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

(docs): Add graph setup documentation for MacOS (#146 )
Thanks @naistran for instructions, and @leothelocust and @seandavi for discussion and confirmation
2025-08-03 12:27:23 -05:00 · 2020-02-21 13:44:16 +08:00 · 2020-02-21 13:17:09 +08:00 · 2020-02-21 10:55:53 +08:00 · 2020-02-20 17:43:30 +08:00 · 2020-02-20 17:33:30 +08:00
21 changed files with 862 additions and 240 deletions
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@ -0,0 +1,30 @@
+---
+name: Bug Report
+about: Something's not working.
+title: ''
+labels: ''
+assignees: 'jethrokuan'
+---
+
+### Description
+
+#### Steps to Reproduce
+<!--
+Example:
+
+1. Load Emacs
+2. Run `org-roam--build-cache-async`
+3. Run `org-roam-find-file`
+...
+-->
+
+
+#### Expected Results
+<!-- Example: File A is there -->
+
+#### Actual Results
+<!-- Example: File A is missing -->
+
+### Versions
+- Emacs (`C-h v emacs-version`): vX.X.X
+- Org-roam commit: https://github.com/jethrokuan/org-roam/commit/commithashhere
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ b/.github/ISSUE_TEMPLATE/feature_request.md
@ -0,0 +1,16 @@
+---
+name: Feature Request
+about: Create a feature request to improve Org-roam
+title: ''
+labels: 'enhancement'
+assignees: 'jethrokuan'
+---
+
+### Brief Abstract
+
+### Long Description
+
+### Proposed Implementation (if any)
+
+### Please check the following:
+- [ ] No similar feature requests
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@ -0,0 +1 @@
+###### Motivation for this change
--- a/.gitignore
+++ b/.gitignore
@ -1 +1,2 @@
 /.sandbox/
+**/*.elc
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -1,5 +1,43 @@
 # Changelog

+## 0.1.2 (2020-02-21)
+
+### Breaking Changes
+* [#143][gh-143] `org-roam-mode` is now a global mode. The installation instructions have changed accordingly.
+* [#103][gh-103] Change `org-roam-file-format` to a function: `org-roam-file-name-function` to allow more flexible file name customizaton. Also changes `org-roam-use-timestamp-as-filename` to `org-roam-filename-noconfirm` to better describe what it does.
+
+### New Features
+* [#145][gh-145] `org-roam-show-graph`: Fallback to Emacs SVG viewer
+* [#141][gh-141] add variable `org-roam-new-file-directory` for new Org-roam files
+* [#138][gh-138] add `org-roam-switch-to-buffer`
+* [#124][gh-124], [#141][gh-141] Maintain cache consistency on file rename and delete
+* [#87][gh-87], [#90][gh-90] Support encrypted Org files
+* [#110][gh-110] Add prefix to `org-roam-insert`, for inserting titles down-cased
+* [#99][gh-99] Add keybinding so that `<return>` or `mouse-1` in the backlinks buffer visits the source file of the backlink at point
+
+### Changes
+
+* [#108][gh-108] Locally overwrite the link following behaviour in the org-roam-buffer to open files in the same window `org-roam` was called from
+
+### Bugfixes
+* [#86][gh-86] Fix `org-roam--parse-content` incorrect `:to` computation for nested files
+* [#98][gh-98] Fix `org-roam--find-file` picking up temporary files
+* [#136][gh-136] Misc bugfixes
+
+### Internal
+* [#122][gh-122], [#128][gh-128] Improve performance of post-command-hook
+* [#92][gh-92], [#105][gh-105] Add tests for core functionality
+
+### New Contributors
+* [@frigge](https://github.com/frigge)
+* [@juergenhoetzel](https://github.com/juergenhoetzel)
+* [@chip2n](https://github.com/chip2n)
+* [@l3kn](https://github.com/l3kn)
+* [@jdormit](https://github.com/jdormit)
+* [@herbertjones](https://github.com/herbertjones)
+* [@CeleritasCelery](https://github.com/CeleritasCelery)
+* [@daniel-koudouna](https://github.com/daniel-koudouna)
+
 ## 0.1.1 (2020-02-15)

 Mostly a documentation/cleanup release.
@ -31,6 +69,24 @@ Mostly a documentation/cleanup release.
 [gh-75]: https://github.com/jethrokuan/org-roam/pull/75
 [gh-78]: https://github.com/jethrokuan/org-roam/pull/78
 [gh-82]: https://github.com/jethrokuan/org-roam/pull/82
+[gh-86]: https://github.com/jethrokuan/org-roam/pull/86
+[gh-87]: https://github.com/jethrokuan/org-roam/pull/87
+[gh-90]: https://github.com/jethrokuan/org-roam/pull/90
+[gh-92]: https://github.com/jethrokuan/org-roam/pull/92
+[gh-98]: https://github.com/jethrokuan/org-roam/pull/98
+[gh-99]: https://github.com/jethrokuan/org-roam/pull/99
+[gh-103]: https://github.com/jethrokuan/org-roam/pull/103
+[gh-105]: https://github.com/jethrokuan/org-roam/pull/105
+[gh-108]: https://github.com/jethrokuan/org-roam/pull/108
+[gh-110]: https://github.com/jethrokuan/org-roam/pull/110
+[gh-122]: https://github.com/jethrokuan/org-roam/pull/122
+[gh-124]: https://github.com/jethrokuan/org-roam/pull/124
+[gh-128]: https://github.com/jethrokuan/org-roam/pull/128
+[gh-136]: https://github.com/jethrokuan/org-roam/pull/136
+[gh-138]: https://github.com/jethrokuan/org-roam/pull/138
+[gh-141]: https://github.com/jethrokuan/org-roam/pull/141
+[gh-142]: https://github.com/jethrokuan/org-roam/pull/142
+[gh-143]: https://github.com/jethrokuan/org-roam/pull/143

 # Local Variables:
 # eval: (auto-fill-mode -1)
--- a/README.md
+++ b/README.md
@ -43,22 +43,20 @@ The recommended method is using use-package and straight, or a similar package m
 (use-package org-roam
      :after org
      :hook 
-      ((org-mode . org-roam-mode)
-       (after-init . org-roam--build-cache-async) ;; optional!
-       )
+      (after-init . org-roam-mode)
      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
      :custom
      (org-roam-directory "/path/to/org-files/")
-      :bind
-      ("C-c n l" . org-roam)
-      ("C-c n t" . org-roam-today)
-      ("C-c n f" . org-roam-find-file)
-      ("C-c n i" . org-roam-insert)
-      ("C-c n g" . org-roam-show-graph))
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n g" . org-roam-show-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
 ```

-For more detailed installation instructions, please see [the
-installation
+For more detailed installation instructions (including instructions for
+Spacemacs users), please see [the installation
 documentation](https://org-roam.readthedocs.io/en/develop/installation/).

 ## Knowledge Bases using Org-Roam
@ -74,7 +72,7 @@ A changelog is being maintained [here](CHANGELOG.md)

 To report bugs and suggest new feature use the issue tracker. If you
 have some code which you would like to be merged, then open a pull
-request. Please also see [CONTRIBUTING.md](CONTRIBUTING.md).
+request. Please also see [CONTRIBUTING.md](.github/CONTRIBUTING.md).

 ## License

--- a/doc/configuration.md
+++ b/doc/configuration.md
@ -66,24 +66,20 @@ Org files in all of its main commands (`org-roam-insert`,
 `org-roam-find-file`). Hence, having any unique file name is a decent
 option, and the default workflow uses the timestamp as the filename.

-The format of the filename is specified by the string
-`org-roam-file-format`, which defaults to `"%Y%m%d%H%M%S"`. To see
-valid specifications, see the help (`C-h f`) for `format-time-string`.
+The format of the filename is controlled by the function
+`org-roam-file-name-function`, which defaults to a format like
+`YYYYMMDDHHMMSS_title_here.org`. You may choose to define your own
+function to change this.

-There are several reasons for keeping filenames meaningful. For
-example, one may wish to publish the Org files, and some publishing
-methods such as Org-publish use the file names as slugs for the URLs.
