0.29.1

Release notes for cobrapy 0.29.1

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

0.29.0

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

0.28.0

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).

0.27.0

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

0.26.3

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

0.26.2

Release notes for cobrapy 0.26.2

New features

Fixes

Fix the version numbers, my bad - cd

Other

Deprecated features

Backwards incompatible changes

0.26.1

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

0.26.0

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().

0.25.0

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.

0.24.0

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).