CodeEntropy.config.runtime module

Run orchestration for CodeEntropy.

This module provides the CodeEntropyRunner, which is responsible for: - Creating a new job folder for each run - Loading YAML configuration and merging it with CLI arguments - Setting up logging and displaying a Rich splash screen - Building the MDAnalysis Universe (including optional force merging) - Wiring dependencies and executing the EntropyWorkflow workflow - Providing physical-constants helpers used by entropy calculations

Notes on design: - CodeEntropyRunner focuses on orchestration and simple utilities only. - Computational logic lives in EntropyWorkflow and the level/entropy DAG modules.

class CodeEntropy.config.runtime.CodeEntropyRunner(folder: str)

Bases: object

Coordinate setup and execution of entropy analysis runs.

Responsibilities:

• Bootstrapping: job folder, logging, splash screen

• Configuration: YAML loading + CLI parsing + merge and validation

• Universe creation: MDAnalysis Universe (optionally merging forces)

• Dependency wiring and execution: EntropyWorkflow

• Utilities used by downstream modules: constants and unit conversions

Variables:

folder – Working directory for the current job (e.g., job001).

property DEF_TEMPER: float

Return the default temperature (K) used in the analysis.

property N_AVOGADRO: float

Return Avogadro’s number used in entropy calculations.

change_lambda_units(arg_lambdas: Any) → Any

Unit of lambdas : kJ2 mol-2 A-2 amu-1 change units of lambda to J/s2

static create_job_folder() → str

Create a new job folder (job###) in the current working directory.

The method searches existing folders that start with “job” and picks the next integer suffix. If none exist, it creates job001.

Returns:

The full path to the newly created job folder.

get_KT2J(arg_temper: float) → float

A temperature dependent KT to Joule conversion

load_citation_data() → dict[str, Any] | None

Load CITATION.cff from GitHub.

If the request fails (offline, blocked, etc.), returns None.

Returns:

Parsed CITATION.cff content as a dict, or None if unavailable.

print_args_table(args: Any) → None

Print a Rich table of the run configuration arguments.

Parameters:

args – argparse Namespace or object with attributes for configuration.

read_universe(path: str) → MDAnalysis.Universe

Read a universe from disk (pickle).

Parameters

pathstr

The path to file.

Returns

uMDAnalysis.Universe

A Universe object will all topology, dihedrals,coordinates and force information.

run_entropy_workflow() → None

Run the end-to-end entropy workflow.

This method: - Sets up logging and prints the splash screen - Loads YAML configuration from CWD and parses CLI args - Merges args with YAML per-run config - Optionally submits a master SLURM job and exits - Builds the MDAnalysis Universe (with optional force merging) - Validates user parameters - Constructs dependencies and executes EntropyWorkflow - Saves recorded console output to a log file - Logs run arguments if an error occurs to aid debugging

Raises:

RuntimeError – If the workflow fails for any reason. The original exception is chained to preserve traceback information.

show_splash() → None

Render a Rich splash screen with optional citation metadata.

write_universe(u: MDAnalysis.Universe, name: str = 'default') → str

Write a universe to disk as a pickle.

Parameters

uMDAnalyse.Universe

A Universe object will all topology, dihedrals,coordinates and force information

namestr, Optional. default: ‘default’

The name of file with sub file name .pkl

Returns

namestr

filename of saved universe