diff --git a/README.md b/README.md index bcc99d4..f1c9fd8 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@

- A package manager for Workflow Description Language files. + A bioinformatics workflow orchestration engine and package manager built on top of the Workflow Description Language (WDL).

Request Feature @@ -41,18 +41,24 @@ ## Guiding Principles -* **Modern, reliable foundation for everyday bioinformatics analysis—written in Rust.** `sprocket` aims to package together a fairly comprehensive set of tools and for developing bioinformatics tasks and workflows using the [Workflow Description Language](http://openwdl.org/). It is built with modern, multi-core systems in mind and written in Rust. -* **WDL specification focused.** We aim to implement the various versions of the [OpenWDL specification](https://github.com/openwdl/wdl) to the letter. In other words, `sprocket` aims to be workflow engine independent. In the future, we plan to make `sprocket` extendable for workflow engine teams. +* Provide a **high-performance** workflow execution engine capable of + orchestrating massive bioinformatics workloads (the stated target is 20,000+ + concurrent jobs). +* Remain **simple and accessible user experience** when complexity isn't + warranted. +* Develop a suite of **modern development tools** that brings bioinformatics + development on par with other modern languages. +* Maintain an **community-focused codebase** that enables a diverse set of + contributors from academic, non-profit, and commercial organizations. +* Build on an **open, domain-tailored standard** to ensure the toolset remains + singularly focused on unencumbered innovation within bioinformatics. ## 📚 Getting Started ### Installation Before you can install `sprocket`, you'll need to install -[Rust](https://www.rust-lang.org/). We recommend using -[rustup](https://rustup.rs/) to accomplish this. - -Once Rust is installed, you can install the latest version of `sprocket` by +[Rust](https://www.rust-lang.org/). We recommend using [rustup](https://rustup.rs/) to accomplish this. Once Rust is installed, you can install the latest version of `sprocket` by running the following command. ```bash diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..45aac9c --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,11 @@ +*.log +*.tgz +.DS_Store +.idea +.temp +.vite_opt_cache +.vscode +dist +cache +node_modules +pnpm-global diff --git a/docs/.vitepress/config.mts b/docs/.vitepress/config.mts new file mode 100644 index 0000000..0e7bdc4 --- /dev/null +++ b/docs/.vitepress/config.mts @@ -0,0 +1,41 @@ +import { defineConfig } from 'vitepress' + +export default defineConfig({ + title: "Sprocket", + description: "A bioinformatics workflow orchestration engine and package manager built on top of the Workflow Description Language (WDL)", + themeConfig: { + nav: [ + { text: 'Documentation', link: '/overview' }, + { + text: "v0.5.0", + items: [ + { + text: 'Changelog', + link: 'https://github.com/stjude-rust-labs/sprocket/blob/main/CHANGELOG.md' + } + ] + } + ], + + sidebar: [ + { + text: 'Getting Started', + items: [ + { text: 'Overview', link: '/overview' }, + { text: 'Installation', link: '/installation' }, + ] + }, + { + text: 'Visual Studio Code Extension', + items: [ + { text: 'Getting Started', link: '/vscode/getting-started' }, + ] + } + ], + + + socialLinks: [ + { icon: 'github', link: 'https://github.com/stjude-rust-labs/sprocket' } + ] + } +}) diff --git a/docs/.vitepress/theme/Layout.vue b/docs/.vitepress/theme/Layout.vue new file mode 100644 index 0000000..b5a3716 --- /dev/null +++ b/docs/.vitepress/theme/Layout.vue @@ -0,0 +1,21 @@ + + + diff --git a/docs/.vitepress/theme/index.ts b/docs/.vitepress/theme/index.ts new file mode 100644 index 0000000..def4cfc --- /dev/null +++ b/docs/.vitepress/theme/index.ts @@ -0,0 +1,17 @@ +// https://vitepress.dev/guide/custom-theme +import { h } from 'vue' +import type { Theme } from 'vitepress' +import DefaultTheme from 'vitepress/theme' +import './style.css' + +export default { + extends: DefaultTheme, + Layout: () => { + return h(DefaultTheme.Layout, null, { + // https://vitepress.dev/guide/extending-default-theme#layout-slots + }) + }, + enhanceApp({ app, router, siteData }) { + // ... + } +} satisfies Theme diff --git a/docs/.vitepress/theme/style.css b/docs/.vitepress/theme/style.css