This fork was created to facilitate refactoring aimed at making algorithm implementations more modular.
active 2024-01-21 → 2026-08-10 (UTC)
Activity over time
Daily event counts in the loaded window
Line chart, 933 days from 2024-01-21 to 2026-08-10. Pushes: 218 total, peak 12 in a day. Pull requests: 9 total, peak 2 in a day. Issues: 40 total, peak 4 in a day. Comments: 15 total, peak 3 in a day. Stars: 0 total, peak 0 in a day.
- Pushes
- Pull requests
- Issues
- Comments
- Stars
Stars, PRs, issues and forks are under-captured in the later part of this window. GH Archive progressively stopped capturing non-push events during 2026 — −95% or worse by the end of the window. Every series here except Pushes fades for that reason, so a decline above reflects the archive, not this repository. Pushes stay reliable throughout, so read them, and the contributor counts derived from them, as the real signal. Data health has the measurements.
Top contributors
Pushes, PRs, issues, reviews and comments — stars and forks excluded, so this is contribution rather than popularity
| Contributor | Contributions | Pushes | PRs | Comments |
|---|---|---|---|---|
| wshlavacek | 268 | 212 | 6 | 13 |
| efm46 | 6 | 6 | 0 | 0 |
| LifeWorks | 5 | 0 | 1 | 1 |
| akutuva21 | 2 | 0 | 1 | 1 |
| dynova | 1 | 0 | 1 | 0 |
Recent activity
Latest issues, pull requests and releases
- Issue comment#548wshlavacek2026-08-07 19:41petab1to2_preserve_scale drops the log estimation scale when the v1 parameter table has a prior column
- Issue#548wshlavacek2026-08-07 19:26petab1to2_preserve_scale drops the log estimation scale when the v1 parameter table has a prior column
- Issue#547wshlavacek2026-08-07 17:49After a pre-equilibration, the scored phase runs the pre-equilibration condition's parameters, so every dose in a dose-response simulates identically (Brannmark, Weber)
- Issue#547wshlavacek2026-08-07 16:51After a pre-equilibration, the scored phase runs the pre-equilibration condition's parameters, so every dose in a dose-response simulates identically (Brannmark, Weber)
- Pull request#489wshlavacek2026-07-17 23:42
- Issue#437wshlavacek2026-07-02 21:57Track readiness of our BNGL PEtab linter (BnglModel adapter)
- Issue#468wshlavacek2026-07-02 21:36Profile likelihood: tests and user-guide documentation
- Issue#467wshlavacek2026-07-02 21:04Profile likelihood: outputs (plots + summary table, resumable) and cross-parameter parallelization
- Issue#462wshlavacek2026-06-30 00:49Gradient optimizers: finish #386 deliverable 6 — convergence-vs-baseline test + becker smoke test
- Issue#462wshlavacek2026-06-30 00:49Gradient optimizers: finish #386 deliverable 6 — convergence-vs-baseline test + becker smoke test
- Issue#461wshlavacek2026-06-30 00:35Gradient path: add a discrete-events pre-flight gate (refuse cleanly, don't fail mid-run)
- Issue#425wshlavacek2026-06-28 03:22Design a first-class surface for analytical / user-defined objective functions (generalize `direct_pass`)
- Issue#417wshlavacek2026-06-21 06:29Native .conf grammar for bounded/truncated normal_var, laplace_var (and log forms)
- Issue#430wshlavacek2026-06-21 02:54PEtab v2 interop: multi-model problems (more than one model per problem, import + export)
- Issue#429wshlavacek2026-06-21 00:48PEtab v2 export: emit SBML models as SBML (per-model language; a job may mix BNGL + SBML)
- Issue#410wshlavacek2026-06-07 06:57Per-observable noise models: lift the single global `objfunc` to per-observable selection (PEtab v2 prerequisite)
- Issue#406wshlavacek2026-06-06 03:16Robustify Powell's line search (bracketing + golden-section/Brent) for curved valleys
- Issue#405wshlavacek2026-06-06 01:29Add a rotated/correlated Gaussian analytical target to validate Powell's conjugate-direction update (and CMA-ES rotation)
- Issue#403wshlavacek2026-06-06 01:04Add Powell's method as a second fit-refinement method (complement to Simplex)
- Issue#402wshlavacek2026-06-05 04:07Migrate parse.py scalar/list token lists into the Pydantic schema (single coercion source)
- Pull request#397wshlavacek2026-05-26 07:29
- Issue#391wshlavacek2026-05-19 05:13NFsim path over-binds ~10%: bound mean ~55 vs exact master-equation 50.08
- Issue#389wshlavacek2026-05-16 19:11BngsimNfModel: free parameters embedded in arithmetic expressions are silently zeroed
- Issue#387wshlavacek2026-05-15 05:10Add example notebooks demonstrating end-to-end fitting workflows
- Issue#386wshlavacek2026-05-15 04:56Pluggable optimizer protocol with scipy wrappers for gradient-based methods
Totals cover only the window loaded into ClickHouse and count events, not GitHub's lifetime totals — 0 stars here means stars gained during the window, not the repo's star count.