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poetry.lock
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# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand.
[[package]]
name = "amici"
version = "0.30.0"
description = "Advanced multi-language Interface to CVODES and IDAS"
optional = true
python-versions = ">=3.10"
groups = ["main"]
markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"amici\""
files = [
{file = "amici-0.30.0.tar.gz", hash = "sha256:8e7038b890d8b3336dcd2115590576a8395c87fbcb436134072021c72a22bf01"},
]
[package.dependencies]
cmake-build-extension = "0.6.0"
mpmath = "*"
numpy = [
{version = ">=1.21.4", markers = "python_version >= \"3.10\" and python_version != \"3.11\" and python_version != \"3.12\""},
{version = ">=1.23.2", markers = "python_version == \"3.11\""},
{version = ">=1.26.2", markers = "python_version == \"3.12\""},
]
pandas = ">=2.0.2"
pyarrow = "*"
python-libsbml = "*"
setuptools = ">=48"
sympy = ">=1.12.1"
toposort = "*"
[package.extras]
examples = ["jupyter", "scipy"]
jax = ["diffrax (>=0.6.0)", "equinox (>=0.11.8)", "interpax (>=0.3.3)", "jax (>=0.4.34,<0.4.36)", "jaxlib (>=0.4.34)", "jaxtyping (>=0.2.34)", "optimistix (>=0.0.9)"]
petab = ["petab (>=0.4.0)"]
pysb = ["pysb (>=1.13.1)"]
test = ["antimony (!=2.14)", "antimony (>=2.13)", "beartype", "coverage", "h5py", "pooch", "pytest", "pytest-cov", "pytest-rerunfailures", "scipy", "shyaml"]
vis = ["matplotlib", "seaborn"]
[[package]]
name = "annotated-types"
version = "0.7.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = true
python-versions = ">=3.8"
groups = ["main"]
markers = "(extra == \"cobra\" or extra == \"quantum\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
files = [
{file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
{file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
]
[[package]]
name = "antimony"
version = "2.15.0"
description = "Python bindings for libAntimony"
optional = true
python-versions = "*"
groups = ["main"]
markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"tellurium\""
files = [
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{file = "antimony-2.15.0-py3-none-win_amd64.whl", hash = "sha256:a1c0e39e7d92910bd4c7b92f72ba63d29736aec8e877200bb523b8892b6db241"},
]
[[package]]
name = "anyio"
version = "4.8.0"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
optional = true
python-versions = ">=3.9"
groups = ["main"]
markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"cobra\""
files = [
{file = "anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a"},
{file = "anyio-4.8.0.tar.gz", hash = "sha256:1d9fe889df5212298c0c0723fa20479d1b94883a2df44bd3897aa91083316f7a"},
]
[package.dependencies]
exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
idna = ">=2.8"
sniffio = ">=1.1"
typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
[package.extras]
doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"]
trio = ["trio (>=0.26.1)"]
[[package]]
name = "appdirs"
version = "1.4.4"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
optional = true
python-versions = "*"
groups = ["main"]
markers = "(extra == \"cobra\" or extra == \"tellurium\") and (python_version <= \"3.11\" or python_version >= \"3.12\")"
files = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
{file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
]
[[package]]
name = "appnope"
version = "0.1.4"
description = "Disable App Nap on macOS >= 10.9"
optional = true
python-versions = ">=3.6"
groups = ["main"]
markers = "platform_system == \"Darwin\" and extra == \"tellurium\" and (python_version <= \"3.11\" or python_version >= \"3.12\")"
files = [
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{file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
]
[[package]]
name = "asttokens"
version = "3.0.0"
description = "Annotate AST trees with source code positions"
optional = false
python-versions = ">=3.8"
groups = ["main"]
markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
files = [
{file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
{file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
]
[package.extras]
astroid = ["astroid (>=2,<4)"]
test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
[[package]]
name = "bigraph-builder"
version = "0.0.4"
description = ""
optional = true
python-versions = ">=3.6"
groups = ["main"]
markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"builder\""
files = [
{file = "bigraph-builder-0.0.4.tar.gz", hash = "sha256:15801fb147e221cec09d9042af877281921d09bf69120f4103a6bdd10843f5e0"},
]
[package.dependencies]
bigraph-viz = "*"
process-bigraph = "*"
[[package]]
name = "bigraph-schema"
version = "0.0.49"
description = "A serializable type schema for compositional systems biology"
optional = false
python-versions = ">=3.7"
groups = ["main"]
markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
files = [
{file = "bigraph-schema-0.0.49.tar.gz", hash = "sha256:e4cdd0a52c01ddaac189c6f727c0635fde5c7a2c318ea61ac6c0b65a2844e144"},
]
[package.dependencies]
fire = "*"
numpy = "*"
parsimonious = "*"
pint = "*"
pytest = "*"
[[package]]
name = "bigraph-viz"
version = "0.0.35"
description = "A graphviz-based plotting tool for compositional bigraph schema"
optional = true
python-versions = ">=3.6"
groups = ["main"]
markers = "(python_version <= \"3.11\" or python_version >= \"3.12\") and extra == \"builder\""
files = [
{file = "bigraph-viz-0.0.35.tar.gz", hash = "sha256:ce23459aaccd9650c6ae5457209a29b16d362cdbf64289d89269d4297c7e6cab"},
]
[package.dependencies]
bigraph-schema = "*"
graphviz = "*"
numpy = "*"
[[package]]
name = "certifi"
version = "2024.12.14"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
groups = ["main"]
markers = "python_version <= \"3.11\" or python_version >= \"3.12\""
files = [
{file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
{file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
]
[[package]]
name = "cffi"
version = "1.17.1"
description = "Foreign Function Interface for Python calling C code."
optional = true
python-versions = ">=3.8"
groups = ["main"]
markers = "(platform_python_implementation != \"PyPy\" or implementation_name == \"pypy\") and (platform_python_implementation != \"PyPy\" or extra == \"tellurium\") and (extra == \"quantum\" or extra == \"tellurium\") and (python_version <= \"3.11\" or python_version >= \"3.12\") and (extra == \"quantum\" or implementation_name == \"pypy\")"
files = [
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