new file mode 100644 index 0000000..e0f3370 --- /dev/null +++ b/docs/.vitepress/theme/style.css @@ -0,0 +1,138 @@ +/** + * Customize default theme styling by overriding CSS variables: + * https://github.com/vuejs/vitepress/blob/main/src/client/theme-default/styles/vars.css + */ + +/** + * Colors + * + * Each colors have exact same color scale system with 3 levels of solid + * colors with different brightness, and 1 soft color. + * + * - `XXX-1`: The most solid color used mainly for colored text. It must + * satisfy the contrast ratio against when used on top of `XXX-soft`. + * + * - `XXX-2`: The color used mainly for hover state of the button. + * + * - `XXX-3`: The color for solid background, such as bg color of the button. + * It must satisfy the contrast ratio with pure white (#ffffff) text on + * top of it. + * + * - `XXX-soft`: The color used for subtle background such as custom container + * or badges. It must satisfy the contrast ratio when putting `XXX-1` colors + * on top of it. + * + * The soft color must be semi transparent alpha channel. This is crucial + * because it allows adding multiple "soft" colors on top of each other + * to create a accent, such as when having inline code block inside + * custom containers. + * + * - `default`: The color used purely for subtle indication without any + * special meanings attched to it such as bg color for menu hover state. + * + * - `brand`: Used for primary brand colors, such as link text, button with + * brand theme, etc. + * + * - `tip`: Used to indicate useful information. The default theme uses the + * brand color for this by default. + * + * - `warning`: Used to indicate warning to the users. Used in custom + * container, badges, etc. + * + * - `danger`: Used to show error, or dangerous message to the users. Used + * in custom container, badges, etc. + * -------------------------------------------------------------------------- */ + + :root { + --vp-c-default-1: var(--vp-c-gray-1); + --vp-c-default-2: var(--vp-c-gray-2); + --vp-c-default-3: var(--vp-c-gray-3); + --vp-c-default-soft: var(--vp-c-gray-soft); + + --vp-c-brand-1: var(--vp-c-indigo-1); + --vp-c-brand-2: var(--vp-c-indigo-2); + --vp-c-brand-3: var(--vp-c-indigo-3); + --vp-c-brand-soft: var(--vp-c-indigo-soft); + + --vp-c-tip-1: var(--vp-c-brand-1); + --vp-c-tip-2: var(--vp-c-brand-2); + --vp-c-tip-3: var(--vp-c-brand-3); + --vp-c-tip-soft: var(--vp-c-brand-soft); + + --vp-c-warning-1: var(--vp-c-yellow-1); + --vp-c-warning-2: var(--vp-c-yellow-2); + --vp-c-warning-3: var(--vp-c-yellow-3); + --vp-c-warning-soft: var(--vp-c-yellow-soft); + + --vp-c-danger-1: var(--vp-c-red-1); + --vp-c-danger-2: var(--vp-c-red-2); + --vp-c-danger-3: var(--vp-c-red-3); + --vp-c-danger-soft: var(--vp-c-red-soft); +} + +/** + * Component: Button + * -------------------------------------------------------------------------- */ + +:root { + --vp-button-brand-border: transparent; + --vp-button-brand-text: var(--vp-c-white); + --vp-button-brand-bg: var(--vp-c-brand-3); + --vp-button-brand-hover-border: transparent; + --vp-button-brand-hover-text: var(--vp-c-white); + --vp-button-brand-hover-bg: var(--vp-c-brand-2); + --vp-button-brand-active-border: transparent; + --vp-button-brand-active-text: var(--vp-c-white); + --vp-button-brand-active-bg: var(--vp-c-brand-1); +} + +/** + * Component: Home + * -------------------------------------------------------------------------- */ + +:root { + --vp-home-hero-name-color: transparent; + --vp-home-hero-name-background: -webkit-linear-gradient( + 120deg, + #bd34fe 30%, + #41d1ff + ); + + --vp-home-hero-image-background-image: linear-gradient( + -45deg, + #bd34fe 50%, + #47caff 50% + ); + --vp-home-hero-image-filter: blur(44px); +} + +@media (min-width: 640px) { + :root { + --vp-home-hero-image-filter: blur(56px); + } +} + +@media (min-width: 960px) { + :root { + --vp-home-hero-image-filter: blur(68px); + } +} + +/** + * Component: Custom Block + * -------------------------------------------------------------------------- */ + +:root { + --vp-custom-block-tip-border: transparent; + --vp-custom-block-tip-text: var(--vp-c-text-1); + --vp-custom-block-tip-bg: var(--vp-c-brand-soft); + --vp-custom-block-tip-code-bg: var(--vp-c-brand-soft); +} + +/** + * Component: Algolia + * -------------------------------------------------------------------------- */ + +.DocSearch { + --docsearch-primary-color: var(--vp-c-brand-1) !important; +} diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..1fc6eac --- /dev/null +++ b/docs/index.md @@ -0,0 +1,14 @@ +--- +layout: home + +hero: + name: "Sprocket" + text: "A bioinformatics workflow orchestration engine and package manager" + actions: + - theme: brand + text: Install Sprocket + link: /installation + - theme: alt + text: Overview + link: /overview +--- diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 0000000..e1eef20 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,48 @@ +# Installation + +If you're looking for the latest stable version of the `sprocket` command line +tool, you can download it from any of the [package managers](#package-managers) +listed below. Otherwise, see the [build from source](#build-from-source) section +on how to obtain and build a copy of the source code. + +## Package Managers + +### Homebrew + +::: warning Notice +While we'd like to make `sprocket` easily installable via [Homebrew], we're +waiting to surpass the [75 star +requirement](https://docs.brew.sh/Acceptable-Formulae#niche-or-self-submitted-stuff) +for Homebrew formulas. If you feel so inclined, help us get there by starring [the +repo](https://github.com/stjude-rust-labs/sprocket)! +::: + +### Crates.io + +Before you can build `sprocket`, you'll need to install [Rust]. We recommend +using [rustup] to accomplish this. Once Rust is installed, you can install the +latest version of `sprocket` by running the following command. + +```bash +cargo install sprocket +``` + +This will pull in the latest published version on [crates.io]. + + +## Build From Source + +Both the source code and the instructions to build the `sprocket` command line +tool are available on GitHub at +[`stjude-rust-labs/sprocket`](https://github.com/stjude-rust-labs/sprocket). + +* The [releases](https://github.com/stjude-rust-labs/sprocket/releases) page + contains all of the official releases for the project. +* If desired, you can install either the latest unpublished version (the code + available on `main`) _or_ any experimental features by checking out the + associated feature branch (`git checkout `). + +[Homebrew]: https://brew.sh/ +[Rust]: https://rust-lang.org/ +[rustup]: https://rustup.rs/ +[crates.io]: https://crates.io/crates/sprocket diff --git a/docs/overview.md b/docs/overview.md new file mode 100644 index 0000000..2d00b3e --- /dev/null +++ b/docs/overview.md @@ -0,0 +1,135 @@ +# Introduction + +::: tip Note +**Sprocket** is current an alpha-phase project. To that effect, +this page serves the purpose of describing what we hope Sprocket _will_ become +rather than what it actually is today. If you're using Sprocket, we encourage +you to follow the project on +[GitHub](https://github.com/stjude-rust-labs/sprocket) to stay up to date on +progress. +::: + +**Sprocket** is an bioinformatics workflow orchestration engine and package +manager built on top of the [Workflow Description Language](https://openwdl.org). The project has multiple high-level goals, including to: + +* Provide a **high-performance** workflow execution engine capable of + orchestrating massive bioinformatics workloads (the stated target is 20,000+ + concurrent jobs). +* Remain **simple and accessible user experience** when complexity isn't warranted. +* Develop a suite of **modern development tools** that brings bioinformatics + development on par with other modern languages (e.g., + [`wdl-lsp`](https://github.com/stjude-rust-labs/wdl/tree/main/wdl-lsp)). +* Maintain an **community-focused codebase** that enables a diverse set of + contributors from academic, non-profit, and commercial organizations. +* Build on an **open, domain-tailored standard** to ensure the toolset remains + singularly focused on unencumbered innovation within bioinformatics. + +Sprocket is written in [Rust](https://www.rust-lang.org/) and enjoys all of the +benefits that come with that choice. It also takes heavy inspiration from Rust +in terms of its approach to building developer tools that are a joy to use. The +code that drives Sprocket is split across the [`wdl`] family of crates, the +[`sprocket`] command line tool, and the [Visual Studio Code extension] +([source](https://github.com/stjude-rust-labs/sprocket-vscode)). + +## Project Goals + +### High-Performance