlerPreferredVersions" = { "LSHandlerRoleAll" = "-"; }; LSHandlerRoleAll = "org.yourusername.OrgProtocol"; LSHandlerURLScheme = "org-protocol";}'
+#+END_SRC
+
+Then restart your computer.
+
+
+** 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 of an Org-roam File][Anatomy of an Org-roam File]]):
+
+[[file:images/roam-ref.gif]]
+
+To use this, create a Firefox bookmarklet as follows:
+
+#+BEGIN_SRC javascript
+javascript:location.href =
+'org-protocol://roam-ref?template=r&ref='
++ encodeURIComponent(location.href)
++ '&title='
++ encodeURIComponent(document.title)
+#+END_SRC
+
+or as a keybinding in =qutebrowser=, adding the following to the =autoconfig.yml= file:
+
+#+BEGIN_SRC yaml
+settings:
+  bindings.commands:
+    global:
+      normal:
+        gc: open javascript:void(location.href='org-protocol://roam-ref?template=r&ref='+encodeURIComponent(location.href)+'&title='+encodeURIComponent(document.title))
+#+END_SRC
+
+where =template= is the template key for a template in
+=org-roam-capture-ref-templates= (see [[*The Templating System][The Templating System]]). These templates
+should contain a =#+ROAM_KEY: ${ref}= in it.
+
+* Diagnosing and Repairing Files
+
+Org-roam provides a utility for diagnosing and repairing problematic files via
+=org-roam-doctor=. By default, =org-roam-doctor= runs the check across all Org-roam
+files, and this can take some time. To run the check only for the current file,
+run =C-u M-x org-roam-doctor=.
+
+- Function: org-roam-doctor &optional this-buffer
+
+  Perform a check on Org-roam files to ensure cleanliness. If THIS-BUFFER, run
+  the check only for the current buffer.
+
+The checks run are defined in =org-roam-doctor--checkers=. Each checker is an instance of =org-roam-doctor-checker=. To define a checker, use =make-org-roam-doctor-checker=. Here is a sample definition:
+
+#+BEGIN_SRC emacs-lisp
+(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))))
+#+END_SRC
+
+The =:name= property is the name of the function run. The function takes in the
+Org parse tree, and returns a list of =(point error-message)=. =:description= is a
+short description of what the checker does. =:actions= is an alist containing
+elements of the form =(char . (prompt . function))=. These actions are defined per
+checker, to perform autofixes for the errors. For each error detected,
+=org-roam-doctor= will move the point to the current error, and pop-up a help
+window displaying the error message, as well as the list of actions that can be
+taken provided in =:actions=.
+
+* _ Copying
+:PROPERTIES:
+:COPYING:    t
+:END:
+
+#+BEGIN_QUOTE
+Copyright (C) 2020-2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+You can redistribute this document and/or modify it under the terms
+of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any
+later version.
+
+This document 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.
+#+END_QUOTE
+
+* Appendix
+** Note-taking Workflows
+- Books ::
+  - [[https://www.goodreads.com/book/show/34507927-how-to-take-smart-notes][How To Take Smart Notes]]
+- Articles ::
+  - [[https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1][The Zettelkasten Method - LessWrong 2.0]]
+  - [[https://reddit.com/r/RoamResearch/comments/eho7de/building_a_second_brain_in_roamand_why_you_might][Building a Second Brain in Roam...And Why You Might Want To : RoamResearch]]
+  - [[https://www.nateliason.com/blog/roam][Roam Research: Why I Love It and How I Use It - Nat Eliason]]
+  - [[https://twitter.com/adam_keesling/status/1196864424725774336?s=20][Adam Keesling's Twitter Thread]]
+  - [[https://blog.jethro.dev/posts/how_to_take_smart_notes_org/][How To Take Smart Notes With Org-mode · Jethro Kuan]]
+- Threads ::
+  - [[https://news.ycombinator.com/item?id=22473209][Ask HN: How to Take Good Notes]]
+- Videos ::
+  - [[https://www.youtube.com/watch?v=RvWic15iXjk][How to Use Roam to Outline a New Article in Under 20 Minutes]]
+** Ecosystem
+A number of packages work well combined with Org-Roam:
+
+*** Deft
+   :PROPERTIES:
+   :CUSTOM_ID: deft
+   :END:
+
+[[https://jblevins.org/projects/deft/][Deft]] provides a nice interface
+for browsing and filtering org-roam notes.
+
+#+BEGIN_SRC 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/"))
+#+END_SRC
+
+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
+[[https://github.com/raxod502/el-patch][el-patch]]:
+
+#+BEGIN_SRC 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))))
+#+END_SRC
+
+The Deft interface can slow down quickly when the number of files get
+huge. [[https://github.com/hasu/notdeft][Notdeft]] is a fork of Deft
+that uses an external search engine and indexer.
+
+*** Org-journal
+   :PROPERTIES:
+   :CUSTOM_ID: org-journal
+   :END:
+
+[[https://github.com/bastibe/org-journal][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.
+
+#+BEGIN_SRC 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"))
+#+END_SRC
+
+*** Note-taking Add-ons
+   :PROPERTIES:
+   :CUSTOM_ID: note-taking-add-ons
+   :END:
+
+These are some plugins that make note-taking in Org-mode more enjoyable.
+
+**** Org-download
+    :PROPERTIES:
+    :CUSTOM_ID: org-download
+    :END:
+
+[[https://github.com/abo-abo/org-download][Org-download]] lets you
+screenshot and yank images from the web into your notes:
+
+#+CAPTION: org-download
+[[file:images/org-download.gif]]
+
+#+BEGIN_SRC emacs-lisp
+  (use-package org-download
+    :after org
+    :bind
+    (:map org-mode-map
+          (("s-Y" . org-download-screenshot)
+           ("s-y" . org-download-yank))))
+#+END_SRC
+
+**** mathpix.el
+    :PROPERTIES:
+    :CUSTOM_ID: mathpix.el
+    :END:
+
+[[https://github.com/jethrokuan/mathpix.el][mathpix.el]] uses
+[[https://mathpix.com/][Mathpix's]] API to convert clips into latex
+equations:
+
+#+CAPTION: mathpix
+[[file:images/mathpix.gif]]
+
+#+BEGIN_SRC 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))
+#+END_SRC
+
+**** Org-noter / Interleave
+    :PROPERTIES:
+    :CUSTOM_ID: org-noter-interleave
+    :END:
+
+[[https://github.com/weirdNox/org-noter][Org-noter]] and
+[[https://github.com/rudolfochrist/interleave][Interleave]] are both
+projects that allow synchronised annotation of documents (PDF, EPUB
+etc.) within Org-mode.
+
+**** Bibliography
+    :PROPERTIES:
+    :CUSTOM_ID: bibliography
+    :END:
+
+[[https://github.com/zaeph/org-roam-bibtex][org-roam-bibtex]] offers
+tight integration between
+[[https://github.com/jkitchin/org-ref][org-ref]],
+[[https://github.com/tmalsburg/helm-bibtex][helm-bibtex]] and
+=org-roam=. This helps you manage your bibliographic notes under
+=org-roam=.
+
+**** Spaced Repetition
+    :PROPERTIES:
+    :CUSTOM_ID: spaced-repetition
+    :END:
+
+[[https://github.com/l3kn/org-fc/][Org-fc]] is a spaced repetition
+system that scales well with a large number of files. Other alternatives
+include
+[[https://orgmode.org/worg/org-contrib/org-drill.html][org-drill]], and
+[[https://github.com/abo-abo/pamparam][pamparam]].
+
+* FAQ
+** How do I have 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:
+
+#+BEGIN_SRC emacs-lisp
+  ((nil . ((org-roam-directory . "/path/to/here/"))))
+#+END_SRC
+
+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.
+
+* _ :ignore:
+# Local Variables:
+# eval: (refill-mode +1)
+# before-save-hook: org-make-toc
+# after-save-hook: (lambda nil (progn (require 'ox-texinfo nil t) (org-texinfo-export-to-info)))
+# indent-tabs-mode: nil
+# org-src-preserve-indentation: nil
+# End:

doc/requirements.txt

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

doc/tour.md

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

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

@@ -1,17 +1,24 @@
-site_name: "Org-Roam: Roam + Org-Mode = ♥"
-repo_url: https://github.com/jethrokuan/org-roam/
+site_name: "Org-roam"
+repo_url: https://github.com/org-roam/org-roam/
 edit_uri: edit/master/doc/
 copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
 docs_dir: doc
+extra:
+  social:
+    - type: 'slack'
+      link: 'https://join.slack.com/t/orgroam/shared_invite/zt-clh0g0tx-j8xg1kVxnrWdKt16gmSGPQ'
 nav:
 - Home: index.md
-- A Tour of Org-Roam: tour.md
+- A Tour of Org-roam: tour.md
 - Installation: installation.md
 - Configuration: configuration.md
+- Anatomy of an Org-roam file: anatomy.md
+- The Templating System: templating.md
 - Ecosystem: ecosystem.md
 - Similar Packages: comparison.md
 - "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Graph Setup": graph_setup.md
+- "Appendix: Roam Protocol": roam_protocol.md
+- "Appendix: Org Export": org_export.md
 markdown_extensions:
   - admonition
   - pymdownx.betterem:

