Prettier

You may have stumbled into this error when attempting a Pull Request:

[warn] Code style issues found in 2 files. Forgot to run Prettier?
Error: Process completed with exit code 1.

[warn] Code style issues found in 2 files. Forgot to run Prettier?
Error: Process completed with exit code 1.

The nf-core community aims for a normalized code style. To do so multiple code linting tests are checked and one of them is made with Prettier. It checks that the code style is correctly formatted, it supports many languages (thus many different files) and can be integrated with most editors.

Prefer seeing this in action? There is a bytesize talk on this topic that you can watch: Bytesize 41: Code linting tools

Installation and usage

Command line

One option is to install prettier in your shell environment. To do so, you can use the following command with conda:

conda install prettier

conda install prettier

and afterwards run the command prettier -w . to overwrite the file with a good style or use prettier -c . to only check if your files follow the requirements.

With git as a pre-commit hook

Another solution is to make sure that every time you commit code on a repository, prettier is run on the updated files. To do this, you can use pre-commit. Most nf-core repositories should already come with a .pre-commit-config.yaml config file that instructs pre-commit to run prettier:

- repo: https://github.com/pre-commit/mirrors-prettier
  rev: '' # Use the sha or tag you want to point at
  hooks:
    - id: prettier

- repo: https://github.com/pre-commit/mirrors-prettier
  rev: '' # Use the sha or tag you want to point at
  hooks:
    - id: prettier

To use this, make sure that the pre-commit tool is installed:

pip install pre-commit

pip install pre-commit

and then install the pre-commit hook in the repository working directory:

pre-commit install

pre-commit install

After this, every time you run git commit ... the pre-commit tests will run and fix your formatting.

Editor plugins

You can also install prettier as an extension of your favorite code editor.

In Visual Studio Code

The extension Prettier will do the job for you. It is also available in the pack of useful extension NF-core.

During your pull request

If you already did your PR, you can also add a comment with @nf-core-bot fix linting in your Pull Request and prettier will be used to apply the required fixes to your code.

Black

Black is a tool for formatting Python code in a quick and efficient way. It is designed to be opinionated and enforce consistent standards in whitespace and style.

Most nf-core repositories come with a pyproject.toml configuration file that sets the formatting defaults.

Command line

As with Prettier above, Black can be installed on the command line:

pip install black

pip install black

Then, pass it a path for your files (typically . for the current working directory) and it will search recursively:

black .

black .

In Visual Studio Code

As with Prettier, there is a VSCode plugin that will run Black for you whenever you save a file. See Black Formatter on the VSCode Marketplace for details.