-
Notifications
You must be signed in to change notification settings - Fork 7
/
pyproject.toml
116 lines (103 loc) · 3.5 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
114
115
116
[build-system]
requires = ["scikit-build-core", "cython >= 3.0"]
build-backend = "scikit_build_core.build"
[project]
name = "pyrodigal"
version = "3.6.3"
description = "Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes."
readme = "README.md"
requires-python = ">=3.7"
license = { file = "COPYING" }
authors = [
{ name = "Martin Larralde", email = "martin.larralde@embl.de" },
]
platform = "any"
keywords = ["bioinformatics", "genome", "orf", "gene", "prodigal"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: C",
"Programming Language :: Cython",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Medical Science Apps.",
"Typing :: Typed",
]
dependencies = [
"archspec ~=0.2.0"
]
[project.urls]
"Documentation" = "https://pyrodigal.readthedocs.io/en/stable/"
"Bug Tracker" = "https://github.com/althonos/pyrodigal/issues"
"Changelog" = "https://github.com/althonos/pyrodigal/blob/master/CHANGELOG.md"
"Coverage" = "https://codecov.io/gh/althonos/pyrodigal/"
"Builds" = "https://github.com/althonos/pyrodigal/actions"
"Paper" = "https://doi.org/10.21105/joss.04296"
"PyPI" = "https://pypi.org/project/pyrodigal"
[project.scripts]
pyrodigal = "pyrodigal.cli:main"
[project.optional-dependencies]
test = ["importlib-resources ; python_version < '3.9'"]
isal = ["isal ~=1.1"]
lz4 = ["lz4 ~=4.0"]
zst = ["zstandard ~=0.22"]
[project.entry-points.console_scripts]
pyrodigal = "pyrodigal.cli:main"
[tool.scikit-build]
build-dir = "build/{build_type}"
editable.rebuild = true
editable.verbose = false
[[tool.scikit-build.overrides]]
if.state = "editable"
cmake.build-type = "Debug"
[[tool.scikit-build-overrides]]
if.env.SCCACHE = true
cmake.define.CMAKE_C_COMPILER_LAUNCHER = "sccache"
cmake.define.CMAKE_CXX_COMPILER_LAUNCHER = "sccache"
[[tool.scikit-build-overrides]]
if.env.MOLD = true
cmake.define.CMAKE_LINKER_TYPE = "mold"
[tool.cibuildwheel]
before-build = "pip install scikit-build-core cython"
build-frontend = { name = "pip", args = ["--no-build-isolation"] }
build-verbosity = 1
test-command = "python -m unittest pyrodigal.tests -v"
test-extras = ["test"]
free-threaded-support = false
[tool.coverage.run]
plugins = ["Cython.Coverage"]
[tool.coverage.report]
include = ["src/pyrodigal/*"]
omit = ["src/pyrodigal/tests/*"]
show_missing = true
exclude_lines = [
"pragma: no cover",
"if typing.TYPE_CHECKING:",
"@abc.abstractmethod",
"@abc.abstractproperty",
"raise NotImplementedError",
"return NotImplemented",
"raise UnexpectedError",
"raise AllocationError",
]
[tool.mypy]
disallow_any_decorated = true
disallow_any_generics = true
disallow_any_unimported = false
disallow_subclassing_any = false
disallow_untyped_calls = true
disallow_untyped_defs = true
ignore_missing_imports = true
warn_unused_ignores = true
warn_return_any = true