Orchestration Engine + +Most fundamentally, the Sprocket project was created due to the lack of workflow +engines that were powerful enough to orchestrate tens of thousands or hundreds +of thousands of concurrent jobs. Enabling the next generation of large-scale, +open science will always remain the top-level objective for the project. + +### Simple and Accessible + +Sprocket aims to provide a user experience that works from workflow development, +through local testing, and into production with fairly low overhead between +these environments. Our target audience is individuals who endeavor to develop +and deploy bioinformatics workflows with excellence. Generally speaking, this +means **bioinformaticians** and **bioinformatics software engineers** working at +a moderate to large scale, but Sprocket should work reasonably well for many +other users too. In particular, we aim to keep Sprocket as simple as we possibly +can—only introducing complexity when needed to achieve the project's other +stated goals. + +### Modern Development Tools + +A suite of development tools are included alongside the execution engine and +package manager. We believe that, when you _do_ need to dust off your code +editor and write an analysis workflow, that activity should as enjoyable as it +can be. Supporting tools, such as +[linters](https://github.com/stjude-rust-labs/wdl/tree/main/wdl-lint), +formatters, [syntax +highlighting](https://github.com/stjude-rust-labs/sprocket-vscode/blob/main/syntaxes/wdl.tmGrammar.json), +and overall [editor +integration](https://github.com/stjude-rust-labs/wdl/tree/main/wdl-lsp), are +critical to making that vision a reality. + +### Community-Focused Codebase + +Since the beginning, Sprocket has been architected to maximize the potential for +any interested party to effectively contribute to the codebase. This means that +(a) every part of the code is designed to be read and modified by anyone [there +are no "owners" of any code—only "experts" in that code], (b) strict practices, +such as required documentation for public members, a common commit message +style, and `CHANGELOG.md` entries, are enforced for each contribution, and (c) a +comprehensive testing suite and CI/CD integration mean you can tinker with +confidence. + +### Open, Tailored Standard + +Predictability, openness, and ensured longevity are virtues the project attempts +to uphold. Given that the project is ultimately limited by the upstream workflow +language in these regards, an open standard is critical to justify such a +significant amount of community effort. Though many such standards exist, +generality is, in some respects, at odds with creating a tailored experience +within bioinformatics specifically. + +## Goal-Adjacent + +The following are "goal adjacent", meaning that the project values these things +when they do not otherwise inhibit the primary goals. + +* **Providing robust implementations natively for a handful of reference + backends.** Outside of a few core backends that are used to drive the + development of the project, backends are intended to be developed and + maintained by the backend providers themselves. When that isn't possible, + custom backends should be able to be configured by end-users with a moderate + amount of effort. + +### Non-goals + +The following are non-goals of the project. + +* **Supporting multiple workflow languages or standards.** Ironically, workflow + languages are ideally a simple means to an end: to run large-scale + bioinformatics analyses with as little development and operational friction as + possible. We stand unconvinced that there is a strong technical argument for + multiple workflow languages existing within bioinformatics. +* **Supporting a comprehensive list of backends.** As stated above, we aim to + spur a thriving community of independent backend development that is + compatible with Sprocket. More explicitly, comprehensive support for the quirks of + each backend (not to mention the day-to-day maintenance of these backends) represents a + _significant_ time investment that takes away from core development time. +* **Simplicity at all costs.** Though we aim to make things simple when + possible, complexity will be introduced when deemed necessary (this is + particularly true when it comes to internal implementation details). +* **Native Windows compatibility.