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Releases: opencobra/cobrapy

0.29.1

19 Sep 12:46
3b599e1
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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

31 Oct 18:34
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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

25 Oct 23:07
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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

15 Sep 18:45
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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

12 Apr 21:25
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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

03 Jan 20:32
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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

02 Jan 22:38
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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

08 Nov 21:21
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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

30 Apr 19:36
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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

30 Apr 18:52
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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).