Scimax for VS Code

A scientific computing environment for VS Code inspired by Scimax, the Emacs-based starter kit for scientists and engineers. This project is 100% vibe-engineered with Claude Code. I have endeavored to make sure it is well tested, and used Claude Code to audit it for security and performance issues. I personally use this almost daily.

Roadmap

For time being, I envision this remaining a mono-repository. That is for practical reasons. As the sole maintainer at the moment, I don't have bandwidth to manage many repositories. I also see this as a "batteries included", low friction path to get org-mode in the hands of as many people as possible.

I anticipate several months of bug fixes and feature parity efforts. Those should be reported at https://github.com/jkitchin/scimax_vscode/issues. I am trying to extend some ideas from org-mode to Markdown so it is easier to go between these formats.

My plan is to keep the major version at 0.x.x until it seems "stable", that is not many bug reports, or mostly feature requests. At that point, I plan to separate out the scimax org-parser and non-extension code into a standalone library that will be available on npm to allow additional packages / extensions to be easily built using it. Then, we will have scimax 1.x.x. I do not anticipate any change in functionality for this, but it will add some maintenance and release complexity. I do not know exactly when that will be, but hopefully by Summer 2026, and sooner if all goes well.

Installation

From VSIX

Download the .vsix file from releases
In VS Code, run Extensions: Install from VSIX...
Select the downloaded file

From Source

git clone https://github.com/jkitchin/scimax_vscode.git
cd scimax_vscode
npm install
npm run compile
npm run package

Then install the generated .vsix file.

Dependencies

VS Code 1.85.0 or later
Node.js 18+ (for development)

Features

Org-Mode & Markdown Editing Features

org-mode is simultaneously a markup language and a library of software to manipulate it. It was created in Emacs, and aside from some syntax highlighters here and there, there has not been another editor capable of the things Emacs can do. Until now.

Enhanced editing commands for org-mode, markdown, and LaTeX files.

Timestamp Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Insert Timestamp | Ctrl+c . | Insert timestamp at cursor | | Scimax: Shift Timestamp Up | Shift+Up | Increment date component | | Scimax: Shift Timestamp Down | Shift+Down | Decrement date component | | Scimax: Shift Timestamp Left | Shift+Left | Previous day | | Scimax: Shift Timestamp Right | Shift+Right | Next day | | Scimax: Add/Change Repeater | Ctrl+c Ctrl+r | Add repeater to timestamp |

Table Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Create Table | Ctrl+c \| | Create a new table | | Scimax: Insert Row Below | Alt+Enter | Insert row below current | | Scimax: Insert Row Above | Alt+Shift+Enter | Insert row above current | | Scimax: Delete Row | Alt+Shift+Backspace | Delete current row | | Scimax: Insert Column Right | Alt+Shift+Right | Insert column (in table) | | Scimax: Delete Column | Alt+Shift+Left | Delete column (in table) | | Scimax: Insert Separator | Ctrl+c - | Insert table separator line | | Scimax: Align Table | - | Align table columns |

Heading Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Promote Heading | Alt+Left | Decrease heading level | | Scimax: Demote Heading | Alt+Right | Increase heading level | | Scimax: Promote Subtree | Alt+Shift+Left | Promote heading and children | | Scimax: Demote Subtree | Alt+Shift+Right | Demote heading and children | | Scimax: Move Heading Up | Alt+Up | Move heading up | | Scimax: Move Heading Down | Alt+Down | Move heading down | | Scimax: Insert Heading | Ctrl+Enter | Insert new heading | | Scimax: Insert Subheading | - | Insert subheading |

Task Commands:**

Command	Keybinding	Description
`Scimax: Toggle Checkbox`	`Ctrl+c Ctrl+c`	Toggle checkbox state
`Scimax: Insert Task`	-	Insert a new task
`Scimax: Insert Due Date`	`Ctrl+c Ctrl+d`	Add due date to task
`Scimax: Insert Scheduled Date`	`Ctrl+c Ctrl+s`	Add scheduled date to task
`Scimax: Insert Priority`	-	Add priority to task
`Scimax: Show Agenda`	-	Show agenda view
`Scimax: Show Today's Tasks`	-	Show tasks due today
`Scimax: Show Tasks by Project`	-	Filter tasks by @project
`Scimax: Show Tasks by Tag`	-	Filter tasks by #tag

Folding: (works in org, markdown, and LaTeX) | Command | Keybinding | Description | | ------------------------------- | ----------- | ------------------------------ | | Scimax: Toggle Fold at Cursor | Tab | Toggle fold at current heading | | Scimax: Cycle Global Folding | Shift+Tab | Cycle all headings fold state |

Unified Navigation: (works in org, markdown, and LaTeX) | Keybinding | Description | | ------------- | ---------------------------------------- | | Ctrl+c Ctrl+n | Next heading/section | | Ctrl+c Ctrl+p | Previous heading/section | | Ctrl+c Ctrl+f | Next sibling (same level) | | Ctrl+c Ctrl+b | Previous sibling | | Ctrl+c Ctrl+u | Parent heading/section | | Ctrl+c Ctrl+j | Jump to any heading/section |

See Markdown Compatibility and LaTeX Navigation for full details.

