(release): Org-roam v1.2.2 (#1168)

* remove org-roam-link-make-string
* remove org-roam-link-store-props and org-roam-link-decode

.dir-locals.el

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

.github/FUNDING.yml

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

.github/ISSUE_TEMPLATE/bug_report.md

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

.github/ISSUE_TEMPLATE/feature_request.md

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

.github/workflows/docs.yml

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

.github/workflows/test.yml

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

.gitignore

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

.readthedocs.yml

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

BACKERS.md

@@ -0,0 +1,8 @@
+# Backers
+
+Many thanks to the following backers, your contributions are greatly appreciated!
+
+- Nathan Tran
+- Burke Libbey
+- forkrul
+- Andreas Stuhlmüller

CHANGELOG.md

@@ -1,5 +1,144 @@
 # Changelog
 
+## 1.2.2 (06-10-2020)
+
+In this release we support fuzzy links of the form `[[roam:Title]]`, `[[roam:*Headline]]` and `[[roam:Title*Headline]]`. Completion for these fuzzy links is supported via `completion-at-point`.
+
+Org-roam now does not resolve symlinks. This significantly speeds up cache builds, but may result in some workflows breaking. In particular, Org-roam now cannot figure out if two distinct file paths in the Org-roam directory are the same file, and both files will be processed as if they were different files. This error seems to be unavoidable now that symlinks are not resolved, but this workflow is rare and should not affect most users.
+
+This change requires you to set `org-roam-directory` to the resolved path of a folder. That is:
+
+```elisp
+(setq org-roam-directory (file-truename "/path/to/directory/"))
+```
+
+### Breaking Changes
+
+- [#1164](https://github.com/org-roam/org-roam/pull/1164) Org-roam now stores the database in the user's Emacs directory by default
+- [#910](https://github.com/org-roam/org-roam/pull/910) Deprecate `company-org-roam`, using `completion-at-point` instead. To use this with company, add the `company-capf` backend instead.
+- [#1109](https://github.com/org-roam/org-roam/pull/1109) Org-roam now does not resolve symlinks.
+
+### Features
+
+- [#1163](https://github.com/org-roam/org-roam/pull/1163) Support file-level IDs introduced in Org 9.4
+- [#1093](https://github.com/org-roam/org-roam/pull/1093) Add `vanilla` org-roam-tag-source to extract buffer Org tags
+- [#1079](https://github.com/org-roam/org-roam/pull/1079) Add `org-roam-tag-face` to customize appearance of tags in interactive commands
+- [#1073](https://github.com/org-roam/org-roam/pull/1073) Rename file on title change, when `org-roam-rename-file-on-title-change` is non-nil.
+- [#1071](https://github.com/org-roam/org-roam/pull/1071) Update link descriptions on title changes, and clean-up rename file advice
+- [#1061](https://github.com/org-roam/org-roam/pull/1061) Speed up the extraction of file properties, headlines, and titles
+- [#1046](https://github.com/org-roam/org-roam/pull/1046) New user option to exclude files from Org-roam
+- [#1032](https://github.com/org-roam/org-roam/pull/1032) File changes are now propagated to the database on idle timer. This prevents large wait times during file saves.
+- [#974](https://github.com/org-roam/org-roam/pull/974) Protect region targeted by `org-roam-insert`
+- [#994](https://github.com/org-roam/org-roam/pull/994) Simplify org-roam-store-link
+- [#1062](https://github.com/org-roam/org-roam/pull/1062) Variable `org-roam-completions-everywhere` allows for completions everywhere from word at point
+- [#910](https://github.com/org-roam/org-roam/pull/910), [#1105](https://github.com/org-roam/org-roam/pull/1105) Support fuzzy links of the form [[roam:Title]], [[roam:*Headline]] and [[roam:Title*Headline]]
+
+### Bugfixes
+
+- [#1057](https://github.com/org-roam/org-roam/pull/1057) Improve performance of database builds by preventing generation of LaTeX and image previews.
+- [#1103](https://github.com/org-roam/org-roam/pull/1103) Fix long build-times for Windows on files with URL links
+
+## 1.2.1 (27-07-2020)
+
+This release consisted of a big deal of refactoring and bug fixes. Notably, we fixed several catastrophic failures on db builds with bad setups (#854), and modularized tag and title extractions.
+
+We also added some new features that had been a long time coming:
+
+1. We made the backlinks more outline-friendly by also showing the outline hierarchy for a backlink (#863)
+2. We now support nested captures, which is crucial for `org-roam-protocol` (#966)
+
+### Breaking Changes
+
+- [#908](https://github.com/org-roam/org-roam/pull/908) Normalized titles in database. May break external packages that rely on unnormalized titles.
+
+### Features
+
+- [#814](https://github.com/org-roam/org-roam/pull/814) Implement `org-roam-insert-immediate`
+- [#833](https://github.com/org-roam/org-roam/pull/833) Add customization of file titles with `org-roam-title-to-slug-function`.
+- [#839](https://github.com/org-roam/org-roam/pull/839) Return selected file from `org-roam-insert`
+- [#847](https://github.com/org-roam/org-roam/pull/847) Add GC threshold `org-roam-db-gc-threshold` to temporarily change the threshold on expensive operations.
+- [#847](https://github.com/org-roam/org-roam/pull/847) Use sqlite3 transactions instead of storing the values to be inserted.
+- [#851](https://github.com/org-roam/org-roam/pull/851) Add `'first-directory'` option for `org-roam-tag-sources`
+- [#863](https://github.com/org-roam/org-roam/pull/863) Display outline hierarchy in backlinks buffer
+- [#898](https://github.com/org-roam/org-roam/pull/898) Add `org-roam-random-note` to browse a random note.
+- [#900](https://github.com/org-roam/org-roam/pull/900) Support and index all valid org links
+- [#966](https://github.com/org-roam/org-roam/pull/966) Enable nested captures
+
+### Bugfixes
+
+- [#854](https://github.com/org-roam/org-roam/pull/854) Warn instead of fail when duplicate refs and IDs exist.
+- [#857](https://github.com/org-roam/org-roam/pull/857) Fix tag extraction for symlinked directories.
+- [#894](https://github.com/org-roam/org-roam/pull/894) Perform link fixes on all Org-roam files
+- [#952](https://github.com/org-roam/org-roam/pull/952) Cache `${foo}` template variables so they do not need to be re-entered twice
+
+## 1.2.0 (12-06-2020)
+
+In this release, we improved the linking process by achieving feature parity between links to files and links to headlines. Before, we used the `file:foo::*bar` format to link to the headline `bar` in file `foo`, but this was prone to breakage upon renaming the file or modifying the headline. This is not the case anymore. Now, we use `org-id` to create IDs for those headlines, which are then stored in our database to compute the relationships and jump around. Note that this will work even if you’re not using `org-id` in your global configuration for Org-mode.
+
+This is a major step forward. Supporting the in-file structure of Org-mode files means that we can interface with many of its core-features like TODOs, properties, priorities, etc. UX will have to be figured out, but this release ushers in a new age in terms of functionalities.
+
+We also add `org-roam-unlinked-references`, which naively finds text that could be references to the current Org-roam file.
+
+### Breaking Changes
+
+- [#701](https://github.com/org-roam/org-roam/pull/701) Use `emacsql-sqlite3` instead of `emacsql-sqlite` for better Windows compatibility. This requires the presence of the standard `sqlite3` binary on your machine.
+- [#750](https://github.com/org-roam/org-roam/pull/750) Deprecate `org-roam-buffer-no-delete-other-windows` in favour of `org-roam-buffer-window-parameters`.
+
+### Features
+
+- [#787](https://github.com/org-roam/org-roam/pull/787) Add `org-roam-unlinked-references`
+- [#783](https://github.com/org-roam/org-roam/pull/783) Add support for headlines
+- [#757](https://github.com/org-roam/org-roam/pull/757) Roam global properties are now case-insensitive
+- [#680](https://github.com/org-roam/org-roam/pull/680) , [#703](https://github.com/org-roam/org-roam/pull/703), [#708](https://github.com/org-roam/org-roam/pull/708) Add `org-roam-doctor` checkers for `ROAM_*` properties
+- [#664](https://github.com/org-roam/org-roam/pull/664) Add support for shelling out to `rg` and `find` in `org-roam--list-files`
+- [#679](https://github.com/org-roam/org-roam/pull/679), [#683](https://github.com/org-roam/org-roam/pull/683) Building of the graph now happens in a separate process
+
+### Bugfixes
+
+- [#714](https://github.com/org-roam/org-roam/pull/714) No longer print citelinks in backlinks buffer if there is no `ROAM_KEY` property or `org-ref` is not installed
+- [#759](https://github.com/org-roam/org-roam/pull/759), [#760](https://github.com/org-roam/org-roam/pull/760) Tags are only added to the tags table if there are actually tags present
+- [#700](https://github.com/org-roam/org-roam/pull/700), [#733](https://github.com/org-roam/org-roam/pull/733) Allow symlinks within the `org-roam` directory
+
+## 1.1.1 (18-05-2020)
+
+In this release, we added two new features:
+
+1. `org-roam-doctor`: a linting system that helps you discover possible problems with your Org-roam files. This is in the spirit of keeping notes in top quality.
+2. A tagging system: one can now use sub-directories, and the `#+roam_tags` key add additional meta data to notes. For more information, see [here](https://www.orgroam.com/manual/Tags.html#Tags).
+
+As usual, this release comes with a multitude of bug-fixes and refactorings.
+
+### Breaking Changes
+
+- [#523](https://github.com/org-roam/org-roam/pull/523) remove `org-roam-completion-fuzzy-match` in favor of using completion mechanism's configuration options directly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Deprecate `org-roam-db--maybe-update`, in favour of `org-roam-db--update-maybe`
+- [#604](https://github.com/org-roam/org-roam/pull/604) Deprecate `org-roam-title-include-subdirs`, `org-roam-title-subdir-format` `org-roam-title-subdir-separator`, for a more general tagging system built on subdirectories
+
+### Bugfixes
+
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix backup files being tracked in database
+- [#509](https://github.com/org-roam/org-roam/pull/509) fix external org files being tracked in database
+- [#537](https://github.com/org-roam/org-roam/pull/537) quote graphviz node and edge configuration options to allow multi-word configurations
+- [#545](https://github.com/org-roam/org-roam/pull/545) fix `org-roam--extract-links` to ensure that multiple citations (`cite:key1,key2`) are split correctly
+- [#547](https://github.com/org-roam/org-roam/pull/547) Fix unlinked citations
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix rename-file advice not working for renaming to directories
+- [#660](https://github.com/org-roam/org-roam/pull/660) fix links breaking within file on file movement
+
+### Features
+
+- [#538](https://github.com/org-roam/org-roam/pull/538) Optionally use text in first headline as title
+- [#553](https://github.com/org-roam/org-roam/pull/553) Add prefix argument to `org-roam-db-build-cache` for forcing rebuilds
+- [#560](https://github.com/org-roam/org-roam/pull/560) Apply 'error face to distinguish broken links
+- [#570](https://github.com/org-roam/org-roam/pull/570) Add `org-roam-doctor` to diagnose org-roam files
+- [#625](https://github.com/org-roam/org-roam/pull/625) Add `org-roam-title-sources` to control how titles are retrieved within notes
+- [#604](https://github.com/org-roam/org-roam/pull/604) Add a tagging system. `org-roam-tag-sources` controls how tags are retrieved from notes
+
+### Internal Changes
+
+- [#547](https://github.com/org-roam/org-roam/pull/547) Added `type` column to the `refs` table
+- [#606](https://github.com/org-roam/org-roam/pull/606) Added `org-roam-dev.el` for developer coding standards
+- [#622](https://github.com/org-roam/org-roam/pull/622) Online documentation now points to the Org-based documentation
+
 ## 1.1.0 (21-04-2020)
 
 To the average user, this release is mainly a bugfix release with additional options to customize. However, the changes made to the source is significant. Most notably, in this release:
@@ -8,31 +147,35 @@ To the average user, this release is mainly a bugfix release with additional opt
 2. [@kljohann](https://github.com/kljohann) did some fantastic work on graph generation: allowing building images for connected components within the graph up to a specified distance
 3. We also started supporting `org-ref` natively: cite links now show up in both the graph and the org-roam buffer.
 
-In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer). 
- 
+In the coming months, you can expect work on bigger projects (e.g. revamping the org-roam buffer).
+
 ### Breaking Changes
-* [#385](https://github.com/jethrokuan/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
-* [#473](https://github.com/jethrokuan/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.
+
+- [#385](https://github.com/org-roam/org-roam/pull/385) Deprecate `org-roam-graph-node-shape` in favour of `org-roam-graph-node-extra-config`.
+- [#473](https://github.com/org-roam/org-roam/pull/473) Deprecate `org-roam-date-filename-format` and `org-roam-date-title-format`, in favour of `org-roam-dailies-capture-templates`.
 
 ### New Features
-* [#350](https://github.com/jethrokuan/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
-* [#359](https://github.com/jethrokuan/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
-* [#374](https://github.com/jethrokuan/org-roam/pull/374) Add support for `org-ref` `cite:` links
-* [#380](https://github.com/jethrokuan/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
-* [#385](https://github.com/jethrokuan/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
-* [#398](https://github.com/jethrokuan/org-roam/pull/398), [#418](https://github.com/jethrokuan/org-roam/pull/418) Add graph building for connected components
-* [#435](https://github.com/jethrokuan/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
-* [#439](https://github.com/jethrokuan/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
-* [#465](https://github.com/jethrokuan/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
-* [#488](https://github.com/jethrokuan/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
-* [#491](https://github.com/jethrokuan/org-roam/pull/491) Use TITLE as description when linking before first heading
+
+- [#350](https://github.com/org-roam/org-roam/pull/350) Add `org-roam-db-location` to customize location of org-roam database.
+- [#359](https://github.com/org-roam/org-roam/pull/359) Add `org-roam-verbose` to allow or silence printing of information.
+- [#374](https://github.com/org-roam/org-roam/pull/374) Add support for `org-ref` `cite:` links
+- [#380](https://github.com/org-roam/org-roam/pull/380) Allow `org-roam-buffer-position` to also be `top` or `bottom`
+- [#385](https://github.com/org-roam/org-roam/pull/385) Add `org-roam-graph-node-extra-config` to configure Graphviz nodes
+- [#398](https://github.com/org-roam/org-roam/pull/398), [#418](https://github.com/org-roam/org-roam/pull/418) Add graph building for connected components
+- [#435](https://github.com/org-roam/org-roam/pull/435) Add `org-roam-graph-edge-extra-config` to configure Graphviz edges
+- [#439](https://github.com/org-roam/org-roam/pull/439) Add support for `org-ref` citations to display as edges in graph. Add `org-roam-graph-edge-cites-extra-config` to configure these edges
+- [#465](https://github.com/org-roam/org-roam/pull/465) Add `org-roam-file-extensions` to allow detection of org files with different file extensions
+- [#488](https://github.com/org-roam/org-roam/pull/488) Allow a function for `org-roam-graph-viewer`
+- [#491](https://github.com/org-roam/org-roam/pull/491) Use TITLE as description when linking before first heading
 
 ### Bugfixes
-* [#470](https://github.com/jethrokuan/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.
+
+- [#470](https://github.com/org-roam/org-roam/pull/470) Add workaround for undocumented `file-truename` behaviour in `org-roam--org-roam-file-p`.
 
 ### Internal Changes
-* [#363](https://github.com/jethrokuan/org-roam/pull/363), [#473](https://github.com/jethrokuan/org-roam/pull/473) Modularize org-roam features.
-* [#497](https://github.com/jethrokuan/org-roam/pull/497) Simplify `org-roam--list-files` implementation
+
+- [#363](https://github.com/org-roam/org-roam/pull/363), [#473](https://github.com/org-roam/org-roam/pull/473) Modularize org-roam features.
+- [#497](https://github.com/org-roam/org-roam/pull/497) Simplify `org-roam--list-files` implementation
 
 ## 1.0.0 (23-03-2020)
 
@@ -40,16 +183,18 @@ Org-roam is now on MELPA! We have squashed most of the bugs, and Org-roam has
 been stable for the most part.
 
 ### New Features
-* [#269](https://github.com/jethrokuan/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
-* [#257](https://github.com/jethrokuan/org-roam/pull/257) Add a company-backend `company-org-roam`
-* [#284](https://github.com/jethrokuan/org-roam/pull/284), [#289](https://github.com/jethrokuan/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
-* [#289](https://github.com/jethrokuan/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
-* [#290](https://github.com/jethrokuan/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
-* [#296](https://github.com/jethrokuan/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`
+
+- [#269](https://github.com/org-roam/org-roam/pull/269) Add `org-roam-graphviz-extra-options`
+- [#257](https://github.com/org-roam/org-roam/pull/257) Add a company-backend `company-org-roam`
+- [#284](https://github.com/org-roam/org-roam/pull/284), [#289](https://github.com/org-roam/org-roam/pull/289) Configurable `org-roam-completion-system` with options `'default`, `'ido`, `'ivy` and `'helm`
+- [#289](https://github.com/org-roam/org-roam/pull/289) Add customizable `org-roam-fuzzy-match` to allow fuzzy-matching of candidates
+- [#290](https://github.com/org-roam/org-roam/pull/290) Add `org-roam-date-title-format` and `org-roam-date-filename-format` for customizing Org-roam's date files
+- [#296](https://github.com/org-roam/org-roam/pull/296) Allow multiple exclusion matchers in `org-roam-graph-exclude-matcher`
 
 ### Bugfixes
-* [#293](https://github.com/jethrokuan/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
-* [#275](https://github.com/jethrokuan/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
+
+- [#293](https://github.com/org-roam/org-roam/pull/293) Fix capture templates not working as expected for `org-roam-find-file`
+- [#275](https://github.com/org-roam/org-roam/pull/275) Fix database rebuild when `org-roam-directory` is set locally
 
 ## 1.0.0-rc1 (06-03-2020)
 
@@ -59,82 +204,95 @@ backing storage has been changed to a SQLite database, and a
 templating system using `org-capture` is introduced.
 
 ### Breaking Changes
-* [#200](https://github.com/jethrokuan/org-roam/pull/200) Move Org-roam cache into a SQLite database.
-* [#203](https://github.com/jethrokuan/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.
+
+- [#200](https://github.com/org-roam/org-roam/pull/200) Move Org-roam cache into a SQLite database.
+- [#203](https://github.com/org-roam/org-roam/pull/203) Roam protocol is deprecated, in favour of extending org-roam-protocol.
 
