Release notes for cobrapy x.y.z
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
not work via github actions or local installation by removing the use of obsolete numpy
Release notes for cobrapy 0.25.0
knock_out_model_genesto simulate knock-outs, setting reaction bounds of affected reactions to zero and returning a list of reactions that were knocked-out. Replaces
undelete_model_genessince it is context sensitive.
- Improve reading of matlab models which will include metabolite and reaction annotations.
Release notes for cobrapy 0.22.1
- 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).
Release notes for cobrapy 0.21.0
- Update libSBML dependency to
- Docstring and style changes.
Release notes for cobrapy 0.17.1
- Prevent an error with infeasible solutions in (loopless) FVA.
- Correct a sampling problem with Gurobi as the solver.
- Adjust sampling documentation.
Release notes for cobrapy 0.17.0
- Improve handling of and problems with SBML notes.
- Log SBML messages to a module logger rather than the root logger.
- Repair documentation building.
Release notes for cobrapy 0.15.4
- This release brings a number of bug fixes for SBML I/O (#852).
Backwards incompatible changes
- The deprecated
objective_coefficientwas removed (#871).
Release notes for cobrapy 0.15.3
- Correct multiple issues with the new SBML parser (#822, #839, #840, #843, #844).
validate_sbml_modelproperly captures errors and warnings.
Release notes for cobrapy 0.15.2
- We introduce a new
toleranceattribute both on the global
Configurationobject as well as
Model. The default for this is 1E-07. Many functions that use a zero cut-off will now use the set model tolerance value by default. This value can still be set manually via function arguments but attempting to set a threshold that is lower than the model tolerance now raises an error.
Release notes for cobrapy 0.14.2
- Better identification of the external compartment.
- Fix the installation of all optional dependencies, i.e.,
pip install cobra[all].
Release notes for cobrapy 0.14.0
- Adding boundary reactions is now much more flexible and accepts user-defined identifiers.
- It is now possible to run FVA and loopless FVA in parallel.
- Some utilities and an example of how to perform static optimization dynamic FBA.
Release notes for cobrapy 0.14.1
- Always create an XML declaration when reading SBML from a byte stream.
Release notes for cobrapy 0.13.4
- Internal re-organization of the test suite.
- Upgrade the
ruamel.yamlversion making it compatible with Python 3.7.
- Fix a bug with a regular expression in the Matlab interface.
Release notes for cobrapy 0.13.3
- Make a clean release for PyPI, website, and GitHub.
Release notes for cobrapy 0.13.0
- New properties for the
cobra.Modelthat give access to specific boundary reactions.
- New functions for handling media and computing minimal media. Please read the new documentation chapter on media.
Backwards incompatible changes
Release notes for cobrapy 0.12.1
- Fix/feature that allows summaries to work properly for models with multiple exchange reactions for the same metabolite.
- Require a later optlang version so that Gurobi can now be used for quadratic problems.
- cobrapy can now extract primal values from a wider range of solver states. This is particularly useful to investigate problems in non-optimal states.
Release notes for cobrapy 0.11.2
- Correctly set the constraint for a previous minimization objective in FVA.
Release notes for cobrapy 0.11.1
- Catch all
optlangerrors and re-raise them as
OptimizationErrorwith corresponding message.
Release notes for cobrapy 0.10.0
- The solvers packaged with cobrapy have been removed.
- cobra is now a pure Python package and no longer has compiled extensions.
- Massively simplified continuous testing and deployment.
solverargument and configuration keyword arguments have been removed. Please set the solver on the model and configure it before calling optimization functions.
Release notes for cobrapy 0.10.1
pandashas dropped support for Python 3.4 and we are doing the same for our automated tests. If you are running Python 3.4 and have a working installation of numpy and pandas, adding cobrapy on top of that is no problem.
- Updated some URLs in the links.
Release notes for cobrapy 0.9.0
Model.compartmentis now a dynamic property fetching the compartments from all metabolites therefore always up-to-date. Assigning a dictionary to the same property updates the internal dictionary of compartment descriptions. This change removes the need for the check for missing compartments from
- Guarantee that sampler._reproject always returns a feasible point and will not attempt to reproject already feasible points. #564
Model.summaryno longer fails when calling after the model has changed. Fixed by letting the summary function re-compute a solution (default) or letting user supply a prior computed solution object. #566
In this release we have made major changes to pretty much all corners of cobrapy and we hope that you will enjoy the new features as much as we do, and that any negative impacts on existing workflows will be limited. The major change is the ongoing move away from cobrapy’s internal solver interfaces to those provided by optlang which provides a single unified interface to glpk, cplex and gurobi enhanced by the ability to deal with symbolic expressions.