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v1.9.0: unify on mhc_species=, deprecate human_only (#73)

* v1.9.0: unify on mhc_species=, deprecate human_only (#72)

Replace the two parallel species-filter paths in scanner.scan with a
single parametrized API:

  scan(mhc_species="Homo sapiens",    # new default, matches old behavior
       species_fallback=True,          # new: host/species text fallback
       human_only=None,                # deprecated, emits warning)

Behavior matrix:
- mhc_species="Homo sapiens", species_fallback=True (default) — same as
  old human_only=True: strict mhcgnomes match on MHC restriction with
  host/species text fallback when mhcgnomes can't parse.
- mhc_species="Homo sapiens", species_fallback=False — strict, no
  fallback. New capability; drops rows with unparseable restrictions.
- mhc_species="Mus musculus", species_fallback=True — same logic
  parametrized to mouse (e.g. bare "H-2 class I" + host=Mus musculus
  now matches).  Also new — old mhc_species= path was strict-only.
- mhc_species=None — no species filter.

Deprecation:
- human_only= still works.  Emits DeprecationWarning pointing at
  mhc_species.  human_only=True → mhc_species="Homo sapiens";
  human_only=False → mhc_species=None.  If both are passed,
  mhc_species wins silently.  Slated for removal in hitlist 2.0.

Internal callers migrated:
- builder.py: human_only=False → mhc_species=None.
- report.py: human_only=True → mhc_species="Homo sapiens"; also
  removed a stale hla_only=True that would TypeError if the call
  ever fired (pre-existing bug, caught incidentally).

Tests: +8 new (deprecation warning on True/False, default path stays
warning-free, explicit mhc_species= path stays warning-free,
"both passed" still warns once for human_only, four-way cross
product of mhc_species x species_fallback as a kwarg acceptance
smoke test).  199 passed.

Docstring updated; vestigial "When set, hla_only is ignored" line
removed.

Closes #72.

* Remove accidentally-committed .coverage artifact

1219 of 2794 relevant lines covered (43.63%)

0.44 hits per line

Coverage Regressions

Lines Coverage ∆ File
61
27.85
 4.67% scanner.py
1
0.0
 0.0% report.py
Jobs
ID Job ID Ran Files Coverage
1 24606779853.1 19
43.63
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Source Files on build 24606779853