lanl/bngsim

An embeddable simulation library for biochemical reaction networks

Stars: 2
Forks: 3
Open beginner issues: 0
Indexed issues: 44
Avg merge: 6h 17m
Merged PRs (30d): 84

Dominant language: Python
License: No license data
Last GitHub push: Sep 19, 2026
Latest indexed: Sep 18, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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42 open issues indexed

clone() re-evaluates derived parameters in declaration order, contradicting the documented invariant that derived_param_order is the only order any re-evaluation pass may walk Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

lanl/bngsim#626 · Opened Sep 18, 2026
Import SBML Level 3 multi into rule-based form, rather than refusing it Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

lanl/bngsim#614 · Opened Sep 18, 2026
A required="true" SBML package under a non-sbml.org namespace is invisible to the load-time guard, so the core layer still loads silently Open

latent bug low priority

Difficulty 3/5 1-2 days Newbie friendliness 74/100

lanl/bngsim#613 · Opened Sep 18, 2026
_codegen.py's .net parser agrees with neither documented loader: it dies on the unindexed blocks they read, and compiles a silently zero rate from the functions lines they refuse Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

lanl/bngsim#608 · Opened Sep 17, 2026
Rate kernel returns a propensity of 0.0 for an unresolvable rate parameter, silently killing the reaction (extends #580 to src/model.cpp) Open

latent bug low priority

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

lanl/bngsim#589 · Opened Sep 16, 2026
Decompose _build_model_from_sbml_doc(): 4,013 lines in one function makes every phase of SBML construction untestable in isolation Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#588 · Opened Sep 16, 2026
Ship py.typed: the package's annotations are invisible to every downstream consumer Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 92/100

lanl/bngsim#587 · Opened Sep 16, 2026
No docs build gate: docs/conf.py exists but no workflow runs sphinx-build Open

documentation enhancement

Difficulty 1/5 Under an hour Newbie friendliness 88/100

lanl/bngsim#586 · Opened Sep 16, 2026
Coverage is never measured: pytest-cov is declared but no --cov runs in any workflow Open

enhancement

Difficulty 1/5 Under an hour Newbie friendliness 92/100

lanl/bngsim#585 · Opened Sep 16, 2026
CI false-green floors have gone slack: COLLECTED_FLOOR=3480 against 6029 collected, so 42% of the suite could vanish unnoticed Open

bug

Difficulty 3/5 Half a day Newbie friendliness 78/100

lanl/bngsim#584 · Opened Sep 16, 2026
Add a sanitizer + warnings leg to native-tests.yml: 33k lines of pointer-heavy C++ build with no -Wall and no ASan/UBSan anywhere Open

enhancement

Difficulty 3/5 Half a day Newbie friendliness 76/100

lanl/bngsim#583 · Opened Sep 16, 2026
No automated numeric regression gate: the parity goldens and three cross-engine oracles block nothing Open

enhancement

Difficulty 4/5 1-2 days Newbie friendliness 52/100

lanl/bngsim#582 · Opened Sep 16, 2026
A value that cannot be computed must not silently become 0.0: the shared root cause behind #554, #569 and #571 Open

bug

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#580 · 1 comment · Opened Sep 16, 2026
Six independent expression grammars with no cross-backend equivalence test: the shared root cause behind #554, #555, #556, #564, #565 and #573 Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#579 · 2 comments · Opened Sep 16, 2026
NfsimSimulator::run() leaks the whole NFcore::System whenever anything between create_system() and the stepping loop throws Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 75/100

lanl/bngsim#577 · Opened Sep 16, 2026
The state array handed to the JAX Jacobian callback has no owner, so a callback that retains it reads freed CVODE memory Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

lanl/bngsim#576 · Opened Sep 16, 2026
write_sedml_protocol writes uniformRange numberOfPoints as the point count, not count-1, so a scan gains an extra point for every standards-compliant consumer Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 85/100

lanl/bngsim#575 · Opened Sep 16, 2026
Native Jacobian synthesizes log(state) for A^B, bypassing the GH #336 log-of-state deferral and emitting NaN at A=0 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 68/100

lanl/bngsim#574 · Opened Sep 16, 2026
Exponent with an explicit unary plus (`A^+n`) emits `pow(A, )+n` — valid ExprTk, uncompilable C Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

lanl/bngsim#573 · Opened Sep 16, 2026
NfsimSimulator::run()/simulate() segfault on n_points <= 0 — unguarded t_out[0] read and record(0,...) write into a zero-row Result Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 76/100

lanl/bngsim#570 · Opened Sep 16, 2026
SSA "truly stuck" fast-forward drops function/expression columns, silently reporting 0.0 for every remaining output time Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 76/100

