-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathpyproject.toml
113 lines (102 loc) · 2.72 KB
/
pyproject.toml
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
[project]
name = "oneroof"
version = "0.1.0"
description = "Base-, Variant-, and Consensus-calling under One Proverbial Roof. Work in progress!"
authors = [
{ name = "Nicholas R. Minor", email = "[email protected]" },
{ name = "Andrew J. Lail", email = "[email protected]" },
{ name = "Annabelle Kalweit", email = "[email protected]" },
{ name = "William K. Gardner", email = "[email protected]" }
]
requires-python = ">= 3.10"
keywords = [
"science",
"biology",
"research",
"bioinformatics",
"sequencing",
"genomics",
"virus",
"SARS-CoV-2",
"H5N1",
"influenze",
"haplotyping",
]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dependencies = [
"polars-lts-cpu[numpy,pandas,pyarrow,pydantic,calamine,openpyxl,xlsx2csv,xlsxwriter,async,graph,plot,style,timezone]>=1.17.1",
"xlsxwriter>=3.2.0",
"xlsx2csv>=0.8.4",
"biopython>=1.84",
"pysam>=0.22.1",
"scipy>=1.14.1",
"paramiko>=3.5.0",
"plotnine>=0.14.4",
"loguru>=0.7.0",
"edlib>=1.3.9.post1",
"lxml>=5.3.0",
"pyyaml",
]
[build-system]
requires = ["setuptools >= 40.8.0", "cffi >=1.15.0,!=1.17.0"]
build-backend = "setuptools.build_meta:__legacy__"
[tool.setuptools]
py-modules = ["bin"]
[project.scripts]
"oneroof" = "bin.__main__:main"
[tool.pixi.project]
channels = ["conda-forge", "bioconda", "anaconda"]
platforms = ["osx-64", "linux-64"]
[tool.pixi.pypi-dependencies]
oneroof = { path = ".", editable = true }
[tool.pixi.dependencies]
samtools = ">=1.5,<2"
nextflow = ">=24.4.2,<24.5"
minimap2 = ">=2.28,<3"
fastqc = ">=0.12.1,<0.13"
multiqc = ">=1.19,<2"
bcftools = ">=1.16,<2"
chopper = ">=0.8.0,<0.9"
seqkit = ">=2.8.2,<2.9"
snpeff = ">=5.2,<6"
vsearch = ">=2.28.1,<2.29"
nextclade = ">=3.7.1,<3.8"
cutadapt = ">=4.8,<5"
ivar = ">=1.4.2,<1.5"
seqfu = ">=1.20.3,<1.21"
rasusa = ">=2.0.0,<2.1"
mosdepth = ">=0.3.8,<0.4"
csvtk = { version = ">=0.30.0,<0.31", channel = "bioconda"}
snpsift = ">=5.2,<6"
bbmap = ">=39.1,<40"
bedtools = ">=2.31.1,<3"
[tool.uv]
dev-dependencies = [
"basedpyright>=1.21.0",
"ipykernel>=6.29.5",
"ipython>=8.12.3",
"jupyter>=0.6.4",
"just>=0.8.162",
"mamba>=0.11.3",
"marimo[sql]>=0.9.10",
"pip>=24.2",
"pre-commit>=3.8.0",
"pytest>=8.3.3",
"quarto>=0.1.0",
"ruff>=0.6.4",
"tox>=4.18.1",
]
compile-bytecode = true
[tool.basedpyright]
venvPath = "."
venv = ".venv"
typeCheckingMode = "basic"