setup.cfg

#######################
# 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 = yannik.schaelte@gmail.com
maintainer = Paul Jonas Jost, Maren Philipps, Domagoj Dorešić, Fabian Fröhlich
maintainer_email = paul.jost@uni-bonn.de, maren.philipps@uni-bonn.de, domagoj.doresic@uni-bonn.de, fabian.frohlich@crick.ac.uk

# License information
license = BSD-3-Clause
license_files = LICENSE

# Search tags
classifiers =
    Development Status :: 4 - Beta
    License :: OSI Approved :: BSD License
    Operating System :: OS Independent
    Programming Language :: Python
    Programming Language :: Python :: 3.11
    Programming Language :: Python :: 3.10
    Programming Language :: Python :: 3.9
keywords =
    parameter inference
    optimization
    sampling
    profiles
    ODE
    AMICI
    systems biology

[options]
install_requires =
    numpy >= 1.19.1, != 1.24.0
    scipy >= 1.5.2
    pandas >= 1.5.0
    cloudpickle >= 1.5.0
    matplotlib >= 3.6.2
    more-itertools >= 9.0.0
    seaborn >= 0.11.2
    h5py >= 3.1.0
    tqdm >= 4.46.0
    tabulate >= 0.8.10

python_requires = >=3.9
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
    %(jax)s
    %(julia)s
    %(emcee)s
    %(dynesty)s
    %(mltools)s
    %(doc)s
    %(example)s
    %(select)s
    %(test)s
    %(roadrunner)s
all_optimizers =
    %(ipopt)s
    %(dlib)s
    %(nlopt)s
    %(pyswarm)s
    %(cma)s
    %(pyswarms)s
    %(fides)s
amici =
    amici >= 0.21.0
roadrunner =
    libroadrunner >= 2.6.0
petab =
    petab >= 0.2.0
ipopt =
    cyipopt >= 1.3.0
dlib =
    dlib >= 19.19.0
nlopt =
    nlopt >= 2.6.2
pyswarm =
    pyswarm >= 0.6
cma =
    cma >= 3.0.3
pyswarms =
    pyswarms >= 1.3.0
fides =
    fides >= 0.6.1
mpi =
    mpi4py >= 3.0.3
pymc =
    arviz >= 0.12.1
    scipy < 1.13.0 # https://github.com/ICB-DCM/pyPESTO/issues/1354
    aesara >= 2.8.6
    pymc >= 4.2.1
aesara =
    aesara >= 2.0.5
jax =
    jax >= 0.4.1
    jaxlib >= 0.4.1
emcee =
    emcee >= 3.0.2
dynesty =
    dynesty >= 2.0.3
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 >= 6.2.1
    nbsphinx >= 0.8.9
    nbconvert >= 6.5.0
    sphinx-rtd-theme >= 1.2.0
    sphinx-autodoc-typehints >= 1.18.3
    sphinxcontrib-bibtex >= 2.5.0
    ipython >= 8.4.0
    myst-parser >= 0.18.0
    # pin to avoid `zmq.error.ZMQError: Too many open files` issues
    ipykernel == 6.23.1
    %(example)s
    %(select)s
    %(fides)s
    %(amici)s
    %(petab)s
    %(aesara)s
    %(jax)s
    %(roadrunner)s
example =
    %(julia)s
    %(pymc)s
    %(emcee)s
    %(dynesty)s
    %(nlopt)s
    %(pyswarm)s
    notebook >= 6.1.4
    benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python
select =
    # Remove when vis is moved to PEtab Select version
    networkx >= 2.5.1
    # End remove
    petab-select >= 0.1.12
test =
    pytest >= 5.4.3
    pytest-cov >= 2.10.0
    gitpython >= 3.1.7
    pytest-rerunfailures >= 9.1.1
    autograd >= 1.3

[bdist_wheel]
# Requires Python 3
universal = False