-
-If you wish to maintain manual control of filenames, set
-`org-roam-use-timestamp-as-filename` to `nil`:
+If you wish to be prompted to change the file name on creation, set
+`org-roam-filename-noconfirm` to `nil`:

 ```emacs-lisp
-(setq org-roam-use-timestamp-as-filename nil)
+(setq org-roam-filename-noconfirm nil)
 ```

-When this setting is turned off, the user is instead manually prompted
-for a filename. It is then the user's responsibility to ensure that
-the file names are unique.
+It is then the user's responsibility to ensure that the file names are
+unique.

 ### Autopopulating Titles

@ -94,6 +90,15 @@ typically near the top of the file. The option
 attribute is automatically inserted into the files created via
 Org-roam commands. Setting it to `nil` will disable this behaviour.

+### Encryption
+
+Encryption (via GPG) can be enabled for all new files by setting
+`org-roam-encrypt-files` to `t`. When enabled, new files are created
+with the .org.gpg extension and decryption are handled automatically
+by EasyPG. Note that this causes Emacs to ask for password when the
+cache is built (if you have an encrypted file in `org-roam-directory`)
+as well as each time a new file is created. It might be a good idea to
+cache the password in order to make this more managable.

 ## Org-roam Graph Viewer

--- a/doc/ecosystem.md
+++ b/doc/ecosystem.md
@ -5,7 +5,7 @@ A number of packages work well combined with Org-Roam:
 [Deft][deft] provides a nice interface for browsing and filtering
 org-roam notes.

-```
+```emacs-lisp
 (use-package deft
  :after org
  :bind
@ -14,8 +14,37 @@ org-roam notes.
  (deft-recursive t)
  (deft-use-filter-string-for-filename t)
  (deft-default-extension "org")
-  (deft-directory "/path/to/org-roam-files/")
-  (deft-use-filename-as-title t))
+  (deft-directory "/path/to/org-roam-files/"))
+```
+
+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
@ -29,7 +58,7 @@ powerful alternative to the simple function `org-roam-today`. It
 provides better journaling capabilities, and a nice calendar interface
 to see all dated entries.

-```
+```emacs-lisp
 (use-package org-journal
  :bind
  ("C-c n j" . org-journal-new-entry)
--- a/doc/graph_setup.md
+++ b/doc/graph_setup.md
@ -5,7 +5,7 @@ The gist of the setup is setting up a Bash script to trim off the
 `roam://` prefix from the link, causing the desktop application to
 call `emacsclient path/to/org-roam-file.org`.

-## Setting Up for Linux
+## Linux

 Create a desktop application. I place mine in
 `~/.local/share/applications/roam.desktop`:
@ -37,3 +37,42 @@ running in your shell:
 ```bash
 xdg-mime default roam.desktop x-scheme-handler/roam
 ```
+
+## Mac OS
+
+One solution to this, recommended in [Issue
+#115](https://github.com/jethrokuan/org-roam/issues/115), is to use
+[Platypus](https://github.com/sveinbjornt/Platypus). Here are the
+instructions for setting up with Platypus and Chrome:
+
+1. Create an executable `launch-emacs.sh` script:
+
+```sh
+#!/usr/bin/env bash
+/usr/local/bin/emacsclient --no-wait "${1#*:}"
+```
+
+2. Install and launch Platypus (with [Homebrew](https://brew.sh/)):
+
+```sh
+brew cask install playtpus
+```
+
+3. Playtpus settings:
+
+- App Name: `OrgRoam`
+- Script Type: `env` and `/usr/bin/env`
+- Script Path: `/path/to/your/launch-emacs.sh`
+- Tick Accept dropped items and click Settings
+- Tick Accept dropped files
+- Tick Register as URI scheme handler
+- Add `roam` as a protocol
+- Create the app
+
+To disable the "confirm" prompt in Chrome, you can also make Chrome
+show a checkbox to tick, so that the `OrgRoam` app will be used
+without confirmation. To do this, run in a shell:
+
+```sh
+defaults write com.google.Chrome ExternalProtocolDialogShowAlwaysOpenCheckbox -bool true
+```
--- a/doc/installation.md
+++ b/doc/installation.md
@ -7,18 +7,16 @@ The recommended method is using [use-package][use-package] and
 (use-package org-roam
      :after org
      :hook 
-      ((org-mode . org-roam-mode)
-       (after-init . org-roam--build-cache-async) ;; optional!
-       )
+      (after-init . org-roam-mode)
      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
      :custom
      (org-roam-directory "/path/to/org-files/")
-      :bind
-      ("C-c n l" . org-roam)
-      ("C-c n t" . org-roam-today)
-      ("C-c n f" . org-roam-find-file)
-      ("C-c n i" . org-roam-insert)
-      ("C-c n g" . org-roam-show-graph))
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n g" . org-roam-show-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
 ```

 If not using package.el, you can also clone it into your Emacs
@ -33,17 +31,16 @@ git clone https://github.com/jethrokuan/org-roam/ ~/.emacs.d/elisp/org-roam
      :after org
      :load-path "elisp/"
      :hook 
-      ((org-mode . org-roam-mode)
-       (after-init . org-roam--build-cache-async) ;; optional!
-       )
+      (after-init . org-roam-mode)
+      :straight (:host github :repo "jethrokuan/org-roam" :branch "develop")
      :custom
      (org-roam-directory "/path/to/org-files/")
-      :bind
-      ("C-c n l" . org-roam)
-      ("C-c n t" . org-roam-today)
-      ("C-c n f" . org-roam-find-file)
-      ("C-c n i" . org-roam-insert)
-      ("C-c n g" . org-roam-show-graph))
+      :bind (:map org-roam-mode-map
+              (("C-c n l" . org-roam)
+               ("C-c n f" . org-roam-find-file)
+               ("C-c n g" . org-roam-show-graph))
+              :map org-mode-map
+              (("C-c n i" . org-roam-insert))))
 ```

 Or without use-package:
@ -59,3 +56,38 @@ affect the Roam workflow. Do look through them at the

 [use-package]: https://github.com/jwiegley/use-package
 [straight]: https://github.com/raxod502/straight.el
+
+## Spacemacs
+If you are using Spacemacs, you can easily install org-roam by creating a simple layer that wraps org-roam. Paste the following into a new file `/.emacs.d/private/org-roam/packages.el`.
+```
+(defconst org-roam-packages
+  '((org-roam :location
+        (recipe :fetcher github :repo "jethrokuan/org-roam" :branch "develop"))))
+
+(defun org-roam/init-org-roam ()
+    (use-package org-roam
+        :after org
+        :hook
+        (after-init . org-roam-mode)
+        :custom
+        (org-roam-directory "/path/to/org-files/")
+        :init
+        (progn
+          (spacemacs/declare-prefix "ar" "org-roam")
+          (spacemacs/set-leader-keys
+            "arl" 'org-roam
+            "art" 'org-roam-today
+            "arf" 'org-roam-find-file
+            "arg" 'org-roam-show-graph)
+
+          (spacemacs/declare-prefix-for-mode 'org-mode "mr" "org-roam")
+          (spacemacs/set-leader-keys-for-major-mode 'org-mode
+            "rl" 'org-roam
+            "rt" 'org-roam-today
+            "rb" 'org-roam-switch-to-buffer
+            "rf" 'org-roam-find-file
+            "ri" 'org-roam-insert
+            "rg" 'org-roam-show-graph))))
+```
+
+Next, append `org-roam` to the `dotspacemacs-configuration-layers` list in your `.spacemacs` configuration file. Reload (`SPC f e R`) or restart Emacs to load `org-roam`. It's functions are available under the prefix `SPC a r` and `, r` when visiting an org-mode buffer. 
--- a/org-roam-utils.el
+++ b/org-roam-utils.el
@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 0.1.0
+;; Version: 0.1.2
 ;; Package-Requires: ((emacs "26.1"))

 ;; This file is NOT part of GNU Emacs.
@ -38,6 +38,24 @@
 (require 'subr-x)
 (require 'cl-lib)

+(defun org-roam--file-name-extension (filename)
+  "Return file name extension for FILENAME.
+
+Like file-name-extension, but does not strip version number."
+  (save-match-data
+    (let ((file (file-name-nondirectory filename)))
+      (if (and (string-match "\\.[^.]*\\'" file)
+                     (not (eq 0 (match-beginning 0))))
+          (substring file (+ (match-beginning 0) 1))))))
+
+(defun org-roam--org-file-p (path)
+  "Check if PATH is pointing to an org file."
