openvax / topiary / 24486800730

88%

master: 90%

Build Type

Pull #136

github

Committed by iskandr

Commit Message

Hardening pass: stale docs, promote xfail → happy-path

## Stale docs cleaned

- docs/cached.md: removed the stale `mode="binding_affinity"` param
  from the from_netmhcpan_stdout example — that kwarg no longer exists.
  Added a note explaining multi-kind behavior for -BA runs.  Removed
  the stale --mhc-cache-netmhcpan-mode row from the CLI flag table.
- docs/api.md: updated the CachedPredictor.from_netmhcpan_stdout entry
  to drop mode= and explain multi-kind output.

## Multi-allele fixtures promoted

The three tests in TestMultiAlleleFixturesKnownBroken are now XPASS
(strict) — they pass because from_netmhcpan_stdout now uses
parse_netmhcpan_to_preds, which handles multi-allele stdout correctly
(the old parse_netmhcpan_stdout crashed on per-allele header lines,
which was mhctools#195).

Renamed the class from TestMultiAlleleFixturesKnownBroken to
TestMultiAlleleFixtures and dropped all xfail markers.  Added a
richer assertion for NetMHCpan 4.1 multi-allele: 3 alleles × 2 kinds
= 6 rows expected.

## Net

0 xfail remaining (were 3 strict xfail, now 0).  1141 tests pass
(up from 1138), lint clean, mkdocs clean.

Pull Request Pull Request #136: CachedPredictor CLI + real NetMHC fixtures + README reorder

Coverage Stats

137 of 154 new or added lines in 3 files covered. (88.96%)

2 existing lines in 1 file now uncovered.

3424 of 3882 relevant lines covered (88.2%)

2.65 hits per line