bettercode/pyproject.toml at main · BetterCodeBetterScience/bettercode · 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
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
[project]
name = "bettercode"
version = "0.2.0"
description = "Code for BetterCodeBetterScience book"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    # Core scientific computing
    "numpy>=2.1.2",
    "scipy>=1.14.1",
    "pandas>=2.2.3",
    "matplotlib>=3.9.2",
    "seaborn>=0.13.2",
    "scikit-learn>=1.5.2",
    # Testing
    "pytest>=8.3.3",
    "pytest-cov>=5.0.0",
    "pytest-mock>=3.14.0",
    "pytest-order>=1.2.0",
    "hypothesis>=6.115.3",
    # Development tools
    "ruff>=0.6.9",
    "codespell>=2.4.1",
    "pre-commit>=4.2.0",
    "jupytext>=1.16.4",
    # Book building
    "mystmd>=1.7.0",
    "linkcheckmd>=1.4.0",
    # LLM/AI
    "anthropic>=0.61.0",
    # Neuroimaging
    "nibabel>=5.3.2",
    # Single-cell RNA-seq
    "anndata>=0.12.7",
    "scanpy>=1.11.5",
    "pydeseq2>=0.5.3",
    "gseapy>=1.1.11",
    "leidenalg>=0.11.0",
    "harmonypy>=0.0.10",
    # Databases
    "pymongo[srv]>=4.15.4",
    "neo4j>=6.0.3",
    "chromadb>=1.3.5",
    # Bioinformatics
    "biopython>=1.86",
    "gprofiler-official>=1.0.0",
    "ols-client>=0.2.1",
    # Data formats
    "h5py>=3.15.1",
    # Utilities
    "python-dotenv>=1.0.1",
    "tqdm>=4.66.5",
    "requests>=2.32.0",
    "wonderwords>=2.2.0",
    "pymc>=5.27.0",
    "arviz>=0.23.0",
    "ipywidgets>=8.1.8",
    "pgmpy>=1.0.0",
    "pygraphviz>=1.14",
    "tigramite>=5.2.9.4",
    "torch>=2.9.1",
    "sdv>=1.32.1",
    "fastparquet>=2025.12.0",
    "pyarrow==18.1.0",
    "ipykernel>=7.1.0",
    "openpyxl>=3.1.5",
    "fastcluster>=1.3.0",
    "palmerpenguins>=0.1.4",
    "arch>=8.0.0",
    "rpy2>=3.6.4",
    "line-profiler>=5.0.0",
    "memory-profiler>=0.61.0",
    "dask>=2024.12.0",
    "distributed>=2024.12.0",
    "psutil>=5.9.0",
    "duckdb>=1.4.3",
    "polars>=1.37.1",
    "tabulate>=0.9.0",
    "opt-einsum>=3.4.0",
    "bokeh>=3.8.2",
    "icecream>=2.1.10",
    "mypy>=1.19.1",
    "templateflow>=25.1.1",
    "flake8>=7.0.0",
    "blue>=0.9.0",
    "datasets>=4.0.0",
    "openai>=2.21.0",
]

[build-system]
requires = ["uv_build>=0.10.2,<0.11.0"]
build-backend = "uv_build"

[tool.uv.build-backend]
module-root = "src"
source-exclude = [
    "tests/",
    "data/",
    "docker-example/",
    "notebooks/",
    "*.pyc",
]

# add script entry points here
[project.scripts]
check-links = "bettercode.check_links:main"
dask-parallel-demo = "bettercode.dask_parallel_demo:main"

[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = './book/transcripts,./book/_build/html,.js*,.git*,*.lock,*.bib,.venv*,*.ipynb,*.json'
check-hidden = true
ignore-regex = '\b(BLOSUM|Shapin)\b'
ignore-words = 'project-words.txt'

[tool.pytest.ini_options]
markers = [
    "unit: mark a test as a unit test.",
    "integration: mark a test as an integration test."
]