+  (let ((ext (org-roam--file-name-extension path)))
+    (or (string= ext "org")
+        (and
+         (string= ext "gpg")
+         (string= (org-roam--file-name-extension (file-name-sans-extension path)) "org")))))
+
 (defun org-roam--find-files (dir)
  "Return all `org-roam' files in `DIR'."
  (if (file-exists-p dir)
@ -53,7 +71,7 @@
            (when (not (string-match dir-ignore-regexp file))
              (setq result (append (org-roam--find-files file) result))))
           ((and (file-readable-p file)
-                 (string= (file-name-extension file) "org"))
+                 (org-roam--org-file-p file))
            (setq result (cons (file-truename file) result)))))
        result)))

@ -65,25 +83,28 @@
            (path (org-element-property :path link))
            (start (org-element-property :begin link)))
        (when (and (string= type "file")
-                   (string= (file-name-extension path) "org"))
+                   (org-roam--org-file-p path))
          (goto-char start)
          (let* ((element (org-element-at-point))
+                 (begin (or (org-element-property :content-begin element)
+                            (org-element-property :begin element)))
                 (content (or (org-element-property :raw-value element)
                              (buffer-substring
-                               (or (org-element-property :content-begin element)
-                                   (org-element-property :begin element))
+                               begin
                               (or (org-element-property :content-end element)
-                                   (org-element-property :end element))))))
-            (list :from (or file-path
-                            (file-truename (buffer-file-name (current-buffer))))
-                  :to (file-truename (expand-file-name path org-roam-directory))
-                  :content (string-trim content))))))))
+                                   (org-element-property :end element)))))
+                 (content (string-trim content))
+                 (file-path (or file-path
+                                (file-truename (buffer-file-name (current-buffer))))))
+            (list :from file-path
+                  :to (file-truename (expand-file-name path (file-name-directory file-path)))
+                  :properties (list :content content :point begin))))))))

 (cl-defun org-roam--insert-item (item &key forward backward)
  "Insert ITEM into FORWARD and BACKWARD cache.

-ITEM is of the form: (:from from-path :to to-path :content preview-content)."
-  (pcase-let ((`(:from ,p-from :to ,p-to :content ,content) item))
+ITEM is of the form: (:from from-path :to to-path :properties (:content preview-content :point point))."
+  (pcase-let ((`(:from ,p-from :to ,p-to :properties ,props) item))
    ;; Build forward-links
    (let ((links (gethash p-from forward)))
      (if links
@ -96,14 +117,14 @@ ITEM is of the form: (:from from-path :to to-path :content preview-content)."
    (let ((contents-hash (gethash p-to backward)))
      (if contents-hash
          (if-let ((contents-list (gethash p-from contents-hash)))
-              (let ((updated (cons content contents-list)))
+              (let ((updated (cons props contents-list)))
                (puthash p-from updated contents-hash)
                (puthash p-to contents-hash backward))
            (progn
-              (puthash p-from (list content) contents-hash)
+              (puthash p-from (list props) contents-hash)
              (puthash p-to contents-hash backward)))
        (let ((contents-hash (make-hash-table :test #'equal)))
-          (puthash p-from (list content) contents-hash)
+          (puthash p-from (list props) contents-hash)
          (puthash p-to contents-hash backward))))))

 (defun org-roam--extract-title ()
@ -116,6 +137,33 @@ ITEM is of the form: (:from from-path :to to-path :content preview-content)."
        (org-element-property :value kw)))
    :first-match t))

+(defun org-roam--build-cache (dir)
+  "Build the org-roam caches in DIR."
+  (let ((backward-links (make-hash-table :test #'equal))
+        (forward-links (make-hash-table :test #'equal))
+        (file-titles (make-hash-table :test #'equal)))
+    (let* ((org-roam-files (org-roam--find-files dir))
+           (file-items (mapcar (lambda (file)
+                                 (with-temp-buffer
+                                   (insert-file-contents file)
+                                   (org-roam--parse-content file))) org-roam-files)))
+      (dolist (items file-items)
+        (dolist (item items)
+          (org-roam--insert-item
+           item
+           :forward forward-links
+           :backward backward-links)))
+      (dolist (file org-roam-files)
+        (with-temp-buffer
+          (insert-file-contents file)
+          (when-let ((title (org-roam--extract-title)))
+            (puthash file title file-titles)))
+        org-roam-files))
+    (list
+     :forward forward-links
+     :backward backward-links
+     :titles file-titles)))
+
 (provide 'org-roam-utils)

 ;;; org-roam-utils.el ends here
--- a/org-roam.el
+++ b/org-roam.el
@ -5,7 +5,7 @@
 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
 ;; URL: https://github.com/jethrokuan/org-roam
 ;; Keywords: org-mode, roam, convenience
-;; Version: 0.1.0
+;; Version: 0.1.2
 ;; Package-Requires: ((emacs "26.1") (dash "2.13") (f "0.17.2") (s "1.12.0") (async "1.9.4"))

 ;; This file is NOT part of GNU Emacs.
@ -55,7 +55,14 @@
  "Path to Org-roam files.

 All Org files, at any level of nesting, is considered part of the Org-roam."
-  :type 'directoy
+  :type 'directory
+  :group 'org-roam)
+
+(defcustom org-roam-new-file-directory nil
+  "Path to where new Org-roam files are created.
+
+If nil, default to the org-roam-directory (preferred)."
+  :type 'directory
  :group 'org-roam)

 (defcustom org-roam-buffer-position 'right
@ -68,18 +75,23 @@ Valid values are
                 (const right))
  :group 'org-roam)

-(defcustom org-roam-file-format "%Y%m%d%H%M%S"
-  "The timestamp format to use filenames."
-  :type 'string
-  :group 'org-roam)
+(defcustom org-roam-file-name-function #'org-roam--file-name-timestamp-title
+  "The function used to generate filenames.
+
+The function takes as parameter `TITLE', a string the user inputs."
+  :group 'org-roam
+  :type '(choice (const :tag "Default" org-roam--file-name-timestamp-title)
+                 (function :tag "Personalized function")))

 (defcustom org-roam-link-title-format "%s"
  "The format string used when inserting org-roam links that use their title."
  :type 'string
  :group 'org-roam)

-(defcustom org-roam-use-timestamp-as-filename t
-  "Whether to use timestamp as a file name. If not true, prompt for a file name each time."
+(defcustom org-roam-filename-noconfirm t
+  "Whether to prompt for confirmation of fil name for new files.
+
+If nil, always ask for filename."
  :type 'boolean
  :group 'org-roam)

@ -96,6 +108,11 @@ Valid values are
  :type 'string
  :group 'org-roam)

+(defcustom org-roam-encrypt-files nil
+  "Whether to encrypt new files. If true, create files with .org.gpg extension."
+  :type 'boolean
+  :group 'org-roam)
+
 (defcustom org-roam-graph-viewer (executable-find "firefox")
  "Path to executable for viewing SVG."
  :type 'string
@ -106,6 +123,16 @@ Valid values are
  :type 'string
  :group 'org-roam)

+(defcustom org-roam-graph-max-title-length 100
+  "Maximum length of titles in graphviz graph nodes"
+  :type 'number
+  :group 'org-roam)
+
+(defcustom org-roam-graph-node-shape "ellipse"
+  "Maximum length of titles in graphviz graph nodes"
+  :type 'string
+  :group 'org-roam)
+
 ;;; Polyfills
 ;; These are for functions I use that are only available in newer Emacs

@ -139,9 +166,12 @@ If called interactively, then PARENTS is non-nil."
 (defvar org-roam-titles-cache (make-hash-table :test #'equal)
  "Cache containing titles for org-roam files.")

-(defvar org-roam-current-file nil
+(defvar org-roam--current-buffer nil
  "Currently displayed file in `org-roam' buffer.")

+(defvar org-roam-last-window nil
+  "Last window `org-roam' was called from.")
+
 ;;; Utilities
 (defun org-roam--ensure-cache-built ()
  "Ensures that org-roam cache is built."
@ -149,11 +179,14 @@ If called interactively, then PARENTS is non-nil."
    (org-roam--build-cache-async)
    (user-error "Your Org-Roam cache isn't built yet! Please wait")))

-(defun org-roam--org-roam-file-p ()
-  "Return t if file is part of org-roam system, false otherwise."