Source Block Execution (Babel)

Full literate programming support with native code execution and Jupyter kernel integration.

Commands: | Command | Keybinding | Description | | ---------------------------------- | --------------- | ---------------------------------- | | Scimax: Execute Block | Ctrl+Enter | Execute source block at cursor | | Scimax: Execute and Next | Shift+Enter | Execute block and move to next | | Scimax: Execute All Blocks | - | Execute all source blocks | | Scimax: Execute to Point | - | Execute all blocks up to cursor | | Scimax: Clear Results | - | Clear results for current block | | Scimax: Clear All Results | - | Clear all results in document |

Features:

Language support: Python, JavaScript/TypeScript, Shell (bash), SQL, R, and more
Native Jupyter kernels: Use jupyter-python, jupyter-julia, etc. as block language
Session persistence: Maintain state across block executions
Rich output: Automatic image capture from matplotlib, displayed as org links
Auto-save images: Jupyter outputs saved to .ob-jupyter/ directory

Example:

#+BEGIN_SRC jupyter-python :session main
import matplotlib.pyplot as plt
import numpy as np

x = np.linspace(0, 2*np.pi, 100)
plt.plot(x, np.sin(x))
plt.title("Sine Wave")
plt.show()
#+END_SRC

#+RESULTS:
[[file:.ob-jupyter/output-1736686800000-0.png]]

Source Block Manipulation (scimax-ob)

Jupyter notebook-like editing for org-mode source blocks.

Block Creation: | Command | Keybinding | Description | | ------------------------------------ | --------------- | ------------------------------- | | Scimax: Insert Block Above | - | Insert new block above current | | Scimax: Insert Block Below | Ctrl+c Ctrl+, | Insert new block below current | | Scimax: Insert Block Below (Same) | - | Insert block with same language |

Block Manipulation: | Command | Keybinding | Description | | -------------------------------- | ------------- | ------------------------------ | | Scimax: Split Block | Ctrl+c - | Split block at cursor position | | Scimax: Clone Block | - | Duplicate current block | | Scimax: Kill Block | - | Delete block and its results | | Scimax: Copy Block | - | Copy block to clipboard | | Scimax: Move Block Up | - | Swap block with previous | | Scimax: Move Block Down | - | Swap block with next | | Scimax: Merge with Previous | - | Merge with previous block | | Scimax: Merge with Next | - | Merge with next block |

Navigation: | Command | Keybinding | Description | | -------------------------------- | ------------- | ------------------------------ | | Scimax: Next Source Block | Ctrl+Down | Jump to next block | | Scimax: Previous Source Block | Ctrl+Up | Jump to previous block | | Scimax: Jump to Source Block | Ctrl+c Ctrl+b | Quick pick to jump to block | | Scimax: Jump to Results | - | Jump to current block results |

Text Markup (scimax-org)

Emacs-style text markup with keyboard shortcuts.

Markup Commands: | Command | Keybinding | Result | | ------------------------ | ----------- | ------------------ | | Scimax: Bold | Ctrl+c b | *bold* | | Scimax: Italic | Ctrl+c i | /italic/ | | Scimax: Underline | Ctrl+c u | _underline_ | | Scimax: Code | Ctrl+c \`` | ~code~ | |Scimax: Verbatim |Ctrl+c = |=verbatim= | |Scimax: Strikethrough |Ctrl+c + |+strikethrough+ | |Scimax: Subscript | - |_{subscript} | |Scimax: Superscript | - |^{superscript} | |Scimax: LaTeX Math | - |$math$` |

DWIM Return: Smart return key that creates:

New list items when in a list
New headings when on a heading line
New table rows when in a table

Speed Commands (org-speed-commands)

Single-key shortcuts that work when the cursor is at column 0 of a heading line, just like Emacs org-mode speed commands.

How it works: Place your cursor at the very beginning of a heading line (column 0) and press a single key to execute commands instantly—no modifier keys needed.

Navigation: | Key | Command | Description | |-----|--------------------------|------------------------------| | n | Next heading | Jump to next visible heading | | p | Previous heading | Jump to previous heading | | f | Next sibling | Next heading at same level | | b | Previous sibling | Previous heading at same level | | u | Parent heading | Jump to parent heading | | j | Jump to heading | Quick pick any heading | | g | Go to menu | Show navigation submenu |

Visibility: | Key | Command | Description | |-----|--------------------------|------------------------------| | c | Cycle global | Cycle all headings visibility | | C | Show children | Expand all children | | o | Overview | Fold all headings | | Tab | Toggle fold | Cycle fold at current heading |

Structure Editing: | Key | Command | Description | |-----|--------------------------|------------------------------| | U | Move subtree up | Swap with previous sibling | | D | Move subtree down | Swap with next sibling | | r | Demote subtree | Increase level of subtree | | l | Promote subtree | Decrease level of subtree | | R | Demote heading | Increase level of heading only | | L | Promote heading | Decrease level of heading only | | w | Kill subtree | Cut subtree to clipboard | | y | Yank subtree | Paste subtree from clipboard | | W | Clone subtree | Duplicate subtree below |

