CLI Reference

Overview

The momapy command-line interface (CLI) allows you to render molecular maps directly from the command line without writing Python code. It supports SBGN-ML and CellDesigner map formats and can output to various image formats (SVG, PDF, PNG, JPEG, WebP).

Synopsis

momapy render <input_file_path>... -o <output_file_path> [options]

Subcommand: `render`

Renders one or more molecular maps to an image file.

Arguments

Argument	Description
`input_file_path`	One or more input file paths (SBGN-ML or CellDesigner format)

Options

Option	Short	Description
`--output-file-path`	`-o`	Output file path (required)
`--renderer`	`-r`	Renderer to use: `svg-native`, `skia`, `cairo` (auto-detected if omitted)
`--format`	`-f`	Output format: `svg`, `pdf`, `png`, `jpeg`, `webp` (inferred from extension if omitted)
`--multi-pages`	`-m`	Render one map per page (for multi-input PDF)
`--to-top-left`	`-t`	Move elements to the top-left of the page
`--style-sheet-file-path`	`-s`	Style sheet file path (can be repeated for multiple style sheets)

Renderer/Format Compatibility

Format	svg-native	skia	cairo
SVG	✓	✓	✓
PDF	✗	✓	✓
PNG	✗	✓	✓
JPEG	✗	✓	✗
WebP	✗	✓	✗

Note: The svg-native renderer is always available and has no external dependencies. The skia and cairo renderers require optional dependencies to be installed.

Examples

Basic rendering

Render an SBGN-ML file to SVG:

momapy render my_map.sbgn -o output.svg

Render to PDF

Render to PDF (requires skia or cairo renderer):

momapy render my_map.sbgn -o output.pdf

Specify renderer explicitly

Force the use of a specific renderer:

momapy render my_map.sbgn -o output.pdf -r cairo

Multiple input files

Render multiple maps into a single multi-page PDF:

momapy render map1.sbgn map2.sbgn map3.sbgn -o combined.pdf -m

Apply style sheets

Apply one or more CSS style sheets to customize the appearance:

momapy render my_map.sbgn -o output.svg -s custom_styles.css
momapy render my_map.sbgn -o output.svg -s base.css -s overrides.css

Adjust layout position

Move all elements to the top-left corner of the output:

momapy render my_map.sbgn -o output.svg -t

Installation

The CLI is installed automatically when you install momapy:

1	`pip install momapy`

To use PDF, PNG, JPEG, or WebP output formats, install the optional rendering dependencies:

pip install momapy[skia]  # For skia renderer
pip install momapy[cairo]  # For cairo renderer
pip install momapy[all]    # For all renderers

Getting Help

Display help information:

momapy --help
momapy render --help