org-roam-buffer.el

@@ -0,0 +1,276 @@
+;;; org-roam-buffer.el --- Metadata buffer -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides the org-roam-buffer functionality for org-roam
+;;; Code:
+;;;; Library Requires
+(eval-when-compile (require 'subr-x))
+(require 'cl-lib)
+(require 'dash)
+(require 's)
+
+(defvar org-roam-directory)
+(defvar org-link-frame-setup)
+(defvar org-return-follows-link)
+(defvar org-roam-backlinks-mode)
+(defvar org-roam-last-window)
+(defvar org-ref-cite-types) ;; in org-ref-core.el
+
+(declare-function org-roam-db--ensure-built   "org-roam-db")
+(declare-function org-roam--extract-ref       "org-roam")
+(declare-function org-roam--get-title-or-slug "org-roam")
+(declare-function org-roam--get-backlinks     "org-roam")
+(declare-function org-roam-backlinks-mode     "org-roam")
+
+(defcustom org-roam-buffer-position 'right
+  "Position of `org-roam' buffer.
+Valid values are
+ * left,
+ * right,
+ * top,
+ * bottom."
+  :type '(choice (const left)
+                 (const right)
+                 (const top)
+                 (const bottom))
+  :group 'org-roam)
+
+(defcustom org-roam-buffer-width 0.33
+  "Width of `org-roam' buffer.
+Has an effect if and only if `org-roam-buffer-position' is `left' or `right'."
+  :type 'number
+  :group 'org-roam)
+
+(defcustom org-roam-buffer-height 0.27
+  "Height of `org-roam' buffer.
+Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
+  :type 'number
+  :group 'org-roam)
+
+
+(defcustom org-roam-buffer "*org-roam*"
+  "Org-roam buffer name."
+  :type 'string
+  :group 'org-roam)
+
+(defcustom org-roam-buffer-prepare-hook '(org-roam-buffer--insert-title
+                                          org-roam-buffer--insert-backlinks
+                                          org-roam-buffer--insert-citelinks)
+  "Hook run in the `org-roam-buffer' before it is displayed."
+  :type 'hook
+  :group 'org-roam)
+
+(defcustom org-roam-buffer-no-delete-other-windows nil
+  "The `no-delete-other-windows' parameter of the `org-roam-buffer' window.
+When non-nil, the window will not be closed when deleting other windows."
+  :type 'boolean
+  :group 'org-roam)
+
+(defvar org-roam-buffer--current nil
+  "Currently displayed file in `org-roam' buffer.")
+
+(defun org-roam-buffer--insert-title ()
+  "Insert the org-roam-buffer title."
+  (insert (propertize (org-roam--get-title-or-slug
+                       (buffer-file-name org-roam-buffer--current))
+                       'font-lock-face
+                       'org-document-title)))
+
+(defun org-roam-buffer--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* ((ref (with-temp-buffer
+                   (insert-buffer-substring org-roam-buffer--current)
+                   (org-roam--extract-ref)))
+            (org-ref-p (require 'org-ref nil t)) ; Ensure that org-ref is present
+            (key-backlinks (org-roam--get-backlinks (cdr ref)))
+            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
+      (progn
+        (insert (let ((l (length key-backlinks)))
+                  (format "\n\n* %d %s\n"
+                          l (org-roam-buffer--pluralize "Cite backlink" l))))
+        (dolist (group grouped-backlinks)
+          (let ((file-from (car group))
+                (bls (cdr group)))
+            (insert (format "** [[file:%s][%s]]\n"
+                            file-from
+                            (org-roam--get-title-or-slug file-from)))
+            (dolist (backlink bls)
+              (pcase-let ((`(,file-from _ ,props) backlink))
+                (insert (propertize
+                         (s-trim (s-replace "\n" " "
+                                            (plist-get props :content)))
+                         'help-echo "mouse-1: visit backlinked note"
+                         'file-from file-from
+                         'file-from-point (plist-get props :point)))
+                (insert "\n\n"))))))
+    (insert "\n\n* No cite backlinks!")))
+
+(defun org-roam-buffer--insert-backlinks ()
+  "Insert the org-roam-buffer backlinks string for the current buffer."
+  (if-let* ((file-path (buffer-file-name org-roam-buffer--current))
+            (backlinks (org-roam--get-backlinks file-path))
+            (grouped-backlinks (--group-by (nth 0 it) backlinks)))
+      (progn
+        (insert (let ((l (length backlinks)))
+                     (format "\n\n* %d %s\n"
+                             l (org-roam-buffer--pluralize "Backlink" l))))
+        (dolist (group grouped-backlinks)
+          (let ((file-from (car group))
+                (bls (cdr group)))
+            (insert (format "** [[file:%s][%s]]\n"
+                            file-from
+                            (org-roam--get-title-or-slug file-from)))
+            (dolist (backlink bls)
+              (pcase-let ((`(,file-from _ ,props) backlink))
+                (insert (propertize
+                         (s-trim (s-replace "\n" " "
+                                            (plist-get props :content)))
+                         'help-echo "mouse-1: visit backlinked note"
+                         'file-from file-from
+                         'file-from-point (plist-get props :point)))
+                (insert "\n\n"))))))
+    (insert "\n\n* No backlinks!")))
+
+(defun org-roam-buffer-update ()
+  "Update the `org-roam-buffer'."
+  (org-roam-db--ensure-built)
+  (let* ((source-org-roam-directory org-roam-directory))
+    (with-current-buffer org-roam-buffer
+      ;; When dir-locals.el is used to override org-roam-directory,
+      ;; org-roam-buffer should have a different local org-roam-directory and
+      ;; default-directory, as relative links are relative from the overridden
+      ;; org-roam-directory.
+      (setq-local org-roam-directory source-org-roam-directory)
+      (setq-local default-directory source-org-roam-directory)
+      ;; Locally overwrite the file opening function to re-use the
+      ;; last window org-roam was called from
+      (setq-local org-link-frame-setup
+                  (cons '(file . org-roam--find-file) org-link-frame-setup))
+      (let ((inhibit-read-only t))
+        (erase-buffer)
+        (unless (eq major-mode 'org-mode)
+          (org-mode))
+        (unless org-roam-backlinks-mode
+          (org-roam-backlinks-mode))
+        (make-local-variable 'org-return-follows-link)
+        (setq org-return-follows-link t)
+        (run-hooks 'org-roam-buffer-prepare-hook)
+        (read-only-mode 1)))))
+
+
+(cl-defun org-roam-buffer--update-maybe (&key redisplay)
+  "Reconstructs `org-roam-buffer'.
+This needs to be quick or infrequent, because this is run at
+`post-command-hook'.  If REDISPLAY, force an update of
+`org-roam-buffer'."
+  (let ((buffer (window-buffer)))
+    (when (and (or redisplay
+                   (not (eq org-roam-buffer--current buffer)))
+               (eq 'visible (org-roam-buffer--visibility))
+               (buffer-local-value 'buffer-file-truename buffer))
+      (setq org-roam-buffer--current buffer)
+      (org-roam-buffer-update))))
+
+;;;; Toggling the org-roam buffer
+(define-inline org-roam-buffer--visibility ()
+  "Return whether the current visibility state of the org-roam buffer.
+Valid states are 'visible, 'exists and 'none."
+  (declare (side-effect-free t))
+  (inline-quote
+   (cond
+    ((get-buffer-window org-roam-buffer) 'visible)
+    ((get-buffer org-roam-buffer) 'exists)
+    (t 'none))))
+
+(defun org-roam-buffer--set-width (width)
+  "Set the width of `org-roam-buffer' to `WIDTH'."
+  (unless (one-window-p)
+    (let ((window-size-fixed)
+          (w (max width window-min-width)))
+      (cond
+       ((> (window-width) w)
+        (shrink-window-horizontally  (- (window-width) w)))
+       ((< (window-width) w)
+        (enlarge-window-horizontally (- w (window-width))))))))
+
+(defun org-roam-buffer--set-height (height)
+  "Set the height of `org-roam-buffer' to `HEIGHT'."
+  (unless (one-window-p)
+    (let ((window-size-fixed)
+          (h (max height window-min-height)))
+      (cond
+       ((> (window-height) h)
+        (shrink-window  (- (window-height) h)))
+       ((< (window-height) h)
+        (enlarge-window (- h (window-height))))))))
+
+(defun org-roam-buffer--get-create ()
+  "Set up the `org-roam' buffer at `org-roam-buffer-position'."
+  (let ((window (get-buffer-window))
+        (position
+         (if (member org-roam-buffer-position '(right left top bottom))
+             org-roam-buffer-position
+           (let ((text-quoting-style 'grave))
+             (lwarn '(org-roam) :error
+                    "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
+                    org-roam-buffer-position))
+           'right)))
+    (-> (get-buffer-create org-roam-buffer)
+        (display-buffer-in-side-window
+         `((side . ,position)
+           (window-parameters . ((no-delete-other-windows . ,org-roam-buffer-no-delete-other-windows)))))
+        (select-window))
+    (pcase position
+      ((or 'right 'left)
+       (org-roam-buffer--set-width  (round (* (frame-width)  org-roam-buffer-width))))
+      ((or 'top  'bottom)
+       (org-roam-buffer--set-height (round (* (frame-height) org-roam-buffer-height)))))
+    (select-window window)))
+
+(defun org-roam-buffer-toggle-display ()
+  "Toggle display of the `org-roam-buffer'."
+  (interactive)
+  (setq org-roam-last-window (get-buffer-window))
+  (pcase (org-roam-buffer--visibility)
+    ('visible (delete-window (get-buffer-window org-roam-buffer)))
+    ((or 'exists 'none) (org-roam-buffer--get-create))))
+
+(provide 'org-roam-buffer)
+
+;;; org-roam-buffer.el ends here

