Snakefmt extension for Visual Studio Code

A Visual Studio Code extension that formats Snakemake code using Snakefmt. The extension ships with snakefmt=2.0.3. The bundled snakefmt is used if no path to the executable or interpreter is specified.

Features

This extensions uses snakefmt to format your Snakemake code. It can also supports formatting Python code. It automatically checks if your Snakemake file is formatted according to snakefmt. You can disable this feature by setting snakefmt.disableLinting = true. This feature is disabled per default for Python files and can be enabled with snakefmt.enablePythonLinting = true.

Files or code chunks can be formatted on-demand by right clicking in the document and selecting "Format Document", or by using the associated keyboard shortcut (usually Ctrl+⇧+F on Windows, Ctrl+⇧+I on Linux, and ⇧+⌥+F on macOS).

To automatically format a file on save, add the following to your vscode settings.json file:

{
    "editor.formatOnSave": true
}

Settings

snakefmt.args

Custom arguments passed to snakefmt. Each argument should be provided as a separate string in the array.

Default value: [] Type: string[]

"snakefmt.args": ["--config", "<file>"]

snakefmt.disableLinting

Disable linting of Snakemake files.

Default value: false Type: boolean

"snakefmt.disableLinting": true

snakefmt.enablePythonLinting

Enable linting of Python files with snakefmt.

Default value: false Type: boolean

"snakefmt.enablePythonLinting": true

snakefmt.path

Path or command to be used by the extension to run snakefmt. Accepts an array of a single or multiple strings. If passing a command, each argument should be provided as a separate string in the array.

Note: Using this option may slow down server response time.

Default value: [] Type: string[]

// Use a custom binary
"snakefmt.path": ["~/global_env/snakefmt"]

// Use conda
"snakefmt.path": ["conda", "run", "-n", "fmt_env", "--no-capture-output", "snakefmt"]

snakefmt.interpreter

Path to a Python executable that will be used to launch the formatter server and any subprocess. When set to [], the extension will use the path to the selected Python interpreter.

Default value: [] Type: string[]

"snakefmt.interpreter": ["/path/to/python"]

snakefmt.importStrategy

Defines where snakefmt is imported from. This setting may be ignored if snakefmt.path is set.

• "useBundled": Always use the bundled version of snakefmt.
• "fromEnvironment": Use snakefmt from the environment, falling back to the bundled version if not available.

Default value: "useBundled" Type: "useBundled" | "fromEnvironment"

"snakefmt.importStrategy": "fromEnvironment"

snakefmt.showNotifications

Controls when notifications are shown by this extension.

• "off": All notifications are turned off, any errors or warnings are still available in the logs.
• "onError": Notifications are shown only in the case of an error.
• "onWarning": Notifications are shown for errors and warnings.
• "always": Notifications are shown for anything that the server chooses to show.

Default value: "off" Type: "off" | "onError" | "onWarning" | "always"

"snakefmt.showNotifications": "onError"

snakefmt.trace.server

Controls the level of trace logging for communication between VS Code and the Snakefmt language server. Useful when filing bug reports.

• "off": No trace logging.
• "messages": Log messages sent between client and server.
• "verbose": Log messages and their content.

Default value: "off" Type: "off" | "messages" | "verbose"

"snakefmt.trace.server": "verbose"

Deprecated settings

snakefmt.config

Deprecated: Use snakefmt.args with ["--config", "<file>"] instead.

Snakefmt config file.

Default value: "" Type: string

snakefmt.executable

Deprecated: Use snakefmt.path instead.

Alias for snakefmt.path.

Default value: "" Type: string

Commands

Logging

From the Command Palette (View > Command Palette ...), run the Developer: Set Log Level... command. Select Snakefmt from the Extension logs group. Then select the log level you want to set.

Alternatively, you can set the snakefmt.trace.server setting to verbose to get more detailed logs from the Snakefmt server. This can be helpful when filing bug reports.

To open the logs, click on the language status icon ({}) on the bottom right of the Status bar, next to the Python language mode. Locate the Snakefmt entry and select Open logs.

Source code

Available on github: https://github.com/tfehlmann/vscode-snakefmt-provider

Release Notes

0.11.3

• Update bundled snakefmt to 2.0.3
• Update CI and release tooling to uv 0.11.24

0.11.2

• Update bundled snakefmt to 2.0.2
• Fix Renovate PR creation so dependency updates are no longer blocked behind pending PR-only checks
• Override vulnerable npm transitive dependencies and update ujson to resolve Dependabot alerts

0.11.1

• Update npm and Python test dependencies to resolve Dependabot security alerts

0.11.0

• Update bundled snakefmt to 2.0.0
• Breaking: snakefmt now formats shell blocks in rules by default. Users can opt out with --no-format-shell via snakefmt.args or format_shell = false in pyproject.toml
• Add bundled shfmt-py support required by snakefmt shell formatting
• Update bundled black to 26.5.1

0.10.0

• Update bundled snakefmt to 1.0.0
• Breaking: snakefmt now automatically reorders rule directives by default. Users can opt out with --no-sort via snakefmt.args
• Update bundled black to 26.3.1

0.9.0

• Update bundled snakefmt to 0.11.4
• Require Python 3.11+ (previously 3.8)
• Add automated publishing to VS Code Marketplace and Open VSX
• Update CI to Node 20, Python 3.11+, latest GitHub Action versions
• Migrate to ESLint 10 flat config
• Update all npm and Python dependencies

0.8.0

• Update bundled snakefmt to 0.10.2

0.7.0 (preview release)

• Update bundled snakefmt to 0.8.5
• Fix "There is no formatter for Snakemake files installed" error
• Remove logging setting, switch to VSCode integrated log level

0.6.0

• Update bundled snakefmt to 0.8.1

0.5.0 (preview release)

• Add support for Python 3.11
• Update bundled snakefmt to 0.7.0

0.4.0

• Integrate 0.3.0 preview release features
• Improve linting messages

0.3.0 (preview release)

• Support Python formatting
• Add better linting messages and error highlighting

0.2.0

• Add linting support
• Support for multi-root workspace
• Add bundled snakefmt

0.1.0

Initial release