Notesium - A simple yet powerful system for networked thought

Writing does not make intellectual endeavours easier, it makes them possible. Deepen understanding, insight, and allow for structure to emerge organically by linking notes.

Notesium (pronounced no-tes-ee-im), is an opiniated, simplistic yet powerful system for creating, storing and accessing knowledge by means of notes.

It aspires and is designed to:

• Do one thing, and do it well - per the unix philosophy.
• Support the concepts of Evergreen notes and Zettelkasten.
• Be used with your own text editor (e.g., Vim integration) or embedded Web app.
• Be used with a local folder of markdown files.
• Be as close to zero friction as possible.
• Be lightweight and fast.

Warning: Experimental, proof-of-concept. Here be dragons!

Table of contents

• Features
• Screenshots
• CLI
  • Installation
  • Shell completion
  • Usage
• Web
  • Keybindings
  • Finder
  • Editor modes
  • Table formatting and navigation
  • Syntax highlighting and concealment
• Vim
  • Example integration
  • Keybindings
  • Fzf search syntax
  • Related Vim settings
• Custom URI protocol
  • Example integration
  • Handler registration
• Design assumptions and rationale
  • Filenames are 8 hexidecimal digits
  • Completely flat directory structure
  • Titles are inferred from the first line
  • Notes with one-word titles are considered labels
  • Links are inline
  • Deterministic periodic notes convention
• Versioning
• Regression tests
• Inspiration and thanks
• License

Features

• Blazingly fast and powerful search.
• Preview notes and links, with line highlighting where relevant.
• Visualize the relationships between notes with an interactive graph view.
• Create and edit notes with your own editor or the embedded web app.
• No need to think about file names or folder locations.
• Instantly create a new note with a keybinding.
• Structure emerges organically through bi-directional links.
• Frictionless creation, listing, previewing, and following of links.
• No caching or preprocessing: Everything is computed on the fly.
• List
  • Display a list of all notes in the entire system.
  • Sort the list alphabetically, by date created, or date modified.
  • Prefix titles with associated labels, date created, or date modified.
  • Customize date format for prefixed date created or date modified.
  • Limit the list to label notes (one-word titles).
  • Limit the list to orphan notes (no incoming or outgoing links).
• Links
  • Quickly search and insert an automatically formatted link.
  • Display a list of all links in the entire system.
  • Display a list of all related links to the current note.
  • Limit the list to incoming links to the current note.
  • Limit the list to outgoing links from the current note.
  • Display a list of broken links and jump there instantly.
• Lines
  • Perform a full text search across all notes in the entire system.
  • Optionally prefix each line with the note title for context.
• Stats
  • View counts of notes, labels, orphans, links, lines, words, etc.
• Web
  • Completely self-contained and runs locally.
  • Create and edit notes with web based editor (optional vim-mode).
  • Markdown syntax highlighting, special char and links concealment.
  • Markdown table formatting and navigation.
  • Open multiple notes in tabs, drag to re-order, keybindings to switch.
  • Finder integration for List, Links and Lines with preview.
  • Note deletion with incoming-links verification and confirmation.
  • Daily and Weekly notes support with Date picker and keybindings.
  • Resizable, configurable and optional panels for different use cases:
    • Labels panel: Integrates with List panel, but useful on its own.
    • List panel: Detailed and compact views, sort, filter, preview.
    • Graph panel: Visualize note relationships, emphasizes active note.
    • Note sidebar: Actions, stats and incoming/outgoing link-trees.
  • Force graph to visualize and explore the relationship between notes.
    • Context aware fullscreen and panel views.
    • Emphasize nodes and their links using search filter or node click.
    • Auto track and emphasize active note and its relationships (panel).
    • Note preview in side panel with inline incoming-links (fullscreen).
    • Adjust node size dynamically based on bi-directional link count.
    • Toggle title visibility and automatically scale per zoom level.
    • Tweak forces such as repel force, collide radius, and strength.
    • Drag, pan, or zoom the graph for a better view or focus.