 ### New Features
-* [#182](https://github.com/jethrokuan/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
-* [#216](https://github.com/jethrokuan/org-roam/pull/216) Adds templating functionality by extending org-capture.
-* [#232](https://github.com/jethrokuan/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
-* [#233](https://github.com/jethrokuan/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
-* [#247](https://github.com/jethrokuan/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
-* [#259](https://github.com/jethrokuan/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`
+
+- [#182](https://github.com/org-roam/org-roam/pull/182) Support file name aliases via `#+ROAM_ALIAS`.
+- [#216](https://github.com/org-roam/org-roam/pull/216) Adds templating functionality by extending org-capture.
+- [#232](https://github.com/org-roam/org-roam/pull/232) Adds a prefix key to `org-roam-show-graph`, to generate graph without opening it.
+- [#233](https://github.com/org-roam/org-roam/pull/233) Adds `org-roam-graph-exclude-matcher`, which allows exclusion of nodes from graph.
+- [#247](https://github.com/org-roam/org-roam/pull/247) Add `org-roam-backlink` face, which allows customizing backlinks appearance
+- [#259](https://github.com/org-roam/org-roam/pull/259) Add optional initial-prompt to `org-roam-find-file`
 
 ### Bugfixes
-* [#207](https://github.com/jethrokuan/org-roam/pull/207), [#221](https://github.com/jethrokuan/org-roam/pull/221) small bugfixes to Org-roam graph generation
-* [#230](https://github.com/jethrokuan/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors
+
+- [#207](https://github.com/org-roam/org-roam/pull/207), [#221](https://github.com/org-roam/org-roam/pull/221) small bugfixes to Org-roam graph generation
+- [#230](https://github.com/org-roam/org-roam/pull/230) remove nonspacing marks from filenames, to prevent cross-platform errors
 
 ### New Contributors
-* [@acowley][https://github.com/acowley]
-* [@teesloane][https://github.com/teesloane]
+
+- [@acowley][https://github.com/acowley]
+- [@teesloane][https://github.com/teesloane]
 
 ## 0.1.2 (2020-02-21)
 
 ### Breaking Changes
-* [#143](https://github.com/jethrokuan/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
-* [#103](https://github.com/jethrokuan/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+- [#143](https://github.com/org-roam/org-roam/pull/143) `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+- [#103](https://github.com/org-roam/org-roam/pull/103) Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
 
 ### New Features
-* [#145](https://github.com/jethrokuan/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
-* [#141](https://github.com/jethrokuan/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
-* [#138](https://github.com/jethrokuan/org-roam/pull/138) add `org-roam-switch-to-buffer`
-* [#124](https://github.com/jethrokuan/org-roam/pull/124), [#141](https://github.com/jethrokuan/org-roam/pull/141) Maintain cache consistency on file rename and delete
-* [#87](https://github.com/jethrokuan/org-roam/pull/87), [#90](https://github.com/jethrokuan/org-roam/pull/90) Support encrypted Org files
-* [#110](https://github.com/jethrokuan/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
-* [#99](https://github.com/jethrokuan/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+- [#145](https://github.com/org-roam/org-roam/pull/145) `org-roam-show-graph`: Fallback to Emacs SVG viewer
+- [#141](https://github.com/org-roam/org-roam/pull/141) add variable `org-roam-new-file-directory` for new Org-roam files
+- [#138](https://github.com/org-roam/org-roam/pull/138) add `org-roam-switch-to-buffer`
+- [#124](https://github.com/org-roam/org-roam/pull/124), [#141](https://github.com/org-roam/org-roam/pull/141) Maintain cache consistency on file rename and delete
+- [#87](https://github.com/org-roam/org-roam/pull/87), [#90](https://github.com/org-roam/org-roam/pull/90) Support encrypted Org files
+- [#110](https://github.com/org-roam/org-roam/pull/110) Add prefix to `org-roam-insert`, for inserting titles down-cased
+- [#99](https://github.com/org-roam/org-roam/pull/99) Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
 
 ### Changes
 
-* [#108](https://github.com/jethrokuan/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+- [#108](https://github.com/org-roam/org-roam/pull/108) Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
 
 ### Bugfixes
-* [#86](https://github.com/jethrokuan/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
-* [#98](https://github.com/jethrokuan/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
-* [#136](https://github.com/jethrokuan/org-roam/pull/136) Misc bugfixes
+
+- [#86](https://github.com/org-roam/org-roam/pull/86) Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+- [#98](https://github.com/org-roam/org-roam/pull/98) Fix `org-roam--find-file` picking up temporary files
+- [#136](https://github.com/org-roam/org-roam/pull/136) Misc bugfixes
 
 ### Internal
-* [#122](https://github.com/jethrokuan/org-roam/pull/122), [#128](https://github.com/jethrokuan/org-roam/pull/128) Improve performance of post-command-hook
-* [#92](https://github.com/jethrokuan/org-roam/pull/92), [#105](https://github.com/jethrokuan/org-roam/pull/105) Add tests for core functionality
+
+- [#122](https://github.com/org-roam/org-roam/pull/122), [#128](https://github.com/org-roam/org-roam/pull/128) Improve performance of post-command-hook
+- [#92](https://github.com/org-roam/org-roam/pull/92), [#105](https://github.com/org-roam/org-roam/pull/105) Add tests for core functionality
 
 ### New Contributors
-* [@frigge](https://github.com/frigge)
-* [@juergenhoetzel](https://github.com/juergenhoetzel)
-* [@chip2n](https://github.com/chip2n)
-* [@l3kn](https://github.com/l3kn)
-* [@jdormit](https://github.com/jdormit)
-* [@herbertjones](https://github.com/herbertjones)
-* [@CeleritasCelery](https://github.com/CeleritasCelery)
-* [@daniel-koudouna](https://github.com/daniel-koudouna)
+
+- [@frigge](https://github.com/frigge)
+- [@juergenhoetzel](https://github.com/juergenhoetzel)
+- [@chip2n](https://github.com/chip2n)
+- [@l3kn](https://github.com/l3kn)
+- [@jdormit](https://github.com/jdormit)
+- [@herbertjones](https://github.com/herbertjones)
+- [@CeleritasCelery](https://github.com/CeleritasCelery)
+- [@daniel-koudouna](https://github.com/daniel-koudouna)
 
 ## 0.1.1 (2020-02-15)
 
 Mostly a documentation/cleanup release.
 
 ### New Features
-* [#62](https://github.com/jethrokuan/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) Add the options `org-roam-use-timestamps-as-filename` and `org-roam-file-format`, more in documentation.
 
 ### Breaking Changes
-* [#62](https://github.com/jethrokuan/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
+
+- [#62](https://github.com/org-roam/org-roam/pull/62) The ID (file-name) workflow is no longer first-class, but a fallback when titles don't exist.
 
 ### Changes
-* [#66](https://github.com/jethrokuan/org-roam/pull/66), [#68](https://github.com/jethrokuan/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
-* [#73](https://github.com/jethrokuan/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
-* [#69](https://github.com/jethrokuan/org-roam/pull/69), [#72](https://github.com/jethrokuan/org-roam/pull/72), [#75](https://github.com/jethrokuan/org-roam/pull/75): Major cleanup and de-duplication of code
+
+- [#66](https://github.com/org-roam/org-roam/pull/66), [#68](https://github.com/org-roam/org-roam/pull/68): Improved the quality of the package in preparation of submission to MELPA
+- [#73](https://github.com/org-roam/org-roam/pull/73): Added CI to the project via Github Issues (Thanks [@alphapapa](https://github.com/alphapapa/) for scripts and setup)
+- [#69](https://github.com/org-roam/org-roam/pull/69), [#72](https://github.com/org-roam/org-roam/pull/72), [#75](https://github.com/org-roam/org-roam/pull/75): Major cleanup and de-duplication of code
 
 ### Bugfixes
-* [#67](https://github.com/jethrokuan/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
-* [#71](https://github.com/jethrokuan/org-roam/pull/71), [#78](https://github.com/jethrokuan/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
-* [#82](https://github.com/jethrokuan/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
+
+- [#67](https://github.com/org-roam/org-roam/pull/67): Fixed `org-roam--make-file` not creating files with extensions
+- [#71](https://github.com/org-roam/org-roam/pull/71), [#78](https://github.com/org-roam/org-roam/pull/78): Fixed `org-roam-insert` not inserting correct paths
+- [#82](https://github.com/org-roam/org-roam/pull/82): Fixed nested Org-roam files not being detected as part of Org-roam
 
 <!-- Local Variables: -->
 <!-- eval: (auto-fill-mode -1) -->

Makefile

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

README.md

@@ -1,10 +1,14 @@
 [![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
 
+> **NOTE:** Org-roam builds upon Emacs and Org-mode, both of which are intricate
+> tools that require time investment for mastery. This makes Org-roam less
+> friendly for beginners, but extremely powerful for those familiar with the
+> ecosystem, or willing to invest effort in it.
+
 Org-roam is a [Roam][roamresearch] replica built on top of the
 all-powerful [Org-mode][org].
 
@@ -22,20 +26,20 @@ describing Org-roam and the concepts behind it:
 
 [![Making Connections in your Notes](http://img.youtube.com/vi/Lg61ocfxk3c/0.jpg)](http://www.youtube.com/watch?v=Lg61ocfxk3c "Making Connections in your Notes")
 
-As of February 2020, it is in a very early stage of development. 
-
 Important links:
 
 - **[Documentation][docs]**
-- **[Org-roam Slack][slack]**
+- **[Discourse][discourse]**
+- **[Slack][slack]**
 
 ## A Preview
 
-Here's a screenshot of `org-roam`. The `org-roam` buffer shows
-backlinks for the active org buffer in the left window, as well as the
-surrounding content in the backlink file. The database is built once,
-and updated incrementally. The graph is generated from the link
-structure, and can be used to navigate to the respective files.
+Here's a screencast of Org-roam. The `org-roam-buffer` (window on the
+right) shows backlinks for the active Org-roam buffer (window on the
+left), as well as the surrounding content in the backlink file. The
+database is built once, and updated incrementally. The graph is
+generated from the link structure, and can be used to navigate to the
+respective files.
 
 ![img](doc/images/org-roam-graph.gif)
 
@@ -51,21 +55,48 @@ Here's a sample configuration with using `use-package`:
 
 ```emacs-lisp
 (use-package org-roam
-      :hook 
+      :ensure t
+      :hook
       (after-init . org-roam-mode)
       :custom
       (org-roam-directory "/path/to/org-files/")
       :bind (:map org-roam-mode-map
               (("C-c n l" . org-roam)
                ("C-c n f" . org-roam-find-file)
-               ("C-c n g" . org-roam-show-graph))
+               ("C-c n g" . org-roam-graph))
               :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
+              (("C-c n i" . org-roam-insert))
+              (("C-c n I" . org-roam-insert-immediate))))
 ```
 
+`org-roam-graph` by default expects to find the `dot` executable
+from the `graphviz` package in the `exec-path`.
+Ensure `graphviz` is installed and found if you want to use this
+feature or customize your configuration for `org-roam-graph` to use a
+different tool.
+
 For more detailed installation and configuration instructions (including for
 Doom and Spacemacs users), please see [the
-documentation](https://org-roam.readthedocs.io/en/master/installation/).
+documentation][docs].
+
+## Frequently-asked Questions
+
+Q: How do I create a note whose title already matches one of the candidates (e.g. creating `bar` when `barricade` already exists)?
+
+A: With `ivy`, you need to press `C-M-j` to use the current input instead of the nearest candidate. (Source: [`ivy`’s
+  FAQ](https://github.com/abo-abo/swiper#frequently-asked-questions))
+
+## Getting Help
+
+Before creating a new topic/issue, please be mindful of our time and ensure
+that it has not already been addressed on
+[GitHub][issues] or on
+[Discourse][discourse].
+
+- If you are new to Emacs and have problem setting up Org-roam, please ask your question on [Slack, channel #how-do-i][slack].
+- For quick questions, please ask them on [Slack, channel #troubleshooting][slack].
+- If something is not working as it should, or if you would like to suggest a new feature, please [create a new issue][issues].
+- If you have questions about your workflow with the slip-box method, please find a relevant topic on [Discourse][discourse], or create a new one.
 
 ## Knowledge Bases using Org-roam
 
@@ -90,5 +121,7 @@ General Public License, Version 3
 [roamresearch]: https://www.roamresearch.com/
 [org]: https://orgmode.org/
 [badge-license]: https://img.shields.io/badge/license-GPL_3-green.svg
-[docs]: https://org-roam.readthedocs.io/
+[docs]: https://www.orgroam.com/manual/
+[discourse]: https://org-roam.discourse.group/
 [slack]: https://join.slack.com/t/orgroam/shared_invite/zt-deoqamys-043YQ~s5Tay3iJ5QRI~Lxg
+[issues]: https://github.com/org-roam/org-roam/issues

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@tquelch.com>

doc/Makefile

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

doc/anatomy.md

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

doc/assets/page.css

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

doc/comparison.md

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

doc/configuration.md

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

doc/css/styles.css

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

doc/ecosystem.md

@@ -1,134 +0,0 @@
-A number of packages work well combined with Org-Roam:
-
-## Deft
-
-[Deft][deft] provides a nice interface for browsing and filtering
-org-roam notes.
-
-```emacs-lisp
-(use-package deft
-  :after org
-  :bind
-  ("C-c n d" . deft)
-  :custom
-  (deft-recursive t)
-  (deft-use-filter-string-for-filename t)
-  (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/"))
-```
-
-If the title of the Org file is not the first line, you might not get
-nice titles. You may choose to patch this to use `org-roam`'s
-functionality. Here I'm using [el-patch](https://github.com/raxod502/el-patch):
-
-```emacs-lisp
-(use-package el-patch
-  :straight (:host github
-                   :repo "raxod502/el-patch"
-                   :branch "develop"))
-
-(eval-when-compile
-  (require 'el-patch))
-
-(use-package deft
-  ;; same as above...
-  :config/el-patch
-  (defun deft-parse-title (file contents)
-    "Parse the given FILE and CONTENTS and determine the title.
-If `deft-use-filename-as-title' is nil, the title is taken to
-be the first non-empty line of the FILE.  Else the base name of the FILE is
-used as title."
-    (el-patch-swap (if deft-use-filename-as-title
-                       (deft-base-filename file)
-                     (let ((begin (string-match "^.+$" contents)))
-                       (if begin
-                           (funcall deft-parse-title-function
-                                    (substring contents begin (match-end 0))))))
-                   (org-roam--get-title-or-slug file))))
-```
-
-The Deft interface can slow down quickly when the number of files get
-huge. [Notdeft][notdeft] is a fork of Deft that uses an external
-search engine and indexer.
-
-## Org-journal
-
-[Org-journal](https://github.com/bastibe/org-journal) is a more powerful
-alternative to the simple function `org-roam-dailies-today`. It provides better
-journaling capabilities, and a nice calendar interface to see all dated entries.
-
-```emacs-lisp
-(use-package org-journal
-  :bind
-  ("C-c n j" . org-journal-new-entry)
-  :custom
-  (org-journal-date-prefix "#+TITLE: ")
-  (org-journal-file-format "%Y-%m-%d.org")
-  (org-journal-dir "/path/to/org-roam-files/")
-  (org-journal-date-format "%A, %d %B %Y"))
-```
-
-## Note-taking Add-ons
-
-These are some plugins that make note-taking in Org-mode more
-enjoyable.
-
-### Org-download
-
-[Org-download][org-download] lets you screenshot and yank images from
-the web into your notes:
-
-![org-download](images/org-download.gif)
-
-```emacs-lisp
-(use-package org-download
-  :after org
-  :bind
-  (:map org-mode-map
-        (("s-Y" . org-download-screenshot)
-         ("s-y" . org-download-yank))))
-```
-
-### mathpix.el
-
-[mathpix.el][mathpix-el] uses [Mathpix's](https://mathpix.com/) API to convert clips into
-latex equations:
-
-![mathpix](images/mathpix.gif)
-
-```emacs-lisp
-(use-package mathpix.el
-  :straight (:host github :repo "jethrokuan/mathpix.el")
-  :custom ((mathpix-app-id "app-id")
-           (mathpix-app-key "app-key"))
-  :bind
-  ("C-x m" . mathpix-screenshot))
-```
-
-### Org-noter / Interleave
-
-[Org-noter][org-noter] and [Interleave][interleave] are both projects
-that allow synchronised annotation of documents (PDF, EPUB etc.)
-within Org-mode.
-
-### Org-ref
-
-[Org-ref][org-ref] does citation and bibliography management in
-Org-mode, and a great tool for scientific notes.
-
-### Spaced Repetition
-
-[Org-fc][org-fc] is a spaced repetition system that scales well with a
-large number of files. Other alternatives include
-[org-drill][org-drill], and [pamparam][pamparam].
-
-[deft]: https://jblevins.org/projects/deft/
-[notdeft]: https://github.com/hasu/notdeft
-[org-download]: https://github.com/abo-abo/org-download
-[mathpix-el]: https://github.com/jethrokuan/mathpix.el
-[org-noter]: https://github.com/weirdNox/org-noter
-[interleave]: https://github.com/rudolfochrist/interleave
-[org-ref]: https://github.com/jkitchin/org-ref
-[org-fc]: https://github.com/l3kn/org-fc/
-[org-drill]: https://orgmode.org/worg/org-contrib/org-drill.html
-[pamparam]: https://github.com/abo-abo/pamparam

doc/htmlxref.cnf

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

doc/index.html

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

doc/index.md

@@ -1,62 +0,0 @@
-![org-roam][org-roam-intro-image]
-
-## What is Org-roam?
-
-Org-roam is a [Roam][roamresearch] replica built around the
-all-powerful [Org-mode][org].
-
-Org-roam is a solution for effortless non-hierarchical note-taking
-with Org-mode. With Org-roam, notes flow naturally, making note-taking
-fun and easy. Org-roam should also work as a plug-and-play solution
-for anyone already using Org-mode for their personal wiki.
-
-To understand more about Roam, a collection of links are available in
-[the appendix](notetaking_workflow.md).
-
-Org-roam aims to implement the core features of Roam, leveraging the
-mature ecosystem around Org-mode where possible. Eventually, we hope
-to further introduce features enabled by the Emacs ecosystem.
-
-## Why use Org-roam?
-
-##### Private and Secure
-
-Edit your personal wiki completely offline, entirely in your control.
-Encrypt your notes with GPG.
-
-##### Longevity
-
-Unlike web solutions like Roam research, the notes are first and
-foremost plain Org-mode files -- Org-roam simply builds up an
-auxilliary database to give the personal wiki superpowers. Having your
-notes in plain-text is crucial for the longevity of your wiki. Never
-have to worry about proprietary web solutions being taken down. Edit
-your plain-text notes in notepad if all other editors cease to exist.
-
-##### Free and Open-source
-
-Org-roam is free and open-source, which means that if you feel unhappy
-with any part of Org-roam, you may choose to extend Org-roam, or open
-a PR.
-
-##### Leverage the Org-mode Ecosystem
-
-Over the years, Emacs and Org-mode has developed into a mature system
-for plain-text organization. Building upon Org-mode already puts
-Org-roam light-years ahead of many other solutions.
-
-Emacs is also a fantastic interface for editing text, and we can
-inherit many of the powerful text-navigation and editing packages
-available to Emacs.
-
-There are several packages that are similar to Org-roam, see the
-[Comparison](comparison.md) page for a detailed comparison.
-
-## Project Status
-
-As of March 2020, most of the core functionality and interfaces have
-stabilized, and a stable release is near.
-
-[org-roam-intro-image]: images/org-roam-intro.png
-[roamresearch]: https://www.roamresearch.com/
-[org]: https://orgmode.org/

