Issues

• Build the training, selection and calibration parsers without importing torch, so their options tab-complete quickly

  openvax/mhcflurry#515 · Filter by author iskandr opened on Nov 3, 2026
  1

• Tab completion (argcomplete) and the shared subtle help colors for the mhcflurry command line

  openvax/mhcflurry#514 · Filter by author iskandr opened on Nov 3, 2026

• Align mhcflurry with the openvax stack baseline (.ix/iteritems and six in downloads-generation, runtime FASTA parser, optional pyarrow, numpy floor, Sphinx docs)

  openvax/mhcflurry#513 · Filter by author iskandr opened on Nov 3, 2026

• Three evaluation commands are reachable under seven CLI names

  openvax/mhcflurry#512 · Filter by author iskandr opened on Nov 3, 2026

• 23 mhcflurry eval/train subcommands are listed in help but cannot run (not even --help) outside a source checkout

  openvax/mhcflurry#511 · Filter by author iskandr opened on Nov 3, 2026

• test_predict_scan_command: test_fasta and test_fasta_percentile fail on master under pandas 3.1 (empty c_flank read back as NaN)

  openvax/mhcflurry#510 · Filter by author iskandr opened on Nov 3, 2026

• Move the per-version RELEASE_NOTES_*.md files out of the repo root

  openvax/mhcflurry#508 · Filter by author iskandr opened on Nov 2, 2026

• Adopt pyproject.toml and test.sh like the sibling openvax repos

  openvax/mhcflurry#507 · Filter by author iskandr opened on Nov 2, 2026

• Split class1_neural_network.py: move Keras-config loading out, break up the 852-line fit()

  openvax/mhcflurry#506 · Filter by author iskandr opened on Nov 2, 2026

• Deprecate the 12 top-level *_command.py wrappers and local_parallelism.py, then remove them

  openvax/mhcflurry#505 · Filter by author iskandr opened on Nov 2, 2026

• Share the remaining duplicated CLI flags (--data, --out, --models-dir, --hyperparameters) and accept --allele/--alleles everywhere

  openvax/mhcflurry#504 · Filter by author iskandr opened on Nov 2, 2026

• ruff.toml is ignored: Ruff reads .ruff.toml, so the #415 lint config never took effect

  openvax/mhcflurry#503 · Filter by author iskandr opened on Nov 2, 2026

• Use Biotite for sequence preparation and unify common scientific dependencies

  openvax/mhcflurry#501 · Filter by author iskandr opened on Oct 26, 2026

• Raise minimum supported pandas to 3.0

  openvax/mhcflurry#499 · Filter by author iskandr opened on Oct 20, 2026
  1

• Restore Docker Hub publishing for MHCflurry 2.3.16

  openvax/mhcflurry#498 · Filter by author iskandr opened on Oct 20, 2026

• Raise minimum supported Python to 3.11

  openvax/mhcflurry#495 · Filter by author iskandr opened on Oct 19, 2026
  1

• Consume frozen Hitlist bundles with task-specific labels and retained training lineage

  openvax/mhcflurry#494 · Filter by author iskandr opened on Oct 15, 2026

• DLA: add release-bound capability metadata and a training-disjoint canine evaluation report

  openvax/mhcflurry#490 · Filter by author iskandr opened on Oct 8, 2026

• Prediction baseline tests use 2.0.0 fixture against default 2.3.0 models

  openvax/mhcflurry#489 · Filter by author iskandr opened on Oct 7, 2026

• Historical MS curation builder uses applymap and fillna(method), removed in pandas 3

  openvax/mhcflurry#488 · Filter by author iskandr opened on Oct 6, 2026

• 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

• 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