Screenshots

[Web] Panels: compact notes list and graph panels

[Web] Panels: labels, detailed notes list and note metadata sidepanels

[Web] Graph: visualize the relationships between notes with an interactive force graph

[Web] Graph: filter notes with emphasized matches, and preview note

[Web] List: prefixed with associated labels and sorted alphabetically

[Web] List: prefixed with modification date and sorted per modification time

[Web] Links: display all links

[Web] Links: display links related to the current note

[Web] Links: link insertion triggered by [[

[Web] Lines: full text search

[Vim] List: prefixed with associated labels and sorted alphabetically

[Vim] List: prefixed with modification date and sorted per modification time

[Vim] Links: display all links

[Vim] Links: display links related to the current note

[Vim] Links: link insertion triggered by [[

[Vim] Lines: full text search (light theme)

CLI

Notesium is primarily tested and supported on Linux, with only preliminary tests performed on macOS and Windows.

Installation

Download the latest release for your platform, making sure to give it executable permissions and available in your PATH.

# Example for Linux 64-bit
curl -sLO https://github.com/alonswartz/notesium/releases/latest/download/notesium-linux-amd64
curl -sLO https://github.com/alonswartz/notesium/releases/latest/download/checksums.txt
sha256sum --check --ignore-missing checksums.txt && rm checksums.txt
chmod +x notesium-linux-amd64
mv notesium-linux-amd64 $HOME/.local/bin/notesium

# Example for macOS 64-bit
curl -sLO https://github.com/alonswartz/notesium/releases/latest/download/notesium-darwin-amd64
curl -sLO https://github.com/alonswartz/notesium/releases/latest/download/checksums.txt
shasum -a 256 -c checksums.txt --ignore-missing && rm checksums.txt
chmod +x notesium-darwin-amd64
mv notesium-darwin-amd64 $HOME/bin/notesium

# Example for Windows 64-bit (in PowerShell)
Invoke-WebRequest -Uri "https://github.com/alonswartz/notesium/releases/latest/download/notesium-windows-amd64.exe" -OutFile "./notesium-windows-amd64.exe"
Invoke-WebRequest -Uri "https://github.com/alonswartz/notesium/releases/latest/download/checksums.txt" -OutFile "./checksums.txt"
$hash = Get-FileHash -Path "./notesium-windows-amd64.exe" -Algorithm SHA256
$checksums = Get-Content "./checksums.txt"
if ($checksums -match $hash.Hash) { Write-Output "Checksum verified"; Remove-Item "./checksums.txt" } else { Write-Error "Checksum verification failed!" }
New-Item -ItemType Directory -Path "$env:USERPROFILE\AppData\Local\Microsoft\WindowsApps" -Force
Move-Item -Path "./notesium-windows-amd64.exe" -Destination "$env:USERPROFILE\AppData\Local\Microsoft\WindowsApps\notesium.exe"

Or build from source.

git clone https://github.com/alonswartz/notesium.git
cd notesium
./web/app/make.sh all
go build -ldflags "
    -X main.gitversion=$(git describe --tags --long --always --dirty) \
    -X main.buildtime=$(date -u +%Y-%m-%dT%H:%M:%SZ)"
ln -s $(pwd)/notesium $HOME/.local/bin/notesium

Shell completion

Bash completion is available for all notesium commands and option flags. Add the following line to your $HOME/.bashrc or similar location.

command -v notesium >/dev/null && source <(notesium extract completion.bash)

Usage

$ notesium help
Usage: notesium COMMAND [OPTIONS]

Commands:
  home              Print path to notes directory
  new               Print path for a new note
    --verbose       Output key:value pairs of related info
    --ctime=        Use specified ctime instead of now (YYYY-MM-DDThh:mm:ss)
  list              Print list of notes
    --color         Color code prefix using ansi escape sequences
    --labels        Limit list to only label notes (ie. one word title)
    --orphans       Limit list to notes without outgoing or incoming links
    --sort=WORD     Sort list by date or alphabetically (ctime|mtime|alpha)
    --prefix=WORD   Prefix title with date or linked label (ctime|mtime|label)
    --date=FORMAT   Date format for ctime/mtime prefix (default: 2006-01-02)
  links [filename]  Print list of links
    --color         Color code using ansi escape sequences
    --outgoing      Limit list to outgoing links related to filename
    --incoming      Limit list to incoming links related to filename
    --dangling      Limit list to broken links
  lines             Print all lines of notes (ie. fulltext search)
    --color         Color code prefix using ansi escape sequences
    --prefix=title  Prefix each line with note title
  stats             Print statistics
    --color         Color code using ansi escape sequences
    --table         Format as table with whitespace delimited columns
  web               Start web server
    --webroot=PATH  Path to web root to serve (default: embedded webroot)
    --open-browser  Launch default web browser with web server URL
    --stop-on-idle  Automatically stop when no activity is detected
    --port=INT      Port for web server to listen on (default: random)
    --no-check      Disable daily new version checks
    --writable      Allow writing of notes in NOTESIUM_DIR via API
  extract [path]    Print list of embedded files or contents of file path
  version           Print version
    --verbose       Output key:value pairs of related info
    --check         Check if a newer version is available

