Optlang

Optlang: An algebraic modeling language for mathematical optimization - Published in JOSS (2017)

https://github.com/opencobra/optlang

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: joss.theoj.org, zenodo.org
✓
Committers with academic emails
11 of 29 committers (37.9%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

optlang - sympy based mathematical programming language

Basic Info

Host: GitHub
Owner: opencobra
License: apache-2.0
Language: Python
Default Branch: master
Homepage: http://optlang.readthedocs.org/
Size: 9.59 MB

Statistics

Stars: 263
Watchers: 18
Forks: 52
Open Issues: 32
Releases: 52

Created over 12 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Contributing License Code of conduct Support

README.rst

optlang
=======

*Sympy based mathematical programming language*

|PyPI| |Python Versions| |License| |Code of Conduct| |GitHub Actions| |Coverage Status| |Documentation Status| |Gitter| |JOSS| |DOI|

Optlang is a Python package for solving mathematical optimization
problems, i.e. maximizing or minimizing an objective function over a set
of variables subject to a number of constraints. Optlang provides a
common interface to a series of optimization tools, so different solver
backends can be changed in a transparent way.
Optlang's object-oriented API takes advantage of the symbolic math library
`sympy `__ to allow objective functions
and constraints to be easily formulated from symbolic expressions of
variables (see examples).

Show us some love by staring this repo if you find optlang useful!

Also, please use the GitHub `issue tracker `_
to let us know about bugs or feature requests, or our `gitter channel `_ if you have problems or questions regarding optlang.

Installation
~~~~~~~~~~~~

Install using pip

::

    pip install optlang

This will also install `swiglpk `_, an interface to the open source (mixed integer) LP solver `GLPK `_.
Quadratic programming (and MIQP) is supported through additional optional solvers (see below).

Dependencies
~~~~~~~~~~~~

The following dependencies are needed.

-  `sympy >= 1.0.0 `__
-  `swiglpk >= 1.4.3 `__

The following are optional dependencies that allow other solvers to be used.

-  `cplex `__ (LP, MILP, QP, MIQP)
-  `gurobipy `__ (LP, MILP, QP, MIQP)
-  `scipy `__ (LP)
-  `osqp `__ (LP, QP)



Example
~~~~~~~

Formulating and solving the problem is straightforward (example taken
from `GLPK documentation `__):

.. code-block:: python

    from optlang import Model, Variable, Constraint, Objective

    # All the (symbolic) variables are declared, with a name and optionally a lower and/or upper bound.
    x1 = Variable('x1', lb=0)
    x2 = Variable('x2', lb=0)
    x3 = Variable('x3', lb=0)

    # A constraint is constructed from an expression of variables and a lower and/or upper bound (lb and ub).
    c1 = Constraint(x1 + x2 + x3, ub=100)
    c2 = Constraint(10 * x1 + 4 * x2 + 5 * x3, ub=600)
    c3 = Constraint(2 * x1 + 2 * x2 + 6 * x3, ub=300)

    # An objective can be formulated
    obj = Objective(10 * x1 + 6 * x2 + 4 * x3, direction='max')

    # Variables, constraints and objective are combined in a Model object, which can subsequently be optimized.
    model = Model(name='Simple model')
    model.objective = obj
    model.add([c1, c2, c3])

    status = model.optimize()

    print("status:", model.status)
    print("objective value:", model.objective.value)
    print("----------")
    for var_name, var in model.variables.iteritems():
        print(var_name, "=", var.primal)

The example will produce the following output:

::

    status: optimal
    objective value: 733.333333333
    ----------
    x2 = 66.6666666667
    x3 = 0.0
    x1 = 33.3333333333

Using a particular solver
-------------------------
If you have more than one solver installed, it's also possible to specify which one to use, by importing directly from the
respective solver interface, e.g. :code:`from optlang.glpk_interface import Model, Variable, Constraint, Objective`

Documentation
~~~~~~~~~~~~~

Documentation for optlang is provided at
`readthedocs.org `__.

Citation
~~~~~~~~

Please cite |JOSS| if you use optlang in a scientific publication. In case you would like to reference a specific version of of optlang you can also include the respective Zenodo DOI (|DOI| points to the latest version).

Contributing
~~~~~~~~~~~~

Please read ``__.

