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# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand.
[[package]]
name = "annotated-types"
version = "0.7.0"
description = "Reusable constraint types to use with typing.Annotated"
optional = false
python-versions = ">=3.8"
groups = ["main"]
files = [
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]
[[package]]
name = "antlr4-python3-runtime"
version = "4.13.2"
description = "ANTLR 4.13.2 runtime for Python 3"
optional = false
python-versions = "*"
groups = ["main"]
files = [
{file = "antlr4_python3_runtime-4.13.2-py3-none-any.whl", hash = "sha256:fe3835eb8d33daece0e799090eda89719dbccee7aa39ef94eed3818cafa5a7e8"},
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]
[[package]]
name = "anyio"
version = "4.9.0"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
optional = false
python-versions = ">=3.9"
groups = ["main"]
files = [
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{file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"},
]
[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 (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"]
test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\" and python_version < \"3.14\""]
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 = false
python-versions = "*"
groups = ["main"]
files = [
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]
[[package]]
name = "asttokens"
version = "3.0.0"
description = "Annotate AST trees with source code positions"
optional = false
python-versions = ">=3.8"
groups = ["main"]
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-schema"
version = "0.0.57"
description = "A serializable type schema for compositional systems biology"
optional = false
python-versions = ">=3.7"
groups = ["main"]
files = [
{file = "bigraph-schema-0.0.57.tar.gz", hash = "sha256:29d625a8f63fc416b85ec888218e45e4a21f353900d9f56548c20044c897dacd"},
]
[package.dependencies]
fire = "*"
numpy = "*"
parsimonious = "*"
pint = "*"
pytest = "*"
[[package]]
name = "bigraph-viz"
version = "0.1.5"
description = "A graphviz-based plotting tool for compositional bigraph schema"
optional = false
python-versions = ">=3.6"
groups = ["main"]
files = [
{file = "bigraph-viz-0.1.5.tar.gz", hash = "sha256:0164c9041fdbc2aeb5cb370b40e45b5a170aa295ef75db0be224375c44b2b99d"},
]
[package.dependencies]
bigraph-schema = ">=0.0.51"
graphviz = "*"
numpy = "*"
[[package]]
name = "cachetools"
version = "5.5.2"
description = "Extensible memoizing collections and decorators"
optional = false
python-versions = ">=3.7"
groups = ["dev"]
files = [
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{file = "cachetools-5.5.2.tar.gz", hash = "sha256:1a661caa9175d26759571b2e19580f9d6393969e5dfca11fdb1f947a23e640d4"},
]
[[package]]
name = "certifi"
version = "2025.4.26"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
groups = ["main"]
files = [
{file = "certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3"},
{file = "certifi-2025.4.26.tar.gz", hash = "sha256:0a816057ea3cdefcef70270d2c515e4506bbc954f417fa5ade2021213bb8f0c6"},
]
[[package]]
name = "cfgv"
version = "3.4.0"
description = "Validate configuration and produce human readable error messages."
optional = false
python-versions = ">=3.8"
groups = ["dev"]
files = [
{file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
{file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
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[[package]]
name = "chardet"
version = "5.2.0"
description = "Universal encoding detector for Python 3"
optional = false
python-versions = ">=3.7"
groups = ["dev"]
files = [
{file = "chardet-5.2.0-py3-none-any.whl", hash = "sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970"},
{file = "chardet-5.2.0.tar.gz", hash = "sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7"},
]
[[package]]
name = "click"
version = "8.2.0"
description = "Composable command line interface toolkit"
optional = false
python-versions = ">=3.10"
groups = ["main", "dev"]
files = [
{file = "click-8.2.0-py3-none-any.whl", hash = "sha256:6b303f0b2aa85f1cb4e5303078fadcbcd4e476f114fab9b5007005711839325c"},
{file = "click-8.2.0.tar.gz", hash = "sha256:f5452aeddd9988eefa20f90f05ab66f17fce1ee2a36907fd30b05bbb5953814d"},
]
[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}
[[package]]
name = "cobra"
version = "0.29.1"
description = "COBRApy is a package for constraint-based modeling of metabolic networks."
optional = false
python-versions = "*"
groups = ["main"]
files = [
{file = "cobra-0.29.1-py2.py3-none-any.whl", hash = "sha256:734df889e751171c12ee9c5ec6f2567f47f9997e183822d4290776aa650c9593"},
{file = "cobra-0.29.1.tar.gz", hash = "sha256:47cd4fe80eb329ed75ccfb7ecbaac6275e986685392d52922bc8ad3cbc599674"},
]
[package.dependencies]
appdirs = ">=1.4,<2.0"
depinfo = ">=2.2,<3.0"
diskcache = ">=5.0,<6.0"
future = "*"
httpx = ">=0.24,<1.0"
importlib-resources = "*"
numpy = ">=1.13"
optlang = ">=1.8,<2.0"
pandas = ">=1.0,<3.0"
pydantic = ">=1.6"
python-libsbml = ">=5.19,<6.0"
rich = ">=8.0"
"ruamel.yaml" = ">=0.16,<1.0"
swiglpk = "*"
[package.extras]
array = ["scipy"]
development = ["black", "bumpversion", "isort", "tox"]
[[package]]
name = "colorama"
version = "0.4.6"
description = "Cross-platform colored terminal text."
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
groups = ["main", "dev"]
files = [
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markers = {main = "sys_platform == \"win32\" or platform_system == \"Windows\""}
[[package]]
name = "contourpy"
version = "1.3.2"
description = "Python library for calculating contours of 2D quadrilateral grids"
optional = false
python-versions = ">=3.10"
groups = ["main"]
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