-  (and (buffer-file-name (current-buffer))
-       (f-descendant-of-p (file-truename (buffer-file-name (current-buffer)))
-                          org-roam-directory)))
+(defun org-roam--org-roam-file-p (&optional file)
+  "Return t if FILE is part of org-roam system, defaulting to the name of the current buffer. Else, return nil."
+  (let ((path (or file
+                  (buffer-file-name (current-buffer)))))
+    (and path
+         (org-roam--org-file-p path)
+         (f-descendant-of-p (file-truename path)
+                            (file-truename org-roam-directory)))))

 (defun org-roam--get-title-from-cache (file)
  "Return title of `FILE' from the cache."
@ -167,14 +200,17 @@ If called interactively, then PARENTS is non-nil."
  "Return all org-roam files."
  (org-roam--find-files (file-truename org-roam-directory)))

-(defun org-roam--get-file-path (id &optional absolute)
-  "Convert identifier `ID' to file path.
+(defun org-roam--make-new-file-path (id &optional absolute)
+  "Make new file path from identifier `ID'.

-If `ABSOLUTE', return the absolute file-path. Else, return the relative file-path."
+If `ABSOLUTE', return an absolute file-path. Else, return a relative file-path."
  (let ((absolute-file-path (file-truename
                             (expand-file-name
-                              (concat id ".org")
-                              org-roam-directory))))
+                              (if org-roam-encrypt-files
+                                  (concat id ".org.gpg")
+                                (concat id ".org"))
+                              (or org-roam-new-file-directory
+                                  org-roam-directory)))))
    (if absolute
        absolute-file-path
      (file-relative-name absolute-file-path
@ -195,6 +231,13 @@ If `ABSOLUTE', return the absolute file-path. Else, return the relative file-pat
         (s (s-join "_" s)))
    s))

+(defun org-roam--file-name-timestamp-title (title)
+  "Return a file name (without extension) for new files.
+
+It uses TITLE and the current timestamp to form a unique title."
+  (let ((timestamp (format-time-string "%Y%m%d%H%M%S" (current-time)))
+        (slug (org-roam--title-to-slug title)))
+    (format "%s_%s" timestamp slug)))

 ;;; Creating org-roam files
 (defun org-roam--populate-title (file &optional title)
@ -218,51 +261,54 @@ If not provided, derive the title from the file name."
  "Create an org-roam file at FILE-PATH, optionally setting the TITLE attribute."
  (if (file-exists-p file-path)
      (error (format "Aborting, file already exists at %s" file-path))
+    (make-empty-file file-path t)
    (if org-roam-autopopulate-title
-        (org-roam--populate-title file-path title)
-      (make-empty-file file-path))))
+        (org-roam--populate-title file-path title))
+    (save-excursion
+      (with-current-buffer (find-file-noselect file-path)
+        (org-roam--update-cache)))))

 (defun org-roam--new-file-named (slug)
  "Create a new file named `SLUG'.
 `SLUG' is the short file name, without a path or a file extension."
  (interactive "sNew filename (without extension): ")
-  (let ((file-path (org-roam--get-file-path slug t)))
+  (let ((file-path (org-roam--make-new-file-path slug t)))
    (unless (file-exists-p file-path)
      (org-roam--make-file file-path))
    (find-file file-path)))

-(defun org-roam--get-new-id (&optional title)
-  "Return a new ID, generated from the current time.
-
-Optionally pass it the title, for a smart file name."
-  (if org-roam-use-timestamp-as-filename
-      (format-time-string org-roam-file-format (current-time))
-    (let* ((slug (read-string "Enter ID (without extension): "
-                              (if title
-                                  (org-roam--title-to-slug title)
-                                "")))
-           (file-path (org-roam--get-file-path slug t)))
-      (if (file-exists-p file-path)
-          (user-error "There's already a file at %s")
-        slug))))
+(defun org-roam--get-new-id (title)
+  "Return a new ID, given the note TITLE."
+  (let* ((proposed-slug (funcall org-roam-file-name-function title))
+         (new-slug (if org-roam-filename-noconfirm
+                       proposed-slug
+                     (read-string "Enter ID (without extension): "
+                                  proposed-slug)))
+         (file-path (org-roam--make-new-file-path new-slug t)))
+    (if (file-exists-p file-path)
+        (user-error "There's already a file at %s")
+      new-slug)))

 (defun org-roam-new-file ()
  "Quickly create a new file, using the current timestamp."
  (interactive)
-  (org-roam--new-file-named (org-roam--get-new-id)))
+  (org-roam--new-file-named (format-time-string "%Y%m%d%H%M%S" (current-time))))

 ;;; Inserting org-roam links
-(defun org-roam-insert ()
-  "Find an org-roam file, and insert a relative org link to it at point."
-  (interactive)
+(defun org-roam-insert (prefix)
+  "Find an org-roam file, and insert a relative org link to it at point.
+
+If PREFIX, downcase the title before insertion."
+  (interactive "P")
  (let* ((completions (mapcar (lambda (file)
                                (list (org-roam--get-title-or-slug file)
                                      file))
                              (org-roam--find-all-files)))
         (title (completing-read "File: " completions))
         (absolute-file-path (or (cadr (assoc title completions))
-                                 (org-roam--get-file-path (org-roam--get-new-id title) t)))
-         (current-file-path (-> (current-buffer)
+                                 (org-roam--make-new-file-path (org-roam--get-new-id title) t)))
+         (current-file-path (-> (or (buffer-base-buffer)
+                                    (current-buffer))
                                (buffer-file-name)
                                (file-truename)
                                (file-name-directory))))
@ -271,7 +317,9 @@ Optionally pass it the title, for a smart file name."
    (insert (format "[[%s][%s]]"
                    (concat "file:" (file-relative-name absolute-file-path
                                                        current-file-path))
-                    (format org-roam-link-title-format title)))))
+                    (format org-roam-link-title-format (if prefix
+                                                           (downcase title)
+                                                         title))))))

 ;;; Finding org-roam files
 (defun org-roam-find-file ()
@ -282,15 +330,37 @@ Optionally pass it the title, for a smart file name."
                              (org-roam--find-all-files)))
         (title-or-slug (completing-read "File: " completions))
         (absolute-file-path (or (cadr (assoc title-or-slug completions))
-                                 (org-roam--get-file-path
+                                 (org-roam--make-new-file-path
                                  (org-roam--get-new-id title-or-slug) t))))
    (unless (file-exists-p absolute-file-path)
      (org-roam--make-file absolute-file-path title-or-slug))
    (find-file absolute-file-path)))

-;;; Building the org-roam cache (asynchronously)
+(defun org-roam--get-roam-buffers ()
+  "Return a list of buffers that are org-roam files."
+  (--filter (and (with-current-buffer it (derived-mode-p 'org-mode))
+                 (buffer-file-name it)
+                 (org-roam--org-roam-file-p (buffer-file-name it)))
+            (buffer-list)))
+
+(defun org-roam-switch-to-buffer ()
+  "Switch to an existing org-roam buffer using completing-read."
+  (interactive)
+  (let* ((roam-buffers (org-roam--get-roam-buffers))
+         (names-and-buffers (mapcar (lambda (buffer)
+                                      (cons (or (org-roam--get-title-from-cache
+                                                 (buffer-file-name buffer))
+                                                (buffer-name buffer))
+                                            buffer))
+                                    roam-buffers)))
+    (unless roam-buffers
+      (error "No roam buffers."))
+    (when-let ((name (completing-read "Choose a buffer: " names-and-buffers)))
+      (switch-to-buffer (cdr (assoc name names-and-buffers))))))
+
+;;; Building the org-roam cache
 (defun org-roam--build-cache-async ()
-  "Builds the cache asychronously, saving it into the org-roam caches."
+  "Builds the caches asychronously."
  (interactive)
  (async-start
   `(lambda ()
@ -298,30 +368,7 @@ Optionally pass it the title, for a smart file name."