Environment:
  NOTESIUM_DIR      Path to notes directory (default: $HOME/notes)

Web

Notesium ships with an embedded web interface which is self contained and runs locally. To allow writing of notes, be sure to specify the --writable flag.

notesium web --writable --open-browser

The web interface stores state and preferences such as editor settings, panel state, start-of-week, and sorting preferences. The state is port-specific, meaning that to retain them across sessions, the same port must be used. For example:

notesium web --writable --open-browser --port=8080

Keybindings

Global

Note tabs

For more keybindings see below.

Finder

The finder is typically opened using global keybindings or icons in the ribbon, but is also seamlessly integrated throughout the web interface.

Keybindings

Search syntax

Editor modes

Default mode

Vim mode

The editor supports Vim mode, which attempts to emulate the most useful features of Vim as faithfully as possible, but is not a complete implementation. It does however feature the following:

• All common motions and operators, including text objects
• Operator motion orthogonality
• Commands for write and quit (:w :wq :q :q!)
• Visual mode - characterwise, linewise, blockwise
• Full macro support (q @)
• Incremental highlighted search (/ ? # g# g)
• Search/replace with confirm (:substitute :%s)
• Search history
• Jump lists (C-o C-i)
• Sort (:sort)
• Marks (` ')
• Cross-buffer yank/paste

Prefer the real thing? Notesium supports Vim integration.

Table formatting and navigation

The editor will recognize when the cursor is placed within a table structure (identified by lines starting with the | character), and provide formatting and navigation.

• Automatic table formatting: Pressing Tab not only navigates through the table but also automatically formats it. This includes adjusting cell padding to align text according to the column specifications defined in the header row.
• Column alignment: The alignment for each column is determined by the syntax used in the header separator row (--- left, :---: center, ---: right).
• Dynamic column adjustment: If the cursor is at the end of a row and Tab is pressed, a new column will be added. When the cursor is on the header row, pressing Tab ensures the header separator row exists and matches the column count of the header, adjusting as necessary.
• Concealment support: When concealment is enabled, the formatting logic takes this into account, calculating the maximum length of each column without the concealed text, ensuring a visually consistent table layout.
• Navigation: Move across table cells and rows with the provided keybindings.

Syntax highlighting and concealment

The editor is configured to syntax highlight based on Markdown formatting.

By default, formatting characters such as those used for bold, italic and code will be concealed except on the active-line. In addition, links will also be concealed and only display the title. This setting can be toggled using the icon in the note sidebar.

The following table lists the Markdown syntax of elements that will be formatted and/or syntax highlighted, and indicates whether concealment of the formatting characters is supported.

Vim

Notesium does not supply a Vim plugin, it is up to the user to write their own Vim commands and configure keybindings. That said, below are some fairly generic commands, with preferences configured in the keybindings.

• Dependencies: fzf and fzf.vim.
• Recommended: bat for syntax highlighting in the preview.
• Recommended: vim-markdown for general markdown goodness.
• Recommended: goyo.vim and lightlight.vim for distraction free writing.

Example integration

let $NOTESIUM_DIR = trim(system("notesium home"))
let $NOTESIUM_WEEKSTART = 1 "0 Sunday, 1 Monday, ...

