chore(deps): bump cobra from 0.21.0 to 0.22.1 in /requirements

[dependabot[bot]]

Bumps cobra from 0.21.0 to 0.22.1.

Release notes

Sourced from cobra's releases.

0.22.1

Release notes for cobrapy 0.22.1

Fixes

• Fix an old bug with double gene deletion that was not knocking-out combinations (#1103).
• Lots of syntax, annotation, and docstring fixes (#1081, #1083, #1084, #1085, #1086, #1088, #1090, #1091, #1092, #1093, #1094, #1095, #1096).

Deprecated features

• find_gene_knockout_reactions is deprecated.

0.22.0

Release notes for cobrapy 0.22.0

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.

Test Dispatch ref fix

... (truncated)

Commits

• cb5ff0b Bump version: 0.22.0 → 0.22.1
• 3958d3d chore: prepare release notes 0.22.1
• 4470383 refactor: add deprecation warning to unused function
• bff20d3 fix: knock-out all genes together
• 563eed1 tests: add test case for bug in #1102
• 0b15120 Merge pull request #1096 from opencobra/refactor/flux-analysis-gapfilling
• 48990e5 refactor: add typing annotations and upgrade code style for test_gapfilling.py
• d4838c6 refactor: add typing annotations and upgrade code style for gapfilling.py
• dfd4077 Merge pull request #1095 from opencobra/refactor/flux-analysis-phenotype
• efa23e2 fix: remove incorrect Union type argument numpy.nan
• Additional commits viewable in compare view

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