      (package-initialize)
      (require 'org-roam-utils)
      ,(async-inject-variables "org-roam-directory")
-      (let ((backward-links (make-hash-table :test #'equal))
-            (forward-links (make-hash-table :test #'equal))
-            (file-titles (make-hash-table :test #'equal)))
-        (let* ((org-roam-files (org-roam--find-files org-roam-directory))
-               (file-items (mapcar (lambda (file)
-                                     (with-temp-buffer
-                                       (insert-file-contents file)
-                                       (org-roam--parse-content file))) org-roam-files)))
-          (dolist (items file-items)
-            (dolist (item items)
-              (org-roam--insert-item
-               item
-               :forward forward-links
-               :backward backward-links)))
-          (mapcar (lambda (file)
-                    (with-temp-buffer
-                      (insert-file-contents file)
-                      (when-let ((title (org-roam--extract-title)))
-                        (puthash file title file-titles))))
-                  org-roam-files))
-        (list
-         :forward forward-links
-         :backward backward-links
-         :titles file-titles)))
+      (org-roam--build-cache org-roam-directory))
   (lambda (cache)
     (setq org-roam-forward-links-cache (plist-get cache :forward))
     (setq org-roam-backward-links-cache (plist-get cache :backward))
@ -330,10 +377,20 @@ Optionally pass it the title, for a smart file name."
     (message "Org-roam cache built!"))))

 (defun org-roam--clear-cache ()
+  "Clears all entries in the caches."
+  (interactive)
+  (setq org-roam-cache-initialized nil)
+  (setq org-roam-forward-links-cache (make-hash-table :test #'equal))
+  (setq org-roam-backward-links-cache (make-hash-table :test #'equal))
+  (setq org-roam-titles-cache (make-hash-table :test #'equal)))
+
+(defun org-roam--clear-file-from-cache (&optional filepath)
  "Remove any related links to the file.

 This is equivalent to removing the node from the graph."
-  (let ((file (file-truename (buffer-file-name (current-buffer)))))
+  (let* ((path (or filepath
+                   (buffer-file-name (current-buffer))))
+         (file (file-truename path)))
    ;; Step 1: Remove all existing links for file
    (when-let ((forward-links (gethash file org-roam-forward-links-cache)))
      ;; Delete backlinks to file
@ -356,7 +413,7 @@ This is equivalent to removing the node from the graph."
 (defun org-roam--update-cache ()
  "Update org-roam caches for the current buffer file."
  (save-excursion
-    (org-roam--clear-cache)
+    (org-roam--clear-file-from-cache)
    ;; Insert into title cache
    (org-roam--update-cache-title)
    ;; Insert new items
@ -386,16 +443,48 @@ This is equivalent to removing the node from the graph."
  (let ((time (org-read-date nil 'to-time nil "Date:  ")))
    (org-roam--new-file-named (format-time-string "%Y-%m-%d" time))))

-;;; Org-roam buffer updates
+;;; Org-roam buffer
+(define-derived-mode org-roam-backlinks-mode org-mode "Backlinks"
+  "Major mode for the org-roam backlinks buffer
+
+Bindings:
+\\{org-roam-backlinks-mode-map}")
+
+(define-key org-roam-backlinks-mode-map [mouse-1] 'org-roam-jump-to-backlink)
+(define-key org-roam-backlinks-mode-map (kbd "RET") 'org-roam-jump-to-backlink)
+
+(defun org-roam-jump-to-backlink ()
+  "Jumps to original file and location of the backlink content snippet at point"
+  (interactive)
+  (let ((file-from (get-text-property (point) 'file-from))
+        (p (get-text-property (point) 'file-from-point)))
+    (when (and file-from p)
+      (find-file file-from)
+      (goto-char p)
+      (org-show-context))))
+
+(defun org-roam--find-file (file)
+  "Open FILE in the window `org-roam' was called from."
+  (if (and org-roam-last-window (window-valid-p org-roam-last-window))
+      (progn (with-selected-window org-roam-last-window
+               (find-file file))
+             (select-window org-roam-last-window))
+    (find-file file)))
+
 (defun org-roam-update (file-path)
  "Show the backlinks for given org file for file at `FILE-PATH'."
  (org-roam--ensure-cache-built)
  (let ((buffer-title (org-roam--get-title-or-slug file-path)))
    (with-current-buffer org-roam-buffer
+      ;; Locally overwrite the file opening function to re-use the
+      ;; last window org-roam was called from
+      (setq-local
+       org-link-frame-setup
+       (cons '(file . org-roam--find-file) org-link-frame-setup))
      (let ((inhibit-read-only t))
        (erase-buffer)
-        (when (not (eq major-mode 'org-mode))
-          (org-mode))
+        (when (not (eq major-mode 'org-roam-backlinks-mode))
+          (org-roam-backlinks-mode))
        (make-local-variable 'org-return-follows-link)
        (setq org-return-follows-link t)
        (insert
@ -408,14 +497,165 @@ This is equivalent to removing the node from the graph."
                         (insert (format "** [[file:%s][%s]]\n"
                                         file-from
                                         (org-roam--get-title-or-slug file-from)))
-                         (dolist (content contents)
-                           (insert (concat (propertize (s-trim (s-replace "\n" " " content))
-                                                       'font-lock-face 'org-block)
-                                           "\n\n"))))
+                         (dolist (properties contents)
+                           (let ((content (propertize
+                                           (s-trim (s-replace "\n" " "
+                                                              (plist-get properties :content)))
+                                           'font-lock-face 'org-block
+                                           'help-echo "mouse-1: visit backlinked note"
+                                           'file-from file-from
+                                           'file-from-point (plist-get properties :point))))
+                             (insert (format "%s \n\n" content)))))
                       backlinks))
          (insert "\n\n* No backlinks!")))
-      (read-only-mode 1)))
-  (setq org-roam-current-file file-path))
+      (read-only-mode 1))))
+
+;;; Building the Graphviz graph
+(defun org-roam-build-graph ()
+  "Build graphviz graph output."
+  (org-roam--ensure-cache-built)
+  (with-temp-buffer
+	(insert "digraph {\n")
+	(dolist (file (org-roam--find-all-files))
+	  (let ((title (org-roam--get-title-or-slug file)))
+		(let ((shortened-title (s-truncate org-roam-graph-max-title-length title)))
+		  (insert
+		   (format "  \"%s\" [label=\"%s\", shape=%s, URL=\"roam://%s\", tooltip=\"%s\"];\n"
+				   title
+				   shortened-title
+				   org-roam-graph-node-shape
+				   file
+				   title
+				   )))))
+	  (maphash
+	   (lambda (from-link to-links)
+		 (dolist (to-link to-links)
+		   (insert (format "  \"%s\" -> \"%s\";\n"
+						   (org-roam--get-title-or-slug from-link)
+						   (org-roam--get-title-or-slug to-link)))))
+	   org-roam-forward-links-cache)
+	  (insert "}")
+	  (buffer-string)))
+
+(defun org-roam-show-graph ()
+  "Generate the org-roam graph in SVG format, and display it using `org-roam-graph-viewer'."
+  (interactive)
+  (unless org-roam-graphviz-executable
+    (setq org-roam-graphviz-executable (executable-find "dot")))
+  (unless org-roam-graphviz-executable
+    (user-error "Can't find graphviz executable. Please check if it is in your path"))
+  (declare (indent 0))
+  (let ((temp-dot (expand-file-name "graph.dot" temporary-file-directory))
+        (temp-graph (expand-file-name "graph.svg" temporary-file-directory))
+        (graph (org-roam-build-graph)))
+    (with-temp-file temp-dot
+      (insert graph))
+    (call-process org-roam-graphviz-executable nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
+    (if (and org-roam-graph-viewer (executable-find org-roam-graph-viewer))
+	(call-process org-roam-graph-viewer nil 0 nil temp-graph)
+      (view-file temp-graph))))
+
+;;; Org-roam minor mode
+(cl-defun org-roam--maybe-update-buffer (&key redisplay)
+  "Update `org-roam-buffer' with the necessary information.
+This needs to be quick/infrequent, because this is run at
+`post-command-hook'."
+  (let ((buffer (window-buffer)))
+    (when (and (or redisplay
+                   (not (eq org-roam--current-buffer buffer)))
+               (eq 'visible (org-roam--current-visibility))
+               (buffer-local-value 'buffer-file-truename buffer))
+      (setq org-roam--current-buffer buffer)
+      (org-roam-update (expand-file-name
+                        (buffer-local-value 'buffer-file-truename buffer))))))
+
+(defun org-roam--find-file-hook-function ()
+  "Called by `find-file-hook' when `org-roam-mode' is on."