org-roam-capture.el

@@ -0,0 +1,352 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides capture functionality for org-roam
+;;; Code:
+;;;; Library Requires
+(require 'org-capture)
+(require 'dash)
+(require 's)
+(require 'cl-lib)
+
+;; Declarations
+(defvar org-roam-encrypt-files)
+(defvar org-roam-directory)
+(declare-function  org-roam--get-title-path-completions "org-roam")
+(declare-function  org-roam--get-ref-path-completions   "org-roam")
+(declare-function  org-roam--file-path-from-id          "org-roam")
+(declare-function  org-roam--format-link                "org-roam")
+(declare-function  org-roam--title-to-slug              "org-roam")
+(declare-function  org-roam-completion--completing-read "org-roam-completion")
+
+(defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
+  "The default file name format for Org-roam templates.")
+
+(defvar org-roam-capture--header-default "#+TITLE: ${title}\n"
+  "The default capture header for Org-roam templates.")
+
+(defvar org-roam-capture--file-path nil
+  "The file path for the Org-roam capture.
+This variable is set during the Org-roam capture process.")
+
+(defvar org-roam-capture--info nil
+  "An alist of additional information passed to the Org-roam template.
+This variable is populated dynamically, and is only non-nil
+during the Org-roam capture process.")
+
+(defvar org-roam-capture--context nil
+  "A symbol, that reflects the context for obtaining the exact point in a file.
+This variable is populated dynamically, and is only active during
+an Org-roam capture process.
+
+The `title' context is used in `org-roam-insert' and
+`org-roam-find-file', where the capture process is triggered upon
+trying to create a new file without that `title'.
+
+The `ref' context is used by `org-roam-protocol', where the
+capture process is triggered upon trying to find or create a new
+note with the given `ref'.")
+
+(defvar org-roam-capture-additional-template-props nil
+  "Additional props to be added to the Org-roam template.")
+
+(defconst org-roam-capture--template-keywords '(:file-name :head)
+  "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
+
+(defvar org-roam-capture-templates
+  '(("d" "default" plain (function org-roam-capture--get-point)
+     "%?"
+     :file-name "%<%Y%m%d%H%M%S>-${slug}"
+     :head "#+TITLE: ${title}\n"
+     :unnarrowed t))
+  "Capture templates for Org-roam.
+The capture templates are an extension of
+`org-capture-templates', and the documentation there also
+applies.
+
+`org-capture-templates' are extended in 3 ways:
+
+1. Template expansion capabilities are extended with additional custom syntax.
+   See `org-roam-capture--fill-template' for more details.
+
+2. The `:file-name' key is added, which expands to the file-name
+   of the note if it creates a new file.  This file-name is
+   relative to `org-roam-directory', and is without the
+   file-extension.
+
+3. The `:head' key is added, which contains the template that is
+   inserted on initial creation (added only once).  This is where
+   insertion of any note metadata should go.")
+
+(defvar org-roam-capture-ref-templates
+  '(("r" "ref" plain (function org-roam-capture--get-point)
+     ""
+     :file-name "${slug}"
+     :head "#+TITLE: ${title}
+#+ROAM_KEY: ${ref}\n"
+     :unnarrowed t))
+  "The Org-roam templates used during a capture from the roam-ref protocol.
+Details on how to specify for the template is given in `org-roam-capture-templates'.")
+
+(defun org-roam-capture--get (keyword)
+  "Gets the value for KEYWORD from the `org-roam-capture-template'."
+  (plist-get (plist-get org-capture-plist :org-roam) keyword))
+
+(defun org-roam-capture--put (&rest stuff)
+  "Puts properties from STUFF into the `org-roam-capture-template'."
+  (let ((p (plist-get org-capture-plist :org-roam)))
+    (while stuff
+      (setq p (plist-put p
+                         (pop stuff) (pop stuff))))
+    (setq org-capture-plist
+          (plist-put org-capture-plist :org-roam p))))
+
+(defun org-roam-capture--in-process-p ()
+  "Return non-nil if a `org-roam-capture' buffer exists."
+  (cl-some (lambda (buffer)
+             (and (eq (buffer-local-value 'major-mode 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.
+This is an extension of org-capture's template expansion.
+
+First, it expands ${var} occurrences in STR, using the INFO alist.
+If there is a ${var} with no matching var in the alist, the value
+of var is prompted for via `completing-read'.
+
+Next, it expands the remaining template string using
+`org-capture-fill-template'."
+  (-> str
+      (s-format (lambda (key)
+                  (or (s--aget info key)
+                      (completing-read (format "%s: " key ) nil))) nil)
+      (org-capture-fill-template)))
+
+(defun org-roam-capture--insert-link-h ()
+  "Insert the link into the original buffer, after the capture process is done.
+This is added as a hook to `org-capture-after-finalize-hook'."
+  (when (and (not org-note-abort)
+             (eq (org-roam-capture--get :capture-fn)
+                 'org-roam-insert))
+    (when-let ((region (org-roam-capture--get :region))) ;; Remove previously selected text.
+      (delete-region (car region) (cdr region)))
+    (insert (org-roam--format-link (org-roam-capture--get :file-path)
+                                   (org-roam-capture--get :link-description))))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--insert-link-h))
+
+(defun org-roam-capture--save-file-maybe-h ()
+  "Save the file conditionally.
+The file is saved if the original value of :no-save is not t and
+`org-note-abort' is not t. It is added to
+`org-capture-after-finalize-hook'."
+  (cond
+   ((and (org-roam-capture--get :new-file)
+         org-note-abort)
+    (with-current-buffer (org-capture-get :buffer)
+      (set-buffer-modified-p nil)
+      (kill-buffer)))
+   ((and (not (org-roam-capture--get :orig-no-save))
+         (not org-note-abort))
+    (with-current-buffer (org-capture-get :buffer)
+      (save-buffer))))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h))
+
+(defun org-roam-capture--new-file ()
+  "Return the path to the new file during an Org-roam capture.
+
+This function reads the file-name attribute of the currently
+active Org-roam template.
+
+If the file path already exists, it throw an error.
+
+Else, to insert the header content in the file, `org-capture'
+prepends the `:head' property of the Org-roam capture template.
+
+To prevent the creation of a new file if the capture process is
+aborted, we do the following:
+
+1. Save the original value of the capture template's :no-save.
+
+2. Set the capture template's :no-save to t.
+
+3. Add a function on `org-capture-after-finalize-hook' that saves
+the file if the original value of :no-save is not t and
+`org-note-abort' is not t."
+  (let* ((name-templ (or (org-roam-capture--get :file-name)
+                         org-roam-capture--file-name-default))
+         (new-id (s-trim (org-roam-capture--fill-template
+                          name-templ
+                          org-roam-capture--info)))
+         (file-path (org-roam--file-path-from-id new-id))
+         (roam-head (or (org-roam-capture--get :head)
+                        org-roam-capture--header-default))
+         (org-template (org-capture-get :template))
+         (roam-template (concat roam-head org-template)))
+    (unless (file-exists-p file-path)
+      (make-directory (file-name-directory file-path) t)
+      (org-roam-capture--put :orig-no-save (org-capture-get :no-save)
+                             :new-file t)
+      (org-capture-put :template
+                       ;; Fixes org-capture-place-plain-text throwing 'invalid search bound'
+                       ;; when both :unnarowed t and "%?" is missing from the template string;
+                       ;; may become unnecessary when the upstream bug is fixed
+                       (if (s-contains-p "%?" roam-template)
+                           roam-template
+                         (concat roam-template "%?"))
+                       :type 'plain
+                       :no-save t))
+    file-path))
+
+(defun org-roam-capture--expand-template ()
+  "Expand capture template with information from `org-roam-capture--info'."
+  (org-capture-put :template
+                   (s-format (org-capture-get :template)
+                             (lambda (key)
+                               (or (s--aget org-roam-capture--info key)
+                                   (when-let ((v (completing-read (format "%s: " key ) nil)))
+                                     (push (cons key v) org-roam-capture--info)
+                                     v))) nil)))
+
+(defun org-roam-capture--get-point ()
+  "Return exact point to file for org-capture-template.
+The file to use is dependent on the context:
+
+If the search is via title, it is assumed that the file does not
+yet exist, and Org-roam will attempt to create new file.
+
+If the search is via daily notes, 'time will be passed via
+`org-roam-capture--info'. This is used to alter the default time
+in `org-capture-templates'.
+
+If the search is via ref, it is matched against the Org-roam database.
+If there is no file with that ref, a file with that ref is created.
+
+This function is used solely in Org-roam's capture templates: see
+`org-roam-capture-templates'."
+  (let ((file-path (pcase org-roam-capture--context
+                     ('capture
+                      (or (cdr (assoc 'file org-roam-capture--info))
+                          (org-roam-capture--new-file)))
+                     ('title
+                      (org-roam-capture--new-file))
+                     ('dailies
+                      (org-capture-put :default-time (cdr (assoc 'time org-roam-capture--info)))
+                      (org-roam-capture--new-file))
+                     ('ref
+                      (let ((completions (org-roam--get-ref-path-completions))
+                            (ref (cdr (assoc 'ref org-roam-capture--info))))
+                        (or (cdr (assoc ref completions))
+                            (org-roam-capture--new-file))))
+                     (_ (error "Invalid org-roam-capture-context")))))
+    (org-roam-capture--expand-template)
+    (org-roam-capture--put :file-path file-path)
+    (while org-roam-capture-additional-template-props
+      (let ((prop (pop org-roam-capture-additional-template-props))
+            (val (pop org-roam-capture-additional-template-props)))
+        (org-roam-capture--put prop val)))
+    (set-buffer (org-capture-target-buffer file-path))
+    (widen)
+    (goto-char (point-max))))
+
+(defun org-roam-capture--convert-template (template)
+  "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
+  (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.
+This is added as a hook to `org-capture-after-finalize-hook'.
+Run the hooks defined in `org-roam-capture-after-find-file-hook'."
+  (unless org-note-abort
+    (when-let ((file-path (org-roam-capture--get :file-path)))
+      (find-file file-path))
+    (run-hooks 'org-roam-capture-after-find-file-hook))
+  (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h))
+
+(defcustom org-roam-capture-after-find-file-hook nil
+  "Hook that is run right after an Org-roam capture process is finalized.
+Suitable for moving point."
+  :group 'org-roam
+  :type 'hook)
+
+(defun org-roam-capture--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))
+        org-capture-templates-contexts)
+    (when (= (length org-capture-templates) 1)
+      (setq keys (caar org-capture-templates)))
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
+    (org-capture goto keys)))
+
+;;;###autoload
+(defun org-roam-capture ()
+  "Launches an `org-capture' process for a new or existing note.
+This uses the templates defined at `org-roam-capture-templates'."
+  (interactive)
+  (when (org-roam-capture--in-process-p)
+    (user-error "Nested Org-roam capture processes not supported"))
+  (let* ((completions (org-roam--get-title-path-completions))
+         (title-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 :file-path)))
+    (let ((org-roam-capture--info (list (cons 'title title)
+                                        (cons 'slug (org-roam--title-to-slug title))
+                                        (cons 'file file-path)))
+          (org-roam-capture--context 'capture))
+      (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-capture))
+      (condition-case err
+          (org-roam-capture--capture)
+        (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
+                           (error-message-string err)))))))
+
+(provide 'org-roam-capture)
+
+;;; org-roam-capture.el ends here

org-roam-compat.el

@@ -0,0 +1,101 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This file contains code needed for backward compatibility with older Emacsen
+;; and previous versions of org-roam.
+;;
+;;; Code:
+;;;; Library Requires
+
+;;; Obsolete aliases (remove after next major release)
+;;;; Functions
+(define-obsolete-function-alias 'org-roam--capture-get-point 'org-roam-capture--get-point
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-build-cache 'org-roam-db-build-cache
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-sql         'org-roam-db-query
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--get-db     'org-roam-db--get
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--db-clear   'org-roam-db--clear
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-show-graph  'org-roam-graph-show
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--maybe-update-buffer
+  'org-roam-buffer--update-maybe "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--current-visibility
+  'org-roam-buffer--visibility "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-update         'org-roam-buffer-update
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--set-width     'org-roam-buffer--set-width
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--set-height    'org-roam-buffer--set-height
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam--set-up-buffer 'org-roam-buffer--get-create
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-today 'org-roam-dailies-today
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-tomorrow 'org-roam-dailies-tomorrow
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-yesterday 'org-roam-dailies-yesterday
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-date 'org-roam-dailies-date
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-graph-show  'org-roam-graph
+  "org-roam 1.0.0")
+(define-obsolete-function-alias 'org-roam-graph-build 'org-roam-graph
+  "org-roam 1.0.0")
+(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")
+
+;;;; Variables
+(define-obsolete-variable-alias 'org-roam-graphviz-extra-options
+  'org-roam-graph-extra-config "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam-grapher-extra-options
+  'org-roam-graph-extra-config "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam-graph-node-shape
+  'org-roam-graph-node-extra-config "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam--db-connection
+  'org-roam-db--connection "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam--current-buffer
+  'org-roam-buffer--current "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam-date-title-format
+  'org-roam-dailies-capture-templates "org-roam 1.0.0")
+(define-obsolete-variable-alias 'org-roam-date-filename-format
+  'org-roam-dailies-capture-templates "org-roam 1.0.0")
+
+(provide 'org-roam-compat)
+
+;;; org-roam-compat.el ends here

