MONSDA/setup.py at main · jfallmann/MONSDA · 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
#!/usr/bin/env python

import os
from collections import defaultdict
from glob import glob

from setuptools import find_packages, setup

import versioneer

NAME = "MONSDA"
DESCRIPTION = (
    "MONSDA, Modular Organizer of Nextflow and Snakemake driven HTS Data Analysis"
)
# Set __version__ done by versioneer
# exec(open("MONSDA/__init__.py").read())


def generate_datafiles():
    df = list()
    dirlist = defaultdict(list)

    libs = list()
    for l in glob("MONSDA/lib/*"):
        if any(x in l for x in [".pl", ".pm", ".py", ".sh", ".R", ".groovy"]):
            libs.append(os.path.relpath(l))
    for l in libs:
        dirlist[str(os.path.join("share", os.path.dirname(l)))].append(l)

    scripts = list()
    for s in glob("scripts/**", recursive=True):
        if any(x in s for x in [".pl", ".pm", ".py", ".sh", ".R"]):
            scripts.append(os.path.relpath(s))  # os.path.join(s, os.path.split(s)[1]))
    for s in scripts:
        dirlist[str(os.path.join("share", "MONSDA", os.path.dirname(s)))].append(s)

    workflows = list()
    for d in glob("workflows/*"):
        if "wip" not in d:
            workflows.append(
                os.path.relpath(d)
            )  # os.path.join(d, os.path.split(d)[1]))
    for w in workflows:
        dirlist[os.path.join("share", "MONSDA", os.path.dirname(w))].append(w)

    envs = list()
    for e in glob("envs/*"):
        envs.append(os.path.relpath(e))  # os.path.join(d, os.path.split(d)[1]))
    for e in envs:
        dirlist[os.path.join("share", "MONSDA", os.path.dirname(e))].append(e)

    confs = list()
    for c in glob("configs/*"):
        if any(x in c for x in [".json"]):
            confs.append(os.path.relpath(c))  # os.path.join(d, os.path.split(d)[1]))
    for c in confs:
        dirlist[os.path.join("share", "MONSDA", os.path.dirname(c))].append(c)

    profiles = list()
    for p in glob("profile_*/**"):
        profiles.append(os.path.relpath(p))  # os.path.join(d, os.path.split(d)[1]))
    for p in profiles:
        dirlist[os.path.join("share", "MONSDA", os.path.dirname(p))].append(p)

    dirlist[""].append("LICENSE")

    for k, v in dirlist.items():
        df.append((k, v))

    return df


# requires = open(os.path.abspath("requirements.txt")).read().strip().split("\n")

setup(
    name=NAME,
    version=versioneer.get_version(),
    cmdclass=versioneer.get_cmdclass(),
    description=DESCRIPTION,
    author="Joerg Fallmann",
    author_email="jot.fallmann@gmail.com",
    packages=find_packages(include=["MONSDA", "MONSDA.*"]),
    include_package_data=True,
    data_files=generate_datafiles(),
    entry_points={
        "console_scripts": [
            "monsda = MONSDA.RunMONSDA:main",
            "monsda_configure = MONSDA.Configurator:main",
        ]
    },
    # install_requires=requires,
    install_requires=[
        "biopython>=1.86",
        "fastapi>=0.128.5",
        "isort>=5.13.2",
        "natsort>=8.4.0",
        "numpy>=2.4.2",
        "pandas>=2.3.3",
        "pyyaml>=6.0.3",
        "scipy>=1.17.0",
        "snakemake>=9.16.3",
        "uvicorn>=0.40.0",
    ],
    python_requires=">=3.12.0",
    setup_requires=["pytest-runner"],
    zip_safe=False,
    license="LICENSE",
    url="https://github.com/jfallmann/MONSDA",
    long_description_content_type="text/markdown",
    long_description=open("README.md").read(),
)