ThoughtKnot

ThoughtKnot draws the graphs written in your notes. You can edit a graph beside its note, by typing or by dragging the drawing. It is an Obsidian plugin, and it works on desktop and phone, offline.

Status: in development. It is not in the community plugin directory yet. It is built in nine slices. Slices 1 to 3 are done, and slice 4 is in progress.

At a glance

You want to	Go to
Use it	How to use ThoughtKnot
Know what it sends, and when	Privacy and network use
Build it or change it	Developing and CONTRIBUTING.md
See how it fits together	How the packages fit

What is here

• packages/obsidian: the plugin.
• packages/graph-spec: the graph format library in plain JavaScript. It reads graphs, checks their rules and answers questions about them. It is one file with no dependencies, so a web page or Node can load it.
• python/graph_spec: the same library in Python. It also draws with Graphviz and runs extra checks with Grafeo. Its answers are tested against the JavaScript library on every shared case.
• Each release carries both libraries as one archive, graph-spec-libraries-<version>.tar.gz. SHA256SUMS lists every file in the release with its SHA-256.
• manifest.json, versions.json and styles.css: the files the plugin store reads. CI builds main.js from a tag and attaches it to each release. It is never committed.

How the packages fit

Each layer uses only the one below it. So a new host, such as a VS Code extension or a desktop app, reuses everything below the hosts as it is.

  hosts       packages/obsidian      packages/claude-code
                     \                      /
  core                 packages/core          host-free: reading, drawing, edits, undo
                            |
  format      packages/graph-spec   <=>   python/graph_spec
              (JavaScript)   held to the same answers   (Python)

• packages/graph-spec: the graph format. It reads GQL blocks and runs the spec's rules, with no dependencies. Guide: packages/graph-spec/GUIDE.md.
• python/graph_spec: the same format in Python, function for function. It adds the Graphviz drawing and the Grafeo checks. Shared tests hold the two to the same answers. Guide: python/graph_spec/GUIDE.md.
• packages/core: the editor core, on top of graph-spec. It works out what to draw, the problems and their fixes, zoom, edits and undo. It uses no Obsidian, editor or Node module, so it runs on a phone too. Guide: packages/core/GUIDE.md.
• packages/obsidian: the Obsidian plugin. It puts the core's drawings and edits on Obsidian's page. Guide: packages/obsidian/GUIDE.md.
• packages/claude-code: the Claude Code host. Its /graph <note> command draws a note's graph in a pane. It also serves a browser editor on your own machine, on the same core. Guide: packages/claude-code/GUIDE.md.

Privacy and network use

The plugin makes no network request of its own. There are no analytics, no update checks, no remote images and no databases. Graphviz, the one runtime dependency, is bundled and runs on your device.

The one exception: AI models you set up. The plugin can ask an AI model to propose changes to a graph. It sends content only to AI models you have set up yourself, and only when you send it. AI is off until you turn it on (Use AI models, in the plugin's settings) and set up a model.

What happens on each send

• You choose what is sent. It can be the whole graph, one of its views, or the things you tick. It goes as GQL: each thing with its kinds and properties, the links between them, your question and the instructions. Nothing else from the vault goes: not the note's other text, not another graph, not a comment.
• You see what will be sent before it goes. You also see which model and address it goes to. Nothing goes until you press Send, and nothing is ever sent in the background.
• Each model has a ceiling. This is the highest classification of note it may be sent, and you set it. A note above the ceiling is not sent to that model. A note at your highest classification is never sent to any model.
• A note with no classification counts as the most sensitive level. So by default it goes to no model. To change that, give the note a classification. Or choose a lower level under Unlabelled notes count as, in the settings.
• Credentials are looked for by common patterns. These include a password or secret property, an API key, an access key and a token. They also include a private key, a card number and the key of any model you set up. What matches is never sent. These are patterns, not a promise, so keep secrets out of notes you send.
• A key stays in Obsidian's own secret store. It is never in the vault, the plugin's settings, a note or a log. A model on another machine is reached over https only. A model's address may hold no user name, password or query.
• The answer comes back as a proposal. It is written into the note as a change set beside the graph. You accept or reject each change. An AI never writes to the graph.
• Every send is recorded in the plugin's own data, without the text sent. The record keeps a SHA-256 digest of the text, its size, the kind of choice and how many things and links. It also keeps the model's name and address, the time and the result. The last 200 sends are kept. The command "Clear the record of sends to AI models" clears them.

