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
|
[project]
name = "CNVkit"
description = "Copy number variation toolkit for high-throughput sequencing."
readme = "README.rst"
#license = "Apache-2.0"
license = {text = "Apache-2.0"}
authors = [
{name = "Eric Talevich", email = "me+code@etal.mozmail.com"}
]
maintainers = [
{name = "Eric Talevich", email = "me+code@etal.mozmail.com"}
]
classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Science/Research",
"Intended Audience :: Healthcare Industry",
"License :: OSI Approved :: Apache Software License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX",
"Operating System :: POSIX :: Linux",
"Operating System :: Unix",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
"Topic :: Scientific/Engineering :: Visualization"
]
requires-python = ">=3.8"
dynamic = ["version", "dependencies", "optional-dependencies"]
[project.urls]
homepage = "https://github.com/etal/cnvkit"
documentation = "https://readthedocs.org"
repository = "https://github.com/etal/cnvkit"
changelog = "https://github.com/me/spam/blob/master/CHANGELOG.md"
[project.scripts]
"cnvkit.py" = "cnvlib.cnvkit:main"
# XXX TODO -- move these scripts under cnvlib.cli and skgenome.cli?
#"cnv_annotate.py" = "scripts.cnv_annotate"
#"cnv_expression_correlate.py" = "scripts.cnv_expression_correlate"
#"cnv_updater.py" = "scripts.cnv_updater"
#"genome_instability_index.py" = "scripts.genome_instability_index"
#"guess_baits.py" = "scripts.guess_baits"
#"reference2targets.py" = "scripts.reference2targets"
#"skg_convert.py" = "scripts.skg_convert"
#"snpfilter.sh" = "scripts/snpfilter.sh"
# -- from setup.py --
# scripts=[join(DIR, 'cnvkit.py')] + glob(join(DIR, 'scripts/*.py')),
[build-system]
# Minimum requirements for the build system to execute (PEP 508)
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
packages = ["cnvlib", "cnvlib.segmentation", "skgenome", "skgenome.tabio"]
[tool.setuptools.dynamic]
version = {attr = "cnvlib._version.__version__"}
dependencies = {file = "requirements/core.txt"}
optional-dependencies = {test = {file = "requirements/tests.txt"}}
[tool.pytest.ini_options]
testpaths = ["test"]
[tool.coverage.run]
branch = true
source = ["cnvlib", "skgenome"]
[tool.coverage.paths]
source = ["cnvlib", "skgenome"]
[tool.mypy]
python_version = "3.10"
files = ["src/flask"]
show_error_codes = true
pretty = true
#strict = true
allow_redefinition = true
disallow_subclassing_any = true
#disallow_untyped_calls = true
#disallow_untyped_defs = true
#disallow_incomplete_defs = true
no_implicit_optional = true
local_partial_types = true
#no_implicit_reexport = true
strict_equality = true
warn_redundant_casts = true
warn_unused_configs = true
warn_unused_ignores = true
#warn_return_any = true
#warn_unreachable = true
[[tool.mypy.overrides]]
module = [
"Bio.*",
"matplotlib.*",
"pandas",
"pomegranate",
"pyfaidx",
"reportlab.*",
"scipy.*",
"sklearn.*",
]
ignore_missing_imports = true
|