autocmd BufRead,BufNewFile $NOTESIUM_DIR/*.md inoremap <expr> [[ fzf#vim#complete({
  \ 'source': 'notesium list --sort=mtime',
  \ 'options': '+s -d : --with-nth 3.. --prompt "NotesiumInsertLink> "',
  \ 'reducer': {l->"[". split(l[0],':1: ')[1] ."](".split(l[0],':')[0].")"},
  \ 'window': {'width': 0.5, 'height': 0.5}})

command! -bang NotesiumNew
  \ execute ":e" system("notesium new")

command! -bang NotesiumWeb
  \ let s:options = "--stop-on-idle --open-browser" |
  \ execute ":silent !nohup notesium web ".s:options." > /dev/null 2>&1 &"

command! -bang -nargs=* NotesiumList
  \ let s:spec = {'dir': $NOTESIUM_DIR, 'options': '+s -d : --with-nth 3..'} |
  \ call fzf#vim#grep(
  \   'notesium list '.join(map(split(<q-args>), 'shellescape(v:val)'), ' '), 0,
  \   &columns > 79 ? fzf#vim#with_preview(s:spec, 'right', 'ctrl-/') : s:spec, <bang>0)

command! -bang -nargs=* NotesiumLinks
  \ let s:spec = {'dir': $NOTESIUM_DIR, 'options': '-d : --with-nth 3..'} |
  \ call fzf#vim#grep(
  \   'notesium links '.join(map(split(<q-args>), 'shellescape(v:val)'), ' '), 0,
  \   &columns > 79 ? fzf#vim#with_preview(s:spec, 'right', 'ctrl-/') : s:spec, <bang>0)

command! -bang -nargs=* NotesiumSearch
  \ let s:spec = {'dir': $NOTESIUM_DIR, 'options': '-d : --with-nth 3..'} |
  \ call fzf#vim#grep(
  \   'notesium lines '.join(map(split(<q-args>), 'shellescape(v:val)'), ' '), 0,
  \   &columns > 79 ? fzf#vim#with_preview(s:spec, 'right', 'ctrl-/') : s:spec, <bang>0)

command! -bang -nargs=* NotesiumDaily
  \ let s:cdate = empty(<q-args>) ? strftime('%Y-%m-%d') : <q-args> |
  \ let s:output = system('notesium new --verbose --ctime='.s:cdate.'T00:00:00') |
  \ let s:filepath = matchstr(s:output, 'path:\zs[^\n]*') |
  \ execute 'edit ' . s:filepath |
  \ if getline(1) =~ '^\s*$' |
  \   let s:epoch = matchstr(s:output, 'epoch:\zs[^\n]*') |
  \   call setline(1, '# ' . strftime('%b %d, %Y (%A)', s:epoch)) |
  \ endif

command! -bang -nargs=* NotesiumWeekly
  \ let s:date = empty(<q-args>) ? strftime('%Y-%m-%d') : <q-args> |
  \ let s:output = system('notesium new --verbose --ctime='.s:date.'T00:00:01') |
  \ let s:epoch = str2nr(matchstr(s:output, 'epoch:\zs[^\n]*')) |
  \ let s:day = strftime('%u', s:epoch) |
  \ let s:startOfWeek = empty($NOTESIUM_WEEKSTART) ? 1 : $NOTESIUM_WEEKSTART |
  \ let s:diff = (s:day - s:startOfWeek + 7) % 7 |
  \ let s:weekBegEpoch = s:epoch - (s:diff * 86400) |
  \ let s:weekBegDate = strftime('%Y-%m-%d', s:weekBegEpoch) |
  \ let s:output = system('notesium new --verbose --ctime='.s:weekBegDate.'T00:00:01') |
  \ let s:filepath = matchstr(s:output, 'path:\zs[^\n]*') |
  \ execute 'edit ' . s:filepath |
  \ if getline(1) =~ '^\s*$' |
  \   let s:weekFmt = s:startOfWeek == 0 ? '%U' : '%V' |
  \   let s:yearWeekStr = strftime('%G: Week' . s:weekFmt, s:weekBegEpoch) |
  \   let s:weekBegStr = strftime('%a %b %d', s:weekBegEpoch) |
  \   let s:weekEndStr = strftime('%a %b %d', s:weekBegEpoch + (6 * 86400)) |
  \   let s:title = printf('# %s (%s - %s)', s:yearWeekStr, s:weekBegStr, s:weekEndStr) |
  \   call setline(1, s:title) |
  \ endif

nnoremap <Leader>nn :NotesiumNew<CR>
nnoremap <Leader>nd :NotesiumDaily<CR>
nnoremap <Leader>nw :NotesiumWeekly<CR>
nnoremap <Leader>nl :NotesiumList --prefix=label --sort=alpha --color<CR>
nnoremap <Leader>nm :NotesiumList --prefix=mtime --sort=mtime --color<CR>
nnoremap <Leader>nc :NotesiumList --prefix=ctime --sort=ctime --color --date=2006-01<CR>
nnoremap <Leader>nb :NotesiumLinks --incoming <C-R>=expand("%:t")<CR><CR>
nnoremap <Leader>nk :NotesiumLinks --color <C-R>=expand("%:t")<CR><CR>
nnoremap <Leader>ns :NotesiumSearch --prefix=title --color<CR>
nnoremap <silent> <Leader>nW :NotesiumWeb<CR>

