feat: Enhance config validation (Resolves #33) - #42

src/specimen/util/config_validator.py:97

• This “Clean up legacy 'USER' keyword” block is unreachable because the earlier if value is None or value == "_USER_" or value == "USER": ... continue already handles all value == "USER" cases. Removing this dead code will simplify control flow and prevent confusion when modifying the placeholder logic later.

        # Clean up legacy 'USER' keyword
        if value == "USER":
            logger.warning(
                f"Deprecated 'USER' keyword found at '{current_path}'. Using default: {rule.default}"
            )
            value = rule.default

src/specimen/util/config_validator.py:105

• bool is a subclass of int in Python, so this numeric bounds check will also run for boolean values (and expected_type=int would accept booleans). Excluding bool here avoids surprising validation behavior when the schema contains integer fields and the YAML provides true/false.

        if isinstance(value, (int, float)):

src/specimen/util/config_validator.py:90

• The legacy placeholder for “required user input” in this repo is __USER__ (see specimen/util/set_up.py:309 and the example YAMLs), but this validator only checks for _USER_. That means __USER__ would pass through as a normal string and likely reach downstream code. Also, when value == "_USER_" and the field is required, the code raises before the deprecation log/specific message, so users won’t see the intended guidance. Consider normalizing both __USER__ and _USER_ up front and always raising a consistent error for them.

This issue also appears in the following locations of the same file:

• line 91
• line 105

        # 1. Check Required fields (Replaces _USER_ and USER logic)
        if value is None or value == "_USER_" or value == "USER":
            if rule.required:
                raise ConfigValidationError(
                    f"Missing required configuration parameter: '{current_path}'"

src/specimen/util/init.py:3

• The PR description states that this PR “replac[es] the previously verbose YAML traversal” for config validation, but the current entrypoints still call specimen.util.set_up.validate_config (e.g. specimen/hqtb/workflow.py:49, specimen/cmpb/workflow.py:48-49). Exporting config_validator from specimen.util doesn’t switch any existing code over, so Issue #33 isn’t fully resolved by these changes alone.

__all__ = ["util", "set_up", "config_validator"]

from . import util, set_up, config_validator