org-roam-completion.el

@@ -0,0 +1,111 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides completion for org-roam.
+;;; Code:
+;;;; Library Requires
+(require 'cl-lib)
+(require 's)
+
+(defvar helm-pattern)
+(declare-function helm "ext:helm")
+(declare-function helm-make-source "ext:helm-source" (name class &rest args) t)
+
+(defcustom org-roam-completion-system 'default
+  "The completion system to be used by `org-roam'."
+  :type '(radio
+          (const :tag "Default" default)
+          (const :tag "Ido" ido)
+          (const :tag "Ivy" ivy)
+          (const :tag "Helm" helm)
+          (function :tag "Custom function"))
+  :group 'org-roam)
+
+(defun org-roam-completion--helm-candidate-transformer (candidates _source)
+  "Transforms CANDIDATES for Helm-based completing read.
+SOURCE is not used."
+  (let ((prefix (propertize "[?] "
+                            'face 'helm-ff-prefix)))
+    (cons (propertize helm-pattern
+                      'display (concat prefix helm-pattern))
+          candidates)))
+
+(cl-defun org-roam-completion--completing-read (prompt choices &key
+                                                       require-match initial-input
+                                                       action)
+  "Present a PROMPT with CHOICES and optional INITIAL-INPUT.
+If REQUIRE-MATCH is t, the user must select one of the CHOICES.
+Return user choice."
+  (let (res)
+    (setq res
+          (cond
+           ((eq org-roam-completion-system 'ido)
+            (let ((candidates (mapcar #'car choices)))
+              (ido-completing-read prompt candidates nil require-match initial-input)))
+           ((eq org-roam-completion-system 'default)
+            (completing-read prompt choices nil require-match initial-input))
+           ((eq org-roam-completion-system 'ivy)
+            (if (fboundp 'ivy-read)
+                (ivy-read prompt choices
+                          :initial-input initial-input
+                          :require-match require-match
+                          :action (prog1 action
+                                    (setq action nil))
+                          :caller 'org-roam--completing-read)
+              (user-error "Please install ivy from \
+https://github.com/abo-abo/swiper")))
+           ((eq org-roam-completion-system 'helm)
+            (unless (and (fboundp 'helm)
+                         (fboundp 'helm-make-source))
+              (user-error "Please install helm from \
+https://github.com/emacs-helm/helm"))
+            (let ((source (helm-make-source prompt 'helm-source-sync
+                            :candidates (mapcar #'car choices)
+                            :filtered-candidate-transformer
+                            (and (not require-match)
+                                 #'org-roam-completion--helm-candidate-transformer)))
+                  (buf (concat "*org-roam "
+                               (s-downcase (s-chop-suffix ":" (s-trim prompt)))
+                               "*")))
+              (or (helm :sources source
+                        :action (if action
+                                    (prog1 action
+                                      (setq action nil))
+                                  #'identity)
+                        :prompt prompt
+                        :input initial-input
+                        :buffer buf)
+                  (keyboard-quit))))))
+    (if action
+        (funcall action res)
+      res)))
+
+(provide 'org-roam-completion)
+
+;;; org-roam-completion.el ends here

org-roam-dailies.el

@@ -0,0 +1,84 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides functionality for creating daily notes. This is a
+;; concept borrowed from Roam Research.
+;;
+;;; Code:
+;;; Library Requires
+(require 'org-capture)
+(require 'org-roam-capture)
+(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>"))
+  "Capture templates for daily notes in Org-roam.")
+
+;; Declarations
+(declare-function org-roam--file-path-from-id "org-roam")
+
+(defun org-roam-dailies--file-for-time (time)
+  "Create and find file for TIME."
+  (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
+        (org-roam-capture--info (list (cons 'time time)))
+        (org-roam-capture--context 'dailies))
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
+    (org-roam--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)
+  (org-roam-dailies--file-for-time (current-time)))
+
+(defun org-roam-dailies-tomorrow (n)
+  "Create and find the daily note for tomorrow.
+With numeric argument N, use N days in the future."
+  (interactive "p")
+  (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
+
+(defun org-roam-dailies-yesterday (n)
+  "Create and find the file for yesterday.
+With numeric argument N, use N days in the past."
+  (interactive "p")
+  (org-roam-dailies-tomorrow (- n)))
+
+(defun org-roam-dailies-date ()
+  "Create the file for any date using the calendar interface."
+  (interactive)
+  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
+    (org-roam-dailies--file-for-time time)))
+
+(provide 'org-roam-dailies)
+
+;;; org-roam-dailies.el ends here

