pyDeltaRCM.preprocessor.BasePreprocessor

class pyDeltaRCM.preprocessor.BasePreprocessor

Base preprocessor class.

Defines a prelimiary yaml reading, then handles the YAML “meta” tag parsing, model instatiation, and job running.

Subclasses create the high-level command line API and the high-level python API.

Note

You probably do not need to interact with this class direclty. Check out the Python API.

__init__()

Initialize the base preprocessor.

Methods

__init__()

Initialize the base preprocessor.

construct_file_list()

Construct the file list.

open_input_file_to_dict(input_file)

Open an input file and convert it to a dictionary.

run_jobs([DeltaModel])

Run the set of jobs.

Attributes

config_list

Configuration list.

file_list

File list.

job_list

Job list.

_expand_ensemble()

Create ensemble random seeds and put into matrix.

Ensemble expansion is implemented as a special class of matrix/set expansion where:

  • if set specification is used, each set is duplicated the specified number of times, and a seed is added to each set

  • otherwise, the matrix key is set for the seed field of the model

This approach ensures that the runs will have different outcomes, while allowing all other parameters to remain fixed, and supporting additional keys in the matrix/set.

In the non-set expansion implementation, if the matrix does not yet exist (e.g., only ensemble specified), then the matrix is created.

_expand_matrix()

Expand YAML matrix.

Compute the matrix expansion of parameters listed in matrix key.

_open_yaml(input_file)

Safely open, read, and close a yaml file.

Parameters

file (input) – string or path to file

Returns

yaml file, as a Python dict

Return type

yaml_dict

_prelim_config_parsing()

Preliminary configuration parsing.

Extract .yml file (self.input_file) into a dictionary, if provided. This dictionary provides a few keys used throughout the code.

Here, we check whether the file is valid yaml, and place it into a dictionary.

Additionally, set the self._has_matrix flag, which is used in the _expand_matrix().

property config_list

Configuration list.

A list of dict containing the input configurations for jobs constructed by the preprocessor.

construct_file_list()

Construct the file list.

The job list is constructed by expanding the various multi-job specifications. For example, matrix, set, and ensemble yaml files are created in this stage.

property file_list

File list.

A list of Path to input YAML files for jobs constructed by the preprocessor.

property job_list

Job list.

A list of jobs, type _SerialJob or _ParallelJob, from the jobs executed by the preprocessor.

Note

This will be an empty list before run_jobs has been called.

open_input_file_to_dict(input_file)

Open an input file and convert it to a dictionary.

This method is used by subclassing Preprocessors to complete the first import of the yaml configuration.

Parameters

input_file – Path to the input file as string, or Pathlib Path.

Returns

Input file converted to a dictionary.

Return type

yaml_dict

run_jobs(DeltaModel=None)

Run the set of jobs.

This method can be seen as the actual execution stage of the preprocessor. If –parallel is specified in the command line or YAML file, the jobs will run in parallel.