doc/installation.md

@@ -1,195 +0,0 @@
-## Basic Install and Configuration
-
-Org-roam is now available on MELPA, so you can install it via the following
-command:
-
-```
-M-x package-install RET org-roam RET
-```
-
-Alternatively, you may use package managers such as [straight][straight] or
-[quelpa][quelpa] to install the package.
-
-The recommended method of configuration is to use [use-package][use-package].
-
-```emacs-lisp
-(use-package org-roam
-      :hook
-      (after-init . org-roam-mode)
-      :custom
-      (org-roam-directory "/path/to/org-files/")
-      :bind (:map org-roam-mode-map
-              (("C-c n l" . org-roam)
-               ("C-c n f" . org-roam-find-file)
-               ("C-c n b" . org-roam-switch-to-buffer)
-               ("C-c n g" . org-roam-graph))
-              :map org-mode-map
-              (("C-c n i" . org-roam-insert))))
-```
-
-Or without `use-package`:
-
-```emacs-lisp
-(require 'org-roam)
-(define-key org-roam-mode-map (kbd "C-c n l") #'org-roam)
-(define-key org-roam-mode-map (kbd "C-c n f") #'org-roam-find-file)
-(define-key org-roam-mode-map (kbd "C-c n b") #'org-roam-switch-to-buffer)
-(define-key org-roam-mode-map (kbd "C-c n g") #'org-roam-graph)
-(define-key org-mode-map (kbd "C-c n i") #'org-roam-insert)
-(org-roam-mode +1)
-```
-
-The [Configuration](configuration.md) page details some of the common
-configuration options available.
-
-### Completion
-
-Link auto-completion is offered via
-[company-org-roam](https://github.com/jethrokuan/company-org-roam/), refer to
-the documentation there for further details.
-
-## Spacemacs
-
-If you are using Spacemacs, install org-roam by creating a simple layer that
-wraps Org-roam. Paste the following into a new file
-`~/.emacs.d/private/org-roam/packages.el`.
-
-```emacs-lisp
-(defconst org-roam-packages
-  '(org-roam))
-
-(defun org-roam/init-org-roam ()
-  (use-package org-roam
-    :hook
-    (after-init . org-roam-mode)
-    :custom
-    (org-roam-directory "/path/to/org-files/")
-    :init
-    (progn
-      (spacemacs/declare-prefix "ar" "org-roam")
-      (spacemacs/set-leader-keys
-       "arl" 'org-roam
-       "art" 'org-roam-dailies-today
-       "arf" 'org-roam-find-file
-       "arg" 'org-roam-graph)
-
-      (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
-      (spacemacs/set-leader-keys-for-major-mode 'org-mode
-                                                "rl" 'org-roam
-                                                "rt" 'org-roam-dailies-today
-                                                "rb" 'org-roam-switch-to-buffer
-                                                "rf" 'org-roam-find-file
-                                                "ri" 'org-roam-insert
-                                                "rg" 'org-roam-graph))))
-```
-
-Next, append `org-roam` to the `dotspacemacs-configuration-layers`
-list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or
-restart Emacs to load `org-roam`. It's functions are available under
-the prefix `SPC a r` and `, r` when visiting an org-mode buffer.
-
-If you also have the ranger layer installed, the prefix 'ar' conflict
-with that of the ranger layer. You might want to change it to 'aor'
-(also change the 'ar' to 'aor' in the other key-binding declarations)
-
-## Doom Emacs
-
-[Doom Emacs][doom] has a `+roam` flag on its `org` module for easy
-installation and configuration. Simply add the flag to the `org` section
-of your `~/.doom.d/init.el` and run `~/.emacs.d/bin/doom sync`.
-
-[use-package]: https://github.com/jwiegley/use-package
-[straight]: https://github.com/raxod502/straight.el
-[quelpa]: https://github.com/quelpa/quelpa
-[doom]: https://github.com/hlissner/doom-emacs
-[doom-getting-started]: https://github.com/hlissner/doom-emacs/blob/develop/docs/getting_started.org#configuring-packages
-
-## Windows
-
-On Windows, if you follow the installation instructions above, you will likely get the error message: **"No EmacSQL SQLite binary available, aborting"**, and `org-roam` won't start properly.
-
-You need to do some additional steps to get `org-roam` to work.
-
-Essentially, you will need to have a binary file for `emacsql-sqlite` so that your Emacs can work with `sqlite` database -- `org-roam` uses it to track backlinks. The following options have been reported to work by Windows users in the community.
-
-Option 1. **Windows Subsystem for Linux (WSL)**
-: This option lets you use Linux on your Windows machine. It's Linux, so you don't need to do anything specific for Windows.
-
-Option 2. **mingw-x64**
-: Use mingw-x64. You would spend a bit of time to download it, and get familiar with how it works. You should be able to use Linux tools within your Windows [more contribution welcome].
-
-Option 3. **scoop**
-: Use [scoop](https://scoop.sh/) to install a couple of software tools (make and gcc) and manually compile a binary (`.exe`) file yourself. Find a short step-by-step guide below.
-
-Option 4. **emacsql-sqlite3**
-: Use another Emacs package called [`emacsql-sqlite3`](https://github.com/cireu/emacsql-sqlite3). You can download an [official binary](https://sqlite.org/download.html) for `sqlite3`. `emacsql-sqlite3` lets you use it. For this option to work, you need to adjust the `org-roam` source code, and get your modified version to work in your Emacs environment. Find a suggestion below.
-
-### scoop
-**Step 1.** In PowerShell, install `scoop` ([instruction here](https://scoop.sh/)).
-
-```powershell
-iwr -useb get.scoop.sh | iex
-```
-
-**Step 2.** In PowerShell, install `make` and `gcc` via scoop
-
-```powershell
-scoop install make gcc
-```
-
-**Step 3.** In Emacs, install the `emacsql-sqlite` package for your Emacs if it is not done yet.
-
-**Step 4.** In PowerShell, move to the directory where `emacsql.c` is stored.
-
-With MELPA, it is likely to be under your ELPA folder:
-
-```
-~\AppData\Roaming\.emacs.d\elpa\emacsql-sqlite-20190727.1710\sqlite
-```
-
-With Doom Emacs, it should be under your `.emacs\.local`:
-
-```
-~\.emacs.d\.local\straight\build\emacsql-sqlite\sqlite
-```
-
-Check the files via `dir` command. You should see these files:
-
-```powershell
-Mode                LastWriteTime         Length Name
-----                -------------         ------ ----
--a----       22/03/2020  12:10 PM           5170 emacsql.c
--a----       22/03/2020  12:10 PM            439 Makefile
--a----       22/03/2020  12:10 PM        7516138 sqlite3.c
--a----       22/03/2020  12:10 PM         526684 sqlite3.h
-```
-
-**Step 5.** Compile the `.exe` file with `make`
-
-```powershell
-make emacsql-sqlite CC=gcc LDLIBS=
-```
-
-You will see the process triggered with lots of text automatically scrolling down; it may take a couple of minutes for compilation to finish.
-
-Once compilation is done, check that `emacsql-sqlite.exe` has been added to the directory.
-
-**Step 6.** Relaunch Emacs, use `org-roam`
-
-When you start `org-roam` (e.g. via `org-roam-mode`), now you should no longer see the "No EmacSQL SQLite binary available, aborting" error. You are good to go.
-
-
-### emacsql-sqlite3
-
-1. In Emacs, install the `emacsql-sqlite3` package
-
-2. Using your text editor, etc. modify `org-roam-db.el`:
-
-    1. Replace `(require 'emacsql-sqlite)` with `(require 'emacsql-sqlite3)`
-
-    2. Comment/deactivate the complete `(defconst org-roam-db--sqlite-available-p ... )`
-
-    3. In `(defun org-roam-db ...`, replace `emacsql-sqlite`
-with `emacsql-sqlite3`
-
-3. If you compile `.el` files, ensure to replace `org-roam-db.elc` with the new source you modified.

doc/notetaking_workflow.md

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

doc/org_export.md

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

doc/requirements.txt

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

doc/roam_protocol.md

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

doc/templating.md

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

doc/tour.md

@@ -1,70 +0,0 @@
-Org-roam was built to support a workflow that was not possible with
-vanilla Org-mode. This flow is modelled after the [Zettelkasten
-method][zettelkasten], and many of [Roam Research][roam]'s workflows.
-It is crucial to understand that Org-roam does not auto-magically make
-note-taking better -- it's changing the note-taking workflow that
-does.
-
-To understand more about the methods and madness, the [Note-Taking
-Workflow][appendix:ntw] page contains a page of useful references. The
-author has also written [a post][jethro-blog-post] about how he uses
-Org-roam.
-
-## Activating Org-roam
-
-Org-roam's entry point is the global minor `org-roam-mode`. This sets
-up Emacs with several hooks, for keeping the org-roam cache
-consistently updated, as well as showing the backlinks buffer. 
-
-The cache is a sqlite database named `org-roam.db`, which resides at
-the root of the `org-roam-directory`. Activating `org-roam-mode`
-builds the cache, which may take a while the first time, but is
-generally instantaneous in subsequent runs. To build the cache
-manually again, run `M-x org-roam-db-build-cache`.
-
-## Finding a Note
-
-`org-roam-find-file` shows the list of titles for notes that reside in
-`org-roam-directory`. Selecting a note title will bring you to the
-corresponding note. Entering a title of a note that does not yet exist
-will create a new note with that title.
-
-![org-roam-find-file](images/org-roam-find-file.gif)
-
-Note that in the above image, the [ivy](https://github.com/abo-abo/swiper)
-completion frontend is used. The default frontend has some usability issues with
-non-matching candidates (e.g. when you want to enter a title of a new note,
-there is no completion candidate), so either `ivy` or `helm` is recommended.
-
-## Inserting Links
-
-`org-roam-insert` insert links to existing (or new) notes. Entering a
-non-existent title will also create a new note with that title.
-
-![org-roam-insert](images/org-roam-insert-filetag.gif)
-
-Good usage of Org-roam requires liberally linking files. This allows
-the build-up of a dense knowledge graph.
-
-## The Org-roam Buffer
-
-The Org-roam buffer is often displayed in the side window. It shows
-backlinks for the currently active Org-roam note, along with some
-surrounding context.
-
-![org-roam-buffer](images/org-roam-buffer.gif)
-
-## Exporting the Graph
-
-Org-roam also uses Graphviz to generate a graph, with notes as nodes,
-and links between them as edges. The generated graph can be used to
-navigate to the files, but this requires some additional setup
-described in the [Roam Protocol][appendix:roam-protocol] page.
-
-![org-roam-graph](images/org-roam-graph.gif)
-
-[zettelkasten]: https://zettelkasten.de/
-[appendix:ntw]: notetaking_workflow.md
-[appendix:roam-protocol]: roam_protocol.md
-[roam]: https://www.roamresearch.com/
-[jethro-blog-post]: https://blog.jethro.dev/posts/how_to_take_smart_notes_org/

makem.sh

@@ -155,7 +155,8 @@ function elisp-checkdoc-file {
     (when makem-checkdoc-errors-p
       (kill-emacs 1))))
 
-(setq checkdoc-spellcheck-documentation-flag t)
+(setq sentence-end-double-space nil)
+(setq checkdoc-spellcheck-documentation-flag nil)
 (makem-checkdoc-files-and-exit)
 EOF
     echo $file
@@ -325,7 +326,7 @@ function dirnames {
 
 function filter-files-exclude-default {
     # Filter out paths (STDIN) which should be excluded by default.
-    egrep -v "(/\.cask/|-autoloads.el|.dir-locals)"
+    egrep -v "(/\.cask/|-autoloads.el|-macs.el|.dir-locals)"
 }
 
 function filter-files-exclude-args {
@@ -590,6 +591,12 @@ function debug {
         }
     fi
 }
+
+function error_nonblocking {
+    echo_color red "ERROR ($(ts)): $@" >&2
+    ((errors_nonblocking++))
+}
+
 function error {
     echo_color red "ERROR ($(ts)): $@" >&2
     ((errors++))
@@ -694,7 +701,7 @@ function lint {
     lint-checkdoc
     lint-compile
     lint-declare
-    lint-indent
+    # lint-indent
     lint-package
     lint-regexps
 }
@@ -762,7 +769,7 @@ function lint-package {
         --funcall package-lint-batch-and-exit \
         "${files_project_feature[@]}" \
         && success "Linting package finished without errors." \
-            || error "Linting package failed."
+            || error_nonblocking "Linting package failed."
 }
 
 function lint-regexps {
@@ -831,6 +838,7 @@ test_files_regexp='^((tests?|t)/)|-test.el$|^test-'
 
 emacs_command=("emacs")
 errors=0
+errors_nonblocking=0
 verbose=0
 compile=true
 arg_batch="--batch"
@@ -1071,9 +1079,9 @@ done
 
 if [[ $errors -gt 0 ]]
 then
-    log_color red "Finished with $errors errors."
+    log_color red "Finished with $errors errors and $errors_nonblocking non-blocking errors."
 else
-    success "Finished without errors."
+    success "Finished with $errors errors and $errors_nonblocking non-blocking errors."
 fi
 
 exit $errors

mkdocs.yml

@@ -1,40 +0,0 @@
-site_name: "Org-roam"
-repo_url: https://github.com/jethrokuan/org-roam/
-edit_uri: edit/master/doc/
-copyright: "Copyright (C) 2020 Jethro Kuan and contributors"
-docs_dir: doc
-extra:
-  social:
-    - type: 'slack'
-      link: 'https://join.slack.com/t/orgroam/shared_invite/zt-clh0g0tx-j8xg1kVxnrWdKt16gmSGPQ'
-nav:
-- Home: index.md
-- A Tour of Org-roam: tour.md
-- Installation: installation.md
-- Configuration: configuration.md
-- Anatomy of an Org-roam file: anatomy.md
-- The Templating System: templating.md
-- Ecosystem: ecosystem.md
-- Similar Packages: comparison.md
-- "Appendix: Note-taking Workflow": notetaking_workflow.md
-- "Appendix: Roam Protocol": roam_protocol.md
-- "Appendix: Org Export": org_export.md
-markdown_extensions:
-  - admonition
-  - pymdownx.betterem:
-      smart_enable: all
-  - pymdownx.caret
-  - pymdownx.critic
-  - pymdownx.details
-  - pymdownx.mark
-  - pymdownx.smartsymbols
-  - pymdownx.superfences
-  - pymdownx.tasklist:
-      custom_checkbox: true
-  - pymdownx.tilde
-
-theme:
-  name: 'material'
-  palette:
-    primary: 'deep purple'
-    accent: 'deep purple'

org-roam-buffer.el

@@ -1,12 +1,12 @@
-;;; org-roam-buffer.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-buffer.el --- Metadata buffer -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,17 +34,28 @@
 (require 'cl-lib)
 (require 'dash)
 (require 's)
+(require 'f)
+(require 'ol)
 
 (defvar org-roam-directory)
 (defvar org-link-frame-setup)
 (defvar org-return-follows-link)
 (defvar org-roam-backlinks-mode)
 (defvar org-roam-last-window)
+(defvar org-ref-cite-types) ;; in org-ref-core.el
+(defvar org-roam-mode)
+(defvar org-roam--org-link-bracket-typed-re)
+
 (declare-function org-roam-db--ensure-built   "org-roam-db")
 (declare-function org-roam--extract-ref       "org-roam")
+(declare-function org-roam--extract-titles    "org-roam")
 (declare-function org-roam--get-title-or-slug "org-roam")
 (declare-function org-roam--get-backlinks     "org-roam")
 (declare-function org-roam-backlinks-mode     "org-roam")
+(declare-function org-roam-mode               "org-roam")
+(declare-function org-roam--find-file         "org-roam")
+(declare-function org-roam-format-link        "org-roam")
+(declare-function org-roam-link-get-path      "org-roam-link")
 
 (defcustom org-roam-buffer-position 'right
   "Position of `org-roam' buffer.
@@ -79,77 +90,128 @@ Has an effect if and only if `org-roam-buffer-position' is `top' or `bottom'."
 
 (defcustom org-roam-buffer-prepare-hook '(org-roam-buffer--insert-title
                                           org-roam-buffer--insert-backlinks
-                                          org-roam-buffer--insert-citelinks)
+                                          org-roam-buffer--insert-ref-links)
   "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
+(defcustom org-roam-buffer-window-parameters nil
+  "Additional window parameters for the `org-roam-buffer' side window.
+For example: (setq org-roam-buffer-window-parameters '((no-other-window . t)))"
+  :type '(alist)
   :group 'org-roam)
 
 (defvar org-roam-buffer--current nil
   "Currently displayed file in `org-roam' buffer.")
 
+(defun org-roam-buffer--find-file (file)
+  "Open FILE in the window `org-roam' was called from."
+  (setq file (expand-file-name file))
+  (if (and org-roam-last-window (window-valid-p org-roam-last-window))
+      (progn (with-selected-window org-roam-last-window
+               (org-roam--find-file file))
+             (select-window org-roam-last-window))
+    (org-roam--find-file file)))
+
 (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)))
+                      'font-lock-face
+                      'org-document-title)))
 
-(defun org-roam-buffer--insert-citelinks ()
-  "Insert citation backlinks for the current buffer."
-  (if-let* ((roam-key (with-temp-buffer
-                        (insert-buffer-substring org-roam-buffer--current)
-                        (org-roam--extract-ref)))
-            (key-backlinks (org-roam--get-backlinks (s-chop-prefix "cite:" roam-key)))
-            (grouped-backlinks (--group-by (nth 0 it) key-backlinks)))
-      (progn
-        (insert (format "\n\n* %d Cite backlinks\n"
-                        (length key-backlinks)))
-        (dolist (group grouped-backlinks)
-          (let ((file-from (car group))
-                (bls (cdr group)))
-            (insert (format "** [[file:%s][%s]]\n"
-                            file-from
-                            (org-roam--get-title-or-slug file-from)))
-            (dolist (backlink bls)
-              (pcase-let ((`(,file-from _ ,props) backlink))
-                (insert (propertize
-                         (s-trim (s-replace "\n" " "
-                                            (plist-get props :content)))
-                         'help-echo "mouse-1: visit backlinked note"
-                         'file-from file-from
-                         'file-from-point (plist-get props :point)))
-                (insert "\n\n"))))))
-    (insert "\n\n* No cite backlinks!")))
+(defun org-roam-buffer--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-expand-links (content orig-path)
+  "Crawl CONTENT for relative links and corrects them to be correctly displayed.
+ORIG-PATH is the path where the CONTENT originated."
+  (with-temp-buffer
+    (insert content)
+    (goto-char (point-min))
+    (let (link link-type)
+      (while (re-search-forward org-roam--org-link-bracket-typed-re (point-max) t)
+        (setq link-type (match-string 1)
+              link (match-string 2))
+        (when (and (string-equal link-type "file")
+                   (f-relative-p link))
+          (replace-match (org-roam-link-get-path (expand-file-name link (file-name-directory orig-path)))
+                         nil t nil 2))))
+    (buffer-string)))
+
+(defun org-roam-buffer--insert-ref-links ()
+  "Insert ref backlinks for the current buffer."
+  (when-let ((path (cdr (with-temp-buffer
+                          (insert-buffer-substring org-roam-buffer--current)
+                          (org-roam--extract-ref)))))
+    (if-let* ((key-backlinks (org-roam--get-backlinks path))
+              (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 "Ref Backlink" l))))
+          (dolist (group grouped-backlinks)
+            (let ((file-from (car group))
+                  (bls (cdr group)))
+              (insert (format "** %s\n"
+                              (org-roam-format-link file-from
+                                                     (org-roam--get-title-or-slug file-from)
+                                                     "file")))
+              (dolist (backlink bls)
+                (pcase-let ((`(,file-from _ ,props) backlink))
+                  (insert (propertize (org-roam-buffer-expand-links (plist-get props :content) file-from)
+                           '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 ref 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))
+            (titles (with-current-buffer org-roam-buffer--current
+                      (org-roam--extract-titles)))
+            (backlinks (org-roam--get-backlinks (push file-path titles)))
             (grouped-backlinks (--group-by (nth 0 it) backlinks)))
       (progn
-        (insert (format "\n\n* %d Backlinks\n"
-                        (length backlinks)))
+        (insert (let ((l (length backlinks)))
+                     (format "\n\n* %d %s\n"
+                             l (org-roam-buffer--pluralize "Backlink" l))))
         (dolist (group grouped-backlinks)
           (let ((file-from (car group))
-                (bls (cdr group)))
-            (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"))))))
+                (bls (mapcar (lambda (row)
+                                 (nth 2 row)) (cdr group))))
+            (insert (format "** %s\n"
+                            (org-roam-format-link file-from
+                                                   (org-roam--get-title-or-slug file-from)
+                                                   "file")))
+            ;; Sort backlinks according to time of occurrence in buffer
+            (setq bls (seq-sort-by (lambda (bl)
+                                     (plist-get bl :point))
+                                   #'<
+                                   bls))
+            (dolist (props bls)
+              (insert "*** "
+                      (if-let ((outline (plist-get props :outline)))
+                          (-> outline
+                              (string-join " > ")
+                              (org-roam-buffer-expand-links file-from))
+                        "Top")
+                      "\n"
+                      (propertize
+                       (s-trim (s-replace "\n" " "
+                                          (org-roam-buffer-expand-links (plist-get props :content) file-from)))
+                       'help-echo "mouse-1: visit backlinked note"
+                       'file-from file-from
+                       'file-from-point (plist-get props :point))
+                      "\n\n")))))
     (insert "\n\n* No backlinks!")))
 
 (defun org-roam-buffer-update ()
@@ -178,6 +240,7 @@ When non-nil, the window will not be closed when deleting other windows."
         (run-hooks 'org-roam-buffer-prepare-hook)
         (read-only-mode 1)))))
 
+
 (cl-defun org-roam-buffer--update-maybe (&key redisplay)
   "Reconstructs `org-roam-buffer'.
 This needs to be quick or infrequent, because this is run at
@@ -187,7 +250,7 @@ This needs to be quick or infrequent, because this is run at
     (when (and (or redisplay
                    (not (eq org-roam-buffer--current buffer)))
                (eq 'visible (org-roam-buffer--visibility))
-               (buffer-local-value 'buffer-file-truename buffer))
+               (buffer-file-name buffer))
       (setq org-roam-buffer--current buffer)
       (org-roam-buffer-update))))
 
@@ -226,8 +289,7 @@ Valid states are 'visible, 'exists and 'none."
 
