CodeEntropy.config.argparse module

Configuration and CLI argument management for CodeEntropy.

This module provides:

1. A declarative argument specification (ARG_SPECS) used to build an argparse.ArgumentParser.

2. A ConfigResolver that:

   • loads YAML configuration (if present),

   • merges YAML values with CLI values (CLI wins),

   • adjusts logging verbosity,

   • validates a subset of runtime inputs against the trajectory.

Notes:

• Boolean arguments are parsed via str2bool to support YAML/CLI interop and common string forms like “true”/”false”.

class CodeEntropy.config.argparse.ArgSpec(help: str, default: Any = None, type: Any = None, action: str | None = None, nargs: str | None = None)

Bases: object

Argument specification used to build an argparse parser.

Variables:

• help (str) – Help text shown in CLI usage.

• default (Any) – Default value if not provided via CLI or YAML.

• type (Any) – Python type for parsing (e.g., int, float, str, bool). If bool, ConfigResolver.str2bool will be used.

• action (str | None) – Optional argparse action (e.g., “store_true”).

• nargs (str | None) – Optional nargs spec (e.g., “+”).

action: str | None = None

default: Any = None

help: str

nargs: str | None = None

type: Any = None

class CodeEntropy.config.argparse.ConfigResolver(arg_specs: dict[str, ArgSpec] | None = None)

Bases: object

Load, merge, and validate CodeEntropy configuration.

This class provides a consistent interface for:

• YAML config discovery/loading

• CLI parser construction

• merging YAML values with CLI values (CLI wins)

• setting logging verbosity

• validating trajectory-related numeric parameters

build_parser() → ArgumentParser

Build an ArgumentParser from argument specs.

Returns:

An argparse.ArgumentParser configured with all supported flags.

load_config(directory_path: str) → dict[str, Any]

Load the first YAML config file found in a directory.

The current behavior matches your existing workflow: - searches for *.yaml in directory_path, - loads the first match, - returns {"run1": {}} if none found or file is empty/invalid.

Parameters:

directory_path – Directory to search for YAML files.

Returns:

A configuration dictionary.

resolve(args: Namespace, run_config: dict[str, Any] | None) → Namespace

Merge CLI arguments with YAML configuration and adjust logging level.

Merge rule:

• CLI explicitly-provided values take precedence.

• YAML values fill in missing values.

• Defaults fill in anything still unset.

Parameters:

• args – Parsed CLI arguments.

• run_config – Dict of YAML values for a specific run, or None.

Returns:

The mutated argparse.Namespace with merged values.

Raises:

TypeError – If run_config is not a dict or None.

static str2bool(value: Any) → bool

Convert a string or boolean input into a boolean.

Accepts common string representations:

• True values: “true”, “t”, “yes”, “1”

• False values: “false”, “f”, “no”, “0”

If the input is already a boolean, it is returned as-is.

Parameters:

value – Input value to convert.

Returns:

The corresponding boolean.

Raises:

argparse.ArgumentTypeError – If the input cannot be interpreted as a boolean.

validate_inputs(u: Any, args: Namespace) → None

Validate user inputs against sensible runtime constraints.

Parameters:

• u – MDAnalysis universe (or compatible) with a trajectory.

• args – Parsed/merged arguments.

Raises:

ValueError – If a parameter is invalid.