** For now, Sprocket is intended to be used on + UNIX-like machines. If you're on Windows, we recommend you [install + WSL](https://learn.microsoft.com/en-us/windows/wsl/install) if you haven't + already. + +## Naming + +The name 'Sprocket' was chosen to evoke imagery of a set of independently +developed cogs ("bioinformatics tools") that are composed together to execute a +specific analysis ("workflows"). + +When discussing the command line tool, `sprocket` should be used. When +discussing the project as a whole (and in all other cases), 'Sprocket' should be +used. + +[`wdl`]: https://github.com/stjude-rust-labs/wdl +[`sprocket`]: https://github.com/stjude-rust-labs/sprocket +[Visual Studio Code extension]: + https://marketplace.visualstudio.com/items?itemName=stjude-rust-labs.sprocket-vscode diff --git a/docs/package-lock.json b/docs/package-lock.json new file mode 100644 index 0000000..503cd80 --- /dev/null +++ b/docs/package-lock.json @@ -0,0 +1,1870 @@ +{ + "name": "docs", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "devDependencies": { + "vitepress": "^1.3.2", + "vue": "^3.4.37" + } + }, + "node_modules/@algolia/autocomplete-core": { + "version": "1.9.3", + "resolved": "https://registry.npmjs.org/@algolia/autocomplete-core/-/autocomplete-core-1.9.3.tgz", + "integrity": "sha512-009HdfugtGCdC4JdXUbVJClA0q0zh24yyePn+KUGk3rP7j8FEe/m5Yo/z65gn6nP/cM39PxpzqKrL7A6fP6PPw==", + "dev": true, + "license": "MIT", + "dependencies": { + 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index 0000000..6172273 --- /dev/null +++ b/docs/package.json @@ -0,0 +1,12 @@ +{ + "private": true, + "scripts": { + "docs:dev": "vitepress dev", + "docs:build": "vitepress build", + "docs:preview": "vitepress preview" + }, + "devDependencies": { + "vitepress": "^1.3.2", + "vue": "^3.4.37" + } +} diff --git a/docs/vscode/getting-started.md b/docs/vscode/getting-started.md new file mode 100644 index 0000000..8aba1b8 --- /dev/null +++ b/docs/vscode/getting-started.md @@ -0,0 +1,55 @@ +# Getting Started + +Sprocket provides an extension for the popular [Visual Studio +Code](https://code.visualstudio.com/) editor. You can access the published +version of the extension in the [Visual Studio +Marketplace](https://marketplace.visualstudio.com/items?itemName=stjude-rust-labs.sprocket-vscode). + +This extension has the following features: + +* **Syntax highlighting** using a complete and up-to-date [TextMate grammar]. +* **Code snippets** for common constructs and conventions are included. +* **Document and workspace diagnostics** courtesy of the language server + protocol implementation provided by `sprocket analyzer`. + +The source code for the extension is available to explore, modify, and build +yourself at +[`stjude-rust-labs/sprocket-vscode`](https://github.com/stjude-rust-labs/sprocket-vscode). + +## Installation + +::: warning +The Sprocket Visual Studio Code extension is currently in very early +development. As such, you currently have to download and install the latest +version of the `sprocket` command line tool manually before running the +extension. You may also experience various UX issues, such as needing to +manually restart the Sprocket extension if it crashes. We plan to improve all of +these things as we continue to iterate. +::: + +To use the Sprocket Visual Studio Code extension, you first need to install the +`sprocket` command line tool. You can do so by executing these commands. + +```bash +# (1) Ensure Rust is installed by following the instructions at +# https://rustup.rs. + +# (2) Install the latest version of `sprocket` available. +cargo install --git https://github.com/stjude-rust-labs/sprocket + +# (3) Make sure `sprocket` is accessible from the command line. +sprocket --version +``` + +Next, you can install the extension from the **Extensions** tab in Visual Studio +Code ([guide](https://code.visualstudio.com/docs/editor/extension-marketplace)) +or visit the extension's page in the Visual Studio Marketplace +([link](https://marketplace.visualstudio.com/items?itemName=stjude-rust-labs.sprocket-vscode)). + +## Known Issues + +See the [known +issues](https://github.com/stjude-rust-labs/sprocket-vscode?tab=readme-ov-file#known-issues) +section of the `README.md` for a list of known issues. + +[TextMate grammar]: https://macromates.com/manual/en/language_grammars