org-roam-db.el

@@ -0,0 +1,458 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library is provides the underlying database api to org-roam
+;;
+;;; Code:
+;;;; Library Requires
+(eval-when-compile (require 'subr-x))
+(require 'emacsql)
+(require 'emacsql-sqlite)
+(require 'org-roam-macs)
+
+(defvar org-roam-directory)
+(defvar org-roam-verbose)
+
+(declare-function org-roam--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-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.
+If this is non-nil, the Org-roam sqlite database is saved here.
+
+It is the user's responsibility to set this correctly, especially
+when used with multiple Org-roam instances."
+  :type 'string
+  :group 'org-roam)
+
+(defconst org-roam-db--version 5)
+(defconst org-roam-db--sqlite-available-p
+  (with-demoted-errors "Org-roam initialization: %S"
+    (emacsql-sqlite-ensure-binary)
+    t))
+
+(defvar org-roam-db--connection (make-hash-table :test #'equal)
+  "Database connection to Org-roam database.")
+
+;;;; Core Functions
+(defun org-roam-db--get ()
+  "Return the sqlite db file."
+  (interactive "P")
+  (or org-roam-db-location
+      (expand-file-name "org-roam.db" org-roam-directory)))
+
+(defun org-roam-db--get-connection ()
+  "Return the database connection, if any."
+  (gethash (file-truename org-roam-directory)
+           org-roam-db--connection))
+
+(defun org-roam-db ()
+  "Entrypoint to the Org-roam sqlite database.
+Initializes and stores the database, and the database connection.
+Performs a database upgrade when required."
+  (unless (and (org-roam-db--get-connection)
+               (emacsql-live-p (org-roam-db--get-connection)))
+    (let* ((db-file (org-roam-db--get))
+           (init-db (not (file-exists-p db-file))))
+      (make-directory (file-name-directory db-file) t)
+      (let ((conn (emacsql-sqlite db-file)))
+        (set-process-query-on-exit-flag (emacsql-process conn) nil)
+        (puthash (file-truename org-roam-directory)
+                 conn
+                 org-roam-db--connection)
+        (when init-db
+          (org-roam-db--init conn))
+        (let* ((version (caar (emacsql conn "PRAGMA user_version")))
+               (version (org-roam-db--update-maybe conn version)))
+          (cond
+           ((> version org-roam-db--version)
+            (emacsql-close conn)
+            (user-error
+             "The Org-roam database was created with a newer Org-roam version.  "
+             "You need to update the Org-roam package"))
+           ((< version org-roam-db--version)
+            (emacsql-close conn)
+            (error "BUG: The Org-roam database scheme changed %s"
+                   "and there is no upgrade path")))))))
+  (org-roam-db--get-connection))
+
+;;;; Entrypoint: (org-roam-db-query)
+(defun org-roam-db-query (sql &rest args)
+  "Run SQL query on Org-roam database with ARGS.
+SQL can be either the emacsql vector representation, or a string."
+  (if  (stringp sql)
+      (emacsql (org-roam-db) (apply #'format sql args))
+    (apply #'emacsql (org-roam-db) sql args)))
+
+;;;; Schemata
+(defconst org-roam-db--table-schemata
+  '((files
+     [(file :unique :primary-key)
+      (hash :not-null)
+      (meta :not-null)])
+
+    (links
+     [(from :not-null)
+      (to :not-null)
+      (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)
+      (type :not-null)])))
+
+(defun org-roam-db--init (db)
+  "Initialize database DB with the correct schema and user version."
+  (emacsql-with-transaction db
+    (pcase-dolist (`(,table . ,schema) org-roam-db--table-schemata)
+      (emacsql db [:create-table $i1 $S2] table schema))
+    (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
+
+(defun org-roam-db--update-maybe (db version)
+  "Upgrades the database schema for DB, if VERSION is old."
+  (emacsql-with-transaction db
+    'ignore
+    (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.
+If DB is nil, closes the database connection for the database in
+the current `org-roam-directory'."
+  (unless db
+    (setq db (org-roam-db--get-connection)))
+  (when (and db (emacsql-live-p db))
+    (emacsql-close db)))
+
+(defun org-roam-db--close-all ()
+  "Closes all database connections made by Org-roam."
+  (dolist (conn (hash-table-values org-roam-db--connection))
+    (org-roam-db--close conn)))
+
+;;;; Database API
+;;;;; Initialization
+(defun org-roam-db--initialized-p ()
+  "Whether the cache has been initialized."
+  (and (file-exists-p (org-roam-db--get))
+       (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
+          0)))
+
+(defun org-roam-db--ensure-built ()
+  "Ensures that Org-roam cache is built."
+  (unless (org-roam-db--initialized-p)
+    (error "[Org-roam] your cache isn't built yet! Please run org-roam-db-build-cache")))
+
+;;;;; Clearing
+(defun org-roam-db--clear ()
+  "Clears all entries in the caches."
+  (interactive)
+  (when (file-exists-p (org-roam-db--get))
+    (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 ((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
+   [:insert :into links
+    :values $v1]
+   links))
+
+(defun org-roam-db--insert-titles (file titles)
+  "Insert TITLES for a FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into titles
+    :values $v1]
+   (list (vector file titles))))
+
+(defun org-roam-db--insert-tags (file tags)
+  "Insert TAGS for a FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into tags
+    :values $v1]
+   (list (vector file tags))))
+
+(defun org-roam-db--insert-ref (file ref)
+  "Insert REF for FILE into the Org-roam cache."
+  (let ((key (cdr ref))
+        (type (car ref)))
+    (org-roam-db-query
+     [:insert :into refs :values $v1]
+     (list (vector key file type)))))
+
+;;;;; Fetching
+(defun org-roam-db--get-current-files ()
+  "Return a hash-table of file to the hash of its file contents."
+  (let* ((current-files (org-roam-db-query [:select * :from files]))
+         (ht (make-hash-table :test #'equal)))
+    (dolist (row current-files)
+      (puthash (car row) (cadr row) ht))
+    ht))
+
+(defun org-roam-db--get-titles (file)
+  "Return the titles of FILE from the cache."
+  (caar (org-roam-db-query [:select [titles] :from titles
+                            :where (= file $s1)]
+                           file
+                           :limit 1)))
+
+(defun org-roam-db--connected-component (file)
+  "Return all files reachable from/connected to FILE, including the file itself.
+If the file does not have any connections, nil is returned."
+  (let* ((query "WITH RECURSIVE
+                   links_of(file, link) AS
+                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                           citelinks AS (SELECT * FROM links
+                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                            AND links.\"type\" = '\"cite\"')
+                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"from\", \"file\" FROM citelinks),
+                   connected_component(file) AS
+                     (SELECT link FROM links_of WHERE file = $s1
+                      UNION
+                      SELECT link FROM links_of JOIN connected_component USING(file))
+                   SELECT * FROM connected_component;")
+         (files (mapcar 'car-safe (emacsql (org-roam-db) query file))))
+    files))
+
+(defun org-roam-db--links-with-max-distance (file max-distance)
+  "Return all files connected to FILE in at most MAX-DISTANCE steps.
+This includes the file itself. If the file does not have any
+connections, nil is returned."
+  (let* ((query "WITH RECURSIVE
+                   links_of(file, link) AS
+                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                           citelinks AS (SELECT * FROM links
+                                                  JOIN refs ON links.\"to\" = refs.\"ref\"
+                                                            AND links.\"type\" = '\"cite\"')
+                      SELECT \"from\", \"to\" FROM roamlinks UNION
+                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"file\", \"from\" FROM citelinks UNION
+                      SELECT \"from\", \"file\" FROM citelinks),
+                   -- Links are traversed in a breadth-first search.  In order to calculate the
+                   -- distance of nodes and to avoid following cyclic links, the visited nodes
+                   -- are tracked in 'trace'.
+                   connected_component(file, trace) AS
+                     (VALUES($s1, json_array($s1))
+                      UNION
+                      SELECT lo.link, json_insert(cc.trace, '$[' || json_array_length(cc.trace) || ']', lo.link) FROM
+                      connected_component AS cc JOIN links_of AS lo USING(file)
+                      WHERE (
+                        -- Avoid cycles by only visiting each file once.
+                        (SELECT count(*) FROM json_each(cc.trace) WHERE json_each.value == lo.link) == 0
+                        -- Note: BFS is cut off early here.
+                        AND json_array_length(cc.trace) < ($s2 + 1)))
+                   SELECT DISTINCT file, min(json_array_length(trace)) AS distance
+                   FROM connected_component GROUP BY file ORDER BY distance;")
+         ;; In principle the distance would be available in the second column.
+         (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
+    files))
+
+;;;;; Updating
+(defun org-roam-db--update-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)))
+         (title (org-roam--extract-titles)))
+    (org-roam-db-query [:delete :from titles
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-titles file title)))
+
+(defun org-roam-db--update-tags ()
+  "Update the tags of the current buffer into the cache."
+  (let* ((file (file-truename (buffer-file-name)))
+         (tags (org-roam--extract-tags)))
+    (org-roam-db-query [:delete :from tags
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-tags file tags)))
+
+(defun org-roam-db--update-refs ()
+  "Update the ref of the current buffer into the cache."
+  (let ((file (file-truename (buffer-file-name))))
+    (org-roam-db-query [:delete :from refs
+                        :where (= file $s1)]
+                       file)
+    (when-let ((ref (org-roam--extract-ref)))
+      (org-roam-db--insert-ref file ref))))
+
+(defun org-roam-db--update-cache-links ()
+  "Update the file links of the current buffer in the cache."
+  (let ((file (file-truename (buffer-file-name))))
+    (org-roam-db-query [:delete :from links
+                        :where (= from $s1)]
+                       file)
+    (when-let ((links (org-roam--extract-links)))
+      (org-roam-db--insert-links links))))
+
+(defun org-roam-db--update-file (&optional file-path)
+  "Update Org-roam cache for FILE-PATH."
+  (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-cache-links)
+          (org-roam-buffer--update-maybe :redisplay t))))))
+
+(defun org-roam-db-build-cache (&optional force)
+  "Build the cache for `org-roam-directory'.
+If FORCE, force a rebuild of the cache from scratch."
+  (interactive "P")
+  (when force (delete-file (org-roam-db--get)))
+  (org-roam-db--close) ;; Force a reconnect
+  (org-roam-db) ;; To initialize the database, no-op if already initialized
+  (let* ((org-roam-files (org-roam--list-all-files))
+         (current-files (org-roam-db--get-current-files))
+         all-files all-links all-titles all-refs all-tags)
+    (dolist (file org-roam-files)
+      (let* ((attr (file-attributes file))
+             (atime (file-attribute-access-time attr))
+             (mtime (file-attribute-modification-time attr)))
+        (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)
+              (push (vector file contents-hash (list :atime atime :mtime mtime))
+                    all-files)
+              (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-files
+      (org-roam-db-query
+       [:insert :into files
+        :values $v1]
+       all-files))
+    (when all-links
+      (org-roam-db-query
+       [:insert :into links
+        :values $v1]
+       all-links))
+    (when all-titles
+      (org-roam-db-query
+       [:insert :into titles
+        :values $v1]
+       all-titles))
+    (when all-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)
+                       :links (length all-links)
+                       :tags (length all-tags)
+                       :titles (length all-titles)
+                       :refs (length all-refs)
+                       :deleted (length (hash-table-keys current-files)))))
+      (org-roam-message "files: %s, links: %s, tags: %s, titles: %s, refs: %s, deleted: %s"
+                        (plist-get stats :files)
+                        (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-db.el ends here

org-roam-dev.el

@@ -0,0 +1,40 @@
+;;; 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: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides 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)
+(setq-local sentence-end-double-space nil)
+(provide 'org-roam-dev)
+
+;;; org-roam-dev.el ends here

org-roam-doctor.el

@@ -0,0 +1,231 @@
+;;; 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: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+
+;;; Commentary:
+;;
+;; This library provides `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-roam-macs)
+(require 'org-element)
+
+(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")
+
+(defvar org-roam-verbose)
+
+(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))))))
+
+(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")
+  (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

