sbmlsim/pyproject.toml at develop · matthiaskoenig/sbmlsim · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "sbmlsim"
dynamic = ["version"]
description = "sbmlsim are utilities for the simulation of SBML models."
readme = "README.md"
requires-python = ">=3.13"
authors = [
	{name="Matthias König", email="konigmatt@googlemail.com"}
]
maintainers = [
	{name="Matthias König", email="konigmatt@googlemail.com"}
]
classifiers = [
	"Development Status :: 4 - Beta",
	"Intended Audience :: Science/Research",
	"License :: OSI Approved :: MIT License",
	"Operating System :: OS Independent",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
	"Programming Language :: Python :: Implementation :: CPython",
	"Topic :: Scientific/Engineering",
	"Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = [
	"modeling",
	"standardization",
	"COMBINE",
    "SBML",
]
dependencies = [
    "sbmlutils>=0.9.6",
    "pkdb-analysis>=0.3.1",
    "pymetadata>=0.5.10",
    # from sbmlutils (no version pin)
    "numpy",
    "libroadrunner",
    "python-libsbml",
    "rich",
    "pint",
    "pandas",
    "Jinja2",
    "scipy",
    "sympy",
    "matplotlib",
    "pydantic>=2.12.5",
    # dependencies
    "dill>=0.4.0",
    "SAlib>=1.5.2",
    "petab>=0.8.1",
    # "tables>=3.10.2",
    "statsmodels>=0.14.6",
    "typst>=0.14.5",
    "xarray>=2025.11.0",
    "bottleneck>=1.4.2",
    "psutil>=6.1.1",
    "setproctitle>=1.3.4",
    "plotly>=6.0.0",
    "altair>=5.5.0",
    "seaborn>=0.13.2",
    "xmltodict>=0.14.2",
    "pyDOE>=0.3.8",
    "python-libsedml>=2.0.33",
    "python-libnuml>=1.1.7",
]

[project.optional-dependencies]
dev = [
    "bump-my-version>=1.2.4",
	"ruff>=0.14.0",
	"pre-commit>=4.0.1",
	"mypy>=1.18.2",
    "tox>=4.31.0",
    "pytest>=8.4.2",
    "pytest-cov>=7.0.0",
    "quartodoc>=0.11.1",
]

[project_urls]
Homepage = "https://github.com/matthiaskoenig/sbmlsim"
Repository = "https://github.com/matthiaskoenig/sbmlsim"
Documentation = "https://github.com/matthiaskoenig/sbmlsim"
Issues = "https://github.com/matthiaskoenig/sbmlsim/issues"
Download = "https://pypi.org/project/sbmlsim"

[tool.hatch.version]
path = "./src/sbmlsim/__init__.py"