 (defun org-roam-buffer--get-create ()
   "Set up the `org-roam' buffer at `org-roam-buffer-position'."
-  (let ((window (get-buffer-window))
-        (position
+  (let ((position
          (if (member org-roam-buffer-position '(right left top bottom))
              org-roam-buffer-position
            (let ((text-quoting-style 'grave))
@@ -235,25 +297,39 @@ Valid states are 'visible, 'exists and 'none."
                     "Invalid org-roam-buffer-position: %s. Defaulting to \\='right"
                     org-roam-buffer-position))
            'right)))
-    (-> (get-buffer-create org-roam-buffer)
-        (display-buffer-in-side-window
-         `((side . ,position)
-           (window-parameters . ((no-delete-other-windows . ,org-roam-buffer-no-delete-other-windows)))))
-        (select-window))
-    (pcase position
-      ((or 'right 'left)
-       (org-roam-buffer--set-width  (round (* (frame-width)  org-roam-buffer-width))))
-      ((or 'top  'bottom)
-       (org-roam-buffer--set-height (round (* (frame-height) org-roam-buffer-height)))))
-    (select-window window)))
+    (save-selected-window
+      (-> (get-buffer-create org-roam-buffer)
+          (display-buffer-in-side-window
+           `((side . ,position)
+             (window-parameters . ,org-roam-buffer-window-parameters)))
+          (select-window))
+      (pcase position
+        ((or 'right 'left)
+         (org-roam-buffer--set-width
+          (round (* (frame-width)  org-roam-buffer-width))))
+        ((or 'top  'bottom)
+         (org-roam-buffer--set-height
+          (round (* (frame-height) org-roam-buffer-height))))))))
+
+(defun org-roam-buffer-activate ()
+  "Activate display of the `org-roam-buffer'."
+  (interactive)
+  (unless org-roam-mode (org-roam-mode))
+  (setq org-roam-last-window (get-buffer-window))
+  (org-roam-buffer--get-create))
+
+(defun org-roam-buffer-deactivate ()
+  "Deactivate display of the `org-roam-buffer'."
+  (interactive)
+  (setq org-roam-last-window (get-buffer-window))
+  (delete-window (get-buffer-window org-roam-buffer)))
 
 (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))))
+    ('visible (org-roam-buffer-deactivate))
+    ((or 'exists 'none) (org-roam-buffer-activate))))
 
 (provide 'org-roam-buffer)
 

org-roam-capture.el

@@ -1,12 +1,12 @@
-;;; org-roam-capture.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-capture.el --- Capture functionality -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -31,25 +31,24 @@
 ;;; Code:
 ;;;; Library Requires
 (require 'org-capture)
+(require 'org-roam-macs)
 (require 'dash)
 (require 's)
+(require 'cl-lib)
 
 ;; Declarations
 (defvar org-roam-encrypt-files)
 (defvar org-roam-directory)
+(defvar org-roam-mode)
+(defvar org-roam-title-to-slug-function)
 (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--find-file                  "org-roam")
+(declare-function  org-roam-format-link                "org-roam")
+(declare-function  org-roam-mode                        "org-roam")
 (declare-function  org-roam-completion--completing-read "org-roam-completion")
 
-(defvar org-roam-capture--file-name-default "%<%Y%m%d%H%M%S>"
-  "The default file name format for Org-roam templates.")
-
-(defvar org-roam-capture--header-default "#+TITLE: ${title}\n"
-  "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.")
@@ -78,66 +77,287 @@ note with the given `ref'.")
 (defconst org-roam-capture--template-keywords '(:file-name :head)
   "Keywords used in `org-roam-capture-templates' specific to Org-roam.")
 
-(defvar org-roam-capture-templates
+(defcustom org-roam-capture-templates
   '(("d" "default" plain (function org-roam-capture--get-point)
      "%?"
      :file-name "%<%Y%m%d%H%M%S>-${slug}"
-     :head "#+TITLE: ${title}\n"
+     :head "#+title: ${title}\n"
      :unnarrowed t))
   "Capture templates for Org-roam.
-The capture templates are an extension of
-`org-capture-templates', and the documentation there also
-applies.
+The Org-roam capture-templates  builds on the default behaviours of
+`org-capture-templates' by expanding them in 3 areas:
 
-`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.
 
-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.
+2. The `:file-name' key is added, which defines the naming format
+   to use when creating new notes. 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.")
+   inserted upon the creation of a new file. This is where you
+   your note metadata should go.
 
-(defvar org-roam-capture-ref-templates
+Each template should have the following structure:
+
+\(KEY DESCRIPTION `plain' `(function org-roam-capture--get-point)'
+  TEMPLATE
+  `:file-name' FILENAME-FORMAT
+  `:head' HEADER-FORMAT
+  `:unnarrowed t'
+  OPTIONS-PLIST)
+
+The elements of a template-entry and their placement are the same
+as in `org-capture-templates', except that the entry type must
+always be the symbol `plain', and that the target must always be
+the list `(function org-roam-capture--get-point)'.
+
+Org-roam requires the plist elements `:file-name' and `:head' to
+be present, and it’s recommended that `:unnarrowed' be set to t."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(repeat
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                    "%?"
+                    :file-name "%<%Y%m%d%H%M%S>-${slug}"
+                    :head "#+title: ${title}\n"
+                    :unnarrowed t)
+            (list :tag "Multikey description"
+                  (string :tag "Keys       ")
+                  (string :tag "Description"))
+            (list :tag "Template entry"
+                  (string :tag "Keys              ")
+                  (string :tag "Description       ")
+                  (const :format "" plain)
+                  (const :format "" (function org-roam-capture--get-point))
+                  (choice :tag "Template          "
+                          (string :tag "String"
+                                  :format "String:\n            \
+Template string   :\n%v")
+                          (list :tag "File"
+                                (const :format "" file)
+                                (file :tag "Template file     "))
+                          (list :tag "Function"
+                                (const :format "" function)
+                                (function :tag "Template function ")))
+                  (const :format "File name format  :" :file-name)
+                  (string :format " %v" :value "#+title: ${title}\n")
+                  (const :format "Header format     :" :head)
+                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+                  (const :format "" :unnarrowed) (const :format "" t)
+                  (plist :inline t
+                         :tag "Options"
+                         ;; Give the most common options as checkboxes
+                         :options
+                         (((const :format "%v " :prepend) (const t))
+                          ((const :format "%v " :immediate-finish) (const t))
+                          ((const :format "%v " :jump-to-captured) (const t))
+                          ((const :format "%v " :empty-lines) (const 1))
+                          ((const :format "%v " :empty-lines-before) (const 1))
+                          ((const :format "%v " :empty-lines-after) (const 1))
+                          ((const :format "%v " :clock-in) (const t))
+                          ((const :format "%v " :clock-keep) (const t))
+                          ((const :format "%v " :clock-resume) (const t))
+                          ((const :format "%v " :time-prompt) (const t))
+                          ((const :format "%v " :tree-type) (const week))
+                          ((const :format "%v " :table-line-pos) (string))
+                          ((const :format "%v " :kill-buffer) (const t))))))))
+
+(defcustom org-roam-capture-immediate-template
+  (append (car org-roam-capture-templates) '(:immediate-finish t))
+  "Capture template to use for immediate captures in Org-roam.
+This is a single template, so do not enclose it into a list.
+See `org-roam-capture-templates' for details on templates."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(list :tag "Template entry"
+         :value ("d" "default" plain (function org-roam-capture--get-point)
+                 "%?"
+                 :file-name "%<%Y%m%d%H%M%S>-${slug}"
+                 :head "#+title: ${title}\n"
+                 :unnarrowed t
+                 :immediate-finish t)
+         (string :tag "Keys              ")
+         (string :tag "Description       ")
+         (const :format "" plain)
+         (const :format "" (function org-roam-capture--get-point))
+         (choice :tag "Template          "
+                 (string :tag "String"
+                         :format "String:\n            \
+Template string   :\n%v")
+                 (list :tag "File"
+                       (const :format "" file)
+                       (file :tag "Template file     "))
+                 (list :tag "Function"
+                       (const :format "" function)
+                       (function :tag "Template function ")))
+         (const :format "File name format  :" :file-name)
+         (string :format " %v" :value "#+title: ${title}\n")
+         (const :format "Header format     :" :head)
+         (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+         (const :format "" :unnarrowed) (const :format "" t)
+         (const :format "" :immediate-finish) (const :format "" t)
+         (plist :inline t
+                :tag "Options"
+                ;; Give the most common options as checkboxes
+                :options
+                (((const :format "%v " :prepend) (const t))
+                 ((const :format "%v " :jump-to-captured) (const t))
+                 ((const :format "%v " :empty-lines) (const 1))
+                 ((const :format "%v " :empty-lines-before) (const 1))
+                 ((const :format "%v " :empty-lines-after) (const 1))
+                 ((const :format "%v " :clock-in) (const t))
+                 ((const :format "%v " :clock-keep) (const t))
+                 ((const :format "%v " :clock-resume) (const t))
+                 ((const :format "%v " :time-prompt) (const t))
+                 ((const :format "%v " :tree-type) (const week))
+                 ((const :format "%v " :table-line-pos) (string))
+                 ((const :format "%v " :kill-buffer) (const t))))))
+
+(defcustom org-roam-capture-ref-templates
   '(("r" "ref" plain (function org-roam-capture--get-point)
-     ""
+     "%?"
      :file-name "${slug}"
-     :head "#+TITLE: ${title}
-#+ROAM_KEY: ${ref}\n"
+     :head "#+title: ${title}\n#+roam_key: ${ref}\n"
      :unnarrowed t))
   "The Org-roam templates used during a capture from the roam-ref protocol.
-Details on how to specify for the template is given in `org-roam-capture-templates'.")
+Details on how to specify for the template is given in `org-roam-capture-templates'."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(repeat
+    (choice :value ("d" "default" plain (function org-roam-capture--get-point)
+                    "%?"
+                    :file-name "${slug}"
+                    :head "#+title: ${title}\n#+roam_key: ${ref}\n"
+                    :unnarrowed t)
+            (list :tag "Multikey description"
+                  (string :tag "Keys       ")
+                  (string :tag "Description"))
+            (list :tag "Template entry"
+                  (string :tag "Keys              ")
+                  (string :tag "Description       ")
+                  (const :format "" plain)
+                  (const :format "" (function org-roam-capture--get-point))
+                  (choice :tag "Template          "
+                          (string :tag "String"
+                                  :format "String:\n            \
+Template string   :\n%v")
+                          (list :tag "File"
+                                (const :format "" file)
+                                (file :tag "Template file     "))
+                          (list :tag "Function"
+                                (const :format "" function)
+                                (function :tag "Template function ")))
+                  (const :format "File name format  :" :file-name)
+                  (string :format " %v" :value "#+title: ${title}\n")
+                  (const :format "Header format     :" :head)
+                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+                  (const :format "" :unnarrowed) (const :format "" t)
+                  (plist :inline t
+                         :tag "Options"
+                         ;; Give the most common options as checkboxes
+                         :options
+                         (((const :format "%v " :prepend) (const t))
+                          ((const :format "%v " :immediate-finish) (const t))
+                          ((const :format "%v " :jump-to-captured) (const t))
+                          ((const :format "%v " :empty-lines) (const 1))
+                          ((const :format "%v " :empty-lines-before) (const 1))
+                          ((const :format "%v " :empty-lines-after) (const 1))
+                          ((const :format "%v " :clock-in) (const t))
+                          ((const :format "%v " :clock-keep) (const t))
+                          ((const :format "%v " :clock-resume) (const t))
+                          ((const :format "%v " :time-prompt) (const t))
+                          ((const :format "%v " :tree-type) (const week))
+                          ((const :format "%v " :table-line-pos) (string))
+                          ((const :format "%v " :kill-buffer) (const t))))))))
+
+(defun org-roam-capture-p ()
+  "Return t if the current capture process is an Org-roam capture.
+This function is to only be called when org-capture-plist is
+valid for the capture (i.e. initialization, and finalization of
+the capture)."
+  (plist-get org-capture-plist :org-roam))
 
 (defun org-roam-capture--get (keyword)
-  "Gets the value for KEYWORD from the `org-roam-capture-template'."
+  "Get the value for KEYWORD from the `org-roam-capture-template'."
   (plist-get (plist-get org-capture-plist :org-roam) keyword))
 
 (defun org-roam-capture--put (&rest stuff)
-  "Puts properties from STUFF into the `org-roam-capture-template'."
+  "Put properties from STUFF into the `org-roam-capture-template'."
   (let ((p (plist-get org-capture-plist :org-roam)))
     (while stuff
-      (setq p (plist-put p
-                         (pop stuff) (pop stuff))))
+      (setq p (plist-put p (pop stuff) (pop stuff))))
     (setq org-capture-plist
           (plist-put org-capture-plist :org-roam p))))
 
-(defun org-roam-capture--in-process-p ()
-  "Return non-nil if a `org-roam-capture' buffer exists."
-  (cl-some (lambda (buffer)
-	     (and (eq (buffer-local-value 'major-mode (current-buffer)) 'org-mode)
-		  (plist-get (buffer-local-value 'org-capture-current-plist (current-buffer)) :org-roam)))
-	   (buffer-list)))
+;; FIXME: Pending upstream patch
+;; https://orgmode.org/list/87h7tv9pkm.fsf@hidden/T/#u
+;;
+;; Org-capture's behaviour right now is that `org-capture-plist' is valid only
+;; during the initialization of the Org-capture buffer. The value of
+;; `org-capture-plist' is saved into buffer-local `org-capture-current-plist'.
+;; However, the value for that particular capture is no longer accessible for
+;; hooks in `org-capture-after-finalize-hook', since the capture buffer has been
+;; cleaned up.
+;;
+;; This advice restores the global `org-capture-plist' during finalization, so
+;; the plist is valid during both initialization and finalization of the
+;; capture.
+(defun org-roam-capture--update-plist (&optional _)
+  "Update global plist from local var."
+  (setq org-capture-plist org-capture-current-plist))
 
-(defun org-roam-capture--fill-template (str &optional info)
-  "Expands the template STR, returning the string.
+(advice-add 'org-capture-finalize :before #'org-roam-capture--update-plist)
+
+(defun org-roam-capture--finalize ()
+  "Finalize the `org-roam-capture' process."
+  (let* ((finalize (org-roam-capture--get :finalize))
+         ;; In case any regions were shielded before, unshield them
+         (region (when-let ((region (org-roam-capture--get :region)))
+                   (org-roam-unshield-region (car region) (cdr region))))
+         (beg (car region))
+         (end (cdr region)))
+    (unless org-note-abort
+      (pcase finalize
+        ('find-file
+         (when-let ((file-path (org-roam-capture--get :file-path)))
+           (org-roam--find-file file-path)
+           (run-hooks 'org-roam-capture-after-find-file-hook)))
+        ('insert-link
+         (when-let* ((mkr (org-roam-capture--get :insert-at))
+                     (buf (marker-buffer mkr)))
+           (with-current-buffer buf
+             (when region
+               (delete-region (car region) (cdr region)))
+             (let ((path (org-roam-capture--get :file-path))
+                   (type (org-roam-capture--get :link-type))
+                   (desc (org-roam-capture--get :link-description)))
+               (if (eq (point) (marker-position mkr))
+                   (insert (org-roam-format-link path desc type))
+                 (org-with-point-at mkr
+                   (insert (org-roam-format-link path desc type))))))))))
+    (when region
+      (set-marker beg nil)
+      (set-marker end nil))
+    (org-roam-capture--save-file-maybe)
+    (remove-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
+
+(defun org-roam-capture--install-finalize ()
+  "Install `org-roam-capture--finalize' if the capture is an Org-roam capture."
+  (when (org-roam-capture-p)
+    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--finalize)))
+
+(add-hook 'org-capture-prepare-finalize-hook #'org-roam-capture--install-finalize)
+
+(defun org-roam-capture--fill-template (str)
+  "Expand 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.
+First, it expands ${var} occurrences in STR, using `org-roam-capture--info'.
 If there is a ${var} with no matching var in the alist, the value
 of var is prompted for via `completing-read'.
 
@@ -145,23 +365,13 @@ 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)
+                  (or (s--aget org-roam-capture--info key)
+                      (when-let ((val (completing-read (format "%s: " key) nil)))
+                        (push (cons key val) org-roam-capture--info)
+                        val))) 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 ()
+(defun org-roam-capture--save-file-maybe ()
   "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
@@ -175,8 +385,7 @@ The file is saved if the original value of :no-save is not t and
    ((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))
+      (save-buffer)))))
 
 (defun org-roam-capture--new-file ()
   "Return the path to the new file during an Org-roam capture.
@@ -196,17 +405,14 @@ aborted, we do the following:
 
 2. Set the capture template's :no-save to t.
 
-3. Add a function on `org-capture-after-finalize-hook' that saves
+3. Add a function on `org-capture-before-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))
+  (let* ((name-templ (org-roam-capture--get :file-name))
          (new-id (s-trim (org-roam-capture--fill-template
-                          name-templ
-                          org-roam-capture--info)))
+                          name-templ)))
          (file-path (org-roam--file-path-from-id new-id))
-         (roam-head (or (org-roam-capture--get :head)
-                        org-roam-capture--header-default))
+         (roam-head (org-roam-capture--get :head))
          (org-template (org-capture-get :template))
          (roam-template (concat roam-head org-template)))
     (unless (file-exists-p file-path)
@@ -224,16 +430,6 @@ the file if the original value of :no-save is not t and
                        :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:
@@ -262,10 +458,12 @@ This function is used solely in Org-roam's capture templates: see
                      ('ref
                       (let ((completions (org-roam--get-ref-path-completions))
                             (ref (cdr (assoc 'ref org-roam-capture--info))))
-                        (or (cdr (assoc ref completions))
-                            (org-roam-capture--new-file))))
+                        (if-let ((pl (cdr (assoc ref completions))))
+                            (plist-get pl :path)
+                          (org-roam-capture--new-file))))
                      (_ (error "Invalid org-roam-capture-context")))))
-    (org-roam-capture--expand-template)
+    (org-capture-put :template
+                     (org-roam-capture--fill-template (org-capture-get :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))
@@ -277,33 +475,24 @@ This function is used solely in Org-roam's capture templates: see
 
 (defun org-roam-capture--convert-template (template)
   "Convert TEMPLATE from Org-roam syntax to `org-capture-templates' syntax."
-  (let* ((copy (copy-tree template))
-         converted
-         org-roam-plist
-         key
-         val)
-    ;;put positional args on converted template
-    (dotimes (_ 5)
-      (push (pop copy) converted))
-    (while (setq key (pop copy)
-                 val (pop copy))
-      (if (member key org-roam-capture--template-keywords)
-          (progn
-            (push val org-roam-plist)
-            (push key org-roam-plist))
-        (push key converted)
-        (push val converted)))
-    (append (nreverse converted) `(:org-roam ,org-roam-plist))))
-
-(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))
+  (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)))
+           (when (and custom
+                      (not val))
+             (user-error "Invalid capture template format: %s\nkey %s cannot be nil" template key))
+           (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))))
 
 (defcustom org-roam-capture-after-find-file-hook nil
   "Hook that is run right after an Org-roam capture process is finalized.
@@ -311,33 +500,47 @@ Suitable for moving point."
   :group 'org-roam
   :type 'hook)
 
-(defun org-roam--capture (&optional goto keys)
+(defcustom org-roam-capture-function #'org-capture
+  "Function that is invoked to start the `org-capture' process."
+  :group 'org-roam
+  :type 'function)
+
+(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)))
-    (when (= (length org-capture-templates) 1)
+  (let* ((org-capture-templates (mapcar #'org-roam-capture--convert-template org-roam-capture-templates))
+         (one-template-p (= (length org-capture-templates) 1))
+         org-capture-templates-contexts)
+    (when one-template-p
       (setq keys (caar org-capture-templates)))
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--save-file-maybe-h)
-    (org-capture goto keys)))
+    (if (or one-template-p
+            (eq org-roam-capture-function 'org-capture))
+        (org-capture goto keys)
+      (funcall-interactively org-roam-capture-function))))
 
 ;;;###autoload
-(defun org-roam-capture ()
+(defun org-roam-capture (&optional goto keys)
   "Launches an `org-capture' process for a new or existing note.
-This uses the templates defined at `org-roam-capture-templates'."
-  (interactive)
-  (when (org-roam-capture--in-process-p)
-    (user-error "Nested Org-roam capture processes not supported"))
+This uses the templates defined at `org-roam-capture-templates'.
+Arguments GOTO and KEYS see `org-capture'."
+  (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
   (let* ((completions (org-roam--get-title-path-completions))
-         (title (org-roam-completion--completing-read "File: " completions))
-         (file-path (cdr (assoc title completions))))
+         (title-with-keys (org-roam-completion--completing-read "File: "
+                                                                completions))
+         (res (cdr (assoc title-with-keys completions)))
+         (title (or (plist-get res :title) title-with-keys))
+         (file-path (plist-get res :path)))
     (let ((org-roam-capture--info (list (cons 'title title)
-                                        (cons 'slug (org-roam--title-to-slug title))
+                                        (cons 'slug (funcall org-roam-title-to-slug-function title))
                                         (cons 'file file-path)))
           (org-roam-capture--context 'capture))
-      (setq org-roam-capture-additional-template-props (list :capture-fn 'org-roam-capture))
-      (org-roam--capture))))
+      (condition-case err
+          (org-roam-capture--capture goto keys)
+        (error (user-error "%s.  Please adjust `org-roam-capture-templates'"
+                           (error-message-string err)))))))
 
 (provide 'org-roam-capture)
 

org-roam-compat.el

@@ -1,12 +1,12 @@
-;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-compat.el --- Compatibility Code -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -41,8 +41,6 @@
   "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
@@ -71,17 +69,24 @@
   "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")
+(define-obsolete-function-alias 'org-roam-db--clear 'org-roam-db-clear
+  "org-roam 1.2.0")
 
