All pull requests

Pull requests

• ci: a pull request runs only the nightly-parity legs its files feed (#1387)

  #1391·Montana opened Oct 29, 2026Contributor·

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• parity: start a model's later sensitivity methods after its first (#1386)

  #1390·Montana opened Oct 29, 2026Contributor·

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• bngl: warn when a source's first run starts from a state from_bngl drops (#1366)

  #1388·Montana opened Oct 29, 2026Contributor·

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• network-free: start NFsim and RuleMonkey from the model's species amounts (#1373)

  #1385·Montana opened Oct 29, 2026Contributor·

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• differential: seven reviewed PRs as one merge (#1316-#1320, #1322, #1323)

  #1384·wshlavacek opened Oct 29, 2026Collaborator·

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• ode: stop on the centre of a smooth bump of the clock in a rate law (#1286)

  #1383·Montana opened Oct 29, 2026Contributor·

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• seeds: derive each row's seed from the base, not base + i (#1365)

  #1382·Montana opened Oct 29, 2026Contributor·

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• ssa: count the run's clock from a far t_start, and read held rates inside their interval (#1059)

  #1381·Montana opened Oct 29, 2026Contributor·

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• sensitivity: refuse a parameter that sits on a kink of a rate law (#1332)

  #1380·Montana opened Oct 29, 2026Contributor·

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• ode: warn when the default atol is above species that matter (#1361)

  #1379·Montana opened Oct 29, 2026Contributor·

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• varvol report: Result.species is amount/V_live in a resized compartment, under every method (#1368)

  #1378·Montana opened Oct 29, 2026Contributor·

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• protocol: read simulate/parameter_scan arguments as BNG2.pl does (#1364)

  #1377·Montana opened Oct 29, 2026Contributor·

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• fit gradients: compare data with the target named, species or observables (#1363)

  #1376·Montana opened Oct 29, 2026Contributor·

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• run_batch, run_replicates: meet the stop conditions run() does, row by row (#1369)

  #1375·Montana opened Oct 29, 2026Contributor·

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• run_replicates: start every replicate where the model is; run_batch warns where it does not (#1362)

  #1374·Montana opened Oct 29, 2026Contributor·

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• network-free: hand NFsim and RuleMonkey the parameters the model has changed (#1360)

  #1372·Montana opened Oct 29, 2026Contributor·

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• steady state: the run test retries a NaN f at the clamped state, as the time course does (#1357)

  #1370·Montana opened Oct 28, 2026Contributor·

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• ode: leave a rule-set parameter at its end-of-run value after a compiled warm run (#1358)

  #1359·Montana opened Oct 28, 2026Contributor·

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• sens: read a row ahead from short of the sample, and fire what crosses there (#1276)

  #1356·Montana opened Oct 28, 2026Contributor·

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• events: refuse a fixed fire and a moving one on one instant across two batches (#1277)

  #1353·Montana opened Oct 28, 2026Contributor·

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• tests: pin the steady state the two unmended quotients reach from a jump; warn on another SUNDIALS (#1335)

  #1352·Montana opened Oct 28, 2026Contributor·

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• sbml: refuse a ring of sizes through a value and a jump condition (#1185)

  #1351·Montana opened Oct 28, 2026Contributor·

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• tests: declare what a forced-JIT run cannot pass, so the run is a signal (#1217)

  #1350·Montana opened Oct 28, 2026Contributor·

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• deps: lock antimony 3.2.1 and libroadrunner 2.11.0, with the evaluation (#1288)

  #1349·Montana opened Oct 28, 2026Contributor·

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• codegen: write C for what ExprTk means, or decline before compiling (#1212)

  #1348·Montana opened Oct 28, 2026Contributor·

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