isa-api/pyproject.toml at master · ISA-tools/isa-api · 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
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
[project]
name = "isatools"
version = "0.14.3"
description = "Metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments"
readme = "README.md"
requires-python = ">=3.9,<4"

license = "CPAL-1.0"
license-files = ["LICENSE.txt"]

authors = [
        { name = "ISA Infrastructure Team", email = "isatools@googlegroups.com" },
]
keywords = []


classifiers = [
    "Operating System :: OS Independent",
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Healthcare Industry",
    "Intended Audience :: System Administrators",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "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",
]
dependencies = [
    "setuptools>=77.0.3,<81",
    'numpy~=2.0.2 ; python_version < "3.10"',
    'numpy~=2.2.4 ; python_version >= "3.10"',
    'networkx>=3.2,<3.3 ; python_version < "3.10"',
    'networkx~=3.4.2 ; python_version >= "3.10"',
    "jsonschema>=4.23.0,<5",
    "pandas>=2.2.3,<3",
    "openpyxl>=3.1.5",
    "lxml~=6.0.2",
    "requests~=2.32.4",
    "iso8601~=2.1.0",
    "chardet~=5.2.0",
    "jinja2~=3.1.4",
    "ddt~=1.7.2",
    "deepdiff~=8.6.1",
    "beautifulsoup4~=4.14.2",
    "mzml2isa==1.1.1",
    "biopython>=1.85,<1.86",
    "progressbar2~=4.5.0",
    "PyYAML~=6.0.2",
    "rdflib~=7.2.1",
    "python-dateutil~=2.9.0.post0",
    "Flask>=3.1.1",
    "flask_sqlalchemy>=3.0.2",
    "SQLAlchemy~=2.0.31", #1.4.54
    "graphene~=3.4.3",
    "graphql-core~=3.2.6",
    "ruff>=0.14.1",
    "pytest-timeout>=2.4.0",
]

[project.optional-dependencies]
notebook = ["bokeh~=3.4.2"]

[project.urls]
Code = "https://github.com/ISA-tools/isa-api"
"Bug Tracker" = "https://github.com/ISA-tools/isa-api/issues"
Changelog = "https://github.com/ISA-tools/isa-api/issues"
Documentation = "https://isa-tools.org/isa-api/content/index.html"
Coverage = "https://coveralls.io/github/ISA-tools/isa-api?branch=master"
CI = "https://github.com/ISA-tools/isa-api/actions"

[build-system]
requires = ["uv_build>=0.9.3"]
build-backend = "uv_build"

[tool.uv.build-backend]
module-name = "isatools"
module-root = ""
# data = ["resources/**/*", "net/**/*"]

[dependency-groups]
dev = [
    "pytest>=8.3.5,<9.0.0",
    "coveralls>=4.0.1",
    "sure>=2.0.1",
    "ddt>=1.7.2",
    "deepdiff>=8.6.1",
    "behave>=1.2.6",
    "httpretty>=1.1.4",
    "import-linter>=2.5.2",
    "ruff>=0.14.1",
    "pre-commit>=4.0.1,<5",
]


[tool.setuptools-git-versioning]
enabled = true

[tool.pytest.ini_options]
addopts = "-ra -q -v"

testpaths = [
    "tests"
]
python_files = ["test_*.py", "*_test.py"]


[tool.ruff]
target-version = "py39"
line-length = 120
exclude = ["*.ipynb"]

[tool.ruff.lint]
extend-select = ["E4", "E7", "E9", "F", "I"]
ignore= ["F401", "F403", "F541", "F841", "F405", "G003", "F821"]
fixable = ["ALL"]

[tool.importlinter]
include_external_packages = true
root_packages = ["isatools"]

[[tool.importlinter.contracts]]
name = "Architecture Layer Dependencies"
type = "layers"
layers = [
    "isatools.convert",
    "isatools.isajson",
    "isatools.isatab",
    "isatools.model"
]

[[tool.importlinter.contracts]]
name = "Restricted External Package Imports - Flask, SQLAlchemy"
description = "Use flask and sqlalchemy packages only for database related utilities"
type = "forbidden"
source_modules = [
   "isatools"
]
forbidden_modules = [
    "flask",
    "sqlalchemy"
]
ignore_imports = [
    "isatools.database.models.** -> sqlalchemy",
    "isatools.database.utils -> flask"
]

[[tool.importlinter.contracts]]
name = "Restricted Development Package Imports"
type = "forbidden"
source_modules = [
   "isatools"
]
forbidden_modules = [
    "bokeh", "coveralls", "pytest", "behave"
]
ignore_imports = [

]