Issues

Model.load on BioNetGen's XML (the file NFsim reads) returns an empty model with no error: Model(species=0, reactions=0), a run returns a (3, 0) array, and libsbml's error 20101 is ignored

lanl/bngsim#1712 · opened

on Nov 13, 2026

Tracking: bngsim as the simulator an AI agent can use safely. Twelve issues from a first-use pass made the way an agent makes it

lanl/bngsim#1710 · opened

on Nov 13, 2026

A tool server (Model Context Protocol) for assistants with no shell: load, describe, run and check a model, with digests returned and arrays left in files

lanl/bngsim#1709 · opened

on Nov 13, 2026

python -m bngsim does not exist and no console script runs a simulation: a bngsim command to inspect, run and check a model, with JSON on standard output

lanl/bngsim#1708 · opened

on Nov 13, 2026

A one-call check of a run: the README says to confirm a result at a tighter tolerance or with a second engine, and the differential checks that do it are not in the wheel

lanl/bngsim#1707 · opened

on Nov 13, 2026

No model ships in the wheel and none can be loaded by name: Model.load('BIOMD0000000010') answers "Cannot infer a model format ... (suffix 'missing')"

lanl/bngsim#1706 · opened

on Nov 13, 2026

Model has no description of itself: repr is four counts, and compartments, quantity kinds, reactions and the methods the model admits cannot be read from Python

lanl/bngsim#1705 · opened

on Nov 13, 2026

A digest of a Result's values for a caller that cannot look at a plot: repr gives three counts, and a base install can neither tabulate nor save a Result

lanl/bngsim#1704 · opened

on Nov 13, 2026

A Result does not say what its numbers are or how its run went: no quantity kind or units, no method, no applied tolerances, no start state, no notices

lanl/bngsim#1703 · opened

on Nov 13, 2026

bngsim's errors carry their diagnosis and remedy as prose only: no stable code, no remedy field, no dict form, and four of eight common failures are not a BngsimError

lanl/bngsim#1702 · opened

on Nov 13, 2026

A second run() on one model starts from the state the first run ended in, with the clock back at t_span[0], and neither a warning nor the Result says so: A(0) = 10, then 0.0674

lanl/bngsim#1701 · opened

on Nov 13, 2026

The calls an agent tries first fail with a bare AttributeError or TypeError, and two fail inside bngsim: Model(path) raises "'str' object has no attribute 'param_names'"

lanl/bngsim#1700 · opened

on Nov 13, 2026

Documentation an AI agent can read: no llms.txt or one-file guide on Read the Docs, and the only overview in the wheel is a 491-character docstring that points to a README the wheel does not hold

lanl/bngsim#1699 · opened

on Nov 13, 2026

PyPI calls bngsim an 'Embeddable simulation engine for BioNetGen reaction networks' and lists no keywords: nothing a search or an AI agent reads says it simulates SBML and Antimony models

lanl/bngsim#1698 · opened

on Nov 13, 2026

An intracellular engine for multicellular simulators: an ensemble kernel (one network, N cell states), a wider C API, and a PhysiCell add-on

lanl/bngsim#1697 · opened

on Nov 13, 2026

A bngsim simulator class for PySB: in-process ODE, SSA, network-free and sensitivity runs from a PySB model

lanl/bngsim#1696 · opened

on Nov 13, 2026

Before the preprint: follow the installation page and the quickstart on a clean machine for each published wheel platform. Done on macOS arm64 with Python 3.13, with three findings; Linux x86_64, macOS x86_64 and Windows are not done

lanl/bngsim#1694 · opened

on Nov 12, 2026

The guides' Python examples are fragments, and the suite executes 3 of the 101 blocks: run in page order beside a model.net, 32 of the 101 in the 0.17.1 docs run and 69 raise, 49 of them NameError (19 for want of `import bngsim`)

lanl/bngsim#1693 · opened

on Nov 12, 2026

Model.from_bngl's 'no usable BNG2.pl' error, and capabilities()['missing']['bngl'], end with a sentence for developers: 'For the parity_checks/ suite use `uv sync --extra dev --group parity` instead'

lanl/bngsim#1692 · opened

on Nov 12, 2026

The first example on the README, the docs index and the quickstart cannot be run as written after `pip install bngsim`: each loads a model.net the reader does not have, and the README's last line needs pandas, which the base install does not bring

lanl/bngsim#1691 · opened

on Nov 12, 2026

Forward sensitivities need a C compiler on the user's machine, and neither the installation page nor the sensitivities guide says so: on a wheel install with no `cc`, a run with sensitivity_params raises CodegenToolchainError where a plain run works

lanl/bngsim#1690 · opened

on Nov 12, 2026

Tracking: docs, packaging and first use. Six open issues, and five gaps with none, found from the README, the installation page and a bare `pip install bngsim` 0.17.1