+  (when (org-roam--org-roam-file-p)
+    (add-hook 'post-command-hook #'org-roam--maybe-update-buffer nil t)
+    (add-hook 'after-save-hook #'org-roam--update-cache nil t)))
+
+(defvar org-roam-mode-map
+  (make-sparse-keymap)
+  "Keymap for org-roam commands.")
+
+(defun org-roam--delete-file-advice (file &optional _trash)
+  "Advice for maintaining cache consistency during file deletes."
+  (org-roam--clear-file-from-cache (file-truename file)))
+
+(defun org-roam--rename-file-advice (file new-file &rest args)
+  "Rename backlinks of FILE to refer to NEW-FILE."
+  (when (and (not (auto-save-file-name-p file))
+             (not (auto-save-file-name-p new-file))
+             (org-roam--org-roam-file-p new-file))
+    (org-roam--ensure-cache-built)
+    (org-roam--clear-file-from-cache file)
+
+    (let* ((files (gethash file org-roam-backward-links-cache nil))
+           (path (file-truename file))
+           (new-path (file-truename new-file))
+           (slug (org-roam--get-title-or-slug file))
+           (old-title (format org-roam-link-title-format slug))
+           (new-slug (or (org-roam--get-title-from-cache path)
+                         (org-roam--get-title-or-slug new-path)))
+           (new-title (format org-roam-link-title-format new-slug)))
+      (when files
+        (maphash (lambda (file-from props)
+                   (let* ((file-dir (file-name-directory file-from))
+                          (relative-path (file-relative-name new-path file-dir))
+                          (old-relative-path (file-relative-name path file-dir))
+                          (slug-regex (regexp-quote (format "[[file:%s][%s]]" old-relative-path old-title)))
+                          (named-regex (concat
+                                        (regexp-quote (format "[[file:%s][" old-relative-path))
+                                        "\\(.*\\)"
+                                        (regexp-quote "]]"))))
+                     (with-temp-file file-from
+                       (insert-file-contents file-from)
+                       (while (re-search-forward slug-regex  nil t)
+                         (replace-match (format "[[file:%s][%s]]" relative-path new-title)))
+                       (goto-char (point-min))
+                       (while (re-search-forward named-regex nil t)
+                         (replace-match (format "[[file:%s][\\1]]" relative-path))))
+                     (save-window-excursion
+                       (find-file file-from)
+                       (org-roam--update-cache))))
+                 files))
+      (save-window-excursion
+        (find-file new-path)
+        (org-roam--update-cache)))))
+
+;;;###autoload
+(define-minor-mode org-roam-mode
+  "Minor mode for Org-roam.
+
+When called interactively, toggle `org-roam-mode'. with prefix ARG, enable `org-roam-mode'
+if ARG is posiwive, otherwise disable it.
+
+When called from Lisp, enable `org-roam-mode' if ARG is omitted, nil, or positive.
+If ARG is `toggle', toggle `org-roam-mode'. Otherwise, behave as if called interactively."
+  :lighter "Org-Roam "
+  :keymap  org-roam-mode-map
+  :group 'org-roam
+  :require 'org-roam
+  :global t
+  (cond
+   (org-roam-mode
+    (unless org-roam-cache-initialized
+      (org-roam--build-cache-async))
+    (add-hook 'find-file-hook #'org-roam--find-file-hook-function)
+    (advice-add 'rename-file :after #'org-roam--rename-file-advice)
+    (advice-add 'delete-file :before #'org-roam--delete-file-advice))
+   (t
+    (remove-hook 'find-file-hook #'org-roam--find-file-hook-function)
+    (advice-remove 'rename-file #'org-roam--rename-file-advice)
+    (advice-remove 'delete-file #'org-roam--delete-file-advice)
+    ;; Disable local hooks for all org-roam buffers
+    (dolist (buf (org-roam--get-roam-buffers))
+      (with-current-buffer buf
+        (remove-hook 'post-command-hook #'org-roam--maybe-update-buffer t)
+        (remove-hook 'after-save-hook #'org-roam--update-cache t))))))
+
+(provide 'org-roam)

 ;;; Show/hide the org-roam buffer
 (define-inline org-roam--current-visibility ()
@ -454,93 +694,11 @@ Valid states are 'visible, 'exists and 'none."
 (defun org-roam ()
  "Pops up the window `org-roam-buffer' accordingly."
  (interactive)
+  (setq org-roam-last-window (get-buffer-window))
  (pcase (org-roam--current-visibility)
    ('visible (delete-window (get-buffer-window org-roam-buffer)))
    ('exists (org-roam--setup-buffer))
    ('none (org-roam--setup-buffer))))
-
-;;; The minor mode definition that updates the buffer
-(defun org-roam--maybe-enable ()
-  "Enable org-roam updating for file, if file is an org-roam file."
-  (when (org-roam--org-roam-file-p)
-    (org-roam--enable)))
-
-(defun org-roam--enable ()
-  "Enable org-roam updating for file.
-
-1. If the cache does not yet exist, build it asynchronously.
-2. Setup hooks for updating the cache, and the org-roam buffer."
-  (unless org-roam-cache-initialized
-    (org-roam--build-cache-async))
-  (add-hook 'post-command-hook #'org-roam--maybe-update-buffer nil t)
-  (add-hook 'after-save-hook #'org-roam--update-cache nil t))
-
-(defun org-roam--disable ()
-  "Disable org-roam updating for file.
-
-1. Remove hooks for updating the cache, and the org-roam buffer."
-  (remove-hook 'post-command-hook #'org-roam--maybe-update-buffer)
-  (remove-hook 'after-save-hook #'org-roam--update-cache))
-
-(cl-defun org-roam--maybe-update-buffer (&key redisplay)
-  "Update `org-roam-buffer' with the necessary information.
-This needs to be quick/infrequent, because this is run at
-`post-command-hook'."
-  (with-current-buffer (window-buffer)
-    (when (and (get-buffer org-roam-buffer)
-               (buffer-file-name (current-buffer))
-               (file-exists-p (file-truename (buffer-file-name (current-buffer))))
-               (or redisplay
-                   (not (string= org-roam-current-file
-                                 (file-truename (buffer-file-name (current-buffer)))))))
-      (org-roam-update (file-truename (buffer-file-name (window-buffer)))))))
-
-(define-minor-mode org-roam-mode
-  "Global minor mode to automatically update the org-roam buffer."
-  :require 'org-roam
-  (if org-roam-mode
-      (org-roam--maybe-enable)
-    (org-roam--disable)))
-
-;;; Building the Graphviz graph
-(defun org-roam-build-graph ()
-  "Build graphviz graph output."
-  (org-roam--ensure-cache-built)
-  (with-temp-buffer
-    (insert "digraph {\n")
-    (dolist (file (org-roam--find-all-files))
-      (insert
-       (format "  \"%s\" [URL=\"roam://%s\"];\n"
-               (org-roam--get-title-or-slug file)
-               file)))
-    (maphash
-     (lambda (from-link to-links)
-       (dolist (to-link to-links)
-         (insert (format "  \"%s\" -> \"%s\";\n"
-                         (org-roam--get-title-or-slug from-link)
-                         (org-roam--get-title-or-slug to-link)))))
-     org-roam-forward-links-cache)
-    (insert "}")
-    (buffer-string)))
-
-(defun org-roam-show-graph ()
-  "Generate the org-roam graph in SVG format, and display it using `org-roam-graph-viewer'."
