Cobra

New features

- Add support for the OSQP and COIN-OR CBC solvers (946)

Fixes

- Fix the `Reaction.compartments` attribute not updating after metabolite changes (1055)
- Lots of syntax, annotation, and docstring fixes (1058, 1059, 1060, 1063,
1065, 1066, 1076, 1077, 1080)
- Multiprocessing on windows now sends data to processes via a pickle file which
should speed up any multiprocessing initialization (1070)
- Upgrade optlang and fix some tolerance issues (1011)
- Enable Python 3.9 (1082)

Documentation

- Document boundary reactions (1038)
- Documentation is now built again on each release (1047)
- Clarify pfba in the documentation (1049)

Other

- COBRApy source code releases are now deposited on Zenodo which provides a
citeable DOI (1061)
- COBRApy creates automatic releases to BioSimulators (1064)
- Fix deployment of releases to the website (1068)
- Improve the `pyproject.toml` config (1067)

Backwards incompatible changes

- Remove some particular `cobra.Reaction.lower_bound` and `.upper_bound`
behaviour that has been deprecated for a long time.

Other

* Update libSBML dependency to `python-libsbml==5.19.0`.
* Docstring and style changes.

New features

* There is a new function inspired by
[cameo](https://github.com/biosustain/cameo/) that can load models directly
from [BiGG](http://bigg.ucsd.edu/) or
[BioModels](https://www.ebi.ac.uk/biomodels/) and by default will cache them
locally (995), for example,

py
from cobra.io import load_model

ecoli = load_model("iML1515")
ylipo = load_model("MODEL1604280017")


Fixes

* Over a series of pull requests, synchon has been modernizing parts of the
codebase for Python 3.6+ (993, 999, 1000, 1003)
* Upgrade the dependency python-libsbml-experimental to 5.18.3