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Editor Integration

If your favourite editor is not listed here, we would love to receive a PR with how to include it.

Unless otherwise specified, all instructions assume you have snakefmt installed already.

Table of Contents

PyCharm/JetBrains IDEA

  1. Locate the path to your snakefmt executable.
# linux and macOS
$ which snakefmt
/usr/local/bin/snakefmt  # just an example

# windows
$ where snakefmt
%LocalAppData%\Programs\Python\Python36-32\Scripts\snakefmt.exe  # just an example
  1. Open External tools in PyCharm/IntelliJ IDEA

  • On macOS: PyCharm -> Preferences -> Tools -> External Tools

  • On Windows / Linux / BSD: File -> Settings -> Tools -> External Tools

  1. Click the + icon to add a new external tool with the following values:

    • Name: Snakefmt
    • Description: The uncompromising Snakemake code formatter
    • Program: result of which/where snakefmt from step 1
    • Arguments: "$FilePath$"

  2. Format the currently opened file by selecting Tools -> External Tools -> Snakefmt.

    • Alternatively, you can set a keyboard shortcut by navigating to Preferences/Settings -> Keymap -> External Tools -> External Tools - Snakefmt. We use Alt+s

  3. Optionally, run snakefmt on every file save:

    1. Make sure you have the File Watchers plugin installed.
    2. Go to Preferences or Settings -> Tools -> File Watchers and click + to add a new watcher:
      • Name: Snakefmt
      • File type: Python
      • Scope: Project Files
      • Program: result of which/where snakefmt from step 1
      • Arguments: $FilePath$
      • Output paths to refresh: $FilePath$
      • Working directory: $ProjectFileDir$
    • Uncheck "Auto-save edited files to trigger the watcher" in Advanced Options

Visual Studio Code

  1. Install the extension within Visual Studio (VS) Code by visiting the Snakefmt extension page and following the instructions at the top of the page.

  2. Follow the directions under the extension's Details page. Pay attention in particular to the Requirements section to provide a path to your snakefmt executable (if it isn't already in your PATH environment variable).

  3. See VS Code's documentation on Formatting for more instructions on how to apply formatting within the IDE.

Vim

Credit: plugin inspired by black

  1. Install the plugin.

    Recommended way is via a plugin manager, eg vim-plug:

    Plug 'snakemake/snakefmt'

    or Vundle:

    Plugin 'snakemake/snakefmt'

  2. That's it! Run :Snakefmt to format a buffer, and :SnakefmtVersion for version info.

    If you do not run Vim 7.0+ built with Python3.6+ support, or you have not installed snakefmt, those commands will complain.

  3. If you want to format your file automatically when saving it, write this in your vimrc:

    au BufNewFile,BufRead Snakefile,*.smk set filetype=snakemake
au FileType snakemake autocmd BufWritePre <buffer> execute ':Snakefmt'

  4. If you additionally want syntax highlighting on your snakemake files, install snakemake's syntax highlighter!

Troubleshooting

Under certain circumstances, import errors can occur when using a virtual environment due to Black dependency imports. See the Black Vim integration docs for more details and a potential solution.

emacs

The format-all package supports use of snakefmt out of the box provided snakefmt is available on the exec-path; it should suffice to have snakefmt available on your PATH.

snakefmt can be invoked in a buffer using format-all in the usual way with format-all-buffer, and also by adding a hook to your dotfile to enable the format-all-mode minor mode. If you are using snakemake-mode already, you can do this with:

(add-hook `snakemake-mode-hook #`format-all-mode)

See the format-all repo for more documentation.