Issues · lanl/PyBNF

PEtab v2 cannot carry a negative-binomial noise model or the cumulative-to-incident transform: encode the transform with per-period conditions, and add negative-binomial noise as a versioned PyBNF extension

lanl/PyBNF#974 · opened

on Sep 29, 2026

Add an IBIS sampler (job_type = ibis) that updates the exact posterior as observations arrive, absorbs revised observations, and finishes within wall_time_fit

lanl/PyBNF#973 · opened

on Sep 29, 2026

An edition-2 job cannot set ODE solver tolerances for a BNGL model: the model: line refuses rtol:/atol: for .bngl, and the simulations built from experiment: lines never carry them

lanl/PyBNF#971 · opened

on Sep 26, 2026

Check whether the bngsim SBML backend's sensitivity warm-up (#543) serves a stale chain rule when a condition or fitted value writes a derived parameter (lanl/bngsim#708)

lanl/PyBNF#967 · opened

on Sep 25, 2026

A condition that sets the same target twice (perturbations: L = 2, L = 7) is accepted, and the last value silently wins

lanl/PyBNF#964 · opened

on Sep 25, 2026

Follow-up to the PEtab fixes: three valid jobs are refused, by checks added in PRs #940 and #943 and by numbered BNGL action lines that PyBNF does not recognise

lanl/PyBNF#963 · opened

on Sep 25, 2026

Nine loud failures that block a valid job or give the wrong cause: RuleMonkey experiments, one-time-point data, PEtab import and export cases, error messages that hide their reason, and a crash on deeply nested formulas

lanl/PyBNF#962 · opened

on Sep 25, 2026

A noise formula that uses a fixed model parameter (PEtab noiseFormula `0.5 * v3`) passes every load check, then fails each parameter set as it is scored, so the fit either stops with "Your simulations are failing to run" or finishes with an objective of inf

lanl/PyBNF#961 · opened

on Sep 25, 2026

On the bngsim network-free path, a bifurcate() action is skipped without any message, so the simulations after it start from the seed species instead of the state the bifurcate left

lanl/PyBNF#960 · opened

on Sep 25, 2026

With job_type = ms, an ave_norm_sos (column-mean sigma) objective divides each segment by that segment's own data mean, so the segmented stages fit a differently weighted objective from the one the user asked for

lanl/PyBNF#959 · opened

on Sep 25, 2026

Per-row noise values in a measurement_params file are silently ignored when the column's sigma is column_mean, ave_norm_sos or fix_at, because no formula reads them

lanl/PyBNF#958 · opened

on Sep 25, 2026

The PEtab importer ignores a problem.yaml extension marked `required: true`, where the PEtab v2 spec says a tool that does not support it must reject the problem

lanl/PyBNF#957 · opened

on Sep 25, 2026

The PEtab importer accepts a fixed (estimate = false) parameter row whose name matches nothing in the problem, such as the typo V3 for v3, and drops it without a message

lanl/PyBNF#956 · opened

on Sep 25, 2026

A measurement formula that uses log10, log2 or log(x, b) cannot be evaluated, and the fit reports failed simulations instead of naming the formula; a PEtab import can also silently rewrite exp(n*log10(A)) as A^n

lanl/PyBNF#955 · opened

on Sep 25, 2026

The PEtab importer reads a blank time in the experiments table as 0 instead of refusing the problem, so a pre-equilibration whose -inf was left blank is dropped from a dose-response

lanl/PyBNF#954 · opened

on Sep 25, 2026

An experiment with equil_t_end: but no preequilibrate: loads and fits, but the equilibration it asks for is never run

lanl/PyBNF#953 · opened

on Sep 25, 2026

A data file with a negative time is accepted, and the default backend then starts the simulation at that time, so every reading is compared with the model's value too late

lanl/PyBNF#952 · opened

on Sep 25, 2026

Importing a PEtab problem whose measured period starts at a time other than 0 keeps the measurement times unchanged, so every reading is scored at the wrong time

lanl/PyBNF#951 · opened

on Sep 25, 2026

PEtab import simulates a time course under the wrong condition when its condition is also a dose-response point and an unused condition imports under the same name

lanl/PyBNF#950 · opened

on Sep 25, 2026

PEtab import fits an estimated parameter named `flagREF` as the model's `flag` in every experiment, but the PEtab problem applies it only where a condition sets `flag = flagREF`

lanl/PyBNF#949 · opened

on Sep 25, 2026

When a pre-equilibration condition changes a fitted parameter, the PEtab export resets that parameter to its estimate for the measured phase, which PyBNF's own fit does not do, and the importer reads such a reset as no change

lanl/PyBNF#948 · opened

on Sep 25, 2026

On the bngsim backend, a hand-written parameter_scan or bifurcate puts the scanned parameter back afterwards, while BNG2.pl leaves it at the last scanned value, so the same job fits differently on the two backends

lanl/PyBNF#941 · opened

on Sep 25, 2026

bootstrap with mh or am is accepted at load, then crashes with a TypeError when the first replicate starts, after the whole main fit has run

lanl/PyBNF#935 · opened

on Sep 25, 2026

An interrupted or failed hmc run writes no _end histograms or credible intervals, because its error-exit cleanup crashes on hmc's empty trajectory and only the log says so

lanl/PyBNF#934 · opened

on Sep 25, 2026

Resuming a Bayesian fit with -r keeps the samples.txt rows written after the last checkpoint and then samples those iterations again, so the histograms and credible intervals count them twice

lanl/PyBNF#933 · opened

on Sep 25, 2026