symfit

Symbolic Fitting; fitting as it should be.

https://github.com/tbuli/symfit

Science Score: 33.0%

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

○
CITATION.cff file
○
codemeta.json file
○
.zenodo.json file
✓
DOI references
Found 1 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
36 of 49 committers (73.5%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary

Keywords

curve-fitting least-squares python scipy sympy

Keywords from Contributors

molecular-dynamics protein-structure

Last synced: 6 months ago · JSON representation

Repository

Symbolic Fitting; fitting as it should be.

Basic Info

Host: GitHub
Owner: tBuLi
License: mit
Language: Python
Default Branch: master
Homepage: http://symfit.readthedocs.org
Size: 3.39 MB

Statistics

Stars: 243
Watchers: 9
Forks: 19
Open Issues: 84
Releases: 24

Topics

curve-fitting least-squares python scipy sympy

Created over 11 years ago · Last pushed about 2 years ago

Metadata Files

Readme Contributing License Authors

README.rst

.. image:: https://zenodo.org/badge/24005390.svg
   :target: https://zenodo.org/badge/latestdoi/24005390
.. image:: https://coveralls.io/repos/github/tBuLi/symfit/badge.svg?branch=master
   :target: https://coveralls.io/github/tBuLi/symfit?branch=master


Please cite this DOI if ``symfit`` benefited your publication. Building this has been a lot of work, and as young researchers your citation means a lot to us.
Martin Roelfs & Peter C Kroon, symfit. doi:10.5281/zenodo.1133336

Documentation
=============
http://symfit.readthedocs.org

Project Goals
=============

The goal of this project is simple: to make fitting in Python pythonic.
What does pythonic fitting look like? Well, there's a simple test. If I can
give you pieces of example code and don't have to use any additional words to
explain what it does, it's pythonic.

.. code-block:: python

  from symfit import parameters, variables, Fit, Model
  import numpy as np
   
  xdata = np.array([1.0, 2.0, 3.0, 4.0, 5.0])
  ydata = np.array([2.3, 3.3, 4.1, 5.5, 6.7])
  yerr = np.array([0.1, 0.1, 0.1, 0.1, 0.1])
  
  a, b = parameters('a, b')
  x, y = variables('x, y')
  model = Model({y: a * x + b})
  
  fit = Fit(model, x=xdata, y=ydata, sigma_y=yerr)
  fit_result = fit.execute()

Cool right? So now that we have done a fit, how do we use the results?

.. code-block:: python

  import matplotlib.pyplot as plt
  
  yfit = model(x=xdata, **fit_result.params)[y]
  plt.plot(xdata, yfit)
  plt.show()

.. figure:: http://symfit.readthedocs.org/en/latest/_images/linear_model_fit.png
  :width: 600px
  :alt: Linear Fit

Need I say more? How about I let another code example do the talking?

.. code-block:: python

  from symfit import parameters, Fit, Equality, GreaterThan
  
  x, y = parameters('x, y')
  model = 2 * x * y + 2 * x - x**2 - 2 * y**2
  constraints = [
      Equality(x**3, y),
      GreaterThan(y, 1),
  ]
  
  fit = Fit(- model, constraints=constraints)
  fit_result = fit.execute()

I know what you are thinking. "What if I need to fit to a system of Ordinary Differential Equations?"

.. code-block:: python

  from symfit import variables, Parameter, ODEModel, Fit, D
  import numpy as np
  
  tdata = np.array([10, 26, 44, 70, 120])
  adata = 10e-4 * np.array([44, 34, 27, 20, 14])
          
  a, b, t = variables('a, b, t')
  k = Parameter('k', 0.1)
  
  model_dict = {
      D(a, t): - k * a**2,
      D(b, t): k * a**2,
  }
  
  ode_model = ODEModel(model_dict, initial={t: 0.0, a: 54 * 10e-4, b: 0.0})
  
  fit = Fit(ode_model, t=tdata, a=adata, b=None)
  fit_result = fit.execute()

For more fitting delight, check the docs at http://symfit.readthedocs.org.

Owner

Name: Martin Roelfs
Login: tBuLi
Kind: user

Repositories: 4
Profile: https://github.com/tBuLi

Physicist by day, python enthusiast by night.

GitHub Events

Total

Issues event: 1
Watch event: 8
Issue comment event: 3
Pull request event: 1
Fork event: 3

Last Year

Issues event: 1
Watch event: 8
Issue comment event: 3
Pull request event: 1
Fork event: 3

Committers

Last synced: 10 months ago

All Time

Total Commits: 905
Total Committers: 49
Avg Commits per committer: 18.469
Development Distribution Score (DDS): 0.674

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Martin Roelfs	u**5@k**e	295
Peter	P****6	141
Martin Roelfs	m**s@r**l	88
tBuLi	m**s@t**l	52
Peter	p****n	40
Antony	t**p@w**e	36
Sam Brockie	s**9@c**k	18
Martin Roelfs	t**i@r**l	16
Martin Roelfs	t**i@r**l	16
Peter Kroon	p**n@r**l	15
Martin Roelfs	t**i@r**l	15
Martin Roelfs	M****s	13
Martin Roelfs	t**i@r**l	11
Jochem Smit	j**t@g**m	11
Martin Roelfs	t**i@r**l	10
Martin Roelfs	t**i@r**l	10
=	=	9
Martin Roelfs	t**i@r**l	9
Martin Roelfs	t**i@r**l	8
Martin Roelfs	t**i@r**l	8
Martin Roelfs	t**i@r**l	8
Martin Roelfs	t**i@r**l	7
Martin Roelfs	t**i@r**l	6
Martin Roelfs	t**i@M**l	6
Martin Roelfs	t**i@r**l	6
Martin Roelfs	t**i@r**l	6
Martin Roelfs	t**i@r**l	6
Martin Roelfs	t**i@r**l	4
tbuli	t**i@M**l	3
Martin Roelfs	t**i@r**l	3
and 19 more...

