Issues

• develop.sh creates a stray venv when sourced from a subdirectory in zsh

  openvax/mhcflurry#485 · Filter by author iskandr opened on Oct 2, 2026

• Adopt datacache for safe, versioned model and dataset downloads

  openvax/mhcflurry#484 · Filter by author iskandr opened on Oct 2, 2026

• Align docs presentation with mhctools; preserve the current structure

  openvax/mhcflurry#483 · Filter by author iskandr opened on Oct 2, 2026

• Release docs omit environment tag allowlist prerequisite

  openvax/mhcflurry#479 · Filter by author iskandr opened on Sep 30, 2026

• Interrupted archive extraction leaves a partial bundle marked downloaded and blocks retry

  openvax/mhcflurry#476 · Filter by author iskandr opened on Sep 30, 2026

• making ahocorasick-rs accelerator optional

  openvax/mhcflurry#473 · Filter by author smoe opened on Sep 30, 2026

• Avoid repeating the full ML matrix for unchanged Python code in docs/container updates

  openvax/mhcflurry#471 · Filter by author iskandr opened on Sep 29, 2026

• Isolate processing negative-policy and flank-context effects in controlled comparisons

  openvax/mhcflurry#469 · Filter by author iskandr opened on Sep 29, 2026

• Keep Docker Hub and Bioconda aligned with package releases

  openvax/mhcflurry#467 · Filter by author iskandr opened on Sep 29, 2026
  5

• Legacy archive connection timeout aborts CI downloads without retry

  openvax/mhcflurry#462 · Filter by author iskandr opened on Sep 28, 2026
  1

• Completion monitor exits on unreadable status JSON and suppresses later completion notification

  openvax/mhcflurry#446 · Filter by author iskandr opened on Sep 28, 2026
  1

• Historical training-sample traceability is incomplete: documented limitation and Hitlist follow-up

  openvax/mhcflurry#444 · Filter by author iskandr opened on Sep 27, 2026
  1

• Peptide validation logs a warning and then raises the same message

  openvax/mhcflurry#443 · Filter by author iskandr opened on Sep 27, 2026

• Full-retrain continuation aborts when Modal app is already stopped after timeout

  openvax/mhcflurry#442 · Filter by author iskandr opened on Sep 27, 2026

• Processing preparation labels DataFrame candidate rounds as numeric positions

  openvax/mhcflurry#440 · Filter by author iskandr opened on Sep 26, 2026
  1

• Legacy shim tests assert parameter names instead of calling the shims

  openvax/mhcflurry#437 · Filter by author iskandr opened on Sep 21, 2026

• v2-2020 full candidate fails presentation gate; component swaps localize most loss to processing

  openvax/mhcflurry#431 · Filter by author iskandr opened on Sep 16, 2026
  1

• Final comparison consumer must support remote artifact-only provenance

  openvax/mhcflurry#430 · Filter by author iskandr opened on Sep 16, 2026

• mhcflurry-downloads: --verbose is a no-op, --quiet still prints progress, info output formatting

  openvax/mhcflurry#428 · Filter by author iskandr opened on Sep 15, 2026

• --help for train/select/calibrate commands: empty usage line, stray USR1 hint, missing defaults, inapplicable flags

  openvax/mhcflurry#427 · Filter by author iskandr opened on Sep 15, 2026

• Common CLI mistakes (missing file/column/models dir, bad allele/peptide/flag) end in tracebacks

  openvax/mhcflurry#426 · Filter by author iskandr opened on Sep 15, 2026
  1

• Prediction commands print an object repr, a 21-allele warning and DataFrame reprs at default verbosity

  openvax/mhcflurry#425 · Filter by author iskandr opened on Sep 15, 2026

• Prediction CSVs: 17-digit floats, no units, duplicated flank columns, inconsistent predict-scan columns

  openvax/mhcflurry#424 · Filter by author iskandr opened on Sep 15, 2026

• Track removal of dense-vector encoding remnants marked DEPRECATED (scheduled for removal)

  openvax/mhcflurry#419 · Filter by author iskandr opened on Sep 14, 2026

• Remove dead pylint, Read the Docs, flake8/nose/Coveralls, and duplicate conda CI config

  openvax/mhcflurry#418 · Filter by author iskandr opened on Sep 14, 2026