 ;;;; Variables
 (define-obsolete-variable-alias 'org-roam-graphviz-extra-options
   'org-roam-graph-extra-config "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-grapher-extra-options
   'org-roam-graph-extra-config "org-roam 1.0.0")
-(make-obsolete-variable 'org-roam-graph-node-shape  'org-roam-graph-node-extra-config "org-roam 1.0.0")
-(defcustom org-roam-graph-node-shape "ellipse"
-  "Shape of graph nodes."
-  :type 'string
-  :group 'org-roam)
+(define-obsolete-variable-alias 'org-roam-graph-node-shape
+  'org-roam-graph-node-extra-config "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam--db-connection
   'org-roam-db--connection "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam--current-buffer
@@ -90,6 +95,8 @@
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
 (define-obsolete-variable-alias 'org-roam-date-filename-format
   'org-roam-dailies-capture-templates "org-roam 1.0.0")
+(make-obsolete-variable 'org-roam-buffer-no-delete-other-windows
+  'org-roam-buffer-window-parameters "org-roam 1.1.1")
 
 (provide 'org-roam-compat)
 

org-roam-completion.el

@@ -1,12 +1,12 @@
-;;; org-roam-completion.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-completion.el --- Completion features -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -47,10 +47,10 @@
           (function :tag "Custom function"))
   :group 'org-roam)
 
-(defcustom org-roam-completion-fuzzy-match nil
-  "Whether to fuzzy match Org-roam's completion candidates."
-  :type 'boolean
-  :group 'org-roam)
+(defcustom org-roam-completion-ignore-case t
+  "Whether to ignore case in Org-roam `completion-at-point' completions."
+  :group 'org-roam
+  :type 'boolean)
 
 (defun org-roam-completion--helm-candidate-transformer (candidates _source)
   "Transforms CANDIDATES for Helm-based completing read.
@@ -82,9 +82,7 @@ Return user choice."
                           :require-match require-match
                           :action (prog1 action
                                     (setq action nil))
-                          :caller 'org-roam--completing-read
-                          :re-builder (if org-roam-completion-fuzzy-match 'ivy--regex-fuzzy
-                                        'regexp-quote))
+                          :caller 'org-roam--completing-read)
               (user-error "Please install ivy from \
 https://github.com/abo-abo/swiper")))
            ((eq org-roam-completion-system 'helm)
@@ -96,8 +94,7 @@ https://github.com/emacs-helm/helm"))
                             :candidates (mapcar #'car choices)
                             :filtered-candidate-transformer
                             (and (not require-match)
-                                 #'org-roam-completion--helm-candidate-transformer)
-                            :fuzzy-match org-roam-completion-fuzzy-match))
+                                 #'org-roam-completion--helm-candidate-transformer)))
                   (buf (concat "*org-roam "
                                (s-downcase (s-chop-suffix ":" (s-trim prompt)))
                                "*")))

org-roam-dailies.el

@@ -1,12 +1,12 @@
-;;; org-roam-dialies.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-dailies.el --- Daily notes for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
 ;;;
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -34,42 +34,97 @@
 ;;; Library Requires
 (require 'org-capture)
 (require 'org-roam-capture)
+(require 'org-roam-macs)
 
-(defvar org-roam-dailies-capture-templates
+(defcustom 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.")
+     :head "#+title: %<%Y-%m-%d>"))
+  "Capture templates for daily notes in Org-roam."
+  :group 'org-roam
+  ;; Adapted from `org-capture-templates'
+  :type
+  '(repeat
+    (choice :value ("d" "daily" plain (function org-roam-capture--get-point)
+                    ""
+                    :immediate-finish t
+                    :file-name "%<%Y-%m-%d>"
+                    :head "#+title: %<%Y-%m-%d>")
+            (list :tag "Multikey description"
+                  (string :tag "Keys       ")
+                  (string :tag "Description"))
+            (list :tag "Template entry"
+                  (string :tag "Keys              ")
+                  (string :tag "Description       ")
+                  (const :format "" plain)
+                  (const :format "" (function org-roam-capture--get-point))
+                  (choice :tag "Template          "
+                          (string :tag "String"
+                                  :format "String:\n            \
+Template string   :\n%v")
+                          (list :tag "File"
+                                (const :format "" file)
+                                (file :tag "Template file     "))
+                          (list :tag "Function"
+                                (const :format "" function)
+                                (function :tag "Template function ")))
+                  (const :format "" :immediate-finish) (const :format "" t)
+                  (const :format "File name format  :" :file-name)
+                  (string :format " %v" :value "#+title: ${title}\n")
+                  (const :format "Header format     :" :head)
+                  (string :format "\n%v" :value "%<%Y%m%d%H%M%S>-${slug}")
+                  (plist :inline t
+                         :tag "Options"
+                         ;; Give the most common options as checkboxes
+                         :options
+                         (((const :format "%v " :prepend) (const t))
+                          ((const :format "%v " :jump-to-captured) (const t))
+                          ((const :format "%v " :empty-lines) (const 1))
+                          ((const :format "%v " :empty-lines-before) (const 1))
+                          ((const :format "%v " :empty-lines-after) (const 1))
+                          ((const :format "%v " :clock-in) (const t))
+                          ((const :format "%v " :clock-keep) (const t))
+                          ((const :format "%v " :clock-resume) (const t))
+                          ((const :format "%v " :time-prompt) (const t))
+                          ((const :format "%v " :tree-type) (const week))
+                          ((const :format "%v " :table-line-pos) (string))
+                          ((const :format "%v " :kill-buffer) (const t))
+                          ((const :format "%v " :unnarrowed) (const t))))))))
 
 ;; Declarations
+(defvar org-roam-mode)
 (declare-function org-roam--file-path-from-id "org-roam")
+(declare-function org-roam-mode               "org-roam")
 
 (defun org-roam-dailies--file-for-time (time)
   "Create and find file for TIME."
   (let ((org-roam-capture-templates org-roam-dailies-capture-templates)
         (org-roam-capture--info (list (cons 'time time)))
         (org-roam-capture--context 'dailies))
-    (add-hook 'org-capture-after-finalize-hook #'org-roam-capture--find-file-h)
-    (org-roam--capture)))
+    (setq org-roam-capture-additional-template-props (list :finalize 'find-file))
+    (org-roam-capture--capture)))
 
 (defun org-roam-dailies-today ()
   "Create and find the daily note for today."
   (interactive)
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (current-time)))
 
 (defun org-roam-dailies-tomorrow (n)
   "Create and find the daily note for tomorrow.
 With numeric argument N, use N days in the future."
   (interactive "p")
+  (unless org-roam-mode (org-roam-mode))
   (org-roam-dailies--file-for-time (time-add (* n 86400) (current-time))))
 
 (defun org-roam-dailies-yesterday (n)
   "Create and find the file for yesterday.
 With numeric argument N, use N days in the past."
   (interactive "p")
-  (org-roam-tomorrow (- n)))
+  (unless org-roam-mode (org-roam-mode))
+  (org-roam-dailies-tomorrow (- n)))
 
 (defun org-roam-dailies-date ()
   "Create the file for any date using the calendar interface."
@@ -78,4 +133,5 @@ With numeric argument N, use N days in the past."
     (org-roam-dailies--file-for-time time)))
 
 (provide 'org-roam-dailies)
+
 ;;; org-roam-dailies.el ends here

org-roam-db.el

@@ -1,12 +1,12 @@
-;;; org-roam-db.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-db.el --- Org-roam database API -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -33,21 +33,30 @@
 ;;;; Library Requires
 (eval-when-compile (require 'subr-x))
 (require 'emacsql)
-(require 'emacsql-sqlite)
+(require 'emacsql-sqlite3)
+(require 'seq)
+(require 'org-macs)
 (require 'org-roam-macs)
 
 (defvar org-roam-directory)
+(defvar org-roam-enable-headline-linking)
 (defvar org-roam-verbose)
+(defvar org-roam-file-name)
 
-(declare-function org-roam--extract-titles      "org-roam")
-(declare-function org-roam--extract-ref         "org-roam")
-(declare-function org-roam--extract-links       "org-roam")
-(declare-function org-roam--list-files          "org-roam")
-(declare-function org-roam-buffer--update-maybe "org-roam-buffer")
+(declare-function org-roam--org-roam-file-p                "org-roam")
+(declare-function org-roam--extract-titles                 "org-roam")
+(declare-function org-roam--extract-ref                    "org-roam")
+(declare-function org-roam--extract-tags                   "org-roam")
+(declare-function org-roam--extract-ids                    "org-roam")
+(declare-function org-roam--extract-links                  "org-roam")
+(declare-function org-roam--list-all-files                 "org-roam")
+(declare-function org-roam--path-to-slug                   "org-roam")
+(declare-function org-roam--file-name-extension            "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.
+(defcustom org-roam-db-location (expand-file-name "org-roam.db" user-emacs-directory)
+  "The full path to file where the Org-roam database is stored.
 If this is non-nil, the Org-roam sqlite database is saved here.
 
 It is the user's responsibility to set this correctly, especially
@@ -55,25 +64,31 @@ when used with multiple Org-roam instances."
   :type 'string
   :group 'org-roam)
 
-(defconst org-roam-db--version 2)
-(defconst org-roam-db--sqlite-available-p
-  (with-demoted-errors "Org-roam initialization: %S"
-    (emacsql-sqlite-ensure-binary)
-    t))
+(defcustom org-roam-db-gc-threshold gc-cons-threshold
+  "The value to temporarily set the `gc-cons-threshold' threshold to.
+During large, heavy operations like `org-roam-db-build-cache',
+many GC operations happen because of the large number of
+temporary structures generated (e.g. parsed ASTs). Temporarily
+increasing `gc-cons-threshold' will help reduce the number of GC
+operations, at the cost of temporary memory usage.
+
+This defaults to the original value of `gc-cons-threshold', but
+tweaking this number may lead to better overall performance. For
+example, to reduce the number of GCs, one may set it to a large
+value like `most-positive-fixnum'."
+  :type 'int
+  :group 'org-roam)
+
+(defconst org-roam-db--version 9)
 
 (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)
+  (gethash (expand-file-name org-roam-directory)
            org-roam-db--connection))
 
 (defun org-roam-db ()
@@ -82,18 +97,17 @@ Initializes and stores the database, and the database connection.
 Performs a database upgrade when required."
   (unless (and (org-roam-db--get-connection)
                (emacsql-live-p (org-roam-db--get-connection)))
-    (let* ((db-file (org-roam-db--get))
-           (init-db (not (file-exists-p db-file))))
-      (make-directory (file-name-directory db-file) t)
-      (let ((conn (emacsql-sqlite db-file)))
+    (let ((init-db (not (file-exists-p org-roam-db-location))))
+      (make-directory (file-name-directory org-roam-db-location) t)
+      (let ((conn (emacsql-sqlite3 org-roam-db-location)))
         (set-process-query-on-exit-flag (emacsql-process conn) nil)
-        (puthash (file-truename org-roam-directory)
+        (puthash (expand-file-name org-roam-directory)
                  conn
                  org-roam-db--connection)
         (when init-db
           (org-roam-db--init conn))
         (let* ((version (caar (emacsql conn "PRAGMA user_version")))
-               (version (org-roam-db--maybe-update conn version)))
+               (version (org-roam-db--update-maybe conn version)))
           (cond
            ((> version org-roam-db--version)
             (emacsql-close conn)
@@ -119,7 +133,12 @@ SQL can be either the emacsql vector representation, or a string."
   '((files
      [(file :unique :primary-key)
       (hash :not-null)
-      (last-modified :not-null)])
+      (meta :not-null)])
+
+    (ids
+     [(id :unique :primary-key)
+      (file :not-null)
+      (level :not-null)])
 
     (links
      [(from :not-null)
@@ -127,13 +146,18 @@ SQL can be either the emacsql vector representation, or a string."
       (type :not-null)
       (properties :not-null)])
 
+    (tags
+     [(file :unique :primary-key)
+      (tags)])
+
     (titles
      [(file :not-null)
-      titles])
+      title])
 
     (refs
      [(ref :unique :not-null)
-      (file :not-null)])))
+      (file :not-null)
+      (type :not-null)])))
 
 (defun org-roam-db--init (db)
   "Initialize database DB with the correct schema and user version."
@@ -142,16 +166,16 @@ SQL can be either the emacsql vector representation, or a string."
       (emacsql db [:create-table $i1 $S2] table schema))
     (emacsql db (format "PRAGMA user_version = %s" org-roam-db--version))))
 
-(defun org-roam-db--maybe-update (db version)
+(defun org-roam-db--update-maybe (db version)
   "Upgrades the database schema for DB, if VERSION is old."
   (emacsql-with-transaction db
     'ignore
-    (when (= version 1)
-      (progn
-        (warn "No good way to perform a DB upgrade, rebuilding from scratch...")
-        (delete-file (org-roam-db--get))
-        (org-roam-db-build-cache)))
-    version))
+    (if (< version org-roam-db--version)
+        (progn
+          (org-roam-message (format "Upgrading the Org-roam database from version %d to version %d"
+                                    version org-roam-db--version))
+          (org-roam-db-build-cache t))))
+  version)
 
 (defun org-roam-db--close (&optional db)
   "Closes the database connection for database DB.
@@ -170,8 +194,8 @@ the current `org-roam-directory'."
 ;;;; Database API
 ;;;;; Initialization
 (defun org-roam-db--initialized-p ()
-  "Whether the cache has been initialized."
-  (and (file-exists-p (org-roam-db--get))
+  "Whether the Org-roam cache has been initialized."
+  (and (file-exists-p org-roam-db-location)
        (> (caar (org-roam-db-query [:select (funcall count) :from titles]))
           0)))
 
@@ -181,36 +205,31 @@ the current `org-roam-directory'."
     (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."
+(defun org-roam-db-clear ()
+  "Clears all entries in the Org-roam cache."
   (interactive)
-  (when (file-exists-p (org-roam-db--get))
-    (org-roam-db-query [:delete :from files])
-    (org-roam-db-query [:delete :from titles])
-    (org-roam-db-query [:delete :from links])
-    (org-roam-db-query [:delete :from refs])))
-
+  (when (file-exists-p org-roam-db-location)
+    (dolist (table (mapcar #'car org-roam-db--table-schemata))
+      (org-roam-db-query `[:delete :from ,table]))))
 
 (defun org-roam-db--clear-file (&optional filepath)
   "Remove any related links to the file at FILEPATH.
 This is equivalent to removing the node from the graph."
-  (let* ((path (or filepath
-                   (buffer-file-name)))
-         (file (file-truename path)))
-    (org-roam-db-query [:delete :from files
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db-query [:delete :from links
-                        :where (= from $s1)]
-                       file)
-    (org-roam-db-query [:delete :from titles
-                        :where (= file $s1)]
-                       file)
-    (org-roam-db-query [:delete :from refs
-                        :where (= file $s1)]
-                       file)))
+  (let ((file (expand-file-name (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
@@ -223,14 +242,59 @@ This is equivalent to removing the node from the graph."
   (org-roam-db-query
    [:insert :into titles
     :values $v1]
-   (list (vector file titles))))
+   (mapcar (lambda (title)
+             (vector file title)) titles)))
+
+(defun org-roam-db--insert-ids (ids)
+  "Insert IDS into the Org-roam cache.
+Returns t if the insertion was successful, nil otherwise.
+Insertions can fail when there is an ID conflict."
+  (condition-case nil
+      (progn
+        (org-roam-db-query
+         [:insert :into ids
+          :values $v1]
+         ids)
+        t)
+    (error
+     (unless (listp ids)
+       (setq ids (list ids)))
+     (lwarn '(org-roam) :error
+            (format "Duplicate IDs in %s, one of:\n\n%s\n\nskipping..."
+                    (aref (car ids) 1)
+                    (string-join (mapcar (lambda (hl)
+                                           (aref hl 0)) ids) "\n")))
+     nil)))
+
+(defun org-roam-db--insert-tags (file tags)
+  "Insert TAGS for a FILE into the Org-roam cache."
+  (org-roam-db-query
+   [:insert :into tags
+    :values $v1]
+   (list (vector file tags))))
 
 (defun org-roam-db--insert-ref (file ref)
-  "Insert REF for FILE into the Org-roam cache."
-  (org-roam-db-query
-   [:insert :into refs
-    :values $v1]
-   (list (vector ref file))))
+  "Insert REF for FILE into the Org-roam cache.
+Returns t if successful, and nil otherwise.
+Insertions can fail if the key is already in the database."
+  (let ((key (cdr ref))
+        (type (car ref)))
+    (condition-case nil
+        (progn
+          (org-roam-db-query
+           [:insert :into refs :values $v1]
+           (list (vector key file type)))
+          t)
+      (error
+       (lwarn '(org-roam) :error
+              (format "Duplicate ref %s in:\n\nA: %s\nB: %s\n\nskipping..."
+                      key
+                      file
+                      (caar (org-roam-db-query
+                             [:select file :from refs
+                              :where (= ref $v1)]
+                             (vector key)))))
+       nil))))
 
 ;;;;; Fetching
 (defun org-roam-db--get-current-files ()
@@ -243,22 +307,32 @@ This is equivalent to removing the node from the graph."
 
 (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)))
+  (caar (org-roam-db-query [:select [title] :from titles
+                            :where (= file $s1)
+                            :limit 1]
+                           file)))
+
+(defun org-roam-db--get-tags ()
+  "Return all distinct tags from the cache."
+  (let ((rows (org-roam-db-query [:select :distinct [tags] :from tags]))
+        acc)
+    (dolist (row rows)
+      (dolist (tag (car row))
+        (unless (member tag acc)
+          (push tag acc))))
+    acc))
 
 (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\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    connected_component(file) AS
@@ -270,16 +344,17 @@ If the file does not have any connections, nil is returned."
     files))
 
 (defun org-roam-db--links-with-max-distance (file max-distance)
-  "Return all files reachable from/connected to FILE in at most MAX-DISTANCE steps,
-including the file itself.  If the file does not have any connections, nil is returned."
+  "Return all files connected to FILE in at most MAX-DISTANCE steps.
+This includes the file itself. If the file does not have any
+connections, nil is returned."
   (let* ((query "WITH RECURSIVE
                    links_of(file, link) AS
-                     (WITH roamlinks AS (SELECT * FROM links WHERE \"type\" = '\"roam\"'),
+                     (WITH filelinks AS (SELECT * FROM links WHERE NOT \"type\" = '\"cite\"'),
                            citelinks AS (SELECT * FROM links
                                                   JOIN refs ON links.\"to\" = refs.\"ref\"
                                                             AND links.\"type\" = '\"cite\"')
-                      SELECT \"from\", \"to\" FROM roamlinks UNION
-                      SELECT \"to\", \"from\" FROM roamlinks UNION
+                      SELECT \"from\", \"to\" FROM filelinks UNION
+                      SELECT \"to\", \"from\" FROM filelinks UNION
                       SELECT \"file\", \"from\" FROM citelinks UNION
                       SELECT \"from\", \"file\" FROM citelinks),
                    -- Links are traversed in a breadth-first search.  In order to calculate the
@@ -301,108 +376,178 @@ including the file itself.  If the file does not have any connections, nil is re
          (files (mapcar 'car-safe (emacsql (org-roam-db) query file max-distance))))
     files))
 
+(defun org-roam-db--file-hash (&optional file-path)
+  "Compute the hash of FILE-PATH, a file or current buffer."
+  (if file-path
+      (with-temp-buffer
+        (set-buffer-multibyte nil)
+        (insert-file-contents-literally file-path)
+        (secure-hash 'sha1 (current-buffer)))
+    (org-with-wide-buffer
+     (secure-hash 'sha1 (current-buffer)))))
+
 ;;;;; Updating
+(defun org-roam-db--update-meta ()
+  "Update the metadata of the current buffer into the cache."
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (attr (file-attributes file))
+         (atime (file-attribute-access-time attr))
+         (mtime (file-attribute-modification-time attr))
+         (hash (org-roam-db--file-hash)))
+    (org-roam-db-query [:delete :from files
+                        :where (= file $s1)]
+                       file)
+    (org-roam-db--insert-meta file hash (list :atime atime :mtime mtime))))
+
 (defun org-roam-db--update-titles ()
   "Update the title of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name))))
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (titles (or (org-roam--extract-titles)
+                     (list (org-roam--path-to-slug file)))))
     (org-roam-db-query [:delete :from titles
                         :where (= file $s1)]
                        file)
-    (org-roam-db--insert-titles file (org-roam--extract-titles))))
+    (org-roam-db--insert-titles file titles)))
+
+(defun org-roam-db--update-tags ()
+  "Update the tags of the current buffer into the cache."
+  (let* ((file (or org-roam-file-name (buffer-file-name)))
+         (tags (org-roam--extract-tags file)))
+    (org-roam-db-query [:delete :from tags
+                        :where (= file $s1)]
+                       file)
+    (when tags
+      (org-roam-db--insert-tags file tags))))
 