Funding
~~~~~~~

The development of optlang was partly support by the Novo Nordisk Foundation.

Future outlook
~~~~~~~~~~~~~~

-  `Mosek `__ interface (provides academic
   licenses)
-  `GAMS `__ output (support non-linear problem
   formulation)
-  `DEAP `__ (support for heuristic
   optimization)
-  Interface to `NEOS `__ optimization
   server (for testing purposes and solver evaluation)
-  Automatically handle fractional and absolute value problems when
   dealing with LP/MILP/QP solvers (like GLPK,
   `CPLEX `__
   etc.)

.. |PyPI| image:: https://img.shields.io/pypi/v/optlang.svg
   :target: https://pypi.org/project/optlang/
   :alt: Current PyPI Version
.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/optlang.svg
   :target: https://pypi.org/project/optlang/
   :alt: Supported Python Versions
.. |License| image:: https://img.shields.io/pypi/l/optlang.svg
   :target: https://www.apache.org/licenses/LICENSE-2.0
   :alt: Apache Software License Version 2.0
.. |Code of Conduct| image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg
   :target: .github/CODE_OF_CONDUCT.md
   :alt: Code of Conduct
.. |GitHub Actions| image:: https://github.com/opencobra/optlang/actions/workflows/main.yml/badge.svg
   :target: https://github.com/opencobra/optlang/actions/workflows/main.yml
   :alt: GitHub Actions
.. |Coverage Status| image:: https://codecov.io/gh/opencobra/optlang/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/opencobra/optlang
   :alt: Codecov
.. |Documentation Status| image:: https://readthedocs.org/projects/optlang/badge/?version=latest
   :target: https://readthedocs.org/projects/optlang/?badge=latest
   :alt: Documentation Status
.. |JOSS|  image:: http://joss.theoj.org/papers/cd848071a664d696e214a3950c840e15/status.svg
   :target: http://joss.theoj.org/papers/cd848071a664d696e214a3950c840e15
   :alt: Publication
.. |DOI| image:: https://zenodo.org/badge/5031/biosustain/optlang.svg
   :target: https://zenodo.org/badge/latestdoi/5031/biosustain/optlang
   :alt: Zenodo Source Code
.. |Gitter| image:: https://badges.gitter.im/biosustain/optlang.svg
   :target: https://gitter.im/biosustain/optlang?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
   :alt: Join the chat at https://gitter.im/biosustain/optlang

Owner

Name: openCOBRA
Login: opencobra
Kind: organization
Location: Terra

Website: opencobra.github.io
Repositories: 33
Profile: https://github.com/opencobra

Community driven constraint-based reconstruction, analysis and modelling of biology

GitHub Events

Total

Create event: 2
Release event: 1
Issues event: 11
Watch event: 14
Issue comment event: 7
Push event: 13
Pull request review comment event: 4
Pull request review event: 8
Pull request event: 6
Fork event: 2

Last Year

Create event: 2
Release event: 1
Issues event: 11
Watch event: 14
Issue comment event: 7
Push event: 13
Pull request review comment event: 4
Pull request review event: 8
Pull request event: 6
Fork event: 2

Committers

Last synced: 8 months ago

All Time

Total Commits: 632
Total Committers: 29
Avg Commits per committer: 21.793
Development Distribution Score (DDS): 0.527

Past Year

Commits: 6
Committers: 2
Avg Commits per committer: 3.0
Development Distribution Score (DDS): 0.167

