#+title: Denote Explorer: Explore your Denote Digital Garden #+author: Peter Prevos
The Denote-Explorer package provides auxiliary functions to maintain and explore your collection of Denote files. Denote-Explore provides three groups of Emacs commands:
- /Summary statistics/: Count and visualise notes, attachments and keywords.
- /Random walks/: Generate new ideas using serendipity.
- /Janitor/: Manage your denote collection.
- /Knowledge graphs/: Visualise your Denote network as a network graph.
Read the [[https://lucidmanager.org/productivity/denote-explore][Denote-Explorer manual]] for a comprehensive explanation of all functionality (=C-h R denote-explore=).
Visualising networks of Denote files with SVG or PDF files will require the [[https://graphviz.org/][GraphViz]] package to be available. The D3.js visualisation type downloads an external JavaScript file from [[https://d3js.org/][d3js.org]].
Denote-Explore package is available on MELPA and is easily installed with the use-package macro.
The configuration below customises all available variables and binds all available commands to the =C-c e= prefix. Modify this configuration to suit your needs, as one person's sensible defaults are another person's nightmare. To get started you don't need to configure anything, so (use-package denote-explore) is sufficient.
#+begin_src elisp
(use-package denote-explore
:custom
;; Where to store network data and in which format
(denote-explore-network-directory "
Alternatively, you can install it directly from GitHub:
#+begin_src elisp :eval no (unless (package-installed-p 'denote-explore) (package-vc-install '(denote-explore :url "https://github.com/pprevos/denote-explore/"))) #+end_src
- Change Log Major version numbers coincide with Denote major versions.
** Version 4.1
- Minor compatibility issues with Denote 4.1. No upgrades.
** Version 4.01
- Various bug fixes and refactoring
- Added
denote-explore-random-signaturefunction - Add ability to ignore files by keyword for determining isolatedness ([[https://github.com/pprevos/denote-explore/pull/41][Pull request 41]])
- Added
denote-explore-list-keywordsfunction ([[https://github.com/pprevos/denote-explore/pull/42][Pull request 42]])
** Version 4.0
- Compatibility check with Denote 4
- Minor update to denoter-explore-sync-metadata
- Updated denote-explore-rename-keyword
- Clarifications in the manual
- Added error message when 'missing' link is not found in buffer
- Clarifications in the manual
** Version 3.3.3
- Fixed bug in keyword renaming function.
** version 3.3.2
- Refactoring of missing links functionality
- Added table of missing file links in Denote files
- Renamed
denote-explore-dead-linkstodenote-explore-missing-links
** Version 3.3.1
- Fixed issues in the manual.
- Clarified duplicate detection.
- Fixed bug in
denote-explore-barchart-backlinks. - Added
denote-explore-random-regex-ignorevariable to exclude files from random walks.
** Version 3.3
- Knowledge Graphs
- New visualisation type: Sequences of Denote signatures
- Changed GraphViz geometry for sequence graphs
- Full rewrite of most functions.
- Increased efficiency in detecting edges (links between files)
- Ability to draw graphs without attachments by using the universal argument when generating and regenerating graphs
- D3.js Visualisations
- New slider to change the number of node labels (from none to every node)
- Added number of isolated notes to info tooltip (when isolated nodes > 0)
- New visualisation type: Sequences of Denote signatures
- Janitor
- New function
denote-explore-dead-linksto find dead links - Optimised single and zero keywords detection
- Change behaviour and optimisation for
denote-explore-isolated-notes denote-explore-sort-keywordsreplaced bydenote-explore-sync-metadata- Refactored
denote-explore-rename-keyword - Renamed duplicate notes functions to remove double verb and UI improvements.
denote-explore-sync-metadatabug fix
- New function
- Statistics
- New function
denote-explore-barchart-timelineto show number of nodes and/or attachment created per year - The File type bar chart can also show only attachments.
denote-explore-barchart-degreeallows text-only option- Added all used keywords to
denote-explore-count-keywords - Fixed bug in random walk functions
- New function
** Version 3.2
- First version formally registered (for inclusion in Guin)
- D3.js Visualisation
- Community graphs can filter out nodes where degree = 0 (isolated notes)
- Preview images and PDF files in tooltips
- Updated manual
- Bug fixes
- GraphViz network
- D3.js file type legend colours
- Random walk functions
- Updated code commentary
- Updated counting and related bar chart functions
** Version 3.1
- Removed dependency on R for D3.js graphs. D3 now uses a template in which a JSON file is inserted. This format is now the default.
- Fixed bugs in renaming functions
- Protection against using quotation marks in note title when visualising networks in GraphViz.
- Fixed backlinks barchart visualisation
- Updates documentation strings.