Where requests go

Requests go straight from your device to the address you gave, through Obsidian's own request function. There is no server of ours in between, and no AI vendor's library inside the plugin.

Obsidian follows redirects; point a model only at an address you trust. Obsidian also adds headers of its own to each request, beyond those shown before you send.

Developing

You need Node 24 or later. CONTRIBUTING.md says how the code is written and how each rule is checked.

npm ci
git config core.hooksPath .githooks
npm test
npm run typecheck
npm run lint
npm run build

The second line turns on the pre-commit check. It refuses any staged file that looks confidential or personal:

• a classification other than Public in a note's frontmatter, or a note's uuid line;
• a path into a home folder;
• a personal email address, a phone number or a card number.

CI runs the same check over every file, so a commit that skipped the hook is still caught.

A fresh clone needs only these steps. CI runs them exactly as written here, in a fresh clone:

• on every merge to main;
• before every release;
• on every pull request that changes them or what they install.

So setting up never depends on a maintainer's machine.

This is a one-person project and takes no outside contributions. Only collaborators can open pull requests and issues, and each pull request's conversation is locked when it opens.

Testing in Obsidian, on desktop and phone

The plugin is tested from installed files, not from the plugin store.

1. npm run build writes main.js once. npm run dev writes it on every save.
2. node scripts/reset-test-vault.mjs copies main.js, manifest.json and styles.css into the test vault's .obsidian/plugins/thoughtknot/, as real files.
3. Reload the plugin in Obsidian.

Obsidian Sync carries the files to a phone when it syncs installed community plugins. A new build reaches the vault only when you run the reset again. Releases are still built only by CI, from a tag.

To try the drawing in an ordinary browser first, run node packages/obsidian/harness/build.mjs <folder>. It builds a page that draws a sample note with the real plugin and a small stand-in for Obsidian. Serve the folder and open it.

The Python library has its own pinned setup (uv, Python 3.14):

cd python/graph_spec
uv sync --locked
uv run --locked python -m unittest discover -s tests

A host that uses the Python library sets three values after importing it: graph_spec.CLASSIFICATION_NOTE, graph_spec.OWNER_ENGINE and graph_spec.WRITTEN_BY. The defaults name no machine or person. No classification note is read until one is set.

Supply chain

• Exact pins. Every dependency is pinned to an exact version. The lockfile is committed, and installs use npm ci.
• No install scripts. .npmrc sets ignore-scripts=true.
• Verified. CI runs npm audit signatures before every build.
• Slow to adopt, quick to patch. Dependabot proposes version updates each week, after a seven-day wait. Security updates come at once.
• Pinned actions. Every GitHub Action is pinned to a full commit hash. CI runs with read-only permissions, and only the release job may write.
• Built by CI. Releases are built from a version tag, with no v in front. Each has SHA256SUMS for every file. Once the repository is public, each also gets a build provenance attestation. GitHub keeps those only for public repositories owned by a person.
• Fit to be public, checked every time. scripts/public-readiness.mjs runs in CI and before every release. It checks every branch and tag for secrets and for anything confidential or personal. It checks that every commit comes from a no-reply address. It also sets up a fresh clone from the steps above alone.
• GitHub settings checked too. The same script (--settings) checks the repository's settings. Collaborators only may open pull requests and issues. Every action is pinned and the token is read-only. A fork's workflows run only once approved. Secret scanning with push protection, Dependabot alerts and fixes, and CodeQL are on.
• Dependencies reviewed, advisories re-read. Each pull request's dependency changes are checked against published advisories. The Graphviz inside the engine is checked against them each week.
• No test framework. Tests use the runner built into Node.

Licence

Mozilla Public License 2.0 (MPL-2.0). See LICENSE.

• Anyone may use, fork and change the code, and send a pull request.
• A changed file stays under the same licence, so its changes stay open.
• The code may still sit inside a larger work under other terms.
• Releases before this change stay MIT.

The layout engine, @viz-js/viz, compiles Graphviz (Eclipse Public License 2.0) into WebAssembly. See THIRD_PARTY_NOTICES.md, which ships with every release.