" overrides for journal
if $NOTESIUM_DIR =~ '**/journal/*'
  nnoremap <Leader>nl :NotesiumList --prefix=label --sort=mtime --color<CR>
endif

Keybindings

Fzf search syntax

Related Vim settings

" junegunn/fzf.vim
let $FZF_DEFAULT_OPTS="--reverse --filepath-word --no-separator --no-scrollbar "
let g:fzf_buffers_jump = 1
let g:fzf_layout = { 'window': { 'width': 0.85, 'height': 0.85 } }
let g:fzf_colors = {
    \ 'fg':      ['fg', 'Normal'],
    \ 'bg':      ['bg', 'Normal'],
    \ 'hl':      ['fg', 'Comment'],
    \ 'fg+':     ['fg', 'CursorLine', 'CursorColumn', 'Normal'],
    \ 'bg+':     ['bg', 'CursorLine', 'CursorColumn'],
    \ 'hl+':     ['fg', 'Statement'],
    \ 'info':    ['fg', 'PreProc'],
    \ 'pointer': ['fg', 'Exception'],
    \ 'marker':  ['fg', 'Keyword'],
    \ 'spinner': ['fg', 'Label'],
    \ 'header':  ['fg', 'Comment'] }

" preservim/vim-markdown
let g:vim_markdown_folding_style_pythonic = 1
let g:vim_markdown_folding_level = 2
let g:vim_markdown_frontmatter = 1
let g:vim_markdown_auto_insert_bullets = 0
let g:vim_markdown_new_list_item_indent = 0
let g:vim_markdown_toc_autofit = 1
let g:vim_markdown_conceal_code_blocks = 0

let g:markdown_fenced_languages = ['json', 'sh', 'shell=bash']
hi def link mkdHeading htmlH1
autocmd FileType markdown setlocal conceallevel=2

Custom URI protocol

Notesium does not support handling the custom URI protocol notesium:// itself directly, as this is very dependent on user preference. It is up to the user to write their own script.

Example integration

An example integration can been found in contrib/xdg-urxvt-nvim.sh, which supports opening the notes listing as well as opening a note for editing - in a new urxvt terminal window and neovim instance.

xdg-open notesium:///home/user/notes
xdg-open notesium:///home/user/notes/625d563f.md

For Vim users, opening the listing is useful when integrated with a launcher or desktop keybinding. Opening a note for editing is useful, for example, when using the web/app or web/graph.

Handler registration

To register the x-scheme-handler with the desktop environment, create the file $HOME/.local/share/applications/notesium.desktop with contents similar to the following (don't forget to update the Exec path):

[Desktop Entry]
Name=Notesium
Exec=/home/github/alonswartz/notesium/contrib/xdg-urxvt-nvim.sh %u
MimeType=x-scheme-handler/notesium;
Type=Application
Terminal=false
NoDisplay=true

Design assumptions and rationale

Filenames are 8 hexidecimal digits

There are only two hard things in Computer Science: cache invalidation and naming things. ~ Phil Karlton

Naming is hard. With regards to notes, common conventions are to use the current date, or note title, or both in concatenated form.

• Titles: Considering notes evolve, it is likely not to be certain exactly what the note will encompass. And even if it is, having to decide on a title can paralyze or cause cognitive overload prior to writing the content. Existing and future collisions also need to be accounted for. If a better title is thought of later, or the context of the note changes, renaming the file would break existing links.

• Dates: The current timestamp seems like a good choice, but depending on the format used, it could result in overly long filenames, especially considering the uniqueness requirement. Additionally, timezones and daylight saving could result in collisions and interfere with sorting.

