parse_arcade_simulations#

Workflow for parsing ARCADE simulations into tidy data.

Working location structure:

(name)
├── data
│   ├── data.CELLS
│   │   └── (name)_(key)_(seed).CELLS.tar.xz
│   └── data.LOCATIONS
│       └── (name)_(key)_(seed).LOCATIONS.tar.xz
└── results
    └── (name)_(key)_(seed).csv

Data from data.CELLS and data.LOCATIONS are parsed into results. If the results file already exists, additional parsing will merge results based on cell id and tick.

Flows

run_flow

Main parse arcade simulations flow.

run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#: Main parse arcade simulations flow.

Configs

`ContextConfig`	Context configuration for parse arcade simulations flow.
`ParametersConfig`	Parameter configuration for parse arcade simulations flow.
`SeriesConfig`	Series configuration for parse arcade simulations flow.

class ContextConfig[source]#

Context configuration for parse arcade simulations flow.

working_location: str#: Location for input and output files (local path or S3 bucket).

manifest_location: str#: Location of manifest file (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for parse arcade simulations flow.

regions: list[str]#: List of subcellular regions to parse.

include_filters: list[str]#: List of Unix filename patterns for files to include in parsing.

exclude_filters: list[str]#: List of Unix filename patterns for files to exclude from parsing.

class SeriesConfig[source]#

Series configuration for parse arcade simulations flow.

name: str#: Name of the simulation series.

manifest_key: str#: Key for manifest file.

extensions: list[str]#: List of file extensions in complete run.