** Version 3.0
- Compatability with Denote 3.0
- Renamed barchart functions to all start with
denote-explore-barchart-. - Using universal argument with
denote-explore-barchart-extensionsvisualises only attachment file types. - All functions that rename files updated for compatability with Denote 3.0
- Enhanced info manual
** Version 1.6
- New functions:
denote-explore-backlinks-barchartto view top-n notes with backlinksdenote-explore-random-regexto jump to random note matching a regular expression.denote-explore-identify-duplicate-notes-dired: View notes with duplicates ID in Dired.
** Version 1.5.1
- Fixed various compilation errors.
- Enhanced output for
denote-explore-identify-duplicate-notes - Update customization types for note ignore variables
- Updated
defgroupdefinition anddefcustomtypes
** Version 1.5
- Published Info mode manual
- Clarified obsolete variables and functions
denote-explore-network-keywordsno longer interactive- Updates to Denote functions
** Version 1.4.2
- Geneal code refactoring with assistance from Prot
- Added ability to filter keywords network by minimum weight of edges
- Added ability for free text in
denote-explore-network-graphviz-filetype - GEXF format now includes the total degree for each node
- Enforced consistency with use of universal argument (its use will include attachments)
denote-explore--retrieve-titledeprecated. Now using Denote function.- Updated manual with clarifications
** Version 1.4.1
- Fixed bugs with random links and keywords from nil file-name
- New variable
denote-explore-network-regex-ignoreto ignore files matching a regular expression when creating neighbourhood or community graphs.
** Version 1.4
- Network visualisation
- SVG output includes links to source file.
- Configure [[https://graphviz.org/docs/outputs/][GraphViz output format]] with
denote-explore-network-graphviz-filetype(SVG (default) or PDF advised). - Improved scaling of GraphViz graphics.
denote-explore-network-regeneraterecreates the previous graph
- New functions:
denote-explore-isolated-notesto select Denote files without any links or backlinks.denote-explore-degree-barchartdraws the distribution of total number of (back)links per file ([[https://en.wikipedia.org/wiki/Degree_distribution][Degree distribution - Wikipedia]]).
- Updated functions:
denote-explore-rename-keywordallows renaming more than one keyword to a new version.denote-explore-sync-metadataenforces renaming confirmation.
- Minor bug fixes.
** Version 1.3
- Complete rewrite of the graph visualisation functionality. Now includes three formats (JavaScript, GraphViz and GEXF) and three graph types (notes that match a regular expression, note neighbourhood and keyword graph).
- Fixed bugs in =denote-explore--retrieve-title= and =denote-explore--retrieve-keywords=.
- Enhanced function and variable documentation.
** Version 1.2
- Removed =pandoc= dependency in network generation.
denote-explore-identify-duplicate-notesreplacesdenote-explore-identify-duplicate-identifiers. This new version either detects duplicate identifiers, or duplicate file names (using the universal argument). Comparing duplicate filenames ignores any duplicate identifiers caused by exporting Org mode files.
** Version 1.1
- Added helper function to call R script for network visualisation.
- =denote-explore-dashboard.el= deprecated.
- Added to MELPA.
** Version 1.0 This version is a complete rewrite of the code to improve coding quality and compatibility with internal changes since Denote version 2.2.
Also major changes to the network visualisation, which can now take a regular expression for partial networks. Most of the code is now undertaken in Emacs Lisp, which saves the network in JSON format.
The functionality for a Dashboard widget has been moved to a separate file to not enforce the requirements for those users not seeking to implement the widget.
New functionality since the previous version:
denote-explore-identify-duplicate-identifiers: Provide a list of duplicate identifiers.denote-explore-single-keywords: Select a note or attachment with a keyword that is only used once.denote-explore-zero-keywords: Select a note or attachment without any keywords.denote-explore-sort-keywords: Order the keywords of all Denote notes and attachments alphabetically.denote-explore-rename-keyword: Rename or remove a keyword across the whole Denote collection.denote-explore-sync-metadata: Synchronise the filenames with the metadata for all Denote files.
- Ideas for future development Some random ideas for future development. Feel free to suggest other ideas.
- Functions to rename Denote attachments using EXIF metadata.
- Store the Denote metadata in a [[https://www.gnu.org/software/emacs/manual/html_node/elisp/Hash-Tables.html][hash table]] that is updated after every modification to a Denote file for more efficient visualisation.
- Ring of previously-generated networks instead of overwriting
denote-explore-network-previous - Use [[https://github.com/alphapapa/org-graph-view/][org-graph-view]] for live neighbourhood view of the current buffer
- [[https://graphviz.org/pdf/cluster.1.pdf][Community detection]]?
- Create a Denote widget for the Emacs Dashboard with links to statistics.