gnomad_toolbox.scripts

Script to copy Jupyter notebooks and configurations to a user-specified directory.

Module Functions

gnomad_toolbox.scripts.load_config([config_file])	Load configuration from a JSON file.
gnomad_toolbox.scripts.save_config(config[, ...])	Save configuration to a JSON file.
gnomad_toolbox.scripts.set_config(key, value)	Add a key-value pair to the configuration file, supporting nested keys.
gnomad_toolbox.scripts.get_config(key[, ...])	Retrieve a value from the configuration file by key, supporting nested keys.
gnomad_toolbox.scripts.copy_directory(src, dest)	Copy a directory to a destination.
gnomad_toolbox.scripts.copy_notebooks(...[, ...])	Copy Jupyter notebooks and configurations to a user-specified directory.
gnomad_toolbox.scripts.run_jupyter_cli()	Launch Jupyter Lab or Notebook using the configured directory.

Script to copy Jupyter notebooks and configurations to a user-specified directory.

gnomad_toolbox.scripts.load_config(config_file='/home/runner/.gnomad_toolbox_config.json')

Load configuration from a JSON file.

Parameters:

config_file (str) – Path to the configuration file.

Return type:

dict

Returns:

The configuration dictionary.

gnomad_toolbox.scripts.save_config(config, config_file='/home/runner/.gnomad_toolbox_config.json')

Save configuration to a JSON file.

Parameters:

• config (dict) – The configuration dictionary.

• config_file (str) – Path to the configuration file.

Return type:

None

Returns:

None.

gnomad_toolbox.scripts.set_config(key, value, config_file='/home/runner/.gnomad_toolbox_config.json')

Add a key-value pair to the configuration file, supporting nested keys.

Parameters:

• key (str) – The key to save, with nesting indicated by periods.

• value (Union[str, dict]) – The value to save.

• config_file (str) – Path to the configuration file.

Return type:

None

Returns:

None.

gnomad_toolbox.scripts.get_config(key, config_file='/home/runner/.gnomad_toolbox_config.json')

Retrieve a value from the configuration file by key, supporting nested keys.

Parameters:

• key (str) – The key to retrieve, with nesting indicated by periods.

• config_file (str) – Path to the configuration file.

Return type:

Optional[str]

Returns:

The value associated with the key, or None if the key doesn’t exist.

gnomad_toolbox.scripts.copy_directory(src, dest, overwrite=False)

Copy a directory to a destination.

Parameters:

• src (str) – Source directory.

• dest (str) – Destination directory.

• overwrite (bool) – Whether to overwrite if the destination exists.

Return type:

None

Returns:

None.

gnomad_toolbox.scripts.copy_notebooks(destination, overwrite=False)

Copy Jupyter notebooks and configurations to a user-specified directory.

Parameters:

• destination (str) – The target directory.

• overwrite (bool) – Whether to overwrite existing files/directories.

Return type:

None

Returns:

None.

gnomad_toolbox.scripts.run_jupyter_cli()

Launch Jupyter Lab or Notebook using the configured directory.

Return type:

None

Returns:

None.