ATOMICA/pyproject.toml at main · mims-harvard/ATOMICA · 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
[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "atomica"
version = "0.1.0"
description = "ATOMICA"
readme = "README.md"
requires-python = ">=3.9"
dependencies = [
    # Core PyTorch and ML libraries
    "torch==2.1.1",
    "torch-scatter==2.1.2",
    "torch-cluster==1.6.3",
    "numpy==1.26.4",
    "scipy==1.13.1",

    # Chemistry and structure libraries
    "rdkit-pypi==2022.9.5",
    "openbabel-wheel==3.1.1.20",
    "biopython==1.84",
    "biotite==0.40.0",
    "e3nn==0.5.1",

    # Data processing
    "pandas==2.2.3",
    "pyarrow==21.0.0",
    "orjson==3.10.16",

    # Utilities
    "tqdm==4.66.5",
    "joblib==1.4.2",
    "networkx==3.2.1",
    "sympy==1.13.3",

    # ML utilities
    "scikit-learn==1.5.2",

    # Logging and experiment tracking
    "wandb==0.18.2",
    "tensorboard==2.18.0",

    # Visualization
    "matplotlib==3.9.2",
    "seaborn==0.13.2",
    "plotly==5.24.1",
    "umap-learn==0.5.6",
]

[project.optional-dependencies]
dev = [
    "pytest",
    "black",
    "flake8",
    "jupyter",
    "ipywidgets",
]

# Interaction profiling features (optional)
interaction_profiler = [
    "plip",  # Protein-Ligand Interaction Profiler
]

# GPU acceleration (install with --extra-index-url for CUDA builds)
gpu = []  # Instructions in https://github.com/mims-harvard/ATOMICA/blob/main/setup/install_atomica_uv.sh for torch+cu118, torch-scatter+cu118, torch-cluster+cu118

# All optional features
all = [
    "atomica[dev,interaction_profiler]",
]

[project.scripts]
atomica-train = "atomica.train:cli"
atomica-embeddings = "atomica.get_embeddings:cli"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-dir]
"" = "src"

[tool.setuptools.package-data]
atomica = [
    "data/tokenizer/vocabs/*.txt",
    "data/converter/*.txt",
]

# Build dependencies for packages that need torch at build time
[tool.uv.extra-build-dependencies]
torch-scatter = ["torch==2.1.1"]
torch-cluster = ["torch==2.1.1"]