Top Committers

Name	Email	Commits
Nikolaus Sonnenschein	n**n@g**m	299
KristianJensen	j**9@g**m	145
Christian Diener	c**r@g**m	54
KristianJensen	k**j@n**l	34
KristianJensen	k**j@n**k	17
carrascomj	c**j@g**m	12
braceal	b**l@u**u	11
KristianJensen	k**j@n**k	6
Joao Cardoso	j**a@b**k	6
KristianJensen	k**j@n**k	6
Nikolaus Sonnenschein	n**n@g**m	6
Moritz E. Beber	m**r@p**t	5
Henning Redestig	h**d@g**m	5
KristianJensen	k**j@n**k	5
KristianJensen	k**j@n**k	3
Ali Kaafarani	a**i@k**o	2
Elad Noor	n**r@e**h	2
João Cardoso	j**o@s**m	2
KristianJensen	k**j@n**k	2
long-m-r	l****r	1
Kristian Jensen	d**e@c**m	1
KristianJensen	k**j@n**k	1
KristianJensen	k**j@n**k	1
Willy Mroczowski	w**y@m**e	1
Peter St. John	p**n@g**m	1
Matthias König	k**t@g**m	1
Alexandre Detiste	a**e@g**m	1
Frames White	o**x@u**u	1
Justin Taylor	t****m	1

Committer Domains (Top 20 + Academic)

ucc.asn.au: 1 mroczowski.de: 1 nnfcb-l0281.win.dtu.dk: 1 nnfcb-l0275.eduroam.wireless.dtu.dk: 1 chr-hansen.com: 1 nnfcb-l0267.win.dtu.dk: 1 silicolife.com: 1 ethz.ch: 1 kvikshaug.no: 1 nnfcb-l0107.win.dtu.dk: 1 nnfcb-l0189.win.dtu.dk: 1 posteo.net: 1 nnfcb-l0135.win.dtu.dk: 1 biosustain.dtu.dk: 1 nnfcb-d0100.win.dtu.dk: 1 umich.edu: 1 nnfcb-l0280.win.dtu.dk: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 73
Total pull requests: 53
Average time to close issues: about 1 year
Average time to close pull requests: 2 months
Total issue authors: 34
Total pull request authors: 15
Average comments per issue: 1.7
Average comments per pull request: 2.43
Merged pull requests: 48
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 5
Average time to close issues: 29 days
Average time to close pull requests: about 1 month
Issue authors: 4
Pull request authors: 2
Average comments per issue: 0.75
Average comments per pull request: 0.2
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Midnighter (23)
cdiener (13)
NGC2023 (3)
braceal (2)
matthiaskoenig (2)
KristianJensen (2)
axelvonkamp (2)
Paulocracy (2)
serdar- (1)
djinnome (1)
Theorell (1)
sjpfenninger (1)
taylo5jm (1)
hredestig (1)
DManowitz (1)

Pull Request Authors

cdiener (33)
KristianJensen (7)
Midnighter (4)
phantomas1234 (4)
carrascomj (2)
Palaract (2)
oxinabox (2)
a-detiste (2)
DWesl (1)
taylo5jm (1)
pablo-angulo (1)
braceal (1)
kvikshaug (1)
ConnectedSystems (1)
hredestig (1)

Top Labels

Issue Labels

enhancement (9) bug (4) in progress (2) epic (1) refine (1)

Pull Request Labels

in progress (6) ready (2) enhancement (2)

Packages

Total packages: 1
Total downloads:
- pypi 38,445 last-month
Total docker downloads: 801

Total dependent packages: 16
Total dependent repositories: 105
Total versions: 71
Total maintainers: 2

pypi.org: optlang

Formulate optimization problems using sympy expressions and solve them using interfaces to third-party optimization software (e.g. GLPK).

Homepage: https://github.com/opencobra/optlang
Documentation: https://optlang.readthedocs.io
License: Apache-2.0
Latest release: 1.8.3
published about 1 year ago

Versions: 71
Dependent Packages: 16
Dependent Repositories: 105
Downloads: 38,445 Last month
Docker Downloads: 801

Rankings

Dependent packages count: 0.7%

Docker downloads count: 1.4%

Dependent repos count: 1.5%

Average: 2.9%

Downloads: 2.9%

Stargazers count: 4.6%

Forks count: 6.0%

Maintainers (2)

midnighter Nikolaus.Sonnenschein

Last synced: 7 months ago

Dependencies

.github/workflows/main.yml actions

actions/checkout v2 composite
actions/create-release v1 composite
actions/setup-python v2 composite

requirements_rtd.txt pypi

sphinx-rtd-theme >=0.1.6

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

Optlang

Science Score: 46.0%

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: optlang

Rankings

Maintainers (2)

Dependencies