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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "biosimulators-processes"
version = "0.2.5"
description = "Core implementations of process-bigraph.composite.Process aligning with BioSimulators simulator tools."
authors = ["Alex Patrie <[email protected]>"]
readme = "README.md"
packages = [{include = "biosimulators_processes"}]
[tool.poetry.dependencies]
python = ">=3.10"
termcolor = "^2.4.0"
jupyterlab = "^4.2.1"
bigraph-viz = "*"
bigraph-builder = "*"
numpy = "^1.26.4"
python-libsbml = "^5.20.2"
docker = "^7.1.0"
notebook = "^7.2.0"
toml = "^0.10.2"
pyyaml = "^6.0.1"
pydantic = "^2.7.2"
seaborn = "^0.13.2"
h5py = "^3.11.0"
bigraph-schema = "*"
process-bigraph = "*"
cobra = {version = "^0.29.0", optional = true, extras = ["imageio"]}
smoldyn = {version = "*", optional = true, extras = ["simulariumio"]}
amici = {version = "^0.25.1", optional = true}
copasi-basico = {version = "^0.69", optional = true}
tellurium = {version = "^2.2.10", optional = true}
pymongo = {version = "^4.8.0", optional = true}
biosimulators-utils = {version = "^0.1.188", optional = true, extras = ["logging"]}
simulariumio = {version = "^1.11.0", optional = true}
imageio = {version = "*", optional = true}
[tool.poetry.extras]
simulators = ["smoldyn", "amici", "cobra", "copasi-basico", "tellurium"]
amici = ["amici"]
cobra = ["cobra"]
copasi = ["copasi-basico"]
tellurium = ["tellurium"]
utc = ["amici", "copasi-basico", "tellurium"]
mongo = ["pymongo"]
simularium = ["simulariumio"]
[tool.poetry.group.dev.dependencies]
pytest = "^8.2.1"
mypy = "^1.10.0"
flake8 = "^7.0.0"
[tool.pytest.ini_options]
testpaths = ["biosimulator_processes", "test_suite"]
addopts = "--ignore=setup.py"
python_files = "*.py"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"