TODO & Priority: | Key | Command | Description | |-----|--------------------------|------------------------------| | t | Cycle TODO | Cycle through TODO states | | , | Cycle priority | Cycle priority up | | 1 | Priority A | Set priority [#A] | | 2 | Priority B | Set priority [#B] | | 3 | Priority C | Set priority [#C] | | 0 | No priority | Remove priority |

Planning: | Key | Command | Description | |-----|--------------------------|------------------------------| | s | Schedule | Add/edit SCHEDULED timestamp | | d | Deadline | Add/edit DEADLINE timestamp | | . | Insert timestamp | Insert timestamp at point |

Metadata: | Key | Command | Description | |-----|--------------------------|------------------------------| | : | Set tags | Edit tags for heading | | e | Set effort | Set Effort property | | P | Set property | Add/edit any property |

Clocking: | Key | Command | Description | |-----|--------------------------|------------------------------| | I | Clock in | Start clock on this heading | | O | Clock out | Stop current clock |

Archive: | Key | Command | Description | |-----|--------------------------|------------------------------| | a | Archive subtree | Archive to archive file | | A | Toggle ARCHIVE tag | Add/remove :ARCHIVE: tag | | $ | Archive to sibling | Archive under Archive sibling |

Special: | Key | Command | Description | |-----|--------------------------|------------------------------| | N | Narrow to subtree | Show only this subtree | | S | Widen | Show full buffer | | ? | Speed help | Show all speed commands |

Configuration:

{
  "scimax.speedCommands.enabled": true
}

Toggle speed commands on/off with Ctrl+c Ctrl+x s.

Export System

Export org documents to multiple formats with full org-mode export option support.

Commands: | Command | Description | | -------------------------------- | ---------------------------------- | | Scimax: Export to HTML | Export current file to HTML | | Scimax: Export to Markdown | Export to GitHub-flavored MD | | Scimax: Export to LaTeX | Export to LaTeX document | | Scimax: Export to PDF | Export to PDF via LaTeX/Pandoc | | Scimax: Export to Word | Export to DOCX via Pandoc | | Scimax: Export to Jupyter | Export to Jupyter Notebook (.ipynb)| | Scimax: Export Dispatch | Show export options dialog |

Features:

Full org-mode syntax support (headings, lists, tables, blocks)
Source block syntax highlighting in exports
Table of contents generation
Custom CSS/templates for HTML export

DOCX Export (Pandoc-based): The Word export uses Pandoc for high-quality document generation:

LaTeX equations render properly as native Word equations
Bibliography support via --citeproc - citations are resolved and a bibliography is generated
Citation formats: Both org-ref (cite:key) and org-cite ([cite:@key]) are supported

Jupyter Notebook Export (ox-ipynb compatible): Export org files to Jupyter Notebook format for interactive computing:

Source blocks become code cells with proper kernel metadata
Markdown cells for prose, headings, and formatted text
Images are embedded as base64 or linked
Participant mode: Strip solutions/answers for assignments (:participant t header)
Compatible with ox-ipynb from Emacs

Export Options: Control what appears in exports using #+OPTIONS: in your org file: | Option | Effect | |-------------|-------------------------------------| | toc:2 | Table of contents to depth 2 | | num:t | Number sections | | p:nil | Remove statistics cookies [1/3] | | todo:nil | Remove TODO keywords | | tags:nil | Remove heading tags | | pri:nil | Remove priority cookies [#A] | | prop:nil | Remove PROPERTIES drawers | | d:nil | Remove all drawers |

Example:

#+TITLE: My Document
#+OPTIONS: toc:2 num:t p:nil todo:nil tags:nil

* Introduction
Content here...

bibliography:~/references.bib

Requirements: Pandoc must be installed for DOCX/PDF export.

Capture Templates (org-capture)

Quick note capture with customizable templates, inspired by Emacs org-capture.

Commands: | Command | Keybinding | Description | | --------------------------------- | ---------- | ---------------------------------- | | Scimax: Capture | Ctrl+c c | Show capture template picker | | Scimax: Quick Capture TODO | Ctrl+c t | Quick capture a TODO item | | Scimax: Quick Capture Note | - | Quick capture a note | | Scimax: Create Capture Template | - | Create a new capture template | | Scimax: List Capture Templates | - | Show all available templates |

Built-in Templates:

Todo (t): Capture a TODO item to todo.org
Note (n): Capture a note with timestamp
Journal (j): Capture to today's journal entry in a datetree
Code Snippet (s): Capture selected code with language and source link
Meeting Notes (m): Capture meeting notes with attendees and agenda
Link (l): Capture a link with description
Idea (i): Capture an idea for the ideas file

Features:

Template variables: %t (timestamp), %T (active timestamp), %U (inactive timestamp)
Context variables: %a (annotation link), %i (selected text), %c (clipboard)
Prompt variables: %^{prompt} for user input
Datetree filing: Automatically file under date hierarchy
File targeting: Capture to specific files or headlines

Configuration:

{
  "scimax.capture.templates": [...],
  "scimax.capture.defaultFile": "~/capture.org",
  "scimax.capture.datetreeFormat": "year-month-day",
  "scimax.capture.autoSave": true
}

Enhanced Tables (scimax-tables)

Spreadsheet-like table editing with export capabilities.

