Metadata-Version: 2.1
Name: dfba
Version: 0.1.8
Summary: Object-oriented software for dynamic flux-balance simulations.
Home-page: https://gitlab.com/davidtourigny/dynamic-fba
Author: David S. Tourigny, Moritz E. Beber
Author-email: dst2156@cumc.columbia.edu, morbeb@biosustain.dtu.dk
License: GNU GPL v3+
Download-URL: https://pypi.org/project/dfba/
Description: =============================
        Dynamic Flux Balance Analysis
        =============================
        
        .. image:: https://img.shields.io/pypi/v/dfba.svg
           :target: https://pypi.org/project/dfba/
           :alt: Current PyPI Version
        
        .. image:: https://img.shields.io/pypi/pyversions/dfba.svg
           :target: https://pypi.org/project/dfba/
           :alt: Supported Python Versions
        
        .. image:: https://img.shields.io/pypi/l/dfba.svg
           :target: http://www.gnu.org/licenses/
           :alt: GPLv3+
        
        .. image:: https://gitlab.com/davidtourigny/dynamic-fba/badges/master/pipeline.svg
           :target: https://travis-ci.org/davidtourigny/dynamic-fba/commits/master
           :alt: Pipeline Status
        
        .. image:: https://gitlab.com/davidtourigny/dynamic-fba/badges/master/coverage.svg
           :target: https://gitlab.com/davidtourigny/dynamic-fba/commits/master
           :alt: Coverage Report
        
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
           :target: https://github.com/ambv/black
           :alt: Black
        
        .. _`Harwood et al., 2016`: https://link.springer.com/article/10.1007/s00211-015-0760-3
        .. _GLPK: https://www.gnu.org/software/glpk/
        .. _SUNDIALS: https://computation.llnl.gov/projects/sundials
        .. _Python: https://www.python.org/
        .. _cobrapy: https://github.com/opencobra/cobrapy
        .. _optlang: https://github.com/biosustain/optlang
        .. _symengine: https://github.com/symengine/symengine
        
        This project provides an object-oriented software package for dynamic
        flux-balance analysis (DFBA) simulations using implementations of the direct
        method or Algorithm 1 described in the paper `Harwood et al., 2016`_. The main
        algorithms for solving embedded LP problems are written in *C++* and use the GNU
        Linear Programming Kit (GLPK_) and the Suite of Nonlinear and
        Differential/Algebraic Equation Solvers (SUNDIALS_) CVODE or IDA. Extension
        modules to cobrapy_ are provided for easy generation and simulation of DFBA
        models.
        
        Installation
        ============
        
        .. _GLPK: https://www.gnu.org/software/glpk/
        .. _SUNDIALS: https://computation.llnl.gov/projects/sundials
        .. _Python: https://www.python.org/
        .. _cobrapy: https://github.com/opencobra/cobrapy
        .. _optlang: https://github.com/biosustain/optlang
        .. _symengine: https://github.com/symengine/symengine
        
        Currently, we do not provide Python wheels for this package and therefore `Installing from
        source`_ is a bit more involved. The quickest way to run the software
        is from the provided `Docker <https://docs.docker.com/>`_ image:
        
        .. code-block:: console
        
            docker run --rm -it davidtourigny/dfba:latest
        
        
        Installing from source
        ----------------------
        
        Currently this package is compatible with most UNIX-like operating systems.
        Provided the following `Dependencies`_ are installed, the module
        can be installed from the root of the repository using the command:
        
        .. code-block:: console
        
            pip install .
        
        Dependencies
        ~~~~~~~~~~~~
        
        .. _`build_glpk.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_glpk.sh
        .. _`build_pybind11.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_pybind11.sh
        .. _`build_sundials.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_sundials.sh
        .. _Dockerfile: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/Dockerfile
        .. _`pybind11`: https://github.com/pybind/pybind11
        
        
        * A version of Python_ 3.6 or higher is required
        * You need `cmake <https://cmake.org/>`_ for the build process
        * You will need `git <https://git-scm.com/>`_ to clone this repository to access
          the scripts and build files
        * You need a working compiler with C++11 support, for example, by installing
          ``build-essential`` on Debian-derived Linux systems
        * GLPK_ version 4.65 is required or can be installed using `build_glpk.sh`_
        * SUNDIALS_ version 5.0.0 or higher is required or can be installed using `build_sundials.sh`_
        * pybind11_ is required or can be installed using `build_pybind11.sh`_
        
        Be aware that some of these packages have their own dependencies that must
        therefore be installed also (e.g. GLPK_ depends on `GMP <https://gmplib.org/>`_
        and pybind11_ requires `pytest <https://docs.pytest.org/en/latest/>`_).
        
        
        Alternatively, a Dockerfile_ is provided for building a `Docker <https://docs.docker.com/>`_
        image to run the software from an interactive container. The `Docker <https://docs.docker.com/>`_ image can be
        built in one step by issuing the command:
        
        .. code-block:: console
        
            make build
        
        from the root of this repository. It can then be started using:
        
        .. code-block:: console
        
            make run
        
        Documentation
        =============
        
        Documentation for dfba is provided at `readthedocs <https://dynamic-fba.readthedocs.io>`_
        
        Authors
        =======
        
        * David S. Tourigny
        * Moritz E. Beber
        
        Additional contributors
        =======================
        
        * Jorge Carrasco Muriel (visualization and documentation)
        
        Funding
        =======
        
        * David S. Tourigny is a Simons Foundation Fellow of the Life Sciences Research
          Foundation.
        
        Copyright
        =========
        
        * Copyright © 2018,2019 Columbia University Irving Medical Center, New York, USA
        * Copyright © 2019 Novo Nordisk Foundation Center for Biosustainability,
          Technical University of Denmark
        * Free software distributed under the `GNU General Public License v3 or later
          (GPLv3+) <http://www.gnu.org/licenses/>`_.
        
Keywords: dynamic,flux-balance analysis,FBA,DFBA,DAE
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: development
Provides-Extra: matplotlib
Provides-Extra: plotly
