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setup.cfg
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setup.cfg
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#######################
# Setup Configuration #
#######################
[metadata]
name = pypesto
version = attr: pypesto.version.__version__
description = python-based Parameter EStimation TOolbox
long_description = file: README.md
long_description_content_type = text/markdown
# URLs
url = https://github.com/icb-dcm/pypesto
download_url = https://github.com/icb-dcm/pypesto/releases
project_urls =
Bug Tracker = https://github.com/icb-dcm/pypesto/issues
Documentation = https://pypesto.readthedocs.io
Changelog = https://pypesto.readthedocs.io/en/latest/changelog.html
# Author information
author = The pyPESTO developers
author_email = [email protected],[email protected]
maintainer = Yannik Schaelte, Jakob Vanhoefer, Paul Jost
# License information
license = BSD-3-Clause
license_file = LICENSE
# Search tags
classifiers =
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Operating System :: OS Independent
Programming Language :: Python
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.8
keywords =
parameter inference
optimization
sampling
profiles
ODE
AMICI
systems biology
[options]
install_requires =
numpy >= 1.19.1
scipy >= 1.5.2
pandas >= 1.5.0
cloudpickle >= 1.5.0
# bug: https://github.com/matplotlib/matplotlib/issues/24127
matplotlib >= 3.6.0, < 3.6.1
seaborn >= 0.11.2
h5py >= 3.1.0
tqdm >= 4.46.0
tabulate >= 0.8.10
python_requires = >=3.8
include_package_data = True
# Where is my code
packages = find:
[options.packages.find]
include = pypesto*
[options.extras_require]
all =
%(amici)s
%(petab)s
%(all_optimizers)s
%(mpi)s
%(pymc)s
%(aesara)s
%(emcee)s
%(mltools)s
%(doc)s
%(example)s
%(select)s
%(test)s
%(test_petab)s
all_optimizers =
%(ipopt)s
%(dlib)s
%(nlopt)s
%(pyswarm)s
%(cmaes)s
%(pyswarms)s
%(fides)s
amici =
amici >= 0.11.27
petab =
petab >= 0.1.14
ipopt =
ipopt
dlib =
dlib >= 19.19.0
nlopt =
nlopt >= 2.6.2
pyswarm =
pyswarm >= 0.6
cmaes =
cma >= 3.0.3
pyswarms =
pyswarms >= 1.3.0
fides =
fides >= 0.6.1
mpi =
mpi4py >= 3.0.3
pymc =
arviz >= 0.12.1
aesara >= 2.8.6
pymc >= 4.2.1
aesara =
aesara >= 2.0.5
emcee =
emcee >= 3.0.2
mltools =
umap-learn[plot] >= 0.5.3
scikit-learn >= 0.24.1
julia =
julia >= 0.5.7
ipython >= 8.4.0
pygments >= 2.12.0
doc =
sphinx >= 5.1.0
nbsphinx >= 0.8.9
nbconvert >= 6.5.0
sphinx-rtd-theme >= 1.0.0
sphinx-autodoc-typehints >= 1.18.3
ipython >= 8.4.0
myst-parser >= 0.18.0
%(select)s
example =
notebook >= 6.1.4
select =
# Remove when vis is moved to PEtab Select version
networkx >= 2.5.1
# End remove
petab-select >= 0.1.1
test =
pytest >= 5.4.3
pytest-cov >= 2.10.0
gitpython >= 3.1.7
pytest-rerunfailures >= 9.1.1
autograd >= 1.3
test_petab =
petabtests >= 0.0.0a6
benchmark-models-petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python
[bdist_wheel]
# Requires Python 3
universal = False