ensembl-genes/pyproject.toml at main · Ensembl/ensembl-genes · 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
[project]
name = "ensembl-genes"
version = "0.1.0"
description = "Tools for genome annotation"
requires-python = ">=3.11"
authors = [
    {name = "Ensembl", email = "dev@ensembl.org"},
]
maintainers = [
    {name = "Ensembl", email = "dev@ensembl.org"},
]
license = "Apache-2.0"
license-files = ["LICENSE", "NOTICE"]
classifiers = [
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
    "pymysql",
    "requests",
    "sqlalchemy >=1.4.16",
    "xmltodict",
    "pandas"
]

[project.optional-dependencies]
docs = [
    "sphinx>=7,<10",

    "mkdocs<2",
    "mkdocs-material",
    "mkdocs-gen-files",
    "mkdocstrings[python]",
    "mkdocs-literate-nav",
    "mkdocs-section-index",
    "mkdocs-coverage",
]

cicd = [
    "black>=24,<25",
    "pylint>=3,<5",
    "pytest>=7,<10",
    "mypy",
    "types-PyMySQL",
    "types-requests",
    "coverage>=7,<8",
]

[project.urls]
repository = "https://github.com/Ensembl/ensembl-genes"

[project.scripts]
pre_release_ftp = "ensembl.genes.automation.pre_release_ftp:main"
main_static_content = "ensembl.genes.content.main_static_content:main"
start_pipeline_from_registry = "ensembl.genes.info_from_registry.start_pipeline_from_registry:main"
beta_patcher = "ensembl.genes.metadata.beta_patcher:main"
core_meta_data = "ensembl.genes.metadata.core_meta_data:main"
busco_lineage_selector = "ensembl.genes.metrics.busco_lineage_selector:main"
busco_metakeys_patch = "ensembl.genes.metrics.busco_metakeys_patch:main"
check_busco_score = "ensembl.genes.metrics.check_busco_score:main"
write_yaml = "ensembl.genes.projects.write_yaml:main"
pid_overlap = "ensembl.genes.stable_id.pid_overlap:main"
bioproject_tracking = "ensembl.genes.tracking.bioproject_tracking:main"
live_tracking = "ensembl.genes.tracking.live_tracking:main"
check_for_transcriptomic = "ensembl.genes.transcriptomic_data.check_for_transcriptomic:main"
get_transcriptomic_data = "ensembl.genes.transcriptomic_data.get_transcriptomic_data:main"
select_transcriptomic_data = "ensembl.genes.transcriptomic_data.select_transcriptomic_data:main"


[build-system