@@ -0,0 +1,296 @@
+;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library provides graphing functionality for org-roam.
+;;
+;;; Code:
+(require 'xml) ;xml-escape-string
+(require 's)   ;s-truncate, s-replace
+(require 'org-roam-macs)
+(require 'org-roam-db)
+
+;;;; Declarations
+(defvar org-roam-directory)
+(declare-function org-roam--org-roam-file-p  "org-roam")
+(declare-function org-roam--path-to-slug     "org-roam")
+
+;;;; Options
+(defcustom org-roam-graph-viewer (executable-find "firefox")
+  "Method to view the org-roam graph.
+It may be one of the following:
+  - a string representing the path to the executable for viewing the graph.
+  - a function accepting a single argument: the graph file path.
+  - nil uses `view-file' to view the graph."
+  :type '(choice
+          (string   :tag "Path to executable")
+          (function :tag "Function to display graph" eww-open-file)
+          (const    :tag "view-file"))
+  :group 'org-roam)
+
+(defcustom org-roam-graph-executable "dot"
+  "Path to graphing executable, or its name."
+  :type 'string
+  :group 'org-roam)
+
+(defcustom org-roam-graph-extra-config nil
+  "Extra options passed to graphviz.
+Example:
+ '((\"rankdir\" . \"LR\"))"
+  :type '(alist)
+  :group 'org-roam)
+
+(defcustom org-roam-graph-node-extra-config
+  '(("shape"      . "underline")
+    ("style"      . "rounded,filled")
+    ("fillcolor"  . "#EEEEEE")
+    ("color"      . "#C9C9C9")
+    ("fontcolor"  . "#111111"))
+  "Extra options for graphviz nodes.
+Example:
+ '((\"color\" . \"skyblue\"))"
+  :type '(alist)
+  :group 'org-roam)
+
+(defcustom org-roam-graph-edge-extra-config
+  '(("color" . "#333333"))
+  "Extra options for graphviz edges.
+Example:
+ '((\"dir\" . \"back\"))"
+  :type '(alist)
+  :group 'org-roam)
+
+(defcustom org-roam-graph-edge-cites-extra-config '(("color" . "red"))
+  "Extra options for graphviz edges for citation links.
+Example:
+ '((\"dir\" . \"back\"))"
+  :type '(alist)
+  :group 'org-roam)
+
+(defcustom org-roam-graph-max-title-length 100
+  "Maximum length of titles in graph nodes."
+  :type 'number
+  :group 'org-roam)
+
+(defcustom org-roam-graph-shorten-titles 'truncate
+  "Determines how long titles appear in graph nodes.
+Recognized values are the symbols `truncate' and `wrap', in which
+cases the title will be truncated or wrapped, respectively, if it
+is longer than `org-roam-graph-max-title-length'.
+
+All other values including nil will have no effect."
+  :type '(choice
+          (const :tag "truncate" truncate)
+          (const :tag "wrap" wrap)
+          (const :tag "no" nil))
+  :group 'org-roam)
+
+(defcustom org-roam-graph-exclude-matcher nil
+  "Matcher for excluding nodes from the generated graph.
+Any nodes and links for file paths matching this string is
+excluded from the graph.
+
+If value is a string, the string is the only matcher.
+
+If value is a list, all file paths matching any of the strings
+are excluded."
+  :type '(choice
+          (string :tag "Matcher")
+          (list :tag "Matchers"))
+  :group 'org-roam)
+
+;;;; Functions
+(defun org-roam-graph--expand-matcher (col &optional negate where)
+  "Return the exclusion regexp from `org-roam-graph-exclude-matcher'.
+COL is the symbol to be matched against.  if NEGATE, add :not to sql query.
+set WHERE to true if WHERE query already exists."
+  (let ((matchers (pcase org-roam-graph-exclude-matcher
+                    ('nil nil)
+                    ((pred stringp) `(,(concat "%" org-roam-graph-exclude-matcher "%")))
+                    ((pred listp) (mapcar (lambda (m)
+                                            (concat "%" m "%"))
+                                          org-roam-graph-exclude-matcher))
+                    (_ (error "Invalid org-roam-graph-exclude-matcher"))))
+        res)
+    (dolist (match matchers)
+      (if where
+          (push :and res)
+        (push :where res)
+        (setq where t))
+      (push col res)
+      (when negate
+        (push :not res))
+      (push :like res)
+      (push match res))
+    (nreverse res)))
+
+(defun org-roam-graph--dot-option (option &optional wrap-key wrap-val)
+  "Return dot string of form KEY=VAL for OPTION cons.
+If WRAP-KEY is non-nil it wraps the KEY.
+If WRAP-VAL is non-nil it wraps the VAL."
+  (concat wrap-key (car option) wrap-key
+          "="
+          wrap-val (cdr option) wrap-val))
+
+(defun org-roam-graph--dot (node-query)
+  "Build the graphviz dot string for NODE-QUERY.
+The Org-roam database titles table is read, to obtain the list of titles.
+The links table is then read to obtain all directed links, and formatted
+into a digraph."
+  (org-roam-db--ensure-built)
+  (org-roam--with-temp-buffer
+    (let* ((nodes (org-roam-db-query node-query))
+           (edges-query
+            `[:with selected :as [:select [file] :from ,node-query]
+              :select :distinct [to from] :from links
+              :where (and (in to selected) (in from selected))])
+           (edges-cites-query
+            `[:with selected :as [:select [file] :from ,node-query]
+              :select :distinct [file from]
+              :from links :inner :join refs :on (and (= links:to refs:ref)
+                                                     (= links:type "cite")
+                                                     (= refs:type "cite"))
+              :where (and (in file selected) (in from selected))])
+           (edges       (org-roam-db-query edges-query))
+           (edges-cites (org-roam-db-query edges-cites-query)))
+      (insert "digraph \"org-roam\" {\n")
+      (dolist (option org-roam-graph-extra-config)
+        (insert (org-roam-graph--dot-option option) ";\n"))
+      (dolist (attribute '("node" "edge"))
+        (insert (format " %s [%s];\n" attribute
+                        (mapconcat (lambda (var)
+                                     (org-roam-graph--dot-option var nil "\""))
+                                   (symbol-value
+                                    (intern (concat "org-roam-graph-" attribute "-extra-config")))
+                                   ","))))
+      (dolist (node nodes)
+        (let* ((file (xml-escape-string (car node)))
+               (title (or (caadr node)
+                          (org-roam--path-to-slug file)))
+               (shortened-title (pcase org-roam-graph-shorten-titles
+                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
+                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                  (_ title)))
+               (node-properties
+                `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
+                  ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
+                  ("tooltip" . ,(xml-escape-string title)))))
+          (insert
+           (format "  \"%s\" [%s];\n" file
+                   (mapconcat (lambda (n)
+                                (org-roam-graph--dot-option n nil "\""))
+                              node-properties ",")))))
+      (dolist (edge edges)
+        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
+                                  ,@(mapcar #'xml-escape-string edge)))))
+      (insert (format "  edge [%s];\n"
+                      (mapconcat #'org-roam-graph--dot-option
+                                 org-roam-graph-edge-cites-extra-config ",")))
+      (dolist (edge edges-cites)
+        (insert (apply #'format `("  \"%s\" -> \"%s\";\n"
+                                  ,@(mapcar #'xml-escape-string edge)))))
+      (insert "}")
+      (buffer-string))))
+
+(defun org-roam-graph--build (&optional node-query)
+  "Generate a graph showing the relations between nodes in NODE-QUERY."
+  (let ((name org-roam-graph-executable))
+    (unless (stringp name)
+      (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'")
+                  name))
+    (let* ((node-query (or node-query
+                           `[:select [file titles]
+                             :from titles
+                             ,@(org-roam-graph--expand-matcher 'file t)]))
+           (graph (org-roam-graph--dot node-query))
+           (temp-dot (make-temp-file "graph." nil ".dot" graph))
+           (temp-graph (make-temp-file "graph." nil ".svg")))
+      (call-process name nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
+      temp-graph)))
+
+(defun org-roam-graph--open (file)
+  "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
+  (pcase org-roam-graph-viewer
+    ((pred stringp)
+     (if (executable-find org-roam-graph-viewer)
+         (condition-case err
+             (call-process org-roam-graph-viewer nil 0 nil file)
+           (error (user-error "Failed to open org-roam graph: %s" err)))
+       (user-error "Executable not found: \"%s\"" org-roam-graph-viewer)))
+    ((pred functionp) (funcall org-roam-graph-viewer file))
+    ('nil (view-file file))
+    (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
+
+(defun org-roam-graph--build-connected-component (file &optional max-distance)
+  "Build a graph of nodes connected to FILE.
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
+  (let* ((file (file-truename file))
+         (files (or (if (and max-distance (>= max-distance 0))
+                        (org-roam-db--links-with-max-distance file max-distance)
+                      (org-roam-db--connected-component file))
+                    (list file)))
+         (query `[:select [file titles]
+                  :from titles
+                  :where (in file [,@files])]))
+    (org-roam-graph--build query)))
+
+;;;; Commands
+;;;###autoload
+(defun org-roam-graph (&optional arg file node-query)
+  "Build and possibly display a graph for FILE from NODE-QUERY.
+If FILE is nil, default to current buffer's file name.
+ARG may be any of the following values:
+  - nil       show the graph.
+  - `\\[universal-argument]'     show the graph for FILE.
+  - `\\[universal-argument]' N   show the graph for FILE limiting nodes to N steps.
+  - `\\[universal-argument] \\[universal-argument]' build the graph.
+  - `\\[universal-argument]' -   build the graph for FILE.
+  - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
+  (interactive "P")
+  (let ((file (or file (buffer-file-name (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 file (abs arg))))
+                         (when (>= arg 0)
+                           (org-roam-graph--open graph))))
+      ('(16)           (org-roam-graph--build node-query))
+      ('-              (org-roam-graph--build-connected-component file))
+      (_ (user-error "Unrecognized ARG: %s" arg)))))
+
+(provide 'org-roam-graph)
+
+;;; org-roam-graph.el ends here

org-roam-macs.el

@@ -0,0 +1,69 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; This library implements macros and utility functions used throughout
+;; org-roam.
+;;
+;;
+;;; Code:
+;;;; Library Requires
+
+(defvar org-roam-verbose)
+
+(defmacro org-roam--with-temp-buffer (&rest body)
+  "Execute BODY within a temp buffer.
+Like `with-temp-buffer', but propagates `org-roam-directory'."
+  (declare (indent 0) (debug t))
+  (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
+    `(let ((,current-org-roam-directory org-roam-directory))
+       (with-temp-buffer
+         (let ((org-roam-directory ,current-org-roam-directory))
+           ,@body)))))
+
+(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

@@ -0,0 +1,91 @@
+;;; 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/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.1.1
+;; Package-Requires: ((emacs "26.1") (org "9.3"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+;;; Commentary:
+;;
+;; We extend org-protocol, adding custom Org-roam handlers. The setup
+;; instructions for `org-protocol' can be found in org-protocol.el.
+;;
+;; We define 2 protocols:
+;;
+;; 1. "roam-file": This protocol simply opens the file given by the FILE key
+;; 2. "roam-ref": This protocol creates or opens a note with the given REF
+;;
+;;; Code:
+(require 'org-protocol)
+(require 'org-roam)
+
+;;;; Functions
+(defun org-roam-protocol-open-ref (info)
+  "Process an org-protocol://roam-ref?ref= style url with INFO.
+
+It opens or creates a note with the given ref.
+
+  javascript:location.href = \\='org-protocol://roam-ref?template=r&ref=\\='+ \\
+        encodeURIComponent(location.href) + \\='&title=\\=' \\
+        encodeURIComponent(document.title) + \\='&body=\\=' + \\
+        encodeURIComponent(window.getSelection())"
+  (when-let* ((alist (org-roam--plist-to-alist info))
+              (decoded-alist (mapcar (lambda (k.v)
+                                       (let ((key (car k.v))
+                                             (val (cdr k.v)))
+                                         (cons key (org-link-decode val)))) alist)))
+    (unless (assoc 'ref decoded-alist)
+      (error "No ref key provided"))
+    (when-let ((title (cdr (assoc 'title decoded-alist))))
+      (push (cons 'slug (org-roam--title-to-slug title)) decoded-alist))
+    (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
+           (org-roam-capture--context 'ref)
+           (org-roam-capture--info decoded-alist)
+           (template (cdr (assoc 'template decoded-alist))))
+      (raise-frame)
+      (org-roam--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)
+  "This handler simply opens the file with emacsclient.
+
+INFO is an alist containing additional information passed by the protocol URL.
+It should contain the FILE key, pointing to the path of the file to open.
+
+  Example protocol string:
+
+org-protocol://roam-file?file=/path/to/file.org"
+  (when-let ((file (plist-get info :file)))
+    (raise-frame)
+    (find-file file))
+  nil)
+
+(push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)
+      org-protocol-protocol-alist)
+(push '("org-roam-file"  :protocol "roam-file"   :function org-roam-protocol-open-file)
+      org-protocol-protocol-alist)
+
+(provide 'org-roam-protocol)
+
+;;; org-roam-protocol.el ends here

