py-quast: drop vestigial boost pin, fix Python 3.12+ compat, fix bundled minimap2 permissions

[gonzabotmdp]

Summary

Three independent, real issues found installing/using py-quast@5.2.0 for a genome-assembly QC pipeline:

1. Vestigial depends_on("boost@1.56.0"). setup.py never references boost at all (confirmed by grepping the full sdist) -- the pin is most likely inherited by copy-paste from the vendored BamTools/bedtools copies bundled inside quast_libs/ for offline use, but those vendored copies aren't what actually gets built; Spack's own separate bedtools2/glimmer/bwa dependencies (already declared below) are. The pin drags in an ancient (2014) boost version purely for no reason. Dropped it (plus the now-unused Boost.with_default_variants import).

2. distutils removal (Python 3.12+). quast_libs/qconfig.py does from distutils.version import LooseVersion just to check the running Python version falls within quast's own supported range. packaging.version.Version is a drop-in for the comparison usage here (Version(str), <, <=). Added depends_on("py-packaging") and swapped the import.

3. Bundled minimap2 fails for any user but the one who ran spack install. quast_libs/minimap2 is quast's own vendored minimap2 source, compiled lazily on first use via qutils.compile_tool() -- by design for a normal per-user pip install, but under Spack the install tree is only writable by whoever ran the install. Any other user running quast.py -r (reference alignment, the single most common invocation) hits a PermissionError trying to write quast_libs/minimap2/minimap2. Added a @run_after("install") hook that compiles it once during spack install itself (while install-tree write access is still available), so the binary is already built and world-readable/executable before any user touches it.

Testing

Installed py-quast@5.2.0, confirmed quast.py --version works, confirmed the bundled minimap2 binary is present with rwxr-xr-x permissions immediately after install (no lazy-compile step needed), and confirmed a real quast.py -r <reference> run (previously failing with PermissionError for a second, non-owner user) completes.