Committer Domains (Top 20 + Academic)

rug.nl: 3 rn-145-97-187-198.eduroam.rug.nl: 1 rn-145-97-186-211.eduroam.rug.nl: 1 rn-145-97-185-13.eduroam.rug.nl: 1 rn-145-97-172-193.eduroam.rug.nl: 1 rn-145-97-186-254.eduroam.rug.nl: 1 rn-145-97-186-104.eduroam.rug.nl: 1 rn-145-97-185-203.eduroam.rug.nl: 1 rn-145-97-173-23.eduroam.rug.nl: 1 rn-145-97-173-161.eduroam.rug.nl: 1 rn-145-97-184-144.eduroam.rug.nl: 1 rn-145-97-186-38.eduroam.rug.nl: 1 rn-145-97-186-222.eduroam.rug.nl: 1 rn-145-97-184-164.eduroam.rug.nl: 1 rn-145-97-185-166.eduroam.rug.nl: 1 rn-145-97-173-38.eduroam.rug.nl: 1 cam.ac.uk: 1 telfort.nl: 1 fwn-nb4-edu-28-49.fmnsedu.rug.nl: 1 rn-145-97-184-169.eduroam.rug.nl: 1 rn-145-97-175-131.eduroam.rug.nl: 1 rn-145-97-173-99.eduroam.rug.nl: 1 rn-145-97-173-49.eduroam.rug.nl: 1 rn-145-97-173-43.eduroam.rug.nl: 1 rn-145-97-173-199.eduroam.rug.nl: 1 rn-145-97-173-14.eduroam.rug.nl: 1 ipp-hgw.mpg.de: 1 rn-145-97-172-197.eduroam.rug.nl: 1 rn-145-97-173-32.eduroam.rug.nl: 1 rn-145-97-184-34.eduroam.rug.nl: 1 rn-145-97-185-3.eduroam.rug.nl: 1 rn-145-97-187-73.eduroam.rug.nl: 1 rn-145-97-172-244.eduroam.rug.nl: 1 rn-145-97-187-164.eduroam.rug.nl: 1 rn-145-97-185-66.eduroam.rug.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 62
Total pull requests: 47
Average time to close issues: 3 months
Average time to close pull requests: 4 months
Total issue authors: 29
Total pull request authors: 10
Average comments per issue: 3.79
Average comments per pull request: 4.04
Merged pull requests: 28
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 3
Average time to close issues: N/A
Average time to close pull requests: 3 months
Issue authors: 1
Pull request authors: 2
Average comments per issue: 1.0
Average comments per pull request: 0.67
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Jhsmit (7)
pckroon (6)
stephanlachnit (5)
lhdp0110 (5)
tBuLi (5)
JohnGoertz (4)
antonykamp (3)
nfhktwrbq (3)
patquem (2)
kvr2007 (2)
brocksam (2)
tokamage (1)
bartrex13 (1)
bhclowers (1)
MrAnimaniac (1)

Pull Request Authors

Jhsmit (18)
pckroon (12)
tBuLi (4)
antonykamp (4)
brocksam (2)
paulftw (2)
stephanlachnit (2)
osvalB (1)
ford--prefect (1)
elgalu (1)

Top Labels

Issue Labels

feature request (3) enhancement (2) easy first issue (1) bug (1)

Pull Request Labels

hacktoberfest-accepted (8) WIP (2)

Packages

Total packages: 2
Total downloads:
- pypi 2,205 last-month

Total dependent packages: 6
(may contain duplicates)
Total dependent repositories: 12
(may contain duplicates)
Total versions: 35
Total maintainers: 1

pypi.org: symfit

Symbolic Fitting; fitting as it should be.

Homepage: https://github.com/tBuLi/symfit
Documentation: https://symfit.readthedocs.io/
License: MIT
Latest release: 0.5.6
published about 3 years ago

Versions: 29
Dependent Packages: 4
Dependent Repositories: 11
Downloads: 2,205 Last month

Rankings

Dependent packages count: 2.4%

Dependent repos count: 4.4%

Stargazers count: 4.6%

Average: 5.2%

Downloads: 5.8%

Forks count: 8.9%

Maintainers (1)

tBuLi

Last synced: 6 months ago

conda-forge.org: symfit

Homepage: The package home page
License: MIT
Latest release: 0.5.5
published almost 4 years ago

Versions: 6
Dependent Packages: 2
Dependent Repositories: 1

Rankings

Dependent packages count: 19.6%

Dependent repos count: 24.2%

Stargazers count: 25.9%

Average: 27.5%

Forks count: 40.1%

Last synced: 6 months ago

Dependencies

requirements.txt pypi

numpy >=1.12
scipy >=1.0
setuptools *
sympy >=1.2
toposort *

requirements_docs.txt pypi

IPython *
ipykernel *
nbsphinx *
sphinx *

.github/workflows/deploy_pypi.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/deploy_pypi_test.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/generate_docs.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/test.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/test_and_coveralls.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite