Cobra

New features

Fixes

* Fixes the incorrect bounds in the CycleFree loop removal.
* Fixes reduced costs and shadow prices not available when using non-convex models.
* Fixed a bug with SBML group parsing that affects the Debian package.
* Fixed a bug where load_matlab_model would not work with numpy 2.0.

Other

* Adding a duplicate boundary reaction (with `add_boundary`) no longer errors, but instead just returns the existing reaction.
* Automatic detection of the external compartment now recognizes CARVEME and GAPSEQ ids and will no longer
show a warning for models generated with those tools.

Deprecated features

Backwards incompatible changes

New features

* Added a new "hybrid" solver that exposes an HIGHS/OSQP combinations for large scale
LPs, MILPs, and QPs.

Fixes

Repaired the broken Biomodels Web IO.

Other

Deprecated features

* The OSQP solver is deprecated in favor of the hybrid solver which also uses OSQP but
will not attempt to solve LPs with OSQP anymore. Setting the `model.solver = "osqp"`
will now use the hybrid interface and will raise an error in a future release.

Backwards incompatible changes

Fixes

* Allowed for pandas versions >=1.0 and <3.0 (1364).

Other

* Updated the GitHub Actions used (1364).

Backwards incompatible changes

* Updated the package `depinfo` to version >2 (1361).

New features

Fixes

COBRApy is now compatible with pydantic version 2.

COBRApy is now compatible with the latest numpy versions and pin to a lower version
has been removed.

`loopless_solution` now fixes the objective to its optimum as in the
originally published method and returns the objective value in the solution object.

Repair a broken test for `fix_objective_as_constraint`.

Other

Backwards compatibility for pickled models has been improved.

Deprecated features

Backwards incompatible changes

New features

Fixes

Fixed an issue where reaction bounds were being overwritten by global model min/max values
when writing sbml model to file. See [1300](https://github.com/opencobra/cobrapy/pull/1312).

Fix an issue where [`runfrog`](https://github.com/matthiaskoenig/fbc_curation/issues/98) does
not work via github actions or local installation by removing the use of obsolete numpy
aliases for `float` and `bool`.

Fix a bug where installing httpx>=0.24 would break cobrapy IO.

Other

Deprecated features

Backwards incompatible changes

New features

Fixes

Fix the version numbers, my bad - cd

Other

Deprecated features

Backwards incompatible changes