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setup.cfg
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setup.cfg
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##########################
# Setup.py Configuration #
##########################
# Configuring setup()
[metadata]
name = mira
version = 0.8.0
license = BSD-2-Clause
license_files =
LICENSE
[options]
install_requires =
pydantic>=2.0.0
sympy
typing_extensions
networkx
tqdm
sbmlmath; python_version >= "3.10"
requests
jsonschema
tabulate
pysd
more_itertools
zip_safe = false
include_package_data = True
python_requires = >=3.9
# Where is my code
packages = find:
[options.packages.find]
exclude =
notebooks
[options.extras_require]
ode =
numpy
scipy
sympy
tests =
pytest
coverage
pygraphviz
pandas
matplotlib
matplotlib_venn
dkg-client =
neo4j
networkx
pystow
tqdm
dkg-construct =
bioontologies>=0.3.1
pyobo>=0.9.1
bioregistry>=0.6.13
click
pystow
tabulate
tqdm
biomappings
rdflib
dkg-embed =
grape
metaregistry =
bioregistry[web]
more_click
web =
fastapi>=0.100.0
httpx
flask
flasgger
bootstrap-flask
gilda
click
neo4j
networkx
pystow
tabulate
pygraphviz
python-libsbml
lxml
bioregistry
scipy
numpy
uvicorn =
uvicorn
gunicorn =
gunicorn
docs =
bioregistry
bioontologies
biomappings
sphinx<7.0.0
sphinx-rtd-theme>=0.5.1
sphinx-autodoc-typehints
sphinx-automodapi
autodoc-pydantic
m2r2
pygraphviz
pyobo
mock
wget
sbml =
python-libsbml
lxml
bioregistry
sbmlmath =
# sbmlmath is py3.9+ only. For version below 3.9, use the following install command locally:
# pip install sbmlmath@git+https://github.com/dweindl/sbmlmath.git --python-version py39 --ignore-requires-python
# It might be necessary to install sbmlmath, pint and lxml using --no-deps as well.
pint
lxml>=4.6.4
sbmlmath
biomodels =
pystow
viz =
pygraphviz
[mypy]
plugins = pydantic.mypy
##########################
# Darglint Configuration #
##########################
[darglint]
docstring_style = numpy
strictness = short
#########################
# Flake8 Configuration #
# (.flake8) #
#########################
[flake8]
ignore =
E203
E501 # line length
DAR005 # missing type annotation in documentation
DAR103 # type annotation mismatch
max-line-length = 120
import-order-style = pycharm
application-import-names =
mira
tests