Named Tables & Export: | Command | Keybinding | Description | | ------------------------ | ----------------- | ------------------------------- | | Scimax: Go to Named Table | - | Jump to table by #+NAME: | | Scimax: Export Table | Ctrl+c Ctrl+e t | Export to CSV/TSV/HTML/LaTeX | | Scimax: Import Table | - | Create table from clipboard | | Scimax: Sum Column | - | Sum numbers in current column | | Scimax: Average Column | - | Average numbers in column | | Scimax: Sort by Column | Ctrl+c ^ | Sort table by current column |

Journal System (scimax-journal)

A date-organized journaling system for daily notes, research logs, and documentation.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Open Today's Journal | Ctrl+Shift+J / Cmd+Shift+J | Open or create today's journal entry | | Scimax: New Journal Entry | - | Create a new journal entry for a specific date | | Scimax: Previous Journal Entry | Alt+[ | Navigate to previous journal entry | | Scimax: Next Journal Entry | Alt+] | Navigate to next journal entry | | Scimax: Go to Journal Date | - | Jump to a specific date's journal | | Scimax: Search Journal | - | Full-text search across all journal entries | | Scimax: Show Journal Calendar | - | Open the calendar webview | | Scimax: This Week's Entries | - | Show journal entries from the current week | | Scimax: Quick Log Entry | - | Quick append a timestamped log entry | | Scimax: Insert Timestamp | - | Insert current timestamp at cursor | | Scimax: Show Journal Statistics | - | Display word count, streaks, task completion |

Templates: Choose from default, minimal, research, meeting, or standup templates.

Configuration:

{
  "scimax.journal.directory": "~/scimax-journal",
  "scimax.journal.format": "markdown",
  "scimax.journal.template": "default",
  "scimax.journal.dateFormat": "YYYY-MM-DD",
  "scimax.journal.autoTimestamp": true,
  "scimax.journal.weekStartsOn": "monday"
}

Project Management (projectile-style)

Quick project switching and file finding, inspired by Emacs projectile. Projects are defined by a directory containing a git repo, or a project marker file like .projectile.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Switch Project | Ctrl+c p p | Switch to a known project | | Scimax: Find File in Project | Ctrl+c p f | Find file in current project | | Scimax: Search in Project | Ctrl+c p s | Search text in project files | | Scimax: Open Project Root | Ctrl+c p d | Open project root directory | | Scimax: Add Project | Ctrl+c p a | Add a project to the list | | Scimax: Remove Project | - | Remove project from tracking | | Scimax: Scan Directory for Projects | - | Scan a directory for projects | | Scimax: Project Info | - | Show project statistics | | Scimax: Cleanup Non-existent Projects | - | Remove deleted projects |

Project Detection: Automatically detects projects via: .projectile, .git, .scimax, package.json, pyproject.toml, Cargo.toml, go.mod, pom.xml, build.gradle, .project

Notebooks (scimax-notebook)

Project-based organization for scientific research and software development.

Commands: | Command | Description | | --------- | ------------- | | Scimax: New Notebook | Create a new notebook project | | Scimax: Open Notebook | Switch to a different notebook | | Scimax: Open Notebook Master File | Open README.org or main file | | Scimax: Recent Files in Notebook | Browse recently modified files | | Scimax: Search in Notebook | Scoped search within notebook | | Scimax: Notebook Agenda | Show agenda for current notebook | | Scimax: Add Collaborator | Add a team member to notebook | | Scimax: Archive Notebook | Create git archive (zip) | | Scimax: Notebook Settings | Edit .scimax/config.json | | Scimax: Index Notebook | Reindex notebook files | | Scimax: Notebook Info | Show notebook statistics | | Scimax: Remove Notebook from Tracking | Untrack a notebook |

Templates:

empty: Basic structure with README.org
research: Scientific research with data/, figures/, scripts/, references.bib
software: Software project with src/, tests/, docs/
notes: Note-taking with journal/ directory

Configuration:

{
  "scimax.notebook.directory": "~/notebooks",
  "scimax.notebook.defaultTemplate": "research",
  "scimax.notebook.autoDetect": true
}

Bibliography & Citations (org-ref)

Full bibliography management with BibTeX support, DOI fetching, and citation insertion. Projects are defined by a directory containing a git repo, or a project marker file like .projectile.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Insert Citation | Ctrl+c ] | Insert a citation at cursor | | Scimax: Insert Reference Link | Ctrl+u Ctrl+c ] | Insert ref:/eqref:/pageref: link | | Scimax: Fetch BibTeX from DOI | - | Fetch bibliography entry from DOI | | Scimax: Search References | - | Search all bibliography entries | | Scimax: Open Bibliography | - | Open a .bib file | | Scimax: Find Citations of Reference | - | Find all citations of a reference | | Scimax: Copy BibTeX Entry | - | Copy BibTeX to clipboard | | Scimax: Extract Bibliography from File | - | Extract all cited references to a new .bib file | | Scimax: Show Citing Works (OpenAlex) | - | Show papers that cite a DOI | | Scimax: Show Related Works (OpenAlex) | - | Show related papers for a DOI | | Scimax: Search OpenAlex | - | Search the OpenAlex academic database | | Scimax: Transpose Citation Left | Shift+Left | Swap citation with previous (when on citation) | | Scimax: Transpose Citation Right | Shift+Right | Swap citation with next (when on citation) | | Scimax: Sort Citations Alphabetically | Shift+Up | Sort citation keys alphabetically (when on citation) | | Scimax: Sort Citations by Year | Shift+Down | Sort citation keys by year (when on citation) | | Scimax: Delete Citation at Cursor | Ctrl+Shift+K | Delete citation key at cursor (when on citation) |

