Releases: ICB-DCM/pyABC
Releases · ICB-DCM/pyABC
pyABC 0.10.14
General:
- Speed up parameter handling (30% internal speed-up) (#387)
- Streamline testing via tox and pre-commit hooks, add flake8 config file (#408)
- Update to python 3.9 (#411)
- Extract PEtab bounds and nominal parameters (#416)
- Allow specifying parameter names in density plots (#416)
- Normalize look-ahead sampling by subpopulation ESS (#418, #421)
Documentation:
- Update contribution and issue guidelines (#408)
- Add example on yaml2sbml usage (#416)
- Clean up user docs on parallelization and storage (#419)
Fixes:
- Fix redis for later started workers (#410)
- Fix PEtab parameter scale import, support all PEtab prior distributions (#413)
Database:
pyABC 0.10.13
- Update branch name master -> main in agreement with
https://github.com/github/renaming (#406). - Notebook improvements:
- Add ground truth to noise notebook.
- Rename notebook "quickstart" -> "model_selection".
- Split notebook tests in 2, extend, reduce test matrix (python 3.7).
- Improve output at the beginning and end (e.g. no
end_time
at beginning;
show duration). - Add walltime plots (
plot_total_walltime
,plot_walltime
,
plot_eps_walltime
). - Make sure
ABCSMC.run()
is always properly finished (sampler, history)
by a wrapper (all #401). - Redis sampler with look-ahead mode:
- Fix insufficient logging of look-ahead samples.
- Log all accepted particles.
- Add
plot_lookahead_...
plots for look-ahead mode diagnostics. - Add global figure parameter settings for pyABC (all #405).
pyABC 0.10.12
- Check components for their adaptivity for correct application of look-ahead
mode (#397).
pyABC 0.10.11
- Require pandas >= 1.2.0 for PEtab.
pyABC 0.10.10
- Uniquely identify redis runs via a uuid.
- Secure proper termination of processes for redis and dask (all #338).
- Rework redis sampler, implement a look-ahead mode for pre-defined (#338)
and adaptive algorithms (#374) for near-perfect parallel efficiency. - Allow subprocessing in multiprocessed redis workers (#377).
- Add a static-scheduling redis sampler (#379).
- Check whether epsilon is nan before sampling (#382).
- Remove useless IdentityFakeDistance (#390).
pyABC 0.10.9
0.10.9 (2020-11-28)
- Add stopping criterion for total walltime (#370).
0.10.8 (2020-11-27) (forgotten to release 🙈 )
pyABC 0.10.7
pyABC 0.10.6
pyABC 0.10.5
pyABC 0.10.4
- Refactor
__all__
imports and docs API build (#312). - Fix json export of aggregated adaptive distances (#316).
- Apply additional flake8 checks on code quality (#317).
- Assert model input is of type
pyabc.Parameter
(#318). - Extend noise notebook to estimated noise parameters (#319).
- Implement optional pickling for multicore samplers; add MacOS
pipeline tests (#320).