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Snakefmt extension for Visual Studio Code

A Visual Studio Code extension that formats Snakemake code using Snakefmt. The extension ships with snakefmt=0.10.2. 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

Settings Default Description
snakefmt.args [] Custom arguments passed to snakefmt. E.g "snakefmt.args" = ["--config", "<file>"]
snakefmt.config "" Snakefmt config file. Deprecated. Use snakefmt.args instead. Usage "snakefmt.config" = "<file>"
snakefmt.disableLinting false Disable linting of snakemake files.
snakefmt.enablePythonLinting false Enable linting of python files with snakefmt.
snakefmt.path [] Setting to provide custom snakefmt executable. Example 1: ["~/global_env/snakefmt"] Example 2: ["conda", "run", "-n", "fmt_env", "--no-capture-output", "snakefmt"]
snakefmt.executable "" Alias for snakefmt.path. Deprecated. Use snakefmt.path instead.
snakefmt.interpreter [] Path to a python interpreter to use to run the formatter server.
snakefmt.importStrategy useBundled Setting to choose where to load snakefmt from. useBundled picks snakefmt bundled with the extension. fromEnvironment uses snakefmt available in the environment.
snakefmt.showNotification off Setting to control when a notification is shown.

Commands

Command Description
Snakefmt: Restart server Force re-start the format server.

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

0.8.0

  • 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