-  (interactive)
-  (unless org-roam-graphviz-executable
-    (setq org-roam-graphviz-executable (executable-find "dot")))
-  (unless org-roam-graphviz-executable
-    (user-error "Can't find graphviz executable. Please check if it is in your path"))
-  (declare (indent 0))
-  (let ((temp-dot (expand-file-name "graph.dot" temporary-file-directory))
-        (temp-graph (expand-file-name "graph.svg" temporary-file-directory))
-        (graph (org-roam-build-graph)))
-    (with-temp-file temp-dot
-      (insert graph))
-    (call-process org-roam-graphviz-executable nil 0 nil temp-dot "-Tsvg" "-o" temp-graph)
-    (call-process org-roam-graph-viewer nil 0 nil temp-graph)))
-
-(provide 'org-roam)
-
 ;;; org-roam.el ends here

 ;; Local Variables:
--- a/shell.nix
+++ b/shell.nix
@ -1,9 +0,0 @@
-let
-  pkgs = import <nixpkgs> {};
-in
-pkgs.mkShell {
-  name = "docs";
-  buildInput = with pkgs; [
-    mkdocs
-  ];
-}
--- a/tests/roam-files/f1.org
+++ b/tests/roam-files/f1.org
@ -0,0 +1,7 @@
+#+TITLE: File 1
+
+link to [[file:nested/f1.org][Nested File 1]] 
+link to [[file:f2.org][File 2]]
+
+Arbitrary [[https://google.com][HTML]] link
+Arbitrary text
--- a/tests/roam-files/f2.org
+++ b/tests/roam-files/f2.org
@ -0,0 +1,3 @@
+#+TITLE: File 2
+
+This file has no links.
--- a/tests/roam-files/f3.org
+++ b/tests/roam-files/f3.org
@ -0,0 +1,5 @@
+#+TITLE: File 3
+
+This file has a link to an file with no title.
+
+[[file:no-title.org][no-title]]
--- a/tests/roam-files/nested/f1.org
+++ b/tests/roam-files/nested/f1.org
@ -0,0 +1,4 @@
+#+TITLE: Nested File 1
+
+Link to [[file:f2.org][Nested File 2]]
+Link to [[file:../f1.org][File 1]]
--- a/tests/roam-files/nested/f2.org
+++ b/tests/roam-files/nested/f2.org
@ -0,0 +1,3 @@
+#+TITLE: Nested File 2
+
+Link to [[file:f1.org][Nested File 1]]
--- a/tests/roam-files/no-title.org
+++ b/tests/roam-files/no-title.org
@ -0,0 +1 @@
+no title in this file :O
--- a/tests/test-org-roam.el
+++ b/tests/test-org-roam.el
@ -3,7 +3,7 @@
 ;; Copyright (C) 2020 Jethro Kuan

 ;; Author: Jethro Kuan <jethrokuan95@gmail.com>
-;; Package-Requires: ((buttercup))
+;; Package-Requires: ((buttercup) (with-simulated-input))

 ;; This program is free software; you can redistribute it and/or modify
 ;; it under the terms of the GNU General Public License as published by
@ -27,9 +27,204 @@
 ;;;; Requirements

 (require 'buttercup)
+(require 'with-simulated-input)
 (require 'org-roam)
+(require 'dash)
+
+(defun abs-path (file-path)
+  (file-truename (expand-file-name file-path org-roam-directory)))
+
+(defun org-roam--test-find-new-file (path)
+  (let ((path (abs-path path)))
+    (make-directory (file-name-directory path) t)
+    (find-file path)))
+
+(defvar org-roam--tests-directory (file-truename (concat default-directory "tests/roam-files"))
+  "Directory containing org-roam test org files.")
+
+(defun org-roam--test-init ()
+  (let ((original-dir org-roam--tests-directory)
+        (new-dir (expand-file-name (make-temp-name "org-roam") temporary-file-directory)))
+    (copy-directory original-dir new-dir)
+    (setq org-roam-directory new-dir))
+  (org-roam-mode +1))
+
+(defun org-roam--test-build-cache ()
+  "Builds the caches synchronously."
+  (let ((cache (org-roam--build-cache org-roam-directory)))
+    (setq org-roam-forward-links-cache (plist-get cache :forward))
+    (setq org-roam-backward-links-cache (plist-get cache :backward))
+    (setq org-roam-titles-cache (plist-get cache :titles))
+    (setq org-roam-cache-initialized t)))

 ;;; Tests
-(describe "Org-roam cache"
-  (it "Mock Test"
-    (expect t :to-be t)))
+(describe "org-roam--build-cache-async"
+          (it "initializes correctly"
+              (org-roam--test-init)
+              (expect org-roam-cache-initialized :to-be nil)
+              (expect (hash-table-count org-roam-forward-links-cache) :to-be 0)
+              (expect (hash-table-count org-roam-backward-links-cache) :to-be 0)
+              (expect (hash-table-count org-roam-titles-cache) :to-be 0)
+
+              (org-roam--build-cache-async)
+              (sleep-for 3) ;; Because it's async
+
+              ;; Caches should be populated
+              (expect org-roam-cache-initialized :to-be t)
+              (expect (hash-table-count org-roam-forward-links-cache) :to-be 4)
+              (expect (hash-table-count org-roam-backward-links-cache) :to-be 5)
+              (expect (hash-table-count org-roam-titles-cache) :to-be 5)
+
+              ;; Forward cache
+              (let ((f1 (gethash (abs-path "f1.org") org-roam-forward-links-cache))
+                    (f2 (gethash (abs-path "f2.org") org-roam-forward-links-cache))
+                    (nested-f1 (gethash (abs-path "nested/f1.org") org-roam-forward-links-cache))
+                    (nested-f2 (gethash (abs-path "nested/f2.org") org-roam-forward-links-cache))
+                    (expected-f1 (list (abs-path "nested/f1.org")
+                                       (abs-path "f2.org")))
+                    (expected-nested-f1 (list (abs-path "nested/f2.org")
+                                              (abs-path "f1.org")))
+                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+
+                (expect f1 :to-have-same-items-as expected-f1)
+                (expect f2 :to-be nil)
+                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
+                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+
+              ;; Backward cache
+              (let ((f1 (hash-table-keys (gethash (abs-path "f1.org") org-roam-backward-links-cache)))
+                    (f2 (hash-table-keys (gethash (abs-path "f2.org") org-roam-backward-links-cache)))
+                    (nested-f1 (hash-table-keys(gethash (abs-path "nested/f1.org") org-roam-backward-links-cache)))
+                    (nested-f2 (hash-table-keys (gethash (abs-path "nested/f2.org") org-roam-backward-links-cache)))
+                    (expected-f1 (list (abs-path "nested/f1.org")))
+                    (expected-f2 (list (abs-path "f1.org")))
+                    (expected-nested-f1 (list (abs-path "nested/f2.org")
+                                              (abs-path "f1.org")))
+                    (expected-nested-f2 (list (abs-path "nested/f1.org"))))
+                (expect f1 :to-have-same-items-as expected-f1)
+                (expect f2 :to-have-same-items-as expected-f2)
+                (expect nested-f1 :to-have-same-items-as expected-nested-f1)
+                (expect nested-f2 :to-have-same-items-as expected-nested-f2))
+
+              ;; Titles Cache
+              (expect (gethash (abs-path "f1.org") org-roam-titles-cache) :to-equal "File 1")
+              (expect (gethash (abs-path "f2.org") org-roam-titles-cache) :to-equal "File 2")
+              (expect (gethash (abs-path "nested/f1.org") org-roam-titles-cache) :to-equal "Nested File 1")
+              (expect (gethash (abs-path "nested/f2.org") org-roam-titles-cache) :to-equal "Nested File 2")
+              (expect (gethash (abs-path "no-title.org") org-roam-titles-cache) :to-be nil)))
+
+(describe "org-roam-insert"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+
+          (it "temp1 -> f1"
+              (let ((buf (org-roam--test-find-new-file "temp1.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:f1.org")))
+
+          (it "temp2 -> nested/f1"
+              (let ((buf (org-roam--test-find-new-file "temp2.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "Nested SPC File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:nested/f1.org")))
+
+          (it "nested/temp3 -> f1"
+              (let ((buf (org-roam--test-find-new-file "nested/temp3.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:../f1.org")))
+
+          (it "a/b/temp4 -> nested/f1"
+              (let ((buf (org-roam--test-find-new-file "a/b/temp4.org")))
+                (with-current-buffer buf
+                  (with-simulated-input
+                   "Nested SPC File SPC 1 RET"
+                   (org-roam-insert nil))))
+              (expect (buffer-string) :to-match (regexp-quote "file:../../nested/f1.org"))))
+
+(describe "rename file updates cache"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+
+          (it "f1 -> new_f1"
