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Script Nodes

A PoPy script file is in YAML format, which consists of nested dictionaries that form a tree structure.

Each node of the tree is either:-

  • a dictionary (dict) with sub nodes
  • or a leave node

A leave node has to be one of the script node types listed below.

auto
The word “auto”, indicating a preference for default behaviour.
bool
A boolean: “true”/”yes”/”y”/”1” or “False”/”no”/”n”/”0”
dict

A dictionary of unspecified structure - the user chooses the keys.

Many of the elements of a script file are known as dictionaries (also known as mappings or associative arrays). These are key:value pairs that can be written as follows using curly brackets:-

my_dictionary1: { key1: value1, key2: value2 }

or alternatively using spacing:-

my_dictionary2:
    key1: value1
    key2: value2

Whichever you use is a matter of convenience and space.

dict_record
A dictionary with a pre-determined structure (i.e. key names and corresponding types)
float
Any number
input_file
The path to a file that already exists. (An error occurs if it does not.)
input_file_as_glob
A pattern (e.g. *.csv) that has only a single match. (An error occurs if there are multiple matching filenames.)
input_files_as_glob
A pattern (e.g. "*.csv") that has at least one match. (An error occurs only if there are no matching filenames.)
input_folder
The path to a folder that already exists. (An error occurs if it does not.)
int
An integer (whole number)
list
A list of values of unspecified type.
list_of
A list of one or more strings taken from the list of options in brackets.
list_record
A list
none
The word “none”, indicating a file that does not exist.
one_of
A string, limited to one of the options given in brackets.
one_of_record
One from a selection of dict_records
output_file
The path to a file that may not yet exist (in contrast to input_file).
output_folder
The path to a folder that may not yet exist (in contrast to input_folder).
pseudocode
verbatim sections of the script file accept Python code with extra PoPy syntax added. For example special variable names such as f[X], r[X] etc. We refer to this code as ‘pseudocode’. Pseudocode is automatically translated into runnable Python functions that are executed by PoPy to process your script.
repeat_dict_record
One or more of a selection of dict_records
repeat_verb_record
One or more of a selection of verbatim records
star
The “*” character, shorthand for “all possibilities”.
str
A string.
verbatim
Several blocks in the script file (namely MODEL_PARAMS, STATES, DERIVATIVES and PREDICTIONS) are reserved for pseudocode of a relatively unstructured kind. This is translated into executable code.
Plot Types
Script File Outputs
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