Releases: SystemsBioinformatics/cbmpy
CBMPy release 0.8.8 update 1
Intermediate release that includes bug fixes, code cleanup and new features to support endPoint FBA. Has alpha support for Flux Balance Constraints V3 features including quadratic objectives, non-stoichiometric user constraints and KeyValue pairs. Try the latest format with cbmpy.writeSBML3FBCV3.
Many thanks to Steven Wijnen for his debugging, testing and help with the QP, constraints and FBCV3 implementation. This release supports his dcFBA/endPointFBA https://github.com/SystemsBioinformatics/dynamic-community-fba package .
See https://systemsbioinformatics.github.io/cbmpy/ and the README.md for more details.
Install
This version is only available from PyPI, install using:
pip install cbmpy
What's Changed
- start 0.8.5 by @bgoli in #53
- Merge pull request #54 from SystemsBioinformatics/master by @bgoli in #55
- Add support for FBCv3 by @bgoli in #58
- CBMPy 0.8.7 dev merge by @bgoli in #60
- tweaked 0.8.8 for a sane pypi release by @bgoli in #61
- fixed typo by @bgoli in #62
Full Changelog: 0.8.4...0.8.8.1
Contributors
Assets 2
CBMPy release 0.8.8
Release 0.8.8
Intermediate release that includes bug fixes, code cleanup and new features to support endPoint FBA. Has alpha support for Flux Balance Constraints V3 features including quadratic objectives, non-stoichiometric user constraints and KeyValue pairs. Try the latest format with cbmpy.writeSBML3FBCV3.
Many thanks to Steven Wijnen for his debugging, testing and help with the QP, constraints and FBCV3 implementation. This release supports his dcFBA/endPointFBA https://github.com/SystemsBioinformatics/dynamic-community-fba package .
See https://systemsbioinformatics.github.io/cbmpy/ and the README.md for more details.
Install
This version is only available from PyPI, install using:
pip install cbmpy
What's Changed
- start 0.8.5 by @bgoli in #53
- Merge pull request #54 from SystemsBioinformatics/master by @bgoli in #55
- Add support for FBCv3 by @bgoli in #58
- CBMPy 0.8.7 dev merge by @bgoli in #60
Full Changelog: 0.8.4...0.8.8
Contributors
Assets 2
CBMPy release 0.8.4
Current release
This is primarily a bugfix/maintenance release, that adds Python 3.10 and the latest libSBML compatibility.
Many thanks go to all who identified issues and suggested code improvements (see CONTRIBUTORS and RELEASES for details).
About CBMPy
CBMPy (http://cbmpy.sourceforge.net) is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection.
What's Changed
- Dev by @bgoli in #47
- Updating collections import in pyparsing.py by @JoPkb in #49
- 0.8.4 py3.9+ compatability release by @bgoli in #50
- removed pyparsing this time by @bgoli in #51
New Contributors
Full Changelog: 0.8.2...0.8.4
Contributors
Assets 2
CBMPy release 0.8.2
Current release
This is primarily a bugfix/maintenance release, fixing a Python 3.8 and setup.py issues.
Many thanks go to all who identified issues and suggested code improvements (see CONTRIBUTORS and RELEASES for details).
About CBMPy
CBMPy (http://cbmpy.sourceforge.net) is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection. To cater for a diverse range of modelling needs CBMPy supports user interaction via:
interactive console, scripting for advanced use or as a library for software development
GUI, for quick access to a visual representation of the model, analysis methods and annotation tools
SOAP based web services: using the Mariner framework much high level functionality is exposed for integration into web tools
For more information on the development and use of CBMPy (https://github.com/SystemsBioinformatics/cbmpy)
CBMPy release 0.8.1
Current release
This is primarily a bugfix/maintenance release. Many thanks go to all who identified issues and suggested code improvements (see CONTRIBUTORS and RELEASES for details).
About CBMPy
CBMPy (http://cbmpy.sourceforge.net) is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection. To cater for a diverse range of modelling needs CBMPy supports user interaction via:
interactive console, scripting for advanced use or as a library for software development
GUI, for quick access to a visual representation of the model, analysis methods and annotation tools
SOAP based web services: using the Mariner framework much high level functionality is exposed for integration into web tools
For more information on the development and use of CBMPy (https://github.com/SystemsBioinformatics/cbmpy)
CBMPy 0.8.0 release candidate
CBMPy 0.8.0-beta has been released and is available for most major operating systems and Python version 2.7, 3.6 and 3.7 from GitHub, PyPI and Anaconda.org.
This release contains bugfixes and upgrades, as well as new features that are still being developed include support for a new version of GLPK, a new solver framework, enhanced Groups support and upports all newer versions of MetaDraft and MetaToolkit.
CBMPy is archived on Zenodo and all new versions can be reference by DOI: https://doi.org/10.5281/zenodo.3358765
CBMPy test suite
This is the initial release of the CBMPy test suite, once CBMPy is installed you have the option of running either:
- run-nose-tests.py
- run-sbml-test-suite-tests.py
The first set are the CBMPy unit tests, while the second is a set of SBML semantic tests from the SBML test suite.
Requires (install from conda or pip): cbmpy, nose
Brett G. Olivier, Amsterdam, 2019
CBMPy 0.7.25 has been released.
CBMPy 0.7.25 has been released and is available for most major operating systems and Python version 2.7, 3.6 and 3.7 from GitHub, PyPI and Anaconda.org
This release contains new speedups in model construction and analysis, support for user defined constraints advanced support for model annotation and many tweaks and bugfixes. It also supports all newer versions of MetaDraft and MetaToolkit.
CBMPy is archived on Zenodo and all new versions can be reference by DOI: https://doi.org/10.5281/zenodo.3358765
CBMPy release 0.7.21
CBMPy 0.7.21 has been released.
New features include support for model validation, new tree representations of GPR's which allow easy editing of GPR elements. New methods for moving components between models have also been added. CBMPy is now available for Python 2 and Python 3
CBMPy release 0.7.19 release 2
Build system tweaks