lanl/bngsim#569 · Opened Sep 16, 2026
Cold run() records rateOf-bearing functions at t=0 from a stale (zero) derivative buffer, so the initial row of every rateOf expression column is wrong Open

bug

Difficulty 2/5 Half a day Newbie friendliness 90/100

lanl/bngsim#567 · Opened Sep 16, 2026
JAX Jacobian callback: unchecked memcpy of ns*ns doubles from the Python-returned array reads past its end into CVODE's Jacobian Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 74/100

lanl/bngsim#566 · Opened Sep 16, 2026
JAX RHS translator has no mapping for log10(), so jacobian='jax' dies with NameError on a model the ODE backend handles Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

lanl/bngsim#565 · Opened Sep 16, 2026
jacobian='jax' emits jnp.jnp.log for any model using ln(): double substitution in _translate_expr_jax Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

lanl/bngsim#564 · Opened Sep 16, 2026
read_sedml discards the standard SBML XPath @target whenever a dataGenerator carries a human-readable @name Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 74/100

lanl/bngsim#563 · Opened Sep 16, 2026
Named observable/expression access on a squeezed batch Result indexes the time axis, returning silently wrong data Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

lanl/bngsim#560 · Opened Sep 16, 2026
Stop-condition partial Result silently drops sensitivities and seed, and reports a fabricated propensity_backend Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 70/100

lanl/bngsim#559 · Opened Sep 16, 2026
SBML event <delay> referencing a non-constant parameter is constant-folded to the parameter's initial value, so the event fires at the wrong time Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 74/100

lanl/bngsim#558 · Opened Sep 16, 2026
n-ary `max(a,b,c)` / `min(a,b,c)` emit `fmax(a,b,c)` — codegen compile fails with "too many arguments" Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

lanl/bngsim#556 · Opened Sep 16, 2026
Chained power `a^b^c` emits `pow(a, b)pow(, c)` — codegen compile fails on a model the interpreter runs fine Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 82/100

lanl/bngsim#555 · Opened Sep 16, 2026
Committed benchmark reports go stale once the paper repo redirects suite output with --out Open

enhancement question

Difficulty 4/5 3-5 days Newbie friendliness 48/100

lanl/bngsim#551 · Opened Sep 15, 2026
Emitted sensitivity source depends on PYTHONHASHSEED (MODEL0847869198): the same model compiles from two different variants Open

bug low priority

Difficulty 4/5 3-5 days Newbie friendliness 55/100

lanl/bngsim#550 · Opened Sep 15, 2026
Deriving a rate law whose if() condition contains other if() chains spends ~2 s per law in sympy's set-theory rewrite of the condition, and mt_music_sequencer spends its whole derivation budget there Open

enhancement low priority

Difficulty 4/5 3-5 days Newbie friendliness 55/100

lanl/bngsim#540 · Opened Sep 14, 2026
Give every analytical-Jacobian decline a machine-readable kind and record it in the Jacobian characterization harnesses, so a census counts finite-difference models by cause instead of classifying them by hand Open

enhancement low priority

Difficulty 4/5 3-5 days Newbie friendliness 65/100

lanl/bngsim#538 · Opened Sep 14, 2026
SSA/PSA reject every event that carries a delay; add the pending-execution queue the ODE engine already has (the error also cites a plan file that no longer exists) Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#526 · Opened Sep 11, 2026
SBML delay(): support constant-delay DDEs in the ODE engine by method of steps on CVODE (all 54 CSymbolDelay suite cases load_fail today; sensitivities staged) Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 28/100

lanl/bngsim#525 · Opened Sep 11, 2026
Multistart steady-state enumeration: seed the batch solver from initial conditions on the conservation manifold, run Newton without the burst, and cluster the distinct roots with their stability (the in-scope slice of #502) Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#524 · Opened Sep 11, 2026
Refresh vendored NFsim onto upstream master: the Aug 29 – Sep 1 performance campaign and whatever lands after it Open

gated

Difficulty 5/5 Over a week Newbie friendliness 35/100

lanl/bngsim#519 · Opened Sep 11, 2026
Native delayed-reaction / DDE support Open

enhancement gated

Difficulty 5/5 Over a week Newbie friendliness 25/100

lanl/bngsim#505 · 2 comments · Opened Sep 7, 2026
Finite-state projection for low-copy stochastic models Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 30/100

lanl/bngsim#504 · 3 comments · Opened Sep 7, 2026
Numerical continuation and modern bifurcation analysis Open

enhancement high priority

Difficulty 5/5 Over a week Newbie friendliness 25/100

lanl/bngsim#501 · 2 comments · Opened Sep 7, 2026

A short digest of beginner-friendly GitHub issues.