Release notes for cobrapy 0.29.0

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

Release notes for cobrapy 0.28.0

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).

Release notes for cobrapy 0.27.0

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

Release notes for cobrapy 0.26.3

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.

Fix an issue where runfrog 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

Release notes for cobrapy 0.26.2

New features

Fixes

Fix the version numbers, my bad - cd

Other

Deprecated features

Backwards incompatible changes

Release notes for cobrapy 0.26.1

New features

Fixes

Fix automatic building of the documentation.

Fix an issue where SBML models with a "created" date would break lots of the cobrapy functionality.

Temporary fix of restricting numpy to <1.24 as that release introduces breaking changes both in cobrapy and dependencies

Other

Deprecated features

Backwards incompatible changes

Release notes for cobrapy 0.26.0

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().

Release notes for cobrapy 0.25.0

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 GPRs that should work. Made GPRs 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.

Release notes for cobrapy 0.24.0

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).

Release notes for cobrapy 0.23.0

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)