Issues

• BLR fit result depends on the number of BLAS threads

  predictive-clinical-neuroscience/PCNtoolkit#595 · Filter by author gdevenyi opened on Oct 6, 2026

• HBR and ZINB results can not be reproduced: no random seed

  predictive-clinical-neuroscience/PCNtoolkit#594 · Filter by author gdevenyi opened on Oct 6, 2026

• transfer and extend ignore savemodel, saveresults, saveplots and evaluate_model

  predictive-clinical-neuroscience/PCNtoolkit#593 · Filter by author gdevenyi opened on Oct 6, 2026

• HBR predict fails with exactly one observation

  predictive-clinical-neuroscience/PCNtoolkit#592 · Filter by author gdevenyi opened on Oct 6, 2026

• SHASHoLikelihood and SHASHo2Likelihood can not be created

  predictive-clinical-neuroscience/PCNtoolkit#591 · Filter by author gdevenyi opened on Oct 6, 2026

• HBR: an unknown batch-effect level gives changing values, not an error

  predictive-clinical-neuroscience/PCNtoolkit#590 · Filter by author gdevenyi opened on Oct 6, 2026

• BLR default fit stops before the optimum (l_bfgs_b_epsilon=0.1)

  predictive-clinical-neuroscience/PCNtoolkit#582 · Filter by author gdevenyi opened on Oct 6, 2026

• Performance: speed up computational code within floating-point noise (tracking)

  predictive-clinical-neuroscience/PCNtoolkit#576 · Filter by author gdevenyi opened on Oct 6, 2026
  4

• Runner on SLURM/Torque: each job reads and rewrites all result CSV files

  predictive-clinical-neuroscience/PCNtoolkit#575 · Filter by author gdevenyi opened on Oct 6, 2026

• HBR: the command line gives a different model than the Python API

  predictive-clinical-neuroscience/PCNtoolkit#574 · Filter by author gdevenyi opened on Oct 6, 2026

• HBR: default Normal model often does not converge on a simple 2-site problem

  predictive-clinical-neuroscience/PCNtoolkit#573 · Filter by author gdevenyi opened on Oct 5, 2026
  1

• BUG: Migration warning is emitted many times when loading an old model

  buggood for new contributors
  predictive-clinical-neuroscience/PCNtoolkit#569 · Filter by author contsili opened on Oct 5, 2026

• Add a CompositeBasisFunction tutorial

  enhancement
  predictive-clinical-neuroscience/PCNtoolkit#567 · Filter by author contsili opened on Oct 5, 2026

• Runner predict jobs: load only their variables, do not pickle the model

  predictive-clinical-neuroscience/PCNtoolkit#564 · Filter by author gdevenyi opened on Oct 2, 2026

• Make runner faster: write per-job result files and merge once at the end

  development
  predictive-clinical-neuroscience/PCNtoolkit#561 · Filter by author contsili opened on Oct 1, 2026
  1

• Longitudinal scores: Yhat not saved, wrong check in ZGainScore

  enhancementGSoC 2026
  predictive-clinical-neuroscience/PCNtoolkit#559 · Filter by author contsili opened on Sep 29, 2026
  2

• Make fetch_models script to load pretrained models

  enhancement
  predictive-clinical-neuroscience/PCNtoolkit#558 · Filter by author contsili opened on Sep 29, 2026

• BLR: fit() fails when hyp0 is a numpy array, including after load()

  bug
  predictive-clinical-neuroscience/PCNtoolkit#557 · Filter by author contsili opened on Sep 28, 2026
  2

  

• Loaded composite basis is refitted on prediction data

  bug
  predictive-clinical-neuroscience/PCNtoolkit#554 · Filter by author contsili opened on Sep 25, 2026
  2

  

• Website documentation on computing a correlation matrix

  GSoC 2026
  predictive-clinical-neuroscience/PCNtoolkit#552 · Filter by author contsili opened on Sep 23, 2026
  3

• Proposal: shard-based model format for voxel-wise save and load

  enhancement
  predictive-clinical-neuroscience/PCNtoolkit#548 · Filter by author gdevenyi opened on Sep 21, 2026
  7

• Standardized 'run report' after fitting a model

  enhancement
  Feature

  predictive-clinical-neuroscience/PCNtoolkit#545 · Filter by author AuguB opened on Sep 19, 2026
  1

• Create subclasses of HBR for MCMC and VI

  enhancement
  predictive-clinical-neuroscience/PCNtoolkit#539 · Filter by author AuguB opened on Sep 14, 2026
  2

• Format the whole codebase with Ruff

  enhancement
  predictive-clinical-neuroscience/PCNtoolkit#533 · Filter by author contsili opened on Sep 3, 2026

• Tidy saving, loading, computing correlation matrix

  GSoC 2026
  predictive-clinical-neuroscience/PCNtoolkit#527 · Filter by author contsili opened on Aug 14, 2026