Audit fixes

Fixes the following audit errors:

lp_solve:
 * Define method "numpy_include_dir" in the class body, not at the top-level

Doesn't fix the following false positives:

lp_solve:
 * Don't need to interpolate "version" with inreplace

beagle:
 * Head-only (no stable download)

seqtk:
 * Head-only (no stable download)