STADiffuser/setup.py at main · messcode/STADiffuser · 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
"""
Cipyright (c) 2024, My Company
"""
import re
import sys
from setuptools import Command, find_packages, setup
from setuptools.command.install import install


_deps = [
    "scanpy>=1.9.3,<1.11",
    "scikit-learn>=1.3.0,<1.4",
    "scipy>=1.10.1",
    "pandas>=2.0.3,<2.1",
    "anndata>=0.10.7,<0.11",
    "torch>=1.13.1",
    "diffusers>=0.17.1,<0.18",
    "torch-geometric>=2.3.1",
    "tqdm>=4.65.0",
    "rpy2>=3.5.13",
    "jupyter>=1.0.0",
    "ipywidgets==7.6.5",
    "widgetsnbextension==3.5.1",
    "notebook==6.1.5"
]

# set rpy2 "rpy2>=3.5.13,<3.6", to be optional


deps = {b: a for a, b in (re.findall(r"^(([^!=<>~]+)(?:[!=<>~].*)?$)", x)[0] for x in _deps)}


def deps_list(*pkgs):
    return [deps[pkg] for pkg in pkgs]


class DepsTableUpdateCommand(Command):
    """
    A custom command that updates the dependency table.
    usage: python setup.py deps_table_update
    """

    description = "build runtime dependency table"
    user_options = [
        # format: (long option, short option, description).
        (
            "dep-table-update",
            None,
            "updates stadiffuser/dependency_versions_table.py",
        ),
    ]

    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def run(self):
        entries = "\n".join([f'    "{k}": "{v}",' for k, v in deps.items()])
        content = [
            "# THIS FILE HAS BEEN AUTOGENERATED. To update:",
            "# 1. modify the `_deps` dict in setup.py",
            "# 2. run `make deps_table_update`",
            "deps = {",
            entries,
            "}",
            "",
        ]
        target = "stadiffuser/dependency_versions_table.py"
        print(f"updating {target}")
        with open(target, "w", encoding="utf-8", newline="\n") as f:
            f.write("\n".join(content))

extras = {}
extras["rpy2"] = deps_list("rpy2")

version_range_max = max(sys.version_info[1], 10) + 1
install_requires = [
    deps["scanpy"],
    deps["scikit-learn"],
    deps["scipy"],
    deps["torch"],
    deps["torch-geometric"],
    deps["diffusers"],
    deps["tqdm"],
    deps["ipywidgets"],
    deps["jupyter"],
    deps["widgetsnbextension"],
    deps["notebook"],
]


setup(
    name="stadiffuser",
    version="0.1.1",
    description="A versatile simulation framework for spatial transcriptomics data",
    author="Chihao Zhang",
    author_email="zhangchihao11@outlook.com",
    python_requires=">=3.8.0",
    install_requires=list(list(install_requires)),
    extras_require=extras,
    packages=find_packages(),
    entry_points={
        'console_scripts': [
            'stadiffuser-cli=scripts.cli:main',
        ],
    },
)