 (defun org-roam-db--update-refs ()
   "Update the ref of the current buffer into the cache."
-  (let ((file (file-truename (buffer-file-name))))
+  (let ((file (or org-roam-file-name (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 ()
+(defun org-roam-db--update-links ()
   "Update the file links of the current buffer in the cache."
-  (let ((file (file-truename (buffer-file-name))))
+  (let ((file (or org-roam-file-name (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-ids ()
+  "Update the ids of the current buffer into the cache."
+  (let* ((file (or org-roam-file-name (buffer-file-name))))
+    (org-roam-db-query [:delete :from ids
+                        :where (= file $s1)]
+                       file)
+    (when-let ((ids (org-roam--extract-ids file)))
+      (org-roam-db--insert-ids ids))))
+
 (defun org-roam-db--update-file (&optional file-path)
-  "Update Org-roam cache for FILE-PATH."
-  (let (buf)
-    (if file-path
-        (setq buf (find-file-noselect file-path))
-      (setq buf (current-buffer)))
-    (with-current-buffer buf
-      (save-excursion
+  "Update Org-roam cache for FILE-PATH.
+If the file does not exist anymore, remove it from the cache.
+If the file exists, update the cache with information."
+  (setq file-path (or file-path
+                      (buffer-file-name (buffer-base-buffer))))
+  (if (not (file-exists-p file-path))
+      (org-roam-db--clear-file file-path)
+    ;; save the file before performing a database update
+    (when-let ((buf (find-buffer-visiting file-path)))
+      (with-current-buffer buf
+        (save-buffer)))
+    (org-roam--with-temp-buffer file-path
+      (emacsql-with-transaction (org-roam-db)
+        (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)))))
+        (when org-roam-enable-headline-linking
+          (org-roam-db--update-ids))
+        (org-roam-db--update-links)))))
 
-;;;;; org-roam-db-build-cache
-(defun org-roam-db-build-cache ()
-  "Build the cache for `org-roam-directory'."
-  (interactive)
+(defun org-roam-db-build-cache (&optional force)
+  "Build the cache for `org-roam-directory'.
+If FORCE, force a rebuild of the cache from scratch."
+  (interactive "P")
+  (when force (delete-file org-roam-db-location))
   (org-roam-db--close) ;; Force a reconnect
   (org-roam-db) ;; To initialize the database, no-op if already initialized
-  (let* ((org-roam-files (org-roam--list-files org-roam-directory))
+  (let* ((gc-cons-threshold org-roam-db-gc-threshold)
+	 (org-agenda-files nil)
+         (org-roam-files (org-roam--list-all-files))
          (current-files (org-roam-db--get-current-files))
-         (time (current-time))
-         all-files all-links all-titles all-refs)
-    (dolist (file org-roam-files)
-      (org-roam--with-temp-buffer
-        (insert-file-contents file)
-        (let ((contents-hash (secure-hash 'sha1 (current-buffer))))
-          (unless (string= (gethash file current-files)
-                           contents-hash)
-            (org-roam-db--clear-file file)
-            (setq all-files
-                  (cons (vector file contents-hash time) all-files))
-            (when-let (links (org-roam--extract-links file))
-              (setq all-links (append links all-links)))
-            (let ((titles (org-roam--extract-titles)))
-              (setq all-titles (cons (vector file titles) all-titles)))
-            (when-let ((ref (org-roam--extract-ref)))
-              (setq all-refs (cons (vector ref file) all-refs))))
-          (remhash file current-files))))
-    (dolist (file (hash-table-keys current-files))
-      ;; These files are no longer around, remove from cache...
-      (org-roam-db--clear-file file))
-    (when all-files
-      (org-roam-db-query
-       [:insert :into files
-        :values $v1]
-       all-files))
-    (when all-links
-      (org-roam-db-query
-       [:insert :into links
-        :values $v1]
-       all-links))
-    (when all-titles
-      (org-roam-db-query
-       [:insert :into titles
-        :values $v1]
-       all-titles))
-    (when all-refs
-      (org-roam-db-query
-       [:insert :into refs
-        :values $v1]
-       all-refs))
-    (let ((stats (list :files (length all-files)
-                       :links (length all-links)
-                       :titles (length all-titles)
-                       :refs (length all-refs)
-                       :deleted (length (hash-table-keys current-files)))))
-      (when org-roam-verbose
-        (message "files: %s, links: %s, titles: %s, refs: %s, deleted: %s"
-                 (plist-get stats :files)
-                 (plist-get stats :links)
-                 (plist-get stats :titles)
-                 (plist-get stats :refs)
-                 (plist-get stats :deleted)))
-      stats)))
+         (file-count 0)
+         (id-count 0)
+         (link-count 0)
+         (tag-count 0)
+         (title-count 0)
+         (ref-count 0)
+         (deleted-count 0)
+         (processed-count 0))
+    (emacsql-with-transaction (org-roam-db)
+      ;; Two-step building
+      ;; First step: Rebuild files and ids
+      (dolist (file org-roam-files)
+        (org-roam-message "Processed %s/%s files..." processed-count (length org-roam-files))
+        (let* ((attr (file-attributes file))
+               (atime (file-attribute-access-time attr))
+               (mtime (file-attribute-modification-time attr)))
+          (let ((contents-hash (org-roam-db--file-hash file)))
+            (unless (string= (gethash file current-files)
+                             contents-hash)
+              (condition-case nil
+                  (org-roam--with-temp-buffer file
+                    (org-roam-db--clear-file file)
+                    (org-roam-db-query
+                     [:insert :into files
+                      :values $v1]
+                     (vector file contents-hash (list :atime atime :mtime mtime)))
+                    (setq file-count (1+ file-count))
+                    (when org-roam-enable-headline-linking
+                      (when-let ((ids (org-roam--extract-ids file)))
+                        (when (org-roam-db--insert-ids ids)
+                          (setq id-count (+ id-count (length ids))))))
+                    (when-let (links (org-roam--extract-links file))
+                      (org-roam-db-query
+                       [:insert :into links
+                        :values $v1]
+                       links)
+                      (setq link-count (1+ link-count)))
+                    (when-let (tags (org-roam--extract-tags file))
+                      (org-roam-db-query
+                       [:insert :into tags
+                        :values $v1]
+                       (vector file tags))
+                      (setq tag-count (1+ tag-count)))
+                    (let ((titles (or (org-roam--extract-titles)
+                                      (list (org-roam--path-to-slug file)))))
+                      (org-roam-db--insert-titles file titles)
+                      (setq title-count (+ title-count (length titles))))
+                    (when-let* ((ref (org-roam--extract-ref)))
+                      (when (org-roam-db--insert-ref file ref)
+                        (setq ref-count (1+ ref-count)))))
+                (file-error
+                 (setq org-roam-files (remove file org-roam-files))
+                 (org-roam-db--clear-file file)
+                 (lwarn '(org-roam) :warning
+                        "Skipping unreadable file while building cache: %s" file))))
+            (remhash file current-files)
+            (setq processed-count (+ processed-count 1)))))
+      (dolist (file (hash-table-keys current-files))
+        ;; These files are no longer around, remove from cache...
+        (org-roam-db--clear-file file)
+        (setq deleted-count (1+ deleted-count))))
+    (org-roam-message "files: Δ%s, ids: Δ%s, links: Δ%s, tags: Δ%s, titles: Δ%s, refs: Δ%s, deleted: Δ%s"
+                      file-count
+                      id-count
+                      link-count
+                      tag-count
+                      title-count
+                      ref-count
+                      deleted-count)))
 
 (provide 'org-roam-db)
 

org-roam-dev.el

@@ -0,0 +1,46 @@
+;;; org-roam-dev.el --- Org-roam development code -mode -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+
+;; 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)
+
+;;;###autoload
+(define-minor-mode org-roam-dev-mode
+  "Minor mode for setting the dev environment of Org-roam."
+  :lighter " ORD"
+  (when org-roam-dev-mode
+    (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 +1,318 @@
+;;; org-roam-doctor.el --- Linter for Org-roam files -*- coding: utf-8; lexical-binding: t; -*-
+;;
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/jethrokuan/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+
+;; This file is NOT part of GNU Emacs.
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation; either version 3, or (at your option)
+;; any later version.
+;;
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+;;
+;; You should have received a copy of the GNU General Public License
+;; along with GNU Emacs; see the file COPYING.  If not, write to the
+;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+;; Boston, MA 02110-1301, USA.
+
+
+;;; Commentary:
+;;
+;; This library provides `org-roam-doctor', a utility for diagnosing and fixing
+;; Org-roam files. Running `org-roam-doctor' launches a list of checks defined
+;; by `org-roam-doctor--checkers'. Every checker is an instance of
+;; `org-roam-doctor-checker'.
+;;
+;; Each checker is given the Org parse tree (AST), and is expected to return a
+;; list of errors. The checker can also provide "actions" for auto-fixing errors
+;; (see `org-roam-doctor--remove-link' for an example).
+;;
+;; The UX experience is inspired by both org-lint and checkdoc, and their code
+;; is heavily referenced.
+;;
+;;; Code:
+;; Library Requires
+(require 'cl-lib)
+(require 'org)
+(require 'org-element)
+(require 's)
+(require 'dash)
+(require 'org-roam-macs)
+
+(declare-function org-roam-insert "org-roam")
+(declare-function org-roam--get-roam-buffers "org-roam")
+(declare-function org-roam--list-all-files "org-roam")
+(declare-function org-roam--org-roam-file-p "org-roam")
+(declare-function org-roam--str-to-list "org-roam")
+(declare-function org-roam-mode "org-roam")
+
+(defvar org-roam-verbose)
+(defvar org-roam-mode)
+
+(defcustom org-roam-doctor-inhibit-startup t
+  "Inhibit `org-mode' startup when processing files with `org-doctor'.
+When non-nil, images and LaTeX preview will not be generated,
+tables will not be aligned, and headlines will not respect
+startup visability. This significantly improves performance when
+processing multiple files"
+  :type 'boolean
+  :group 'org-roam)
+
+(cl-defstruct (org-roam-doctor-checker (:copier nil))
+  (name 'missing-checker-name)
+  (description "")
+  (actions nil))
+
+(defconst org-roam-doctor--checkers
+  (list
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-broken-links
+    :description "Fix broken links."
+    :actions '(("d" . ("Unlink" . org-roam-doctor--remove-link))
+               ("r" . ("Replace link" . org-roam-doctor--replace-link))
+               ("R" . ("Replace link (keep label)" . org-roam-doctor--replace-link-keep-label))))
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-roam-props
+    :description "Check #+roam_* properties.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-tags
+    :description "Check #+roam_tags.")
+   (make-org-roam-doctor-checker
+    :name 'org-roam-doctor-check-alias
+    :description "Check #+roam_alias.")))
+
+(defconst org-roam-doctor--supported-roam-properties
+  '("roam_tags" "roam_alias" "roam_key")
+  "List of supported Org-roam properties.")
+
+(defun org-roam-doctor-check-roam-props (ast)
+  "Checker for detecting invalid #+roam_* properties.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (let ((key (org-element-property :key kw)))
+          (when (and (string-prefix-p "ROAM_" key t)
+                     (not (member (downcase key) org-roam-doctor--supported-roam-properties)))
+            (push
+             `(,(org-element-property :begin kw)
+               ,(concat "Possible mispelled key: "
+                        (prin1-to-string key)
+                        "\nOrg-roam supports the following keys: "
+                        (s-join ", " org-roam-doctor--supported-roam-properties)))
+             reports)))))
+    reports))
+
+(defun org-roam-doctor-check-tags (ast)
+  "Checker for detecting invalid #+roam_tags.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_tags" nil t)
+          (let ((tags (org-element-property :value kw)))
+            (condition-case nil
+                (org-roam--str-to-list tags)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse tags: "
+                           tags
+                           (when (s-contains? "," tags)
+                             "\nCheck that your tags are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-check-alias (ast)
+  "Checker for detecting invalid #+roam_alias.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'keyword
+      (lambda (kw)
+        (when (string-collate-equalp (org-element-property :key kw) "roam_alias" nil t)
+          (let ((aliases (org-element-property :value kw)))
+            (condition-case nil
+              (org-roam--str-to-list aliases)
+              (error
+               (push
+                `(,(org-element-property :begin kw)
+                  ,(concat "Unable to parse aliases: "
+                           aliases
+                           (when (s-contains? "," aliases)
+                             "\nCheck that your aliases are not comma-separated.")))
+                reports)))))))
+    reports))
+
+(defun org-roam-doctor-broken-links (ast)
+  "Checker for detecting broken links.
+AST is the org-element parse tree."
+  (let (reports)
+    (org-element-map ast 'link
+      (lambda (l)
+        (when (equal "file" (org-element-property :type l))
+          (let ((file (org-element-property :path l)))
+            (or (file-exists-p file)
+                (file-remote-p file)
+                (push
+                 `(,(org-element-property :begin l)
+                   ,(format (if (org-element-lineage l '(link))
+                                "Link to non-existent image file \"%s\"\
+ in link description"
+                              "Link to non-existent local file \"%s\"")
+                            file))
+                 reports))))))
+    reports))
+
+(defun org-roam-doctor--check (buffer checkers)
+  "Check BUFFER for errors.
+CHECKERS is the list of checkers used."
+  (with-current-buffer buffer
+    (save-excursion
+      (goto-char (point-min))
+      (let* ((ast (org-element-parse-buffer))
+             (errors (sort (cl-mapcan
+                            (lambda (c)
+                              (mapcar
+                               (lambda (report)
+                                 (list (set-marker (make-marker) (car report))
+                                       (nth 1 report) c))
+                               (save-excursion
+                                 (funcall
+                                  (org-roam-doctor-checker-name c)
+                                  ast))))
+                            checkers)
+                           #'car-less-than-car)))
+        (dolist (e errors)
+          (pcase-let ((`(,m ,msg ,checker) e))
+            (switch-to-buffer buffer)
+            (goto-char m)
+            (org-reveal)
+            (undo-boundary)
+            (org-roam-doctor--resolve msg checker)
+            (set-marker m nil)))
+        errors))))
+
+;;; Actions
+(defun org-roam-doctor--recursive-edit ()
+  "Launch into a recursive edit."
+  (message "When you're done editing press C-M-c to continue.")
+  (recursive-edit))
+
+(defun org-roam-doctor--skip ()
+  "Skip the current error."
+  (org-roam-message "Skipping..."))
+
+(defun org-roam-doctor--replace-link ()
+  "Replace the current link with a new link."
+  (save-match-data
+    (unless (org-in-regexp org-link-bracket-re 1)
+      (user-error "No link at point"))
+    (let ((orig (buffer-string))
+          (p (point)))
+      (condition-case nil
+          (save-excursion
+            (replace-match "")
+            (org-roam-insert))
+        (quit (progn
+                (replace-buffer-contents orig)
+                (goto-char p)))))))
+
+(defun org-roam-doctor--replace-link-keep-label ()
+  "Replace the current link with a new link, keeping the current link's label."
+  (save-match-data
+    (unless (org-in-regexp org-link-bracket-re 1)
+      (user-error "No link at point"))
+    (let ((orig (buffer-string))
+          (p (point)))
+      (condition-case nil
+          (save-excursion
+            (let ((label (if (match-end 2)
+                             (match-string-no-properties 2)
+                           (org-link-unescape (match-string-no-properties 1)))))
+              (replace-match "")
+              (org-roam-insert nil nil label)))
+        (quit (progn
+                (replace-buffer-contents orig)
+                (goto-char p)))))))
+
+(defun org-roam-doctor--remove-link ()
+  "Unlink the text at point."
+  (unless (org-in-regexp org-link-bracket-re 1)
+    (user-error "No link at point"))
+  (save-excursion
+    (let ((label (if (match-end 2)
+                     (match-string-no-properties 2)
+                   (org-link-unescape (match-string-no-properties 1)))))
+      (delete-region (match-beginning 0) (match-end 0))
+      (insert label))))
+
+(defun org-roam-doctor--resolve (msg checker)
+  "Resolve an error.
+MSG is the error that was found, which is displayed in a help buffer.
+CHECKER is a org-roam-doctor checker instance."
+  (let ((actions (org-roam-doctor-checker-actions checker))
+        c)
+    (push '("e" . ("Edit" . org-roam-doctor--recursive-edit)) actions)
+    (push '("s" . ("Skip" . org-roam-doctor--skip)) actions)
+    (with-output-to-temp-buffer "*Org-roam-doctor Help*"
+      (mapc #'princ
+            (list "Error message:\n   " msg "\n\n"))
+      (dolist (action actions)
+        (princ (format "[%s]: %s\n"
+                       (car action)
+                       (cadr action))))
+      (princ "\n\n"))
+    (shrink-window-if-larger-than-buffer
+     (get-buffer-window "*Org-roam-doctor Help*"))
+    (message "Press key for command:")
+    (unwind-protect
+        (progn
+          (cl-loop
+           do (setq c (char-to-string (read-char-exclusive)))
+           until (assoc c actions)
+           do (message "Please enter a valid key for command:"))
+          (funcall (cddr (assoc c actions)))
+          (redisplay))
+      (when (get-buffer-window "*Org-roam-doctor Help*")
+        (delete-window (get-buffer-window "*Org-roam-doctor Help*"))
+        (kill-buffer "*Org-roam-doctor Help*")))))
+
+;;;###autoload
+(defun org-roam-doctor (&optional checkall)
+  "Perform a check on the current buffer to ensure cleanliness.
+If CHECKALL, run the check for all Org-roam files."
+  (interactive "P")
+  (unless org-roam-mode (org-roam-mode))
+  (let ((files (if checkall
+                  (org-roam--list-all-files)
+                (unless (org-roam--org-roam-file-p)
+                  (user-error "Not in an org-roam file"))
+                `(,(buffer-file-name)))))
+    (org-roam-doctor-start files org-roam-doctor--checkers)))
+
+(defun org-roam-doctor-start (files checkers)
+  "Lint FILES using CHECKERS."
+  (save-window-excursion
+    (let ((existing-buffers (org-roam--get-roam-buffers))
+          (org-inhibit-startup org-roam-doctor-inhibit-startup))
+      (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-faces.el

@@ -0,0 +1,72 @@
+;;; org-roam-faces.el --- Face definitions -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.2
+;; 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 file contains the face definitions for Org-roam.
+
+;;; Code:
+
+(defgroup org-roam-faces nil
+  "Faces used by Org-roam."
+  :group 'org-roam
+  :group 'faces)
+
+;;; Definitions
+(defface org-roam-link
+  '((t :inherit org-link))
+  "Face for Org-roam links."
+  :group 'org-roam-faces)
+
+(defface org-roam-tag
+  '((t :weight bold))
+  "Face for Org-roam tags in minibuffer commands."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-current
+  '((t :inherit org-link))
+  "Face for Org-roam links pointing to the current buffer."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-invalid
+  '((t :inherit (error org-link)))
+  "Face for Org-roam links that are not valid.
+This face is used for links without a destination."
+  :group 'org-roam-faces)
+
+(defface org-roam-link-shielded
+  '((t :inherit (warning org-link)))
+  "Face for Org-roam links that are shielded.
+This face is used on the region target by `org-roam-insertion'
+during an `org-roam-capture'."
+  :group 'org-roam-faces)
+
+;;; _
+
+(provide 'org-roam-faces)
+
+;;; org-roam-faces.el ends here

org-roam-graph.el

@@ -1,12 +1,12 @@
-;;; org-roam-graph.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-graph.el --- Graphing API -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -37,8 +37,10 @@
 
 ;;;; Declarations
 (defvar org-roam-directory)
+(defvar org-roam-mode)
 (declare-function org-roam--org-roam-file-p  "org-roam")
 (declare-function org-roam--path-to-slug     "org-roam")
+(declare-function org-roam-mode              "org-roam")
 
 ;;;; Options
 (defcustom org-roam-graph-viewer (executable-find "firefox")
@@ -53,8 +55,8 @@ It may be one of the following:
           (const    :tag "view-file"))
   :group 'org-roam)
 
-(defcustom org-roam-graph-executable (executable-find "dot")
-  "Path to graphing executable."
+(defcustom org-roam-graph-executable "dot"
+  "Path to graphing executable, or its name."
   :type 'string
   :group 'org-roam)
 
@@ -65,14 +67,20 @@ Example:
   :type '(alist)
   :group 'org-roam)
 
