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

[project]
name = "specimux"
version = "0.7.2"
description = "Dual barcode and primer demultiplexing system for MinION sequenced reads"
readme = "README.md"
license = {file = "LICENSE"}
requires-python = ">=3.10"
authors = [
    {name = "Josh Walker", email = "joshowalker@yahoo.com"},
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
keywords = ["bioinformatics", "demultiplexing", "minion", "nanopore", "sequencing"]

dependencies = [
    "edlib>=1.1.2",
    "biopython>=1.81",
    "pybloomfilter3>=0.7.3",
    "cachetools>=5.3.0",
    "tqdm>=4.65.0",
    "plotly>=5.0.0",  # Included by default for visualization
    "watchdog>=3.0.0",  # File system monitoring for specimux-watch
    "pyyaml>=5.0",  # Profile system
]

[project.optional-dependencies]
# Note: For minimal install without plotly, users would need to install from source
# and modify dependencies. Consider making plotly truly optional if size is a concern.
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "ruff>=0.1.0",
]
test = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
]

[project.scripts]
specimux = "specimux.cli:main"
specimine = "specimux.cli:specimine_main"
specimux-convert = "specimux.cli:converter_main"
specimux-stats = "specimux.cli:trace_main"
specimux-visualize = "specimux.cli:visualize_main"
specimux-watch = "specimux.cli:watch_main"

[project.urls]
Homepage = "https://github.com/joshuaowalker/specimux"
Repository = "https://github.com/joshuaowalker/specimux"
Issues = "https://github.com/joshuaowalker/specimux/issues"

[tool.setuptools.packages.find]
where = ["src"]
include = ["specimux*"]

[tool.setuptools.package-data]
"*" = ["*.txt", "*.fasta", "*.fastq", "*.yaml"]