Features:

Hover preview: Hover over citations to see reference details with source file
DOI tooltips: Hover over DOIs to see metadata from CrossRef + OpenAlex (citation count, open access status, topics)
Autocomplete: Type cite: or @ for citation suggestions
Go to definition: Jump from citation to bibliography entry
Code lens: In .bib files, see citations count and quick actions
Citation styles: cite, citet, citep, citeauthor, citeyear
OpenAlex integration: View citation counts, open access links, citing works, related works
Citation manipulation: Transpose, sort, and delete citations with keyboard shortcuts (like org-ref)

Configuration:

{
  "scimax.ref.bibliographyFiles": ["~/bibliography.bib"],
  "scimax.ref.pdfDirectory": "~/papers",
  "scimax.ref.notesDirectory": "~/notes",
  "scimax.ref.defaultCiteStyle": "cite"
}

Works with Zotero too!

Fuzzy Search (swiper-style)

Fast, interactive search for the current file and all open files, inspired by Emacs swiper.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Fuzzy Search (Current File) | Ctrl+c s | Search lines in current file with live preview | | Scimax: Fuzzy Search (Open Files) | Ctrl+c Shift+s | Search across all open editor tabs | | Scimax: Fuzzy Search (Outline) | Ctrl+c Alt+s | Search headings/symbols in current file |

Features:

Live preview: Cursor moves to match as you type
Match highlighting: Matches highlighted in the editor
Multi-file search: Search all open tabs at once
Outline mode: Jump to headings, functions, classes

Quick navigation to visible text using labeled targets, inspired by Emacs avy.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Jump to Character | Ctrl+c j c | Jump to any occurrence of a character | | Scimax: Jump to 2-Character Sequence | Ctrl+c j j | Jump to a two-character sequence | | Scimax: Jump to Word | Ctrl+c j w | Jump to word starts | | Scimax: Jump to Line | Ctrl+c j l | Jump to any visible line | | Scimax: Jump to Symbol | Ctrl+c j o | Jump to symbols/headings in view | | Scimax: Jump to Subword | Ctrl+c j s | Jump to subword boundaries (camelCase, snake_case) | | Scimax: Jump Copy Line | - | Select a visible line and copy it | | Scimax: Jump Kill Line | - | Select a visible line and delete it |

Features:

Label-based selection: Type a label (a, s, d, f...) to instantly jump
QuickPick fallback: Browse and filter targets in a list
Match highlighting: All targets highlighted in the editor
Works everywhere: Functions in any file type

Edit Marks (Track Changes)

Collaborative editing markup for reviewing changes, inspired by scimax-editmarks.

Commands: | Command | Keybinding | Description | | --------- | ------------ | ------------- | | Scimax: Mark Insertion | Ctrl+c e i | Mark selected text as insertion | | Scimax: Mark Deletion | Ctrl+c e d | Mark selected text for deletion | | Scimax: Insert Edit Comment | Ctrl+c e c | Insert a review comment | | Scimax: Mark Typo Correction | Ctrl+c e t | Mark typo with correction | | Scimax: Accept Edit Mark | Ctrl+c e a | Accept the edit mark at cursor | | Scimax: Reject Edit Mark | Ctrl+c e r | Reject the edit mark at cursor | | Scimax: Accept All Edit Marks | - | Accept all marks in document | | Scimax: Reject All Edit Marks | - | Reject all marks in document | | Scimax: Next Edit Mark | Ctrl+c e ] | Navigate to next edit mark | | Scimax: Previous Edit Mark | Ctrl+c e [ | Navigate to previous edit mark | | Scimax: Show Edit Marks Summary | Ctrl+c e s | Show summary of all edit marks |

Markup Format:

@@+inserted text+@@          # Insertion (green)
@@-deleted text-@@           # Deletion (red, strikethrough)
@@>comment text<@@           # Comment (yellow, italic)
@@~old text|new text~@@      # Typo correction (orange)

Also supports CriticMarkup format: {++insert++}, {--delete--}, {>>comment<<}, {~~old~>new~~}

File Database (scimax-db)

SQLite database powered by libsql with FTS5 full-text search and vector semantic search.

