openvax / vaxrank / 25144038521
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Linker grammar ((BASE)N / GnSm / AnY) + BioNTech-canonical default (#251)

* Linker grammar: (BASE)N / GnSm / AnY + BioNTech-canonical default + #247 plan

Compositional names parsed at lookup time (vaxrank.vaccine_library.get_linker):

- (BASE)N — repeat any base linker N times. Example: '(G2S)3' → 'GGSGGSGGS'.
  2A linkers (codon-frozen, positional skipping mechanism) are rejected
  with an explicit error.
- GnSm — n glycines + 1 serine, that unit repeated m times. Example: 'G6S'
  → 'GGGGGGS', 'G2S5' → 'GGSGGSGGSGGSGGS'.
- AnY — n alanines + tyrosine. Example: 'A3Y' → 'AAAY'. The synthesized
  Linker.citation explicitly notes that AAY (= A2Y) is the canonical form
  (Velders 2001) and longer A-stretches are mechanistic extrapolations
  without independent primary-literature validation.

Repeat counts are capped at 100 to prevent accidental megasequences.

CLI:
- --mrna-linker / --peptide-linker now use a type=callable validator
  (_linker_arg) that calls get_linker. Drops the static argparse choices=
  list since arbitrary compositional forms are now valid.

Default mRNA linker switched from G4S3 (15 aa) to G4S2 (10 aa) to match
BioNTech FixVac / iNeST canonical (Sahin et al. Nature 2017,
doi:10.1038/nature23003; Kreiter et al. J Immunol 180:309, 2008,
doi:10.4049/jimmunol.180.1.309). G4S3 stays in the library for callers
that explicitly want it.

Tests added (+9):
  - (BASE)N parsing for G2S and AAY
  - 2A repeat rejection
  - count-out-of-range rejection (zero, > 100)
  - GnSm parsing for G6S and G2S5; static G4S3 still wins lookup
  - AnY parsing for A3Y / A4Y / A8Y
  - AnY citation flags the extrapolation for n != 2
  - (G2S)3 and G2S3 produce the same amino_acids
  - unknown compositional form raises with the available-linkers hint

Issue #247 updated with the concrete junction-aware swap algorithm
discussed in the design conversation: per-junction independent linker
swap with mhcflurry-presentation rank scoring, default A2Y +
candidates A3Y/A... (continued)
Source Files on build 25144038521
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