Notesium addresses this by using the UNIX epoch time, and further encoding it in hexidecimal, resulting in 8 characters for the identifier (e.g., 625d563f.md). This can later be easily decoded and formatted depending on the use case.

The .md extension is required so external tools can easily identify the filetype for syntax highlighting, as well as limit the processing of files by the parser.

Completely flat directory structure

It is better to prefer associative ontologies to hierarchical taxonomies.

Folders are often thought of as categories, but notes don't always fit neatly into just one category, which could result in decision paralysis when creating a new note, and can prematurely constrain what may emerge.

Links would also be broken when renaming a folder or moving a note from one folder to another.

Notesium assumes a flat directory structure, having all notes be siblings to one another, in one directory. Utilizing bi-directional links allows for the structure to emerge over time. Additionally, the label convention allows for a meta-hierarchical taxonomy to be created which can be useful in certain circumstances.

Titles are inferred from the first line

Note titles are like APIs, and when titled well they become an abstraction.

Notesium assumes note titles are on the first line of the note, in markdown H1 format, for example: # this is the title of a note.

Notes with one-word titles are considered labels

Even though tags are an ineffective association structure, Notesium supports the concept of labels, but there is no special label syntax. Instead, a label is just a regular note, and only considered a label if its title is one-word.

This becomes useful, for example, when issuing the following list command, each note title will be prefixed with its associated label (multiple times for each associated label), color coded, and sorted alphabetically, effectively creating a hierarchical taxonomy listing, which can further be filtered and searched.

notesium list --prefix=label --sort=alpha --color

Links are inline

Notes should be densely linked, allowing for structure to emerge organically, and may even help you see unexpected connections which may surprise you.

Notesium assumes note links use the inline markdown syntax, for example: [link text](625d563f.md). This makes it easier to parse, and simple to insert links with a keybinding.

Even though links are short, for an improved reading experience in Vim consider enabling conceallevel (see Related Vim settings). This is implemented in the web app and enabled by default.

Deterministic periodic notes convention

Notesium itself does not directly support periodic notes, instead the embedded Web app and Vim integration support daily and weekly notes using a creation-time convention (00:00:00 for daily and 00:00:01 on the first day of the week for weekly).

This convention results in deterministic, unique filenames, enabling instant identification of a specific periodic note, without the need for manual organization or special formatting - eliminating overhead and the need to search the entire notes directory for keywords or regular expressions.

Additionally, past and future periodic notes can also be created using this convention while retaining chronological order.

$ notesium new --ctime=2024-07-04T00:00:00
/home/user/notesium/notes/6685bbd0.md

$ notesium list --sort=ctime --prefix=ctime --date=15:04:05 | grep 00:00:00
6685bbd0.md:1: 00:00:00 Jul 04, 2024 (Thursday)
6681c750.md:1: 00:00:00 Jul 01, 2024 (Monday)
668075d0.md:1: 00:00:00 Jun 30, 2024 (Sunday)

Versioning

Versions are specified using git tags, based on semantic versioning, and use the format MAJOR.MINOR.PATCH. While the MAJOR version is 0, MINOR version bumps are considered MAJOR bumps per the semver spec.

Regression tests

Test suites for all commands and their options (except for --color) are included in the tests/ directory, along with fixtures acting as a notes corpus. The tests are dependent on bats-core.

Some tests are dependent on the modification datetime of the notes (sorting and prefixing), in which case the test suite will duplicate the corpus to a temporary directory and modify the mtime deterministically.

These test suites can be paused prior to teardown for manual inspection and additional testing by setting the PAUSE environmental variable.

# run all test suites
bats tests

# run a specific test suite
bats tests/list.bats

# run a subset of tests within a specific test suite
bats tests/list.bats --filter "mtime"

# run a specific test suite, but pause prior to teardown (--tap recommended)
PAUSE=y bats tests/list.bats --tap

Inspiration and thanks

• Niklas Luhmann: Zettelkasten method.
• Andy Matuschak: Insightful notes.
• Sonke Ahrens: How to take smart notes (book).
• Junegunn Choi: Fzf and Vim plugins.
• The people behind Vim and Neovim.
• The people behind VueJS, Codemirror, TailwindCSS and D3.js.
• Projects such as Obsidian, Logseq, Roam Research, and countless others...

License

The MIT License (MIT)

Copyright (c) 2023-2024 Alon Swartz