Contributing

We’d love to accept community contributions, especially to add new tools to:

• Janis-bioinformatics
• Janis-unix
• Or other tool suites!

There are a couple of best standard we’d love to follow when contributing to Janis.

Documentation

There are a couple of ways that can you provide documentation to your tools:

Tool and workflow inputs

There’s a doc parameter that can be filled when creating a ToolInput or Workflow.input that is used to drive the Janis documentation and table of inputs for a tool.

ToolInput(
	"inputId", 
	DataType, 
	doc="<Explain what this input does>", 
	**kwargs
)

w = WorkflowBuilder()
w.input(
	"inputId", 
	DataType, 
	doc="<Explain what this input does>", 
	**kwargs
)

Tool documentation

This differs if you’re using a class based tool, or using of the builders.

Class based

A CommandTool and Workflow both have a bind_metadata method that you can return a ToolMetadata or WorkflowMetadata from respectively.

CommandTool:

def bind_metadata(self):  
	from datetime import date  

	return ToolMetadata(
		contributors=["<Add your name here>"],
		dateCreated=date(2018, 12, 24),
		dateUpdated=date(2020),
		institution="<who produces the tool>",
		keywords=["list", "of", "keywords"],
		documentationUrl="<url to original documentation>",
		short_documentation="Short subtitle of tool",
		documentation="""Extensive tool documentation here """.strip(),
		doi=None,
		citation=None,
  )

Workflow

def bind_metadata(self):  
	from datetime import date  

	return ToolMetadata(
		contributors=["<Add your name here>"],
		dateCreated=date(2018, 12, 24),
		dateUpdated=date(2020),
		institution="<who produces the tool>",
		keywords=["list", "of", "keywords"],
		documentationUrl="<url to original documentation>",
		short_documentation="Short subtitle of tool",
		documentation="""Extensive tool documentation here """.strip(),
		doi=None,
		citation=None,
  ).   

Builders

The builders have a parameter called metadata which takes a ToolMetadata or WorkflowMetadata for a CommandToolBuilder or WorkflowBuilder respectively:

Example

wf = WorkflowBuilder(
    "workflowId",
    **kwargs,
    metadata=WorkflowMetadata(
        **meta_kwargs
    ),
)

# OR

clt = CommandTooBuilder(
    "commandtoolId",
    **kwargs,
    metadata=ToolMetadata(
        **meta_kwargs
    ),
)

Code formatting

Janis uses the opinionated Black Python code formatter. It ensures that there are no personal opinions about how to format code, and anecdotally saves a lot of mental power from not thinking about this.

The projects include a pyproject.toml , and it’s a git pre-commit dependency.

Installation

You can install Black (+ pre-commit) inside a janis-* directory with:

pip3 install -r requirements.txt

You can manually run black with:

black {source_file_or_directory}

Editor integration

See more: https://github.com/psf/black

We’d recommend configuring Black to run on save within your editor with the following guides:

• PyCharm / IntelliJ IDEA

• Vim

• VSCode + Python extension, simplified instructions:

  • Install the [extension]

  • Within VSCode, go to your settings.json

    • Command + Shift + P
    • (type) Preferences: Open Settings (JSON)

  • Add the following lines:

        "python.formatting.provider": "black",
        "editor.formatOnSave": true