Commands: | Command | --------- | Scimax: Reindex Files | Scimax: Search All Files | Scimax: Semantic Search (AI) | Scimax: Hybrid Search | Scimax: Search Headings | Scimax: Search by Tag | Scimax: Search by Property | Scimax: Search Code Blocks | Scimax: Search by Hashtag | Scimax: Show TODO Items | Scimax: Show Agenda | Scimax: Show Upcoming Deadlines | Scimax: Browse Indexed Files | Scimax: Set Search Scope | Scimax: Configure Embedding | Scimax: Show Database Stats | Scimax: Optimize Database | Scimax: Clear Database | Description | | ------------- | | Reindex all files in workspace | | Full-text search with BM25 ranking | | Find by meaning using embeddings | | Combined keyword + semantic search | | Search document headings | | Filter headings by org-mode tags | | Search by property drawer values | | Search source code blocks by language | | Find files containing #hashtags | | List all TODO items | | View deadlines and scheduled items | | See deadlines in next 2 weeks | | Browse all indexed files | | Limit searches to directory/project | Service | Setup Ollama for semantic search | | Display indexing statistics | | Clean up stale entries (VACUUM) | | Reset the database |

Features:

SQLite with FTS5: Fast full-text search with BM25 ranking, scalable to 10k+ files
Vector Search: Semantic search using embeddings (cosine similarity)
Hybrid Search: Reciprocal rank fusion of keyword + semantic results
Auto-indexing: Files are automatically indexed on save
Tag inheritance: Inherited tags from parent headings
Agenda view: Deadlines, scheduled items, and TODOs with overdue detection
Scoped search: Limit searches to specific directories
Batched reindexing: Memory-safe reindexing with configurable batch size and progress reporting
Cancellable operations: Long-running reindex can be cancelled via progress notification

Embedding Provider for Semantic Search: | Provider | Model | Dimensions | Setup | | ------------------ | ---------------- | ---------- | ------------------------------ | | Ollama (local) | nomic-embed-text | 768 | ollama pull nomic-embed-text | | Ollama (local) | all-minilm | 384 | ollama pull all-minilm | | Ollama (local) | mxbai-embed-large| 1024 | ollama pull mxbai-embed-large|

Configuration:

{
  "scimax.db.directories": [],
  "scimax.db.ignorePatterns": ["**/node_modules/**", "**/.git/**"],
  "scimax.db.autoIndex": true,
  "scimax.db.embeddingProvider": "ollama",
  "scimax.db.ollamaUrl": "http://localhost:11434",
  "scimax.db.ollamaModel": "nomic-embed-text"
}

The extension adds a Scimax activity bar icon with these views:

View	Description
Calendar	Interactive calendar for journal navigation
Journal Entries	List of recent journal files
Projects	Quick project switching (projectile-style)

Keyboard Shortcuts Summary

General

Shortcut	Command
`Alt+X`	Command Palette (Emacs M-x)
`Ctrl+Shift+J` / `Cmd+Shift+J`	Open Today's Journal
`Ctrl+Alt+V` / `Ctrl+Cmd+V`	Database Menu (quick access to search commands)

Help (Emacs-style)

Shortcut	Command
`Ctrl+h k`	Describe Key (type a key sequence to see its command)
`Ctrl+h b`	List all keybindings
`Ctrl+h f`	Describe Command (find command by name)

Capture

Shortcut	Command
`Ctrl+c c`	Capture (template picker)
`Ctrl+c t`	Quick Capture TODO

Shortcut	Command	When
`Alt+[`	Previous Journal Entry	In journal file
`Alt+]`	Next Journal Entry	In journal file

Citations & References

Shortcut	Command	When
`Ctrl+c ]`	Insert Citation	In org/markdown/latex
`Ctrl+u Ctrl+c ]`	Insert Reference Link	In org/markdown/latex
`Shift+Left`	Transpose Citation Left	On citation
`Shift+Right`	Transpose Citation Right	On citation
`Shift+Up`	Sort Citations Alphabetically	On citation
`Shift+Down`	Sort Citations by Year	On citation
`Ctrl+Shift+K`	Delete Citation	On citation

Fuzzy Search

Shortcut	Command	When
`Ctrl+c s`	Fuzzy Search (Current File)	In editor
`Ctrl+c Shift+s`	Fuzzy Search (Open Files)	In editor
`Ctrl+c Alt+s`	Fuzzy Search (Outline)	In editor

Shortcut	Command	When
`Ctrl+c j c`	Jump to Character	In editor
`Ctrl+c j j`	Jump to 2-Char Sequence	In editor
`Ctrl+c j w`	Jump to Word	In editor
`Ctrl+c j l`	Jump to Line	In editor
`Ctrl+c j o`	Jump to Symbol	In editor
`Ctrl+c j s`	Jump to Subword	In editor

Edit Marks (Track Changes)

Shortcut	Command	When
`Ctrl+c e i`	Mark Insertion	In editor
`Ctrl+c e d`	Mark Deletion	In editor
`Ctrl+c e c`	Insert Comment	In editor
`Ctrl+c e t`	Mark Typo	In editor
`Ctrl+c e a`	Accept Edit Mark	In editor
`Ctrl+c e r`	Reject Edit Mark	In editor
`Ctrl+c e ]`	Next Edit Mark	In editor
`Ctrl+c e [`	Previous Edit Mark	In editor
`Ctrl+c e s`	Show Summary	In editor

