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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
enhancementNew feature or requestNew feature or requestStatus: Open.#971 In lanl/PyBNF;Edition 2: refuse hand-written BNGL actions other than generate_network and setOption, at config load and at PEtab import, so the conf alone defines the protocol
enhancementNew feature or requestNew feature or requestStatus: Open.#969 In lanl/PyBNF;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)
exploratoryExploratory/optional: an open question or proposal to evaluate before committing to buildExploratory/optional: an open question or proposal to evaluate before committing to buildStatus: Open.#967 In lanl/PyBNF;A condition that sets the same target twice (perturbations: L = 2, L = 7) is accepted, and the last value silently wins
bugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#964 In lanl/PyBNF;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
bugSomething isn't workingSomething isn't workinghigh priorityUrgent or important workUrgent or important workStatus: Open.#963 In lanl/PyBNF;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
bugSomething isn't workingSomething isn't workingStatus: Open.#962 In lanl/PyBNF;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 infbugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#961 In lanl/PyBNF;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
bugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#960 In lanl/PyBNF;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
bugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#958 In lanl/PyBNF;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 problembugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#957 In lanl/PyBNF;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
bugSomething isn't workingSomething isn't workingsilent-incorrectnessCompletes without error, but the reported result is wrong, incomplete, or missingCompletes without error, but the reported result is wrong, incomplete, or missingStatus: Open.#956 In lanl/PyBNF;