drylab env

• Generates a Conda environment YAML file based on a paper's DOI or PDF.

• Uses drylab.config.json by default if no flags are provided.

Usage

drylab env [--pdf ./paper.pdf | --doi <doi>] [--output ./env.yaml]

If drylab.config.json is present in the current directory, --pdf and --doi are optional.

What it does

• Sends a DOI or paper PDF to the DryLab API

• Receives an auto-generated env.yaml file

• Writes the environment file to disk (default: env.yaml)

• Reads from drylab.config.json by default if no flags are passed

Examples

# simplest usage — uses config file if available
drylab env

# generate from local paper
drylab env --pdf ./paper.pdf

# generate from DOI directly
drylab env --doi 10.1038/s41592-020-01005-z

# save output to custom location
drylab env --pdf ./paper.pdf --output ./custom-env.yaml

Options

Flag	Description
--pdf <path>	Path to paper PDF (overrides config)
--doi <doi>	DOI of the paper (overrides config)
--output <path>	Output path for env.yaml (default: env.yaml)

If both --pdf and --doi are passed, --pdf takes precedence. If no input is passed and drylab.config.json is missing, it will error.

Output

By default, this writes:

env.yaml

This file can be used with conda env create -f env.yaml.

Integration with config

If drylab.config.json exists and contains:

{
  "pdfPath": "./paper.pdf",
  "envFileName": "env.yaml"
  //... rest of config file items
}

Then drylab env will auto-use those values. You can override them anytime with CLI flags.