Project Management

Shortcut	Command
`Ctrl+c p p`	Switch Project
`Ctrl+c p f`	Find File in Project
`Ctrl+c p s`	Search in Project
`Ctrl+c p d`	Open Project Root
`Ctrl+c p a`	Add Project

Org-Mode & Markdown Editing

Shortcut	Command	When
`Tab`	Toggle Fold	On heading
`Shift+Tab`	Cycle Global Folding	In org/markdown/latex
`Ctrl+Enter`	Execute Block / Insert Heading	In org/markdown
`Shift+Enter`	Execute Block and Move to Next	In org/markdown
`Ctrl+c Ctrl+c`	Toggle Checkbox	In org/markdown
`Ctrl+c .`	Insert Timestamp	In org/markdown
`Ctrl+c Ctrl+d`	Insert Due Date	In org/markdown
`Ctrl+c Ctrl+s`	Insert Scheduled Date	In org/markdown
`Ctrl+c Ctrl+r`	Add Repeater	In org/markdown
`Ctrl+c \\|`	Create Table	In org/markdown
`Ctrl+c -`	Insert Table Separator / Split Block	In org/markdown
`Shift+Up/Down`	Adjust Timestamp	On timestamp
`Shift+Left/Right`	Previous/Next Day or Cycle TODO	On timestamp/heading
`Alt+Left/Right`	Promote/Demote Heading	On heading
`Alt+Up/Down`	Move Heading/Subtree Up/Down	On heading
`Alt+Enter`	Insert Table Row Below	In table
`Alt+Shift+Enter`	Insert Table Row Above	In table
`Alt+Shift+Left/Right`	Promote/Demote Subtree or Delete/Insert Column	Context-dependent

Text Markup

| Shortcut | Command | Result | | ------------ | ------------------ | ------------------- | | Ctrl+c b | Bold | *text* | | Ctrl+c i | Italic | /text/ | | Ctrl+c u | Underline | _text_ | | Ctrl+c \`` | Code | ~text~ | |Ctrl+c = | Verbatim |=text= | |Ctrl+c + | Strikethrough |+text+` |

Shortcut	Command	When
`Ctrl+Down`	Next Source Block	In org/md
`Ctrl+Up`	Previous Source Block	In org/md
`Ctrl+c Ctrl+,`	Insert Block Below	In org/md
`Ctrl+c Ctrl+b`	Jump to Source Block	In org/md
`Ctrl+c Ctrl+j`	Jump to Heading	In org/md
`Ctrl+c Ctrl+o`	Open Link at Point	In org/md
`Ctrl+c Ctrl+l`	Insert Link	In org/md
`Ctrl+c Ctrl+t`	Cycle TODO State	In org/md

File Formats

The extension supports:

Org-mode (.org): Full parsing of headings, properties, tags, timestamps, source blocks, links
Markdown (.md): Structural editing parity with org-mode (headings, code blocks, navigation, speed commands)
LaTeX (.tex): Section navigation, structure editing, environments, hover tooltips, completion
BibTeX (.bib): Bibliography entries with all standard fields

Comparison with Emacs Scimax

This package almost achieves feature parity with Emacs Scimax. If there are features missing it is likely because I don't use them anymore or frequently.

Feature	Emacs Scimax	VS Code Scimax
Journal	scimax-journal	Full support
Bibliography	org-ref	Full support + OpenAlex
Database	org-db-v3	Full support with semantic search
Notebooks	scimax-notebook	Full support
Projectile	projectile	Full support
Swiper	swiper/ivy	Full support (fuzzy search)
Avy	avy	Full support (jump)
Spell Check	jinx/flyspell	Use LTeX extension
Track Changes	scimax-editmarks	Full support (editmarks)
Literate Programming	ob-ipython/ob-*	Full support (Babel + Jupyter)
Text Markup	scimax-org	Full support (bold, italic, etc.)
Block Manipulation	scimax-ob	Full support (split, merge, navigate)
Export	ox-*	Full support (HTML, LaTeX, MD, PDF, DOCX, ipynb)
Tables	org-table	Full support + export to CSV/HTML
Speed Commands	org-speed-commands	Full support (37 commands)
Clocking	org-clock	Full support (in/out, reports, tables)
Contacts	org-contacts	Not yet
Capture Templates	org-capture	Full support (templates, datetree)
Markdown Support	-	Full structural editing parity
LaTeX Navigation	AUCTeX	Full support (sections, environments)

Scimax VS Code Codebase Statistics

Metric	Count
TypeScript files	299
Lines of TypeScript	~173,900
Test files	69
Unit tests	2683
Documentation files	47
Commands	942
Keybindings	409

Supported Languages (Babel Execution)

Python, JavaScript, TypeScript, Shell (bash/sh), SQL, R, Julia, plus any Jupyter kernel via jupyter-* prefix.

Parser Performance

Benchmarks on typical documents (may vary by system):

Document Size	Parse Time (avg)
Small (~3.5K chars, 177 lines)	<5ms
Medium (~9K chars, 428 lines)	<10ms
Large (~34K chars, 1571 lines)	<25ms

The parser scales linearly with document size and handles documents with hundreds of headings, source blocks, and deeply nested structures efficiently.

