Cobra

New features

* View number of genes in model notebook representation.
* added support for Python 3.11

Fixes

* serializes GPRs to strings to avoid massive storage usage
* Reformatted example files (e_coli_core.xml, mini_cobra.xml, mini.json, mini.yml, textbook.xml.gz) to be more compliant with identifiers.org.
* ncbigi is not a valid identifiers.org, so it was replaced with ncbiprotein.
* make sbml.py subsystem reading add partonomy, which matches the definition
of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
* Correct reading and writing of subsystem in mat.
* General cleanup of code in mat.py
* fix the pandas deprecation warning in `find_external_compartment`
* fix an issue where creating a Formula object would give a recursion error

Other

* Resolve `flake8` issues and add missing type annotations and docstrings in `src/cobra/io` and `tests/test_io` (1212).
* Updated model.py and test_model.py to Python 3.6+, including type annotations and docstrings.
* Resolve remaining `flake8` issues and enable the check in GitHub Actions Lint workflow (1272).

Deprecated features

* dropped support for Python 3.6

Backwards incompatible changes
* Removed `model.add_reaction()` and replaced remaining usages of it with `model.add_reactions()`
* Removed the following tests: test_add_remove_reaction_benchmark, test_add_reaction,
test_add_reaction_context, test_add_reaction_from_other_model, test_add_cobra_reaction
* Removed `model.__add__` and `model.__iadd__` - use `model.merge` to replace them.
* Remove `Model().description()`.
* Remove `Model().get_metabolite_compartments()`.

New features

* Add `knock_out_model_genes` to simulate knock-outs, setting
reaction bounds of affected reactions to zero and returning a list
of reactions that were knocked-out. Replaces `delete_model_genes`
and `undelete_model_genes` since it is context sensitive.
* Improve reading of matlab models which will include metabolite
and reaction annotations.

Fixes

* `model.copy()` will now correctly copy GPRs.
* Fix an error where matlab models can not be read if their bounds exceed the
configuration default in some cases.
* Fixed some bugs in `GPR().from_string()` where it was using the unmodified string,
leading to errors with `GPR`s that should work. Made `GPR`s that have empty
parenthesis fail more comprehensibly.

Other

* Move tests to a different directory, from `src/cobra/test` to `tests` (1191).
* Add two tests for `GPR` fixes:
* `test_gpr_wrong_input()`
* `test_gpr_that_needs_two_replacements()`
* Clean up Python syntax (1152, 1153, 1171, 1173, 1182)

Deprecated features

* Deprecate `delete_model_genes`, `undelete_model_genes`

Backwards incompatible changes

* Remove `find_gene_knockout_reactions` from `delete.py`
* Remove `_find_gene_knockout_reactions_fast`,
`_gene_knockout_computation`, `_get_removed `
from `test_delete.py`
* Remove `pymatlib` direct transfer of models to matlab process.
Please use `save_matlab_model()` and then read the model in matlab.

New features

* Gene-protein-reaction association rules are now represented by a structured object `GPR`.
`Reaction.gene_reaction_rule` still returns a string and a string can be assigned
to it that will modify the underlying `GPR` instance.
* The `Reaction` class has gained another attribute `Reaction.gpr` which allows direct
access to the `GPR` instance (1143).

Fixes

* Syntax update and type annotations (1151).

Fixes

- Make compatible with Python 3.10
- Use the internal semantic GPR parser in the SBML module
- Setting a growth medium will not reset export flux bounds anymore

Other

- Clean up code (1116, 1114, 1113, 1111, 1110, 1097)

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.

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.