Clui
Command-line interface for snailz.
Each subcommand takes options --output (output file path), --params (parameter file), and --seed (random number seed) along with command-specific parameters. If a parameter file is given, it is read first and additional parameters override its values. If a parameter file is not given, all other parameters are required.
cli()
Command-line interface for snailz.
Source code in src/snailz/clui.py
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all(params, output)
Generate all data files.
Source code in src/snailz/clui.py
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assays(baseline=None, delay=None, degrade=None, mutant=None, noise=None, oops=None, output=None, params=None, people=None, plate_size=None, seed=None, specimens=None)
Generate assays for specimens.
Source code in src/snailz/clui.py
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convert(input, kind, output)
Convert JSON data to CSV format.
Converts grid, specimens, or assays data from JSON to CSV format. If output is not specified, writes to standard output.
Source code in src/snailz/clui.py
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database(assays, output, people, specimens)
Create a SQLite database from CSV files.
Source code in src/snailz/clui.py
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grid(depth=None, output=None, params=None, seed=None, size=None)
Generate grid.
Source code in src/snailz/clui.py
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init(output=None, overwrite=False)
Initialize parameter files for snailz.
Creates JSON parameter files in the specified directory (or current directory if not specified). Creates the directory if it doesn't exist.
By default, will not overwrite existing files unless --overwrite is specified.
Source code in src/snailz/clui.py
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mangle(seed, dir, people)
Modify assay files by reassigning people.
This command takes assay files in a directory and reassigns the people who performed the assays using the provided seed for random number generation.
Source code in src/snailz/clui.py
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people(locale=None, number=None, output=None, params=None, seed=None)
Generate people.
Source code in src/snailz/clui.py
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specimens(grid=None, length=None, max_mass=None, min_mass=None, mut_scale=None, mutations=None, number=None, output=None, params=None, seed=None, start_date=None, end_date=None)
Generate specimens.
Source code in src/snailz/clui.py
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_get_params(caller, param_class, supplied, params_file, **converters)
Get and check parameter values.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
caller
|
str
|
Name of the calling function for error messages |
required |
param_class
|
Type[BaseModelType]
|
Pydantic parameter class |
required |
supplied
|
tuple[tuple[str, object], ...]
|
Tuple of (name, value) pairs for CLI parameters |
required |
params_file
|
str | Path | None
|
Path to JSON parameter file, or None |
required |
converters
|
Callable
|
Optional converters for specific parameter values |
{}
|
Returns:
Type | Description |
---|---|
BaseModelType
|
An instance of the param_class with validated parameters |
Source code in src/snailz/clui.py
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_write_content(output, content)
Write content to standard output or a file.
Source code in src/snailz/clui.py
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