org-roam-utils.el

@@ -1,169 +0,0 @@
-;;; org-roam-utils.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
-
-;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
-
-;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
-;; Keywords: org-mode, roam, convenience
-;; Version: 0.1.2
-;; Package-Requires: ((emacs "26.1"))
-
-;; This file is NOT part of GNU Emacs.
-
-;; This program is free software; you can redistribute it and/or modify
-;; it under the terms of the GNU General Public License as published by
-;; the Free Software Foundation; either version 3, or (at your option)
-;; any later version.
-;;
-;; This program is distributed in the hope that it will be useful,
-;; but WITHOUT ANY WARRANTY; without even the implied warranty of
-;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;; GNU General Public License for more details.
-;;
-;; You should have received a copy of the GNU General Public License
-;; along with GNU Emacs; see the file COPYING.  If not, write to the
-;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
-;; Boston, MA 02110-1301, USA.
-
-;;; Commentary:
-;;
-;; This library is an attempt at injecting Roam functionality into Org-mode.
-;; This is achieved primarily through building caches for forward links,
-;; backward links, and file titles.
-;;
-;;; Code:
-
-(require 'org)
-(require 'org-element)
-(require 'subr-x)
-(require 'cl-lib)
-
-(defun org-roam--file-name-extension (filename)
-  "Return file name extension for FILENAME.
-
-Like file-name-extension, but does not strip version number."
-  (save-match-data
-    (let ((file (file-name-nondirectory filename)))
-      (if (and (string-match "\\.[^.]*\\'" file)
-                     (not (eq 0 (match-beginning 0))))
-          (substring file (+ (match-beginning 0) 1))))))
-
-(defun org-roam--org-file-p (path)
-  "Check if PATH is pointing to an org file."
-  (let ((ext (org-roam--file-name-extension path)))
-    (or (string= ext "org")
-        (and
-         (string= ext "gpg")
-         (string= (org-roam--file-name-extension (file-name-sans-extension path)) "org")))))
-
-(defun org-roam--find-files (dir)
-  "Return all `org-roam' files in `DIR'."
-  (if (file-exists-p dir)
-      (let ((files (directory-files dir t "." t))
-            (dir-ignore-regexp (concat "\\(?:"
-                                       "\\."
-                                       "\\|\\.\\."
-                                       "\\)$"))
-            result)
-        (dolist (file files)
-          (cond
-           ((file-directory-p file)
-            (when (not (string-match dir-ignore-regexp file))
-              (setq result (append (org-roam--find-files file) result))))
-           ((and (file-readable-p file)
-                 (org-roam--org-file-p file))
-            (setq result (cons (file-truename file) result)))))
-        result)))
-
-(defun org-roam--parse-content (&optional file-path)
-  "Parse the current buffer, and return a list of items for processing."
-  (org-element-map (org-element-parse-buffer) 'link
-    (lambda (link)
-      (let ((type (org-element-property :type link))
-            (path (org-element-property :path link))
-            (start (org-element-property :begin link)))
-        (when (and (string= type "file")
-                   (org-roam--org-file-p path))
-          (goto-char start)
-          (let* ((element (org-element-at-point))
-                 (begin (or (org-element-property :content-begin element)
-                            (org-element-property :begin element)))
-                 (content (or (org-element-property :raw-value element)
-                              (buffer-substring
-                               begin
-                               (or (org-element-property :content-end element)
-                                   (org-element-property :end element)))))
-                 (content (string-trim content))
-                 (file-path (or file-path
-                                (file-truename (buffer-file-name (current-buffer))))))
-            (list :from file-path
-                  :to (file-truename (expand-file-name path (file-name-directory file-path)))
-                  :properties (list :content content :point begin))))))))
-
-(cl-defun org-roam--insert-item (item &key forward backward)
-  "Insert ITEM into FORWARD and BACKWARD cache.
-
-ITEM is of the form: (:from from-path :to to-path :properties (:content preview-content :point point))."
-  (pcase-let ((`(:from ,p-from :to ,p-to :properties ,props) item))
-    ;; Build forward-links
-    (let ((links (gethash p-from forward)))
-      (if links
-          (puthash p-from
-                   (if (member p-to links)
-                       links
-                     (cons p-to links)) forward)
-        (puthash p-from (list p-to) forward)))
-    ;; Build backward-links
-    (let ((contents-hash (gethash p-to backward)))
-      (if contents-hash
-          (if-let ((contents-list (gethash p-from contents-hash)))
-              (let ((updated (cons props contents-list)))
-                (puthash p-from updated contents-hash)
-                (puthash p-to contents-hash backward))
-            (progn
-              (puthash p-from (list props) contents-hash)
-              (puthash p-to contents-hash backward)))
-        (let ((contents-hash (make-hash-table :test #'equal)))
-          (puthash p-from (list props) contents-hash)
-          (puthash p-to contents-hash backward))))))
-
-(defun org-roam--extract-title ()
-  "Extract the title from `BUFFER'."
-  (org-element-map
-      (org-element-parse-buffer)
-      'keyword
-    (lambda (kw)
-      (when (string= (org-element-property :key kw) "TITLE")
-        (org-element-property :value kw)))
-    :first-match t))
-
-(defun org-roam--build-cache (dir)
-  "Build the org-roam caches in DIR."
-  (let ((backward-links (make-hash-table :test #'equal))
-        (forward-links (make-hash-table :test #'equal))
-        (file-titles (make-hash-table :test #'equal)))
-    (let* ((org-roam-files (org-roam--find-files dir))
-           (file-items (mapcar (lambda (file)
-                                 (with-temp-buffer
-                                   (insert-file-contents file)
-                                   (org-roam--parse-content file))) org-roam-files)))
-      (dolist (items file-items)
-        (dolist (item items)
-          (org-roam--insert-item
-           item
-           :forward forward-links
-           :backward backward-links)))
-      (dolist (file org-roam-files)
-        (with-temp-buffer
-          (insert-file-contents file)
-          (when-let ((title (org-roam--extract-title)))
-            (puthash file title file-titles)))
-        org-roam-files))
-    (list
-     :forward forward-links
-     :backward backward-links
-     :titles file-titles)))
-
-(provide 'org-roam-utils)
-
-;;; org-roam-utils.el ends here

tests/roam-files/alias.org

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

tests/roam-files/bar.org

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

tests/roam-files/base.org

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

tests/roam-files/f1.org

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

tests/roam-files/f3.org

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

tests/roam-files/foo.org

@@ -0,0 +1,8 @@
+#+TITLE: Foo
+
+This is the foo file. It contains a link to [[file:bar.org][Bar]].
+
+To make the tests more robust, here are some arbitrary links:
+
+- [[https:google.com][Google]]
+- [[mailto:foo@john.com][mail to foo]]

tests/roam-files/nested/bar.org

@@ -0,0 +1,3 @@
+#+TITLE: Nested Bar
+
+This file is nested, 1 level deeper. It links to both [[file:../foo.org][Foo]] and [[file:foo.org][Nested Foo]].

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

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

tests/roam-files/nested/f1.org

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

tests/roam-files/nested/f2.org

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

tests/roam-files/nested/foo.org

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

tests/roam-files/no-title.org

@@ -1 +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

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

tests/roam-files/web_ref.org

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

tests/test-org-roam.el

@@ -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
 
@@ -19,212 +19,450 @@
 ;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 ;;; Commentary:
-
-;;
-
 ;;; Code:
 
-;;;; Requirements
-
 (require 'buttercup)
 (require 'with-simulated-input)
 (require 'org-roam)
 (require 'dash)
 
-(defun abs-path (file-path)
+(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)
-  (let ((path (abs-path path)))
+(defun test-org-roam--find-file (path)
+  "PATH."
+  (let ((path (test-org-roam--abs-path path)))
     (make-directory (file-name-directory path) t)
     (find-file path)))
 
-(defvar org-roam--tests-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 ()
-  (let ((original-dir org-roam--tests-directory)
+(defun test-org-roam--init ()
+  "."
+  (let ((original-dir test-org-roam-directory)
         (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
     (copy-directory original-dir new-dir)
-    (setq org-roam-directory new-dir))
-  (org-roam-mode +1))
+    (setq org-roam-directory new-dir)
+    (org-roam-mode +1)
+    (sleep-for 2)))
 
-(defun org-roam--test-build-cache ()
-  "Builds the caches synchronously."
-  (let ((cache (org-roam--build-cache org-roam-directory)))
-    (setq org-roam-forward-links-cache (plist-get cache :forward))
-    (setq org-roam-backward-links-cache (plist-get cache :backward))
-    (setq org-roam-titles-cache (plist-get cache :titles))
-    (setq org-roam-cache-initialized t)))
+(defun test-org-roam--teardown ()
+  (org-roam-mode -1)
+  (delete-file (org-roam-db--get))
+  (org-roam-db--close))
+
+(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--build-cache-async"
+(xdescribe "org-roam-db-build-cache"
+  (before-each
+    (test-org-roam--init))
+
+  (after-each
+    (test-org-roam--teardown))
+
   (it "initializes correctly"
-              (org-roam--test-init)
-              (expect org-roam-cache-initialized :to-be nil)
-              (expect (hash-table-count org-roam-forward-links-cache) :to-be 0)
-              (expect (hash-table-count org-roam-backward-links-cache) :to-be 0)
-              (expect (hash-table-count org-roam-titles-cache) :to-be 0)
+    ;; Cache
+    (expect (caar (org-roam-db-query [:select (funcall count) :from files])) :to-be 8)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links])) :to-be 5)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from titles])) :to-be 8)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from titles
+                                      :where titles :is-null])) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)
 
-              (org-roam--build-cache-async)
-              (sleep-for 3) ;; Because it's async
+    ;; Links
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
 
-              ;; Caches should be populated
-              (expect org-roam-cache-initialized :to-be t)
-              (expect (hash-table-count org-roam-forward-links-cache) :to-be 4)
-              (expect (hash-table-count org-roam-backward-links-cache) :to-be 5)
-              (expect (hash-table-count org-roam-titles-cache) :to-be 5)
+    ;; Links -- File-to
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= to $s1)]
+                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= to $s1)]
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
+    (expect (caar (org-roam-db-query [:select (funcall count) :from links
+                                      :where (= to $s1)]
+                                     (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
+    ;; TODO Test titles
+    (expect (org-roam-db-query [:select * :from titles])
+            :to-have-same-items-as
+            (list (list (test-org-roam--abs-path "alias.org")
+                        (list "t1" "a1" "a 2"))
+                  (list (test-org-roam--abs-path "bar.org")
+                        (list "Bar"))
+                  (list (test-org-roam--abs-path "foo.org")
+                        (list "Foo"))
+                  (list (test-org-roam--abs-path "nested/bar.org")
+                        (list "Nested Bar"))
+                  (list (test-org-roam--abs-path "nested/foo.org")
+                        (list "Nested Foo"))
+                  (list (test-org-roam--abs-path "no-title.org")
+                        (list "Headline title"))
+                  (list (test-org-roam--abs-path "web_ref.org") nil)
+                  (list (test-org-roam--abs-path "unlinked.org")
+                        (list "Unlinked"))))
 