-(defcustom org-roam-graph-node-extra-config nil
+(defcustom org-roam-graph-node-extra-config
+  '(("shape"      . "underline")
+    ("style"      . "rounded,filled")
+    ("fillcolor"  . "#EEEEEE")
+    ("color"      . "#C9C9C9")
+    ("fontcolor"  . "#111111"))
   "Extra options for graphviz nodes.
 Example:
  '((\"color\" . \"skyblue\"))"
   :type '(alist)
   :group 'org-roam)
 
-(defcustom org-roam-graph-edge-extra-config nil
+(defcustom org-roam-graph-edge-extra-config
+  '(("color" . "#333333"))
   "Extra options for graphviz edges.
 Example:
  '((\"dir\" . \"back\"))"
@@ -91,6 +99,19 @@ Example:
   :type 'number
   :group 'org-roam)
 
+(defcustom org-roam-graph-shorten-titles 'truncate
+  "Determines how long titles appear in graph nodes.
+Recognized values are the symbols `truncate' and `wrap', in which
+cases the title will be truncated or wrapped, respectively, if it
+is longer than `org-roam-graph-max-title-length'.
+
+All other values including nil will have no effect."
+  :type '(choice
+          (const :tag "truncate" truncate)
+          (const :tag "wrap" wrap)
+          (const :tag "no" nil))
+  :group 'org-roam)
+
 (defcustom org-roam-graph-exclude-matcher nil
   "Matcher for excluding nodes from the generated graph.
 Any nodes and links for file paths matching this string is
@@ -144,7 +165,7 @@ The Org-roam database titles table is read, to obtain the list of titles.
 The links table is then read to obtain all directed links, and formatted
 into a digraph."
   (org-roam-db--ensure-built)
-  (org-roam--with-temp-buffer
+  (org-roam--with-temp-buffer nil
     (let* ((nodes (org-roam-db-query node-query))
            (edges-query
             `[:with selected :as [:select [file] :from ,node-query]
@@ -154,7 +175,8 @@ into a digraph."
             `[:with selected :as [:select [file] :from ,node-query]
               :select :distinct [file from]
               :from links :inner :join refs :on (and (= links:to refs:ref)
-                                                     (= links:type "cite"))
+                                                     (= links:type "cite")
+                                                     (= refs:type "cite"))
               :where (and (in file selected) (in from selected))])
            (edges       (org-roam-db-query edges-query))
            (edges-cites (org-roam-db-query edges-cites-query)))
@@ -163,17 +185,23 @@ into a digraph."
         (insert (org-roam-graph--dot-option option) ";\n"))
       (dolist (attribute '("node" "edge"))
         (insert (format " %s [%s];\n" attribute
-                        (mapconcat #'org-roam-graph--dot-option
+                        (mapconcat (lambda (var)
+                                     (org-roam-graph--dot-option var nil "\""))
                                    (symbol-value
                                     (intern (concat "org-roam-graph-" attribute "-extra-config")))
                                    ","))))
       (dolist (node nodes)
         (let* ((file (xml-escape-string (car node)))
-               (title (or (caadr node)
+               (title (or (cadr node)
                           (org-roam--path-to-slug file)))
-               (shortened-title (s-truncate org-roam-graph-max-title-length title))
+               (shortened-title (pcase org-roam-graph-shorten-titles
+                                  (`truncate (s-truncate org-roam-graph-max-title-length title))
+                                  (`wrap (s-word-wrap org-roam-graph-max-title-length title))
+                                  (_ title)))
+               (shortened-title (org-roam-string-quote shortened-title))
+               (title (org-roam-string-quote title))
                (node-properties
-                `(("label"   . ,(s-replace "\"" "\\\"" shortened-title))
+                `(("label"   . ,shortened-title)
                   ("URL"     . ,(concat "org-protocol://roam-file?file=" (url-hexify-string file)))
                   ("tooltip" . ,(xml-escape-string title)))))
           (insert
@@ -193,21 +221,32 @@ into a digraph."
       (insert "}")
       (buffer-string))))
 
-(defun org-roam-graph--build (&optional node-query)
-  "Generate a graph showing the relations between nodes in NODE-QUERY."
-  (unless org-roam-graph-executable
-    (user-error "Can't find %s executable.  Please check if it is in your path"
+(defun org-roam-graph--build (&optional node-query callback)
+  "Generate a graph showing the relations between nodes in NODE-QUERY.
+Execute CALLBACK when process exits successfully.
+CALLBACK is passed the graph file as its sole argument."
+  (unless (stringp org-roam-graph-executable)
+    (user-error "`org-roam-graph-executable' is not a string"))
+  (unless (executable-find org-roam-graph-executable)
+    (user-error (concat "Cannot find executable \"%s\" to generate the graph.  "
+                        "Please adjust `org-roam-graph-executable'")
                 org-roam-graph-executable))
   (let* ((node-query (or node-query
-                         `[:select [file titles]
-                           :from titles
-                           ,@(org-roam-graph--expand-matcher 'file t)]))
+                         `[:select [file title] :from titles
+                           ,@(org-roam-graph--expand-matcher 'file t)
+                           :group :by file]))
          (graph      (org-roam-graph--dot node-query))
          (temp-dot   (make-temp-file "graph." nil ".dot" graph))
          (temp-graph (make-temp-file "graph." nil ".svg")))
-    (call-process org-roam-graph-executable nil 0 nil
-                  temp-dot "-Tsvg" "-o" temp-graph)
-    temp-graph))
+    (org-roam-message "building graph")
+    (make-process
+     :name "*org-roam-graph--build-process*"
+     :buffer "*org-roam-graph--build-process*"
+     :command `(,org-roam-graph-executable ,temp-dot "-Tsvg" "-o" ,temp-graph)
+     :sentinel (when callback
+                 (lambda (process _event)
+                   (when (= 0 (process-exit-status process))
+                     (funcall callback temp-graph)))))))
 
 (defun org-roam-graph--open (file)
   "Open FILE using `org-roam-graph-viewer' with `view-file' as a fallback."
@@ -216,24 +255,25 @@ into a digraph."
      (if (executable-find org-roam-graph-viewer)
          (condition-case err
              (call-process org-roam-graph-viewer nil 0 nil file)
-           ((error (user-error "Failed to open org-roam graph: %s" err))))
+           (error (user-error "Failed to open org-roam graph: %s" err)))
        (user-error "Executable not found: \"%s\"" org-roam-graph-viewer)))
     ((pred functionp) (funcall org-roam-graph-viewer file))
     ('nil (view-file file))
     (_ (signal 'wrong-type-argument `((functionp stringp null) ,org-roam-graph-viewer)))))
 
-(defun org-roam-graph--build-connected-component (file &optional max-distance)
+(defun org-roam-graph--build-connected-component (file &optional max-distance callback)
   "Build a graph of nodes connected to FILE.
-If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps."
-  (let* ((file (file-truename file))
+If MAX-DISTANCE is non-nil, limit nodes to MAX-DISTANCE steps.
+CALLBACK is passed to `org-roam-graph--build'."
+  (let* ((file (expand-file-name 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]
+         (query `[:select [file title]
                   :from titles
                   :where (in file [,@files])]))
-    (org-roam-graph--build query)))
+    (org-roam-graph--build query callback)))
 
 ;;;; Commands
 ;;;###autoload
@@ -248,17 +288,17 @@ ARG may be any of the following values:
   - `\\[universal-argument]' -   build the graph for FILE.
   - `\\[universal-argument]' -N  build the graph for FILE limiting nodes to N steps."
   (interactive "P")
-  (let ((file (or file (buffer-file-name))))
-    (unless file
-      (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
-    (unless (org-roam--org-roam-file-p file)
-      (user-error "\"%s\" is not an org-roam file" file))
+  (unless org-roam-mode (org-roam-mode))
+  (let ((file (or file (buffer-file-name (buffer-base-buffer)))))
+    (unless (or (not arg) (equal arg '(16)))
+      (unless file
+        (user-error "Cannot build graph for nil file. Is current buffer visiting a file?"))
+      (unless (org-roam--org-roam-file-p file)
+        (user-error "\"%s\" is not an org-roam file" file)))
     (pcase arg
-      ('nil            (org-roam-graph--open (org-roam-graph--build node-query)))
-      ('(4)            (org-roam-graph--open (org-roam-graph--build-connected-component file)))
-      ((pred integerp) (let ((graph (org-roam-graph--build-connected-component (buffer-file-name) (abs arg))))
-                         (when (>= arg 0)
-                           (org-roam-graph--open graph))))
+      ('nil            (org-roam-graph--build node-query #'org-roam-graph--open))
+      ('(4)            (org-roam-graph--build-connected-component file nil #'org-roam-graph--open))
+      ((pred integerp) (org-roam-graph--build-connected-component file (abs arg) (when (>= arg 0) #'org-roam-graph--open)))
       ('(16)           (org-roam-graph--build node-query))
       ('-              (org-roam-graph--build-connected-component file))
       (_ (user-error "Unrecognized ARG: %s" arg)))))

org-roam-link.el

@@ -0,0 +1,310 @@
+;;; org-roam-link.el --- Custom links for Org-roam -*- coding: utf-8; lexical-binding: t; -*-
+
+;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
+;;                  Alan Carroll
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; URL: https://github.com/org-roam/org-roam
+;; Keywords: org-mode, roam, convenience
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
+
+;; 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 adds the custom `roam:' link to Org-roam. `roam:' links allow linking to
+;; Org-roam files via their titles and headlines.
+;;
+;;; Code:
+;;;; Dependencies
+
+(require 'ol)
+(require 'org-roam-compat)
+
+(defvar org-roam-completion-ignore-case)
+(defvar org-roam-directory)
+(declare-function  org-roam--find-file                  "org-roam")
+(declare-function  org-roam-find-file                   "org-roam")
+(declare-function org-roam-format-link                  "org-roam")
+
+(defcustom org-roam-link-auto-replace t
+  "When non-nil, replace Org-roam's roam links with file or id links whenever possible."
+  :group 'org-roam
+  :type 'boolean)
+
+(defcustom org-roam-link-file-path-type 'relative
+  "How the path name in file links should be stored.
+Valid values are:
+
+relative  Relative to the current directory, i.e. the directory of the file
+          into which the link is being inserted.
+absolute  Absolute path, if possible with ~ for home directory.
+noabbrev  Absolute path, no abbreviation of home directory."
+  :group 'org-roam
+  :type '(choice
+          (const relative)
+          (const absolute)
+          (const noabbrev))
+  :safe #'symbolp)
+
+;;; the roam: link
+(org-link-set-parameters "roam"
+                         :follow #'org-roam-link-follow-link)
+
+(defun org-roam-link-follow-link (path)
+  "Navigates to location specified by PATH."
+  (pcase-let ((`(,link-type ,loc ,desc ,mkr) (org-roam-link--get-location path)))
+    (when (and org-roam-link-auto-replace loc desc)
+      (org-roam-link--replace-link link-type loc desc))
+    (pcase link-type
+          ("file"
+           (if loc
+               (org-roam--find-file loc)
+             (org-roam-find-file desc nil nil t)))
+          ("id"
+           (org-goto-marker-or-bmk mkr)))))
+
+;;; Retrieval Functions
+(defun org-roam-link--get-titles ()
+  "Return all titles within Org-roam."
+  (mapcar #'car (org-roam-db-query [:select [titles:title] :from titles])))
+
+(defun org-roam-link--get-headlines (&optional file with-marker use-stack)
+  "Return all outline headings for the current buffer.
+If FILE, return outline headings for passed FILE instead.
+If WITH-MARKER, return a cons cell of (headline . marker).
+If USE-STACK, include the parent paths as well."
+  (let* ((buf (or (and file
+                       (or (find-buffer-visiting file)
+                           (find-file-noselect file)))
+                  (current-buffer)))
+         (outline-level-fn outline-level)
+         (path-separator "/")
+         (stack-level 0)
+         stack cands name level marker)
+    (with-current-buffer buf
+      (save-excursion
+        (goto-char (point-min))
+        (while (re-search-forward org-complex-heading-regexp nil t)
+          (save-excursion
+            (setq name (substring-no-properties (or (match-string 4) "")))
+            (setq marker (point-marker))
+            (when use-stack
+              (goto-char (match-beginning 0))
+              (setq level (funcall outline-level-fn))
+              ;; Update stack.  The empty entry guards against incorrect
+              ;; headline hierarchies, e.g. a level 3 headline
+              ;; immediately following a level 1 entry.
+              (while (<= level stack-level)
+                (pop stack)
+                (cl-decf stack-level))
+              (while (> level stack-level)
+                (push name stack)
+                (cl-incf stack-level))
+              (setq name (mapconcat #'identity
+                                    (reverse stack)
+                                    path-separator)))
+            (push (if with-marker
+                      (cons name marker)
+                    name) cands)))))
+    (nreverse cands)))
+
+(defun org-roam-link--get-file-from-title (title &optional no-interactive)
+  "Return the file path corresponding to TITLE.
+When NO-INTERACTIVE, return nil if there are multiple options."
+  (let ((files (mapcar #'car (org-roam-db-query [:select [titles:file] :from titles
+                                                 :where (= titles:title $v1)]
+                                                (vector title)))))
+    (pcase files
+      ('nil nil)
+      (`(,file) file)
+      (_
+       (unless no-interactive
+         (completing-read "Select file: " files))))))
+
+(defun org-roam-link--get-id-from-headline (headline &optional file)
+  "Return (marker . id) correspondng to HEADLINE.
+If FILE, get headline from FILE instead.
+If there is no corresponding headline, return nil."
+  (save-excursion
+    (with-current-buffer (or (and file
+                                  (or (find-buffer-visiting file)
+                                      (find-file-noselect file)))
+                             (current-buffer))
+      (let ((headlines (org-roam-link--get-headlines file 'with-markers)))
+        (when-let ((marker (cdr (assoc-string headline headlines))))
+          (goto-char marker)
+          (cons marker
+                (when org-roam-link-auto-replace
+                  (org-id-get-create))))))))
+
+;;; Path-related functions
+(defun org-roam-link-get-path (path)
+  "Return the PATH of the link to use.
+Respect `org-link-file-path-type', see the variable documentation for details.
+If DIR is passed, use DIR as the default directory."
+  (pcase org-roam-link-file-path-type
+      ('absolute
+       (abbreviate-file-name (expand-file-name path)))
+      ('noabbrev
+       (expand-file-name path))
+      ('relative
+       (file-relative-name path))))
+
+(defun org-roam-link--split-path (path)
+  "Splits PATH into title and headline.
+Return a list of the form (type title has-headline-p headline star-idx).
+type is one of `title', `headline', `title+headline'.
+title is the title component of the path.
+headline is the headline component of the path.
+star-idx is the index of the asterisk, if any."
+  (save-match-data
+    (let* ((star-index (string-match-p "\\*" path))
+           (title (substring-no-properties path 0 star-index))
+           (headline (if star-index
+                         (substring-no-properties path (+ 1 star-index))
+                       ""))
+           (type (cond ((not star-index)
+                        'title)
+                       ((= 0 star-index)
+                        'headline)
+                       (t 'title+headline))))
+      (list type title headline star-index))))
+
+(defun org-roam-link--get-location (link)
+  "Return the location of Org-roam fuzzy LINK.
+The location is returned as a list containing (link-type loc desc marker).
+nil is returned if there is no matching location.
+
+link-type is either \"file\" or \"id\".
+loc is the target location: e.g. a file path, or an id.
+marker is a marker to the headline, if applicable."
+  (let (mkr link-type desc loc)
+    (pcase-let ((`(,type ,title ,headline _) (org-roam-link--split-path link)))
+      (pcase type
+        ('title+headline
+         (let ((file (org-roam-link--get-file-from-title title)))
+           (if (not file)
+               (org-roam-message "Cannot find matching file")
+             (setq mkr (org-roam-link--get-id-from-headline headline file))
+             (pcase mkr
+               (`(,marker . ,target-id)
+                (setq mkr marker
+                      loc target-id
+                      link-type "id"
+                      desc headline))
+               (_ (org-roam-message "cannot find matching id"))))))
+        ('title
+         (setq loc (org-roam-link--get-file-from-title title)
+               desc title
+               link-type "file"))
+        ('headline
+         (setq mkr (org-roam-link--get-id-from-headline headline))
+         (pcase mkr
+           (`(,marker . ,target-id)
+            (setq mkr marker
+                  loc target-id
+                  desc headline
+                  link-type "id"))
+           (_ (org-roam-message "Cannot find matching headline")))))
+      (list link-type loc desc mkr))))
+
+;;; Conversion Functions
+(defun org-roam-link--replace-link (link-type loc &optional desc)
+  "Replace link at point with a vanilla Org link.
+LINK-TYPE is the Org link type, typically \"file\" or \"id\".
+LOC is path for the Org link.
+DESC is the link description."
+  (save-excursion
+    (save-match-data
+      (unless (org-in-regexp org-link-bracket-re 1)
+        (user-error "No link at point"))
+      (replace-match "")
+      (insert (org-roam-format-link loc desc link-type)))))
+
+(defun org-roam-link-replace-all ()
+  "Replace all roam links in the current buffer."
+  (interactive)
+  (save-excursion
+    (goto-char (point-min))
+    (while (re-search-forward org-link-bracket-re nil t)
+      (let ((context (org-element-context)))
+          (pcase (org-element-lineage context '(link) t)
+            (`nil nil)
+            (link
+             (when (string-equal "roam" (org-element-property :type link))
+               (pcase-let ((`(,link-type ,loc ,desc _) (org-roam-link--get-location (org-element-property :path link))))
+                 (when (and link-type loc)
+                   (org-roam-link--replace-link link-type loc desc))))))))))
+
+(defun org-roam-link--replace-link-on-save ()
+  "Hook to replace all roam links on save."
+  (when org-roam-link-auto-replace
+    (org-roam-link-replace-all)))
+
+;;; Completion
+(defun org-roam-link-complete-at-point ()
+  "Do appropriate completion for the link at point."
+  (let ((end (point))
+        (start (point))
+        collection link-type headline-only-p)
+    (when (org-in-regexp org-link-bracket-re 1)
+      (setq start (match-beginning 1)
+            end (match-end 1))
+      (let ((context (org-element-context)))
+        (pcase (org-element-lineage context '(link) t)
+          (`nil nil)
+          (link
+           (setq link-type (org-element-property :type link))
+           (when (member link-type '("roam" "fuzzy"))
+             (when (string= link-type "roam") (setq start (+ start (length "roam:"))))
+             (pcase-let ((`(,type ,title _ ,star-idx)
+                          (org-roam-link--split-path (org-element-property :path link))))
+               (pcase type
+                 ('title+headline
+                  (when-let ((file (org-roam-link--get-file-from-title title t)))
+                    (setq collection (apply-partially #'org-roam-link--get-headlines file))
+                    (setq start (+ start star-idx 1))))
+                 ('title
+                  (setq collection #'org-roam-link--get-titles))
+                 ('headline
+                  (setq collection #'org-roam-link--get-headlines)
+                  (setq start (+ start star-idx 1))
+                  (setq headline-only-p t)))))))))
+    (when collection
+      (let ((prefix (buffer-substring-no-properties start end)))
+        (list start end
+              (if (functionp collection)
+                  (completion-table-case-fold
+                   (completion-table-dynamic
+                    (lambda (_)
+                      (cl-remove-if (apply-partially #'string= prefix)
+                                    (funcall collection))))
+                   (not org-roam-completion-ignore-case))
+                collection)
+              :exit-function
+              (lambda (str &rest _)
+                (delete-char (- 0 (length str)
+                                (if headline-only-p 1 0)))
+                (insert (concat (unless (string= link-type "roam") "roam:")
+                                (when headline-only-p "*")
+                                str))))))))
+
+(provide 'org-roam-link)
+;;; org-roam-link.el ends here

org-roam-macs.el

@@ -1,12 +1,12 @@
-;;; org-roam-macs.el --- Roam Research replica with Org-mode -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-macs.el --- Macros/utility functions -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
-;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite "1.0.0"))
+;; Version: 1.2.2
+;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (org "9.3") (emacsql "3.0.0") (emacsql-sqlite3 "1.0.2"))
 
 ;; This file is NOT part of GNU Emacs.
 