+              (rename-file (abs-path "f1.org")
+                           (abs-path "new_f1.org"))
+              ;; Cache should be cleared of old file
+              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (hash-table-keys)
+                           (member (abs-path "f1.org"))) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "new_f1.org"))) :not :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "new_f1.org"))
+                           (member (abs-path "nested/f1.org"))) :not :to-be nil)
+              ;; Links are updated
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "nested/f1.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:../new_f1.org][File 1]]")))
+
+
+          (it "f1 -> f1 with spaces"
+              (rename-file (abs-path "f1.org")
+                           (abs-path "f1 with spaces.org"))
+              ;; Cache should be cleared of old file
+              (expect (gethash (abs-path "f1.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (hash-table-keys)
+                           (member (abs-path "f1.org"))) :to-be nil)
+              ;; Links are updated
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "nested/f1.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:../f1 with spaces.org][File 1]]")))
+
+          (it "no-title -> meaningful-title"
+              (rename-file (abs-path "no-title.org")
+                           (abs-path "meaningful-title.org"))
+              ;; File has no forward links
+              (expect (gethash (abs-path "no-title.org")  org-roam-forward-links-cache) :to-be nil)
+              (expect (gethash (abs-path "meaningful-title.org")  org-roam-forward-links-cache) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f3.org"))
+                           (member (abs-path "no-title.org"))) :to-be nil)
+
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f3.org"))
+                           (member (abs-path "meaningful-title.org"))) :not :to-be nil)
+
+              ;; Links are updated with the appropriate name
+              (expect (with-temp-buffer
+                        (insert-file-contents (abs-path "f3.org"))
+                        (buffer-string)) :to-match (regexp-quote "[[file:meaningful-title.org][meaningful-title]]"))))
+
+(describe "delete file updates cache"
+          (before-each
+           (org-roam--test-init)
+           (org-roam--clear-cache)
+           (org-roam--test-build-cache))
+          (it "delete f1"
+              (delete-file (abs-path "f1.org"))
+              (expect (->> org-roam-forward-links-cache
+                           (gethash (abs-path "f1.org"))) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (gethash (abs-path "f1.org"))) :to-be nil)
+              (expect (->> org-roam-backward-links-cache
+                           (gethash (abs-path "nested/f1.org"))
+                           (gethash (abs-path "nested/f2.org"))) :not :to-be nil)))
Author	SHA1	Message	Date
Jethro Kuan	cb029c4ce8	(release): org-roam v0.1.2 (#147 )	2020-02-21 13:44:16 +08:00
Jethro Kuan	571f65cebd	(docs): Add graph setup documentation for MacOS (#146 ) Thanks @naistran for instructions, and @leothelocust and @seandavi for discussion and confirmation	2020-02-21 13:17:09 +08:00
Jürgen Hötzel	316ad40b2c	(feature): `org-roam-show-graph`: fallback to Emacs SVG viewer (#145 ) (#145 )	2020-02-21 10:55:53 +08:00
ffrigge	b78b545d31	(feature): allow customization of graphviz node appearance (#132 )	2020-02-20 17:43:30 +08:00
Jethro Kuan	8523fb43b4	(feature): global org-roam-mode (#143 ) Makes org-roam-mode a global minor mode. This mode adds an advice to find-file-function, which decides whether to turn on the local post-command-hook and after-save-hook. It also advices delete-file and rename-file to ensure cache consistency. Also fixes a bug introduced with #142	2020-02-20 17:33:30 +08:00
Jethro Kuan	dd4b1a97a1	(feature): Add advice to delete-file (#142 ) Closes #119	2020-02-20 16:18:40 +08:00
Jethro Kuan	3a8908f72a	(feature): add a variable `org-roam-new-file-directory` (#141 ) Fixes #140	2020-02-20 14:34:23 +08:00
Jethro Kuan	ddaf855b5d	(chore): some cleanups (#139 ) * move org-roam-switch-to-buffer * add org-roam-switch-to-buffer to docs * Update changelog	2020-02-20 13:38:31 +08:00
Herbert Jones	f458c6caf6	(feature): add org-roam-switch-to-buffer (#138 ) Implement a buffer-switching mechanism for org-roam files. Closes #126	2020-02-20 13:23:32 +08:00
Anthony Cowley	0346d3b16c	(bugfix): handle nil file names in `org-roam--org-roam-file-p` (#136 )	2020-02-20 11:45:12 +08:00
Jeremy Dormitzer	63754d1ccd	(feature): make org-roam-insert work in org-capture buffers (#134 ) In org-capture buffers, (buffer-file-name) will always return nil. But we can get the name of the buffer that we are capturing into via (buffer-base-buffer), then getting the path to the current file works as expected.	2020-02-20 09:15:13 +08:00
Hendrik Cech	05ada41710	(docs): add Spacemacs installation instructions (#133 )	2020-02-20 08:48:47 +08:00
Daniel Koudouna	bdc13cd6bf	(feature): update cache on file rename (#124 )	2020-02-20 08:32:54 +08:00
Troy Hinckley	2522b9d2fa	(bugfi): check for buffer file in post-command-hook (#128 ) If you delete a org-roam buffer it can still trigger an update. Need to make sure that their exists a file for the buffer before we proceed	2020-02-20 00:38:12 +08:00
Troy Hinckley	edbe34a1d9	(chore): add autoload to org-roam-mode (#121 ) With this change it is no longer required to load org-roam before use.	2020-02-19 14:50:36 +08:00
Troy Hinckley	570467b34b	(internal): increase performance of post-command-hook (#122 ) file-truename can be an expensive function on a slow filesystem like NFS. I Removed a lot of the unneeded code and refactored to improve performance. In my testing it took the execution time from 13ms per call to 2µs; over a 1000x speedup. This is important since post-command-hook is called with every character you type.	2020-02-19 02:39:22 +08:00
Jethro Kuan	e84ab1de9a	(chore): Add GitHub templates (#117 )	2020-02-18 13:43:13 +08:00
Jeremy Dormitzer	996923f9d9	(feature): add jump to point from org-roam buffer (#99 )	2020-02-18 11:41:13 +08:00
bdarcus	4a5531cde3	(fix): fix typo (#113 ) this addresses the minor typo noted in #112	2020-02-18 10:12:36 +08:00
Jethro Kuan	2d206134fd	(feature): insert link as downcased title with `org-roam-insert` (#110 )	2020-02-17 23:15:27 +08:00
Leon	883eed0a5e	(change): open file links in org-roam buffer in `org-roam-last-window` (#108 ) Addresses #30 , thanks @l3kn	2020-02-17 21:46:48 +08:00
Jethro Kuan	659babf922	(bugfix): force a cache update on making a new file (#107 )	2020-02-17 19:02:46 +08:00
Jethro Kuan	424de1f0cb	(docs): update changelog (#106 )	2020-02-17 16:01:46 +08:00
Jethro Kuan	618b7f6124	(tests): add tests for org-roam-insert (#105 )	2020-02-17 15:48:54 +08:00
Jethro Kuan	ce305af319	(breaking): change org-roam-file-format to a function (#103 ) This allows for more flexible naming of files. Now filename defaults to yyyymmddhhmmss_title_here.org. Also, remove `org-use-timestamp-as-filename`, and change it to `org-roam-filename-noconfirm` to better describe what it is doing.s	2020-02-17 13:50:40 +08:00
Jethro Kuan	58590a0e9d	(bugfix): fix org-roam--find-file picking up temporary files (#98 ) Fixes #96	2020-02-17 12:07:08 +08:00
Jethro Kuan	9ae03532da	(tests): test org-roam--build-cache-async (#92 )	2020-02-16 20:31:09 +08:00
chip2n	159b64b538	(feature): add support for file encryption by default (#90 ) This is controlled by variable org-roam-encrypt-files	2020-02-16 18:31:51 +08:00
Jethro Kuan	8ec3b441d1	(docs): document deft-title patching (#89 )	2020-02-16 14:29:58 +08:00
Kevin Liu	f048a6b866	(bugfix): org-roam--org-roam-file-p: add a missed file-truename (#88 )	2020-02-16 11:33:31 +08:00
chip2n	9aba7ee094	(feature): support encrypted org files (#87 ) Authored by @chip2n	2020-02-16 03:04:54 +08:00
Jethro Kuan	ba91fc41a7	(bugfix): fix org-roam--parse-content incorrect :to computation (#86 ) * fix org-roam--parse-content incorrect :to computation org-roam--parse-content always computed the to-path relative to the org-roam-directory, when it should be relative to the file-path in question. Fixes #81. * Add to changelog	2020-02-16 00:41:25 +08:00