rebop 0.9.5

A fast stochastic simulator for chemical reaction networks
Documentation 
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
91
92
93
94
95
96
97
98

[build-system]
requires = ["maturin>=1.9.6,<2.0"]
build-backend = "maturin"

[project]
name = "rebop"
authors = [
  { name = "Virgile Andreani", email = "virgile.andreani@proton.me" },
]
requires-python = ">=3.12"
dynamic = ["version"]
dependencies = ["xarray >= 2023.10"]
description = "A fast stochastic simulator for chemical reaction networks"
readme = "README.md"
keywords = ["gillespie-algorithm", "systems-biology", "stochastic", "scientific-computing"]
classifiers = [
    "Programming Language :: Rust",
    "Programming Language :: Python :: Implementation :: CPython",
    "Programming Language :: Python :: Implementation :: PyPy",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

[project.optional-dependencies]
dev = [
  "pytest>=8.3.4,<9",
  "maturin>=1.9.6,<2",
  "pip>=24.3.1,<25",
  "pre-commit>=4.0.1,<5",
]

doc = [
  "mkdocs>=1.6.1,<2",
  "mkdocs-material>=9.5.49,<10",
  "mkdocstrings[python]>=0.27.0,<0.28",
]

[tool.maturin]
python-source = "python"
module-name = "rebop._lib"
features = ["pyo3/extension-module"]

[tool.ruff]
extend-exclude = ["benches/*"]

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = ["ALL"]
ignore = [
  "COM812",  # Incompatible with ruff-format
  "ISC001",  # Incompatible with ruff-format
  "RET504",  # Unnecessary asignment before return
  "PYI021",  # Docstrings should not be included in stubs
]

[tool.ruff.lint.per-file-ignores]
"tests/test_*.py" = ["D", "S101", "PLR2004", "ANN201"]
"examples/*" = ["INP001"]
"examples/*.py" = ["T201"]
"python/rebop/__init__.py" = ["D104"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.pytest.ini_options]
minversion = "7"
testpaths = ["tests"]
log_cli_level = "INFO"
xfail_strict = true
addopts = ["-ra", "--strict-config", "--strict-markers"]
filterwarnings = ["error"]

[tool.mypy]
strict = true
warn_unreachable = true
disallow_untyped_decorators = false
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]

[tool.pixi.workspace]
channels = ["conda-forge"]
platforms = ["linux-64"]

[tool.pixi.pypi-dependencies]
rebop = { path = ".", editable = true }

[tool.pixi.feature.dev.tasks]
build = "maturin develop --extras dev"

[tool.pixi.environments]
dev = { features = ["dev"] }
doc = { features = ["doc"] }