Replace `print()` statements with `warnings.warn()` in production code

[suhaan-24]

Several functions in the codebase use print() to notify users of non-critical conditions (e.g. cohort too small, SNP filter returned no results). This bypasses Python's standard warnings module, meaning users cannot filter or suppress these messages programmatically.
Affected locations:

• hapclust.py — lines 405, 712
• dipclust.py — lines 543, 610
• sample_metadata.py — line 1468
  Each print(...) should be replaced with warnings.warn(...) using stacklevel=2 so the warning points to the caller.