lanl/bngsim#1689 · opened

on Nov 12, 2026

run_protocol skips a setConcentration or setParameter placed before the first simulate of an actions block with no generate_network: A(1) = 36.79 for 18.39, with no warning, on the actions file omex_to_net itself writes

lanl/bngsim#1687 · opened

on Nov 12, 2026

write_sedml_protocol writes no listOfDataGenerators and no listOfOutputs: the SED-ML of a net_to_omex(bngl=...) archive names nothing to record, and its five tasks for a two-run protocol are not told apart from the two experiments

lanl/bngsim#1686 · opened

on Nov 12, 2026

bngsim cannot replay an archive it wrote when an action names a species with a component, a state or a compartment: run_protocol on the archive's SBML raises "the network has no species 'L(r)'", and omex_to_net's actions abort in BNG2.pl

lanl/bngsim#1685 · opened

on Nov 12, 2026

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Issues

Model.load on BioNetGen's XML (the file NFsim reads) returns an empty model with no error: Model(species=0, reactions=0), a run returns a (3, 0) array, and libsbml's error 20101 is ignored

Tracking: bngsim as the simulator an AI agent can use safely. Twelve issues from a first-use pass made the way an agent makes it

A tool server (Model Context Protocol) for assistants with no shell: load, describe, run and check a model, with digests returned and arrays left in files

python -m bngsim does not exist and no console script runs a simulation: a bngsim command to inspect, run and check a model, with JSON on standard output

A one-call check of a run: the README says to confirm a result at a tighter tolerance or with a second engine, and the differential checks that do it are not in the wheel

No model ships in the wheel and none can be loaded by name: Model.load('BIOMD0000000010') answers "Cannot infer a model format ... (suffix 'missing')"

Model has no description of itself: repr is four counts, and compartments, quantity kinds, reactions and the methods the model admits cannot be read from Python

A digest of a Result's values for a caller that cannot look at a plot: repr gives three counts, and a base install can neither tabulate nor save a Result

A Result does not say what its numbers are or how its run went: no quantity kind or units, no method, no applied tolerances, no start state, no notices

bngsim's errors carry their diagnosis and remedy as prose only: no stable code, no remedy field, no dict form, and four of eight common failures are not a BngsimError

A second run() on one model starts from the state the first run ended in, with the clock back at t_span[0], and neither a warning nor the Result says so: A(0) = 10, then 0.0674

The calls an agent tries first fail with a bare AttributeError or TypeError, and two fail inside bngsim: Model(path) raises "'str' object has no attribute 'param_names'"

Documentation an AI agent can read: no llms.txt or one-file guide on Read the Docs, and the only overview in the wheel is a 491-character docstring that points to a README the wheel does not hold

PyPI calls bngsim an 'Embeddable simulation engine for BioNetGen reaction networks' and lists no keywords: nothing a search or an AI agent reads says it simulates SBML and Antimony models

An intracellular engine for multicellular simulators: an ensemble kernel (one network, N cell states), a wider C API, and a PhysiCell add-on

A bngsim simulator class for PySB: in-process ODE, SSA, network-free and sensitivity runs from a PySB model

Before the preprint: follow the installation page and the quickstart on a clean machine for each published wheel platform. Done on macOS arm64 with Python 3.13, with three findings; Linux x86_64, macOS x86_64 and Windows are not done

The guides' Python examples are fragments, and the suite executes 3 of the 101 blocks: run in page order beside a model.net, 32 of the 101 in the 0.17.1 docs run and 69 raise, 49 of them NameError (19 for want of `import bngsim`)

Model.from_bngl's 'no usable BNG2.pl' error, and capabilities()['missing']['bngl'], end with a sentence for developers: 'For the parity_checks/ suite use `uv sync --extra dev --group parity` instead'

The first example on the README, the docs index and the quickstart cannot be run as written after `pip install bngsim`: each loads a model.net the reader does not have, and the README's last line needs pandas, which the base install does not bring

Forward sensitivities need a C compiler on the user's machine, and neither the installation page nor the sensitivities guide says so: on a wheel install with no `cc`, a run with sensitivity_params raises CodegenToolchainError where a plain run works

Tracking: docs, packaging and first use. Six open issues, and five gaps with none, found from the README, the installation page and a bare `pip install bngsim` 0.17.1

run_protocol skips a setConcentration or setParameter placed before the first simulate of an actions block with no generate_network: A(1) = 36.79 for 18.39, with no warning, on the actions file omex_to_net itself writes

write_sedml_protocol writes no listOfDataGenerators and no listOfOutputs: the SED-ML of a net_to_omex(bngl=...) archive names nothing to record, and its five tasks for a two-run protocol are not told apart from the two experiments

bngsim cannot replay an archive it wrote when an action names a species with a component, a state or a compartment: run_protocol on the archive's SBML raises "the network has no species 'L(r)'", and omex_to_net's actions abort in BNG2.pl