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stencila/stencila: Documents with Scientific Intelligence

Documents with Scientific Intelligence

Stencila is a platform for creating and publishing, dynamic, data-driven content. Our aim is to lower the barriers for creating truly programmable documents, and to make it easier to publish them as beautiful, interactive, and semantically rich, articles and applications. Our roots are in scientific communication, but our tools are useful beyond.

This is v2 of Stencila, a rewrite in Rust focussed on the synergies between three recent and impactful innovations and trends:

• Conflict-free replicated data types (CRDTs) for de-centralized collaboration and version control.

• Large language models (LLMs) for assisting in writing and editing, prose and code.

• The blurring of the lines between documents and applications as seen in tools such as Notion and Coda.

We are embarking on a rewrite because CRDTs will now be the foundational synchronization and storage layer for Stencila documents. This requires fundamental changes to most other parts of the platform. Furthermore, a rewrite allow us to bake in, rather than bolt on, new modes of interaction between authors and LLM assistants and add mechanisms to mitigate the risks associated with using LLMs (e.g. by recording the actor, human or LLM, that made the change to a document). Much of the code in the v1 branch will be reused (after some tidy-ups and refactoring), so v2 is not a complete rewrite.

Our general strategy is to iterate horizontally across the feature set, rather than fully developing features sequentially. This will better enable early user testing of workflows and reduce the risk of finding ourselves painted into an architectural corner. So expect initial iterations to have limited functionality and be buggy.

We'll be making alpha and beta releases of v2 early and often across all products (e.g. CLI, desktop, SDKs). We're aiming for a 2.0.0 release by the end of Q3 2024.

🟢 Stable • 🔶 Beta • ⚠️ Alpha • 🚧 Under development • 🧪 Experimental • 🧭 Planned • ❔ Maybe

The Stencila Schema is the data model for Stencila documents (definition here, generated reference documentation here). Most of the schema is well defined but some document node types are still marked as under development. A summary by category:

In v2, documents can be stored as binary Automerge CRDT files, branched and merged, and with the ability to import and export the document in various formats. Collaboration, including real-time, is made possible by exchanging fine-grained changes to the CRDT over the network. In addition, we want to enable interoperability with a Git-based workflow.

Interoperability with existing formats has always been a key feature of Stencila. We are bringing over codecs (a.k.a. converters) from the v1 branch and porting other functionality from encoda to Rust.

Kernels are what executes the code in Stencila CodeChunks and CodeExpressions, as well as in control flow document nodes such as ForBlock and IfBlock. In addition, there are kernels for rendering math (e.g. MathBlock) and styling (e.g. StyledInline) nodes.

Tip

Run stencila kernels (or cargo run -p cli kernels in development) for an up to date list of kernels, including those available through plugins.

Tools are what we call the self-contained Stencila products you can download and use locally on your machine to interact with Stencila documents.

Stencila's software development kits (SDKs) enable developers to create plugins to extend Stencila's core functionality or to build other tools on top of. At this stage we are planning to support Python, Node.js and R but more languages may be added if there is demand.

Making sure Stencila v2 is well tested, fast, secure, and accessible, is important. Here's what where doing towards that:

At this stage, documentation for v2 is mainly reference material, much of it generated:

• Schema
• Formats
• CLI

More reference docs as well as guides and tutorial will be added over the coming months. We will be bootstrapping the publishing of all docs (i.e. to use Stencila itself to publish HTML pages) and expect to have an initial published set in.

Although v2 is in early stages of development, and functionality may be limited or buggy, we are releasing alpha versions of the Stencila CLI and SDKs. Doing so allows us to get early feedback and monitor what impact the addition of features has on build times and distribution sizes.

To install the latest release download stencila-<version>-x86_64-pc-windows-msvc.zip from the latest release and place it somewhere on your PATH.

To install the latest release in /usr/local/bin,

curl -LsSf https://stencila.io/install.sh | bash

To install a specific version, append -s vX.X.X. Or, if you'd prefer to do it manually, download stencila-<version>-x86_64-apple-darwin.tar.gz from the one of the releases and then,

tar xvf stencila-*.tar.gz
cd stencila-*/
sudo mv -f stencila /usr/local/bin # or wherever you prefer

To install the latest release in ~/.local/bin/,

curl -LsSf https://stencila.io/install.sh | bash

To install a specific version, append -s vX.X.X. Or, if you'd prefer to do it manually, download stencila-<version>-x86_64-unknown-linux-gnu.tar.gz from the one of the releases and then,

tar xvf stencila-*.tar.gz
mv -f stencila ~/.local/bin/ # or wherever you prefer

The CLI is also available in a Docker image you can pull from the Github Container Registry,

docker pull stencila/stencila

and use locally like this for example,

docker run -it --rm -v "$PWD":/work -w /work --network host stencila/stencila --help

The same image is also published to the Github Container Registry if you'd prefer to use that,

docker pull ghcr.io/stencila/stencila

Use your favorite package manager to install Stencila's SDK for Python:

python -m pip install stencila

[!NOTE] If you encounter problems with the above command, you may need to upgrade Pip using pip install --upgrade pip.

Use your favorite package manager to install @stencila/node:

npm install @stencila/node

Use your favorite package manager to install @stencila/types:

npm install @stencila/types

This repository is organized into the following modules. Please see their respective READMEs, where available, for guides to contributing to each.

• schema: YAML files which define the Stencila Schema, an implementation of, and extensions to, schema.org, for programmable documents.

• json: A JSON Schema and JSON LD @context, generated from Stencila Schema, which can be used to validate Stencila documents and transform them to other vocabularies

• rust: Several Rust crates implementing core functionality and a CLI for working with Stencila documents.

• python: A Python package, with classes generated from Stencila Schema and bindings to Rust functions, so you can work with Stencila documents from within Python.

• ts: A package of TypeScript types generated from Stencila Schema so you can create type-safe Stencila documents in the browser, Node.js, Deno etc.

• node: A Node.js package, using the generated TypeScript types and bindings to Rust functions, so you can work with Stencila documents from within Node.js.

• prompts: Prompts used to instruct generative AI models in different contexts and for different purposes.

• docs: Documentation, including reference documentation generated from schema and CLI tool.

• examples: Examples of documents conforming to Stencila Schema, mostly for testing purposes.

• scripts: Scripts used for making releases and during continuous integration.

Several Github Action workflows are used for testing and releases. All products (i.e CLI, Docker image, SKDs) are released at the same time with the same version number. To create and release a new version:

bash scripts/bump-version.sh <VERSION>
git push && git push --tags

Stencila is built on the shoulders of many open source projects. Our sincere thanks to all the maintainers and contributors of those projects for their vision, enthusiasm and dedication. But most of all for all their hard work! The following open source projects in particular have an important role in the current version of Stencila. We sponsor these projects where, and to an extent, possible through GitHub Sponsors and Open Collective.

We wouldn’t be doing this without the support of these forward looking organizations.

Thank you to all our contributors (not just the ones that submitted code!). If you made a contribution but are not listed here please create an issue, or PR, like this.

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