wdl

Rust crates for working with Workflow Description Language (WDL) documents.
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⚠️ REPOSITORY WARNING

These crates have moved to the stjude/sprocket repository under the crates directory. Please direct all future development, discusssions, and issues there. Thank you!

📚 Getting Started

The wdl family of crates consists of (a) a number of component crates (any crate that is not explicitly wdl) that are developed and versioned independently, and (b) a convenience crate (the wdl crate) that exists to ease syncing compatible component crates versions. Component crates can be enabled using features and are generally re-exported crates without the wdl- (or wdl_) prefix.

This repository contains crates that can be used to work with WDL within your own Rust projects—if you're looking for a command-line tool built on top of these crates instead, you should check out sprocket.

Convenience Crate

Most users should prefer selecting a version of the convenience crate and enabling features as they wish. For example,

cargo add wdl --features grammar

and then

use wdl::grammar;

Component Crate(s)

You are free to include component crates directly. For example,

cargo add wdl_grammar

and then

use wdl_grammar;

Be aware, however, that versions between component crates are explicitly not compatible. In other words, if you choose not to use the convenience crate, it is not simple to derive which crate versions are compatible, and you'll need to manually sync those. We highly recommend using the convenience crate if you intend to use more than one component crate in conjunction.

Minimum Supported Rust Version

The minimum supported Rust version is currently 1.88.0.

There is a CI job that verifies the declared minimum supported version.

If a contributor submits a PR that uses a feature from a newer version of Rust, the contributor is responsible for updating the minimum supported version in the Cargo.toml.

Contributors may update the minimum supported version as-needed to the latest stable release of Rust.

To facilitate the discovery of what the minimum supported version should be, install the cargo-msrv tool:

cargo install cargo-msrv

And run the following command:

cargo msrv --min 1.88.0

If the reported version is newer than the crate's current minimum supported version, an update is required.

🖥️ Development

The WDL specification requires that command scripts are run with the Bash shell, and therefore developing for the wdl crates will require /bin/bash be on your $PATH. Linux and Mac users should not need to do anything special to meet this requirement, but we recommend Windows users fulfill this criteria by installing Git BASH.

There is an additional requirement for development of the wdl-lint crate, which expects the shellcheck binary be available on your $PATH. See instructions for installing ShellCheck here.

To bootstrap a development environment, please use the following commands.

# Clone the repository
git clone [email protected]:stjude-rust-labs/wdl.git
cd wdl

# Build the crate in release mode
cargo build --release

# List out the examples
cargo run --release --example

🚧️ Tests

Before submitting any pull requests, please make sure the code passes the following checks (from the root directory).

# Run the project's tests.
cargo test --all-features

# Run the tests for the examples.
cargo test --examples --all-features

# Ensure the project doesn't have any linting warnings.
cargo clippy --all-features

# Ensure the project passes `cargo fmt`.
# Currently this requires nightly Rust
cargo +nightly fmt --check

# Ensure the docs build.
cargo doc

Note that the wdl-engine tests require a locally running Docker daemon.

🤝 Contributing

Contributions, issues, and feature requests are all welcome! Feel free to read our contributing guide.

📝 License and Legal

This project is licensed as either Apache 2.0 or MIT at your discretion. Additionally, please see the disclaimer that applies to all crates and command line tools made available by St. Jude Rust Labs.

Copyright © 2023-Present St. Jude Children's Research Hospital.