Pyabc

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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:

* Add database migration scheme based on alembic (419)
* Store proposal ids, increment database version to 0 (419)

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* 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).

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* Check components for their adaptivity for correct application of look-ahead
mode (397).

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* Require pandas >= 1.2.0 for PEtab.

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* 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).

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* Add stopping criterion for total walltime (370).