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PEtab-aligned config redesign: explicit experiments/conditions/data (retire filename→suffix linkage)

enhancementNew feature or requestNew feature or request

Status: Open.

#423 In lanl/PyBNF;

· wshlavacek opened on Jun 16, 2026

PEtab v2 exporter: conditions/experiments chunk (mutants→conditions, suffix→experiments, dose-response)

Status: Open.

#422 In lanl/PyBNF;

· wshlavacek opened on Jun 15, 2026

Test suite is not xdist-safe at high worker counts (shared relative pybnf_output/ dir races)

Status: Open.

#421 In lanl/PyBNF;

· wshlavacek opened on Jun 15, 2026

Native BNGL PEtab linter: a petab Model adapter for BNGL (full petablint oracle), toward upstream libpetab-python (PEtab#436)

Status: Open.

#420 In lanl/PyBNF;

· wshlavacek opened on Jun 15, 2026

Mean/median prediction-centering for every noise model (complete the location axis; neg_bin median)

Status: Open.

#419 In lanl/PyBNF;

· wshlavacek opened on Jun 14, 2026

Generalize the _Cum cumulative→incident transform: decouple it from neg_bin, make it explicit

Status: Open.

#418 In lanl/PyBNF;

· wshlavacek opened on Jun 14, 2026

Native .conf grammar for bounded/truncated normal_var, laplace_var (and log forms)

Status: Open.

#417 In lanl/PyBNF;

· wshlavacek opened on Jun 14, 2026

Dockerfile is broken/outdated: runtime install requires bngsim (no Linux wheel) and bundles only legacy BNG2.pl

bugSomething isn't workingSomething isn't working

Status: Open.

#414 In lanl/PyBNF;

· wshlavacek opened on Jun 7, 2026

Separate the initialization distribution from the prior (PyBNF conflates objective prior and start-point sampling)

Status: Open.

#413 In lanl/PyBNF;

· wshlavacek opened on Jun 7, 2026

Centralize the θ↔u scale transform: ~12 algorithm sites inline base-10 (np.log10/10**/exp10) instead of routing through Scale (ADR-0010 drift)

Status: Open.

#412 In lanl/PyBNF;

· wshlavacek opened on Jun 7, 2026

Truncated/bounded priors: allow reflecting bounds on unbounded-support families (Normal/Laplace/log-*) (PEtab v2 prerequisite)

Status: Open.

#411 In lanl/PyBNF;

· wshlavacek opened on Jun 7, 2026

PEtab v2 problem importer — the 'two-adapter' proof (first step: parameters table → FreeParameter/Prior)

Status: Open.

#407 In lanl/PyBNF;

· wshlavacek opened on Jun 6, 2026