Describe the bug

In PositionalEncoding.forward(), the sequence length check uses assert instead of raising a proper exception. Assertions are stripped when Python is run with the -O (optimize) flag, meaning this validation silently disappears in production.

Relevant code:

• pyaptamer/aptatrans/layers/_encoder.py, line 81

assert x.shape[1] <= self.max_len, (
    f"Input sequence length {x.shape[1]} exceeds maximum length {self.max_len}."
)

Expected behavior

Use an explicit ValueError instead of assert:

if x.shape[1] > self.max_len:
    raise ValueError(
        f"Input sequence length {x.shape[1]} exceeds maximum length {self.max_len}."
    )

This ensures the check always runs regardless of Python optimization flags.

Versions

0.1.0a1