@@ -27,22 +27,75 @@
 
 ;;; Commentary:
 ;;
-;; This library implements macros used throughout org-roam
+;; This library implements macros and utility functions used throughout
+;; org-roam.
 ;;
 ;;
 ;;; Code:
 ;;;; Library Requires
+(require 'dash)
 
-(defmacro org-roam--with-temp-buffer (&rest body)
+(defvar org-roam-verbose)
+
+;;;; Utility Functions
+(defun org-roam--list-interleave (lst separator)
+  "Interleaves elements in LST with SEPARATOR."
+  (when lst
+    (let ((new-lst (list (pop lst))))
+      (dolist (it lst)
+        (nconc new-lst (list separator it)))
+      new-lst)))
+
+(defmacro org-roam--with-temp-buffer (file &rest body)
   "Execute BODY within a temp buffer.
-Like `with-temp-buffer', but propagates `org-roam-directory'."
-  (declare (indent 0) (debug t))
+Like `with-temp-buffer', but propagates `org-roam-directory'.
+If FILE, set `org-roam-temp-file-name' to file and insert its contents."
+  (declare (indent 1) (debug t))
   (let ((current-org-roam-directory (make-symbol "current-org-roam-directory")))
     `(let ((,current-org-roam-directory org-roam-directory))
        (with-temp-buffer
-         (let ((org-roam-directory ,current-org-roam-directory))
+         (let ((org-roam-directory ,current-org-roam-directory)
+               (org-mode-hook nil)
+               (org-inhibit-startup t))
+           (org-mode)
+           (when ,file
+             (insert-file-contents ,file)
+             (setq-local org-roam-file-name ,file))
            ,@body)))))
 
+(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))))
+
+(defun org-roam-string-quote (str)
+  "Quote STR."
+  (->> str
+       (s-replace "\\" "\\\\")
+       (s-replace "\"" "\\\"")))
+
+;;; Shielding regions
+(defun org-roam-shield-region (beg end)
+  "Shield REGION against modifications.
+REGION must be a cons-cell containing the marker to the region
+beginning and maximum values."
+  (when (and beg end)
+    (add-text-properties beg end
+                           '(font-lock-face org-roam-link-shielded
+                                            read-only t)
+                           (marker-buffer beg))
+    (cons beg end)))
+
+(defun org-roam-unshield-region (beg end)
+  "Unshield the shielded REGION."
+  (when (and beg end)
+    (let ((inhibit-read-only t))
+      (remove-text-properties beg end
+                              '(font-lock-face org-roam-link-shielded
+                                               read-only t)
+                              (marker-buffer beg)))
+    (cons beg end)))
+
 (provide 'org-roam-macs)
 
 ;;; org-roam-macs.el ends here

org-roam-protocol.el

@@ -1,10 +1,10 @@
-;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t -*-
+;;; org-roam-protocol.el --- Protocol handler for roam:// links  -*- coding: utf-8; lexical-binding: t; -*-
 
 ;; Copyright © 2020 Jethro Kuan <jethrokuan95@gmail.com>
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; URL: https://github.com/jethrokuan/org-roam
+;; URL: https://github.com/org-roam/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 1.1.0
+;; Version: 1.2.2
 ;; Package-Requires: ((emacs "26.1") (org "9.3"))
 
 ;; This file is NOT part of GNU Emacs.
@@ -37,6 +37,7 @@
 ;;; Code:
 (require 'org-protocol)
 (require 'org-roam)
+(require 'ol) ;; for org-link-decode
 
 ;;;; Functions
 (defun org-roam-protocol-open-ref (info)
@@ -56,14 +57,14 @@ It opens or creates a note with the given ref.
     (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))
+      (push (cons 'slug (funcall org-roam-title-to-slug-function title)) decoded-alist))
     (let* ((org-roam-capture-templates org-roam-capture-ref-templates)
            (org-roam-capture--context 'ref)
            (org-roam-capture--info decoded-alist)
            (template (cdr (assoc 'template decoded-alist))))
       (raise-frame)
-      (org-roam--capture nil template)
-      (message "Item captured.")))
+      (org-roam-capture--capture nil template)
+      (org-roam-message "Item captured.")))
   nil)
 
 (defun org-roam-protocol-open-file (info)
@@ -77,7 +78,7 @@ It should contain the FILE key, pointing to the path of the file to open.
 org-protocol://roam-file?file=/path/to/file.org"
   (when-let ((file (plist-get info :file)))
     (raise-frame)
-    (find-file file))
+    (org-roam--find-file file))
   nil)
 
 (push '("org-roam-ref"  :protocol "roam-ref"   :function org-roam-protocol-open-ref)

tests/roam-files/alias.org

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

tests/roam-files/bar.org

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

tests/roam-files/base.org

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

tests/roam-files/foo.org

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

tests/roam-files/headlines/headline.org

@@ -0,0 +1,14 @@
+#+TITLE: Headline
+
+* Headline 1
+:PROPERTIES:
+:ID:       e84d0630-efad-4017-9059-5ef917908823
+:END:
+
+* No headline here
+Oops.
+
+* Headline 2
+:PROPERTIES:
+:ID:       801b58eb-97e2-435f-a33e-ff59a2f0c213
+:END:

tests/roam-files/nested/bar.org

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

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

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

tests/roam-files/nested/foo.org

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

tests/roam-files/no-title.org

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

tests/roam-files/tags/no_tag.org

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

tests/roam-files/tags/tag.org

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

tests/roam-files/titles/aliases.org

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

tests/roam-files/titles/combination.org

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

tests/roam-files/titles/headline.org

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

tests/roam-files/titles/title.org

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

tests/roam-files/unlinked.org

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

tests/roam-files/web_ref.org

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

tests/test-org-roam-perf.el

@@ -0,0 +1,53 @@
+;;; test-org-roam-perf.el --- Performance Tests for Org-roam -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2020 Jethro Kuan
+
+;; Author: Jethro Kuan <jethrokuan95@gmail.com>
+;; Package-Requires: ((buttercup))
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+;;; Code:
+
+(require 'buttercup)
+(require 'org-roam)
+
+(defconst test-org-roam-perf-zip-url "https://github.com/org-roam/test-org-files/archive/master.zip"
+  "Path to zip for test org-roam files.")
+
+(defun test-org-roam-perf--abs-path (file-path)
+  "Get absolute FILE-PATH from `org-roam-directory'."
+  (expand-file-name file-path org-roam-directory))
+
+(defun test-org-roam-perf--init ()
+  "."
+  (let* ((temp-loc (expand-file-name (make-temp-name "test-org-files-") temporary-file-directory))
+         (zip-file-loc (concat temp-loc ".zip"))
+         (_ (url-copy-file test-org-roam-perf-zip-url zip-file-loc))
+         (_ (shell-command (format "mkdir -p %s && unzip -j -qq %s -d %s" temp-loc zip-file-loc temp-loc))))
+    (setq org-roam-directory temp-loc)))
+
+(describe "Cache Build"
+  (it "cache build from scratch time to be acceptable"
+    (test-org-roam-perf--init)
+    (pcase (benchmark-run 1 (org-roam-db-build-cache t))
+      (`(,time ,gcs ,time-in-gc)
+       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
+       (expect time :to-be-less-than 90))))
+  (it "builds quickly without change"
+    (pcase (benchmark-run 1 (org-roam-db-build-cache))
+      (`(,time ,gcs ,time-in-gc)
+       (message "Elapsed time: %fs (%fs in %d GCs)" time time-in-gc gcs)
+       (expect time :to-be-less-than 5)))))

tests/test-org-roam.el

@@ -1,9 +1,9 @@
-;;; 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
 
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup) (with-simulated-input))
+;; Package-Requires: ((buttercup))
 
 ;; This program is free software; you can redistribute it and/or modify
 ;; it under the terms of the GNU General Public License as published by
@@ -19,291 +19,330 @@
 ;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 ;;; Commentary:
-
-;;
-
 ;;; Code:
 
-;;;; Requirements
-
 (require 'buttercup)
-(require 'with-simulated-input)
 (require 'org-roam)
 (require 'dash)
 
-(defun org-roam-test-abs-path (file-path)
+(defun test-org-roam--abs-path (file-path)
   "Get absolute FILE-PATH from `org-roam-directory'."
-  (file-truename (expand-file-name file-path org-roam-directory)))
+  (expand-file-name file-path org-roam-directory))
 
-(defun org-roam-test-find-new-file (path)
+(defun test-org-roam--find-file (path)
   "PATH."
-  (let ((path (org-roam-test-abs-path path)))
+  (let ((path (test-org-roam--abs-path path)))
     (make-directory (file-name-directory path) t)
     (find-file path)))
 
-(defvar org-roam-test-directory (file-truename (concat default-directory "tests/roam-files"))
+(defvar test-org-roam-directory (expand-file-name "tests/roam-files")
   "Directory containing org-roam test org files.")
 
-(defun org-roam-test-init ()
+(defun test-org-roam--init ()
   "."
-  (org-roam-db--close)
-  (let ((original-dir org-roam-test-directory)
+  (let ((original-dir test-org-roam-directory)
         (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
     (copy-directory original-dir new-dir)
     (setq org-roam-directory new-dir)
-    (org-roam-mode +1)))
+    (org-roam-mode +1)
+    (sleep-for 2)))
+
+(defun test-org-roam--teardown ()
+  (org-roam-mode -1)
+  (delete-file org-roam-db-location)
+  (org-roam-db--close))
+
+(describe "org-roam--str-to-list"
+  (it "nil"
+    (expect (org-roam--str-to-list nil)
+            :to-be
+            nil))
+  (it "\"multi word\" prop 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "prop \"multi word\" 123"
+    (expect (org-roam--str-to-list "\"multi word\" prop 123")
+            :to-equal
+            '("multi word" "prop" "123")))
+  (it "errors on bad input"
+    (expect (org-roam--str-to-list 1)
+            :to-throw)
+    (expect (org-roam--str-to-list "\"hello")
+            :to-throw)))
+
+(describe "Title extraction"
+  :var (org-roam-title-sources)
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (cl-flet
+      ((test (fn file)
+             (let ((buf (find-file-noselect
+                         (test-org-roam--abs-path file))))
+               (with-current-buffer buf
+                 (funcall fn)))))
+    (it "extracts title from title property"
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/title.org")
+              :to-equal
+              '("Title"))
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/aliases.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/headline.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-title
+                    "titles/combination.org")
+              :to-equal
+              '("TITLE PROP")))
+
+    (it "extracts alias"
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/title.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/aliases.org")
+              :to-equal
+              '("roam" "alias"))
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/headline.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/combination.org")
+              :to-equal
+              '("roam" "alias")))
+
+    (it "extracts headlines"
+      (expect (test #'org-roam--extract-titles-alias
+                    "titles/title.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/aliases.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/headline.org")
+              :to-equal
+              '("Headline"))
+      (expect (test #'org-roam--extract-titles-headline
+                    "titles/combination.org")
+              :to-equal
+              '("Headline")))
+
+    (describe "uses org-roam-title-sources correctly"
+      (it "'((title headline) alias)"
+        (expect (let ((org-roam-title-sources '((title headline) alias)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("TITLE PROP" "roam" "alias")))
+      (it "'((headline title) alias)"
+        (expect (let ((org-roam-title-sources '((headline title) alias)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("Headline" "roam" "alias")))
+      (it "'(headline alias title)"
+        (expect (let ((org-roam-title-sources '(headline alias title)))
+                  (test #'org-roam--extract-titles
+                        "titles/combination.org"))
+                :to-equal
+                '("Headline" "roam" "alias" "TITLE PROP"))))))
+
+(describe "Tag extraction"
+  :var (org-roam-tag-sources)
+  (before-all
+    (test-org-roam--init))
+
+  (after-all
+    (test-org-roam--teardown))
+
+  (cl-flet
+      ((test (fn file)
+             (let* ((fname (test-org-roam--abs-path file))
+                    (buf (find-file-noselect fname)))
+               (with-current-buffer buf
+                 (funcall fn fname)))))
+    (it "extracts from prop"
+      (expect (test #'org-roam--extract-tags-prop
+                    "tags/tag.org")
+              :to-equal
+              '("t1" "t2 with space" "t3"))
+      (expect (test #'org-roam--extract-tags-prop
+                    "tags/no_tag.org")
+              :to-equal
+              nil))
+
+    (it "extracts from all directories"
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-all-directories
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("nested" "deeply")))
+
+    (it "extracts from last directory"
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-last-directory
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("deeply")))
+
+    (it "extracts from first directory"
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "base.org")
+              :to-equal
+              nil)
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "tags/tag.org")
+              :to-equal
+              '("tags"))
+      (expect (test #'org-roam--extract-tags-first-directory
+                    "nested/deeply/deeply_nested_file.org")
+              :to-equal
+              '("nested")))
+
+    (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"))))))
+
+(describe "ID extraction"
+  (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 ids"
+      (expect (test #'org-roam--extract-ids
+                    "headlines/headline.org")
+              :to-have-same-items-as
+              `(["e84d0630-efad-4017-9059-5ef917908823" ,(test-org-roam--abs-path "headlines/headline.org") 1]
+                ["801b58eb-97e2-435f-a33e-ff59a2f0c213" ,(test-org-roam--abs-path "headlines/headline.org") 1])))))
+
+(describe "Test roam links"
+  (it ""
+    (expect (org-roam-link--split-path "")
+            :to-equal
+            '(title "" "" nil)))
+  (it "title"
+    (expect (org-roam-link--split-path "title")
+            :to-equal
+            '(title "title" "" nil)))
+  (it "title*"
+    (expect (org-roam-link--split-path "title*")
+            :to-equal
+            '(title+headline "title" "" 5)))
+  (it "title*headline"
+    (expect (org-roam-link--split-path "title*headline")
+            :to-equal
+            '(title+headline "title" "headline" 5)))
+  (it "*headline"
+    (expect (org-roam-link--split-path "*headline")
+            :to-equal
+            '(headline "" "headline" 0))))
 
 ;;; Tests
-(describe "org-roam-db-build-cache"
-  (it "initializes correctly"
-    (org-roam-test-init)
-    (org-roam-db-build-cache)
+(xdescribe "org-roam-db-build-cache"
+  (before-each
+    (test-org-roam--init))
 
+  (after-each
+    (test-org-roam--teardown))
+
+  (it "initializes correctly"
     ;; Cache
     (expect (caar (org-roam-db-query [:select (funcall count) :from files])) :to-be 8)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links])) :to-be 5)
     (expect (caar (org-roam-db-query [:select (funcall count) :from titles])) :to-be 8)
     (expect (caar (org-roam-db-query [:select (funcall count) :from titles
-                                      :where titles :is-null])) :to-be 2)
+                                      :where titles :is-null])) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from refs])) :to-be 1)
 
-    ;; TODO Test files
-
     ;; Links
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "foo.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= from $s1)]
-                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 2)
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 2)
 
     ;; Links -- File-to
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "nested/foo.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "nested/foo.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "nested/bar.org"))) :to-be 1)
+                                     (test-org-roam--abs-path "nested/bar.org"))) :to-be 1)
     (expect (caar (org-roam-db-query [:select (funcall count) :from links
                                       :where (= to $s1)]
-                                     (org-roam-test-abs-path "unlinked.org"))) :to-be 0)
+                                     (test-org-roam--abs-path "unlinked.org"))) :to-be 0)
     ;; TODO Test titles
     (expect (org-roam-db-query [:select * :from titles])
             :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "alias.org")
+            (list (list (test-org-roam--abs-path "alias.org")
                         (list "t1" "a1" "a 2"))
-                  (list (org-roam-test-abs-path "bar.org")
+                  (list (test-org-roam--abs-path "bar.org")
                         (list "Bar"))
-                  (list (org-roam-test-abs-path "foo.org")
+                  (list (test-org-roam--abs-path "foo.org")
                         (list "Foo"))
-                  (list (org-roam-test-abs-path "nested/bar.org")
+                  (list (test-org-roam--abs-path "nested/bar.org")
                         (list "Nested Bar"))
-                  (list (org-roam-test-abs-path "nested/foo.org")
+                  (list (test-org-roam--abs-path "nested/foo.org")
                         (list "Nested Foo"))
-                  (list (org-roam-test-abs-path "no-title.org") nil)
-                  (list (org-roam-test-abs-path "web_ref.org") nil)
-                  (list (org-roam-test-abs-path "unlinked.org")
+                  (list (test-org-roam--abs-path "no-title.org")
+                        (list "Headline title"))
+                  (list (test-org-roam--abs-path "web_ref.org") nil)
+                  (list (test-org-roam--abs-path "unlinked.org")
                         (list "Unlinked"))))
 
     (expect (org-roam-db-query [:select * :from refs])
             :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
+            (list (list "https://google.com/" (test-org-roam--abs-path "web_ref.org") "website")))
 
     ;; Expect rebuilds to be really quick (nothing changed)
     (expect (org-roam-db-build-cache)
             :to-equal
-            (list :files 0 :links 0 :titles 0 :refs 0 :deleted 0))))
-
-(describe "org-roam-insert"
-  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache))
-
-  (it "temp1 -> foo"
-    (let ((buf (org-roam-test-find-new-file "temp1.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert nil))))
-    (expect (buffer-string) :to-match (regexp-quote "file:foo.org")))
-
-  (it "temp2 -> nested/foo"
-    (let ((buf (org-roam-test-find-new-file "temp2.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Nested SPC Foo RET"
-         (org-roam-insert nil))))
-    (expect (buffer-string) :to-match (regexp-quote "file:nested/foo.org")))
-
-  (it "nested/temp3 -> foo"
-    (let ((buf (org-roam-test-find-new-file "nested/temp3.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Foo RET"
-         (org-roam-insert nil))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../foo.org")))
-
-  (it "a/b/temp4 -> nested/foo"
-    (let ((buf (org-roam-test-find-new-file "a/b/temp4.org")))
-      (with-current-buffer buf
-        (with-simulated-input
-         "Nested SPC Foo RET"
-         (org-roam-insert nil))))
-    (expect (buffer-string) :to-match (regexp-quote "file:../../nested/foo.org"))))
-
-(describe "rename file updates cache"
-  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache))
-
-  (it "foo -> new_foo"
-    (rename-file (org-roam-test-abs-path "foo.org")
-                 (org-roam-test-abs-path "new_foo.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (org-roam-test-abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (org-roam-test-abs-path "new_foo.org"))
-            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../new_foo.org][Foo]]")))
-
-  (it "foo -> foo with spaces"
-    (rename-file (org-roam-test-abs-path "foo.org")
-                 (org-roam-test-abs-path "foo with spaces.org"))
-    ;; Cache should be cleared of old file
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-
-    ;; Cache should be updated
-    (expect (org-roam-db-query [:select [to]
-                                :from links
-                                :where (= from $s1)]
-                               (org-roam-test-abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "bar.org"))))
-    (expect (org-roam-db-query [:select [from]
-                                :from links
-                                :where (= to $s1)]
-                               (org-roam-test-abs-path "foo with spaces.org"))
-            :to-have-same-items-as
-            (list (list (org-roam-test-abs-path "nested/bar.org"))))
-
-    ;; Links are updated
-    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "nested/bar.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:../foo with spaces.org][Foo]]")))
-
-  (it "no-title -> meaningful-title"
-    (rename-file (org-roam-test-abs-path "no-title.org")
-                 (org-roam-test-abs-path "meaningful-title.org"))
-    ;; File has no forward links
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "no-title.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "meaningful-title.org"))) :to-be 1)
-
-    ;; Links are updated with the appropriate name
-    (expect (with-temp-buffer
-              (insert-file-contents (org-roam-test-abs-path "meaningful-title.org"))
-              (buffer-string))
-            :to-match
-            (regexp-quote "[[file:meaningful-title.org][meaningful-title]]")))
-
-  (it "web_ref -> hello"
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal
-            (list (list (org-roam-test-abs-path "web_ref.org"))))
-    (rename-file (org-roam-test-abs-path "web_ref.org")
-                 (org-roam-test-abs-path "hello.org"))
-    (expect (org-roam-db-query
-             [:select [file] :from refs
-              :where (= ref $s1)]
-             "https://google.com/")
-            :to-equal (list (list (org-roam-test-abs-path "hello.org"))))
-    (expect (caar (org-roam-db-query
-                   [:select [ref] :from refs
-                    :where (= file $s1)]
-                   (org-roam-test-abs-path "web_ref.org")))
-            :to-equal nil)))
-
-(describe "delete file updates cache"
-  (before-each
-    (org-roam-test-init)
-    (org-roam-db--clear)
-    (org-roam-db-build-cache)
-    (sleep-for 1))
-
-  (it "delete foo"
-    (delete-file (org-roam-test-abs-path "foo.org"))
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from titles
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from refs
-                                      :where (= file $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0)
-    (expect (caar (org-roam-db-query [:select (funcall count)
-                                      :from links
-                                      :where (= from $s1)]
-                                     (org-roam-test-abs-path "foo.org"))) :to-be 0))
-
-  (it "delete web_ref"
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list (list "https://google.com/" (org-roam-test-abs-path "web_ref.org"))))
-    (delete-file (org-roam-test-abs-path "web_ref.org"))
-    (expect (org-roam-db-query [:select * :from refs])
-            :to-have-same-items-as
-            (list))))
+            (list :files 0 :links 0 :tags 0 :titles 0 :refs 0 :deleted 0))))
 
 (provide 'test-org-roam)