Troubleshooting & Logging

Scimax includes a rotating file logger for debugging issues:

Commands: | Command | Description | |----------------------------------|------------------------------------| | Scimax: Open Log File Directory| Open the directory containing logs |

Log Files:

Logs are written to scimax.log in the extension's storage directory
Automatic rotation when file exceeds size limit (default 1MB)
Keeps configurable number of backup files (scimax.log.1, scimax.log.2, etc.)

Configuration:

{
  "scimax.logLevel": "info",       // debug, info, warn, error
  "scimax.logMaxSizeKB": 1024,     // Max log file size before rotation
  "scimax.logBackupCount": 3       // Number of backup files to keep
}

Contributing

Contributions welcome! Please see the GitHub repository.

License

MIT License - see LICENSE file for details.

Inspiration & Acknowledgments

This project is a reimplementation of concepts and workflows from the Emacs ecosystem for VS Code. We gratefully acknowledge the following projects that inspired this work:

Core Inspiration

Org-mode - The foundational system for outlining, task management, and literate programming in Emacs. Org-mode's elegant plain-text format and powerful features are the heart of what we're bringing to VS Code.
Scimax - An Emacs configuration for scientists and engineers by John Kitchin. Scimax extends org-mode with features specifically designed for scientific computing, reproducible research, and technical writing. This VS Code extension is a spiritual successor to Scimax.

Feature Inspirations

org-ref - Bibliography and citation management for org-mode. Our reference management system, including citation links, BibTeX integration, and crossref/OpenAlex lookups, follows org-ref's design.
org-db - A database for indexing and searching org files. Our SQLite-based database with FTS5 full-text search and semantic vector search is inspired by org-db.
Swiper/Ivy - Completion and narrowing framework for Emacs. Our fuzzy search feature brings swiper-style incremental search to VS Code.
Avy - Jump to visible text using a char-based decision tree. Our jump feature implements avy-style navigation.
Projectile - Project management for Emacs. Our project management features draw from projectile's approach.
Hydra - Sticky key bindings for Emacs. Our hydra menu system brings this concept to VS Code.

Org-mode Babel

The source block execution system (Babel) is inspired by org-babel, which pioneered literate programming and reproducible research in plain text documents.

Thank You

Special thanks to the Emacs community and all the developers who have built these incredible tools over the years. While this is a clean-room reimplementation for VS Code, the ideas and workflows we're implementing come from decades of innovation in the Emacs ecosystem.

Should you use this?

I hope so; I use it every day. I have used the previous version of scimax for over a decade in Emacs. So why VS Code now? I have increasingly needed to use VS Code to work with a Kubernetes cluster we use in my research group, and my students have all migrated to VS Code and away from Emacs.

I was never able to get anything resembling the Emacs experience on my own because I lack familiarity with Typescript and the way VS Code works. Claude Code changed that dramatically, and in just a few weeks I was able to create nearly the same Emacs experience I am accustomed to in VS Code, i.e. similar key bindings, similar functionality, across every dimension of org-mode, org-ref, and all the scimax tools I built over the past decade. VS Code is not like Emacs, and it is not generally possible to get exact feature parity; but I think we get pretty close. I was even able to extend much of this to markdown and LaTeX to provide a first-class scientific writing tool.

Are there risks you should be aware of? org-mode in Emacs was created in 2003, and has over two decades of community development and experience. scimax in VS Code does not have that yet. I hope we will build that over time.

I have made some choices, like relying on a Sqlite database to enable full text, semantic search and agenda building across all your org-files, that are not standard in org-mode. It has been the most difficult task to get this working, but I am sure it will be worth it. While I have tried to keep true to the org-mode syntax and experience, I have added the scimax features I find critical for my own work, and that I want to be readily available for you.

Scimax for VS Code

John Kitchin

Scimax for VS Code

Roadmap

Installation

From VSIX

From Source

Dependencies

Features

Org-Mode & Markdown Editing Features

Task Commands:**

Source Block Execution (Babel)

Source Block Manipulation (scimax-ob)

Text Markup (scimax-org)

Speed Commands (org-speed-commands)

Export System

Capture Templates (org-capture)

Enhanced Tables (scimax-tables)

Journal System (scimax-journal)

Project Management (projectile-style)

Notebooks (scimax-notebook)

Bibliography & Citations (org-ref)

Fuzzy Search (swiper-style)

Jump Navigation (avy-style)

Edit Marks (Track Changes)

File Database (scimax-db)

Sidebar Views

Keyboard Shortcuts Summary

General

Help (Emacs-style)

Capture

Journal Navigation

Citations & References

Fuzzy Search

Jump Navigation

Edit Marks (Track Changes)

Project Management

Org-Mode & Markdown Editing

Text Markup

Source Block Navigation & Execution

File Formats

Comparison with Emacs Scimax

Scimax VS Code Codebase Statistics

Supported Languages (Babel Execution)

Parser Performance

Troubleshooting & Logging

Contributing

License

Inspiration & Acknowledgments

Core Inspiration

Feature Inspirations

Org-mode Babel

Thank You

Should you use this?