-              ;; Forward cache
-              (let ((f1 (gethash (abs-path "f1.org") org-roam-forward-links-cache))
-                    (f2 (gethash (abs-path "f2.org") org-roam-forward-links-cache))
-                    (nested-f1 (gethash (abs-path "nested/f1.org") org-roam-forward-links-cache))
-                    (nested-f2 (gethash (abs-path "nested/f2.org") org-roam-forward-links-cache))
-                    (expected-f1 (list (abs-path "nested/f1.org")
-                                       (abs-path "f2.org")))
-                    (expected-nested-f1 (list (abs-path "nested/f2.org")
-                                              (abs-path "f1.org")))
-                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+    (expect (org-roam-db-query [:select * :from refs])
+            :to-have-same-items-as
+            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
 
-                (expect f1 :to-have-same-items-as expected-f1)
-                (expect f2 :to-be nil)
-                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
-                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+    ;; Expect rebuilds to be really quick (nothing changed)
+    (expect (org-roam-db-build-cache)
+            :to-equal
+            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
-              ;; Backward cache
-              (let ((f1 (hash-table-keys (gethash (abs-path "f1.org") org-roam-backward-links-cache)))
-                    (f2 (hash-table-keys (gethash (abs-path "f2.org") org-roam-backward-links-cache)))
-                    (nested-f1 (hash-table-keys(gethash (abs-path "nested/f1.org") org-roam-backward-links-cache)))
-                    (nested-f2 (hash-table-keys (gethash (abs-path "nested/f2.org") org-roam-backward-links-cache)))
-                    (expected-f1 (list (abs-path "nested/f1.org")))
-                    (expected-f2 (list (abs-path "f1.org")))
-                    (expected-nested-f1 (list (abs-path "nested/f2.org")
-                                              (abs-path "f1.org")))
-                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
-                (expect f1 :to-have-same-items-as expected-f1)
-                (expect f2 :to-have-same-items-as expected-f2)
-                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
-                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
-
-              ;; Titles Cache
-              (expect (gethash (abs-path "f1.org") org-roam-titles-cache) :to-equal "File 1")
-              (expect (gethash (abs-path "f2.org") org-roam-titles-cache) :to-equal "File 2")
-              (expect (gethash (abs-path "nested/f1.org") org-roam-titles-cache) :to-equal "Nested File 1")
-              (expect (gethash (abs-path "nested/f2.org") org-roam-titles-cache) :to-equal "Nested File 2")
-              (expect (gethash (abs-path "no-title.org") org-roam-titles-cache) :to-be nil)))
-
-(describe "org-roam-insert"
+(xdescribe "org-roam-insert"
   (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
+    (test-org-roam--init))
 
-          (it "temp1 -> f1"
-              (let ((buf (org-roam--test-find-new-file "temp1.org")))
+  (after-each
+    (test-org-roam--teardown))
+
+  (it "temp1 -> foo"
+    (let ((buf (test-org-roam--find-file "temp1.org")))
       (with-current-buffer buf
         (with-simulated-input
-                   "File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:f1.org")))
+         "Foo RET"
+         (org-roam-insert))))
+    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))
 
-          (it "temp2 -> nested/f1"
-              (let ((buf (org-roam--test-find-new-file "temp2.org")))
+  (it "temp2 -> nested/foo"
+    (let ((buf (test-org-roam--find-file "temp2.org")))
       (with-current-buffer buf
         (with-simulated-input
-                   "Nested SPC File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:nested/f1.org")))
+         "(nested) SPC Nested SPC Foo RET"
+         (org-roam-insert))))
+    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))
 
-          (it "nested/temp3 -> f1"
-              (let ((buf (org-roam--test-find-new-file "nested/temp3.org")))
+  (it "nested/temp3 -> foo"
+    (let ((buf (test-org-roam--find-file "nested/temp3.org")))
       (with-current-buffer buf
         (with-simulated-input
-                   "File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:../f1.org")))
+         "Foo RET"
+         (org-roam-insert))))
+    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))
 
-          (it "a/b/temp4 -> nested/f1"
-              (let ((buf (org-roam--test-find-new-file "a/b/temp4.org")))
+  (it "a/b/temp4 -> nested/foo"
+    (let ((buf (test-org-roam--find-file "a/b/temp4.org")))
       (with-current-buffer buf
         (with-simulated-input
-                   "Nested SPC File SPC 1 RET"
-                   (org-roam-insert nil))))
-              (expect (buffer-string) :to-match (regexp-quote "file:../../nested/f1.org"))))
+         "(nested) SPC Nested SPC Foo RET"
+         (org-roam-insert))))
+    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))
 
-(describe "rename file updates cache"
+(xdescribe "rename file updates cache"
   (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
+    (test-org-roam--init))
 
-          (it "f1 -> new_f1"
-              (rename-file (abs-path "f1.org")
-                           (abs-path "new_f1.org"))
+  (after-each
+    (test-org-roam--teardown))
+
+  (it "foo -> new_foo"
+    (rename-file (test-org-roam--abs-path "foo.org")
+                 (test-org-roam--abs-path "new_foo.org"))
     ;; Cache should be cleared of old file
-              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (hash-table-keys)
-                           (member (abs-path "f1.org"))) :to-be nil)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
 
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "new_f1.org"))) :not :to-be nil)
+    ;; Cache should be updated
+    (expect (org-roam-db-query [:select [to]
+                                :from links
+                                :where (= from $s1)]
+                               (test-org-roam--abs-path "new_foo.org"))
+            :to-have-same-items-as
+            (list (list (test-org-roam--abs-path "bar.org"))))
+    (expect (org-roam-db-query [:select [from]
+                                :from links
+                                :where (= to $s1)]
+                               (test-org-roam--abs-path "new_foo.org"))
+            :to-have-same-items-as
+            (list (list (test-org-roam--abs-path "nested/bar.org"))))
 
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "new_f1.org"))
-                           (member (abs-path "nested/f1.org"))) :not :to-be nil)
     ;; Links are updated
     (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "nested/f1.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:../new_f1.org][File 1]]")))
+              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:../new_foo.org][Foo]]")))
 
-
-          (it "f1 -> f1 with spaces"
-              (rename-file (abs-path "f1.org")
-                           (abs-path "f1 with spaces.org"))
+  (it "foo -> foo with spaces"
+    (rename-file (test-org-roam--abs-path "foo.org")
+                 (test-org-roam--abs-path "foo with spaces.org"))
     ;; Cache should be cleared of old file
-              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (hash-table-keys)
-                           (member (abs-path "f1.org"))) :to-be nil)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+
+    ;; Cache should be updated
+    (expect (org-roam-db-query [:select [to]
+                                :from links
+                                :where (= from $s1)]
+                               (test-org-roam--abs-path "foo with spaces.org"))
+            :to-have-same-items-as
+            (list (list (test-org-roam--abs-path "bar.org"))))
+    (expect (org-roam-db-query [:select [from]
+                                :from links
+                                :where (= to $s1)]
+                               (test-org-roam--abs-path "foo with spaces.org"))
+            :to-have-same-items-as
+            (list (list (test-org-roam--abs-path "nested/bar.org"))))
+
     ;; Links are updated
     (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "nested/f1.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:../f1 with spaces.org][File 1]]")))
+              (insert-file-contents (test-org-roam--abs-path "nested/bar.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))
 
   (it "no-title -> meaningful-title"
-              (rename-file (abs-path "no-title.org")
-                           (abs-path "meaningful-title.org"))
+    (rename-file (test-org-roam--abs-path "no-title.org")
+                 (test-org-roam--abs-path "meaningful-title.org"))
     ;; File has no forward links
-              (expect (gethash (abs-path "no-title.org")  org-roam-forward-links-cache) :to-be nil)
-              (expect (gethash (abs-path "meaningful-title.org")  org-roam-forward-links-cache) :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f3.org"))
-                           (member (abs-path "no-title.org"))) :to-be nil)
-
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f3.org"))
-                           (member (abs-path "meaningful-title.org"))) :not :to-be nil)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "no-title.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--abs-path "meaningful-title.org"))) :to-be 1)
 
     ;; Links are updated with the appropriate name
     (expect (with-temp-buffer
-                        (insert-file-contents (abs-path "f3.org"))
-                        (buffer-string)) :to-match (regexp-quote "[[file:meaningful-title.org][meaningful-title]]"))))
+              (insert-file-contents (test-org-roam--abs-path "meaningful-title.org"))
+              (buffer-string))
+            :to-match
+            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
 
-(describe "delete file updates cache"
+  (it "web_ref -> hello"
+    (expect (org-roam-db-query
+             [:select [file] :from refs
+              :where (= ref $s1)]
+             "https://google.com/")
+            :to-equal
+            (list (list (test-org-roam--abs-path "web_ref.org"))))
+    (rename-file (test-org-roam--abs-path "web_ref.org")
+                 (test-org-roam--abs-path "hello.org"))
+    (expect (org-roam-db-query
+             [:select [file] :from refs
+              :where (= ref $s1)]
+             "https://google.com/")
+            :to-equal (list (list (test-org-roam--abs-path "hello.org"))))
+    (expect (caar (org-roam-db-query
+                   [:select [ref] :from refs
+                    :where (= file $s1)]
+                   (test-org-roam--abs-path "web_ref.org")))
+            :to-equal nil)))
+
+(xdescribe "delete file updates cache"
   (before-each
-           (org-roam--test-init)
-           (org-roam--clear-cache)
-           (org-roam--test-build-cache))
-          (it "delete f1"
-              (delete-file (abs-path "f1.org"))
-              (expect (->> org-roam-forward-links-cache
-                           (gethash (abs-path "f1.org"))) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (gethash (abs-path "f1.org"))) :to-be nil)
-              (expect (->> org-roam-backward-links-cache
-                           (gethash (abs-path "nested/f1.org"))
-                           (gethash (abs-path "nested/f2.org"))) :not :to-be nil)))
+    (test-org-roam--init))
+
+  (after-each
+    (test-org-roam--teardown))
+
+  (it "delete foo"
+    (delete-file (test-org-roam--abs-path "foo.org"))
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from titles
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from refs
+                                      :where (= file $s1)]
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 0)
+    (expect (caar (org-roam-db-query [:select (funcall count)
+                                      :from links
+                                      :where (= from $s1)]
+                                     (test-org-roam--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/" (test-org-roam--abs-path "web_ref.org") "website")))
+    (delete-file (test-org-roam--abs-path "web_ref.org"))
+    (expect (org-roam-db-query [:select * :from refs])
+            :to-have-same-items-as
+            (list))))
+
+(provide 'test-org-roam)
+
+;;; test-org-roam.el ends here