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, with CLI values taking precedence,

   • fills missing defaults,

   • auto-detects conda/mamba settings for HPC runs,

   • 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, such as int, float, str, or bool.

• action (str | None) – Optional argparse action, such as “store_true”.

• nargs (str | None) – Optional nargs spec, such as “+”.

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.

build_parser() → ArgumentParser

Build an ArgumentParser from the argument specs.

Returns:

Configured argparse.ArgumentParser.

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

Load the first YAML config file found in a directory.

Parameters:

directory_path – Directory to search for YAML files.

Returns:

Configuration dictionary.

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

Merge CLI arguments with YAML configuration and fill defaults.

Merge rule:

• CLI explicitly provided values take precedence.

• YAML values fill in values not provided by CLI.

• Defaults fill in anything still unset.

• HPC conda/mamba settings are auto-detected if missing.

Parameters:

• args – Parsed CLI arguments.

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

Returns:

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.

Parameters:

value – Input value to convert.

Returns:

Corresponding boolean value.

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 object with a trajectory.

• args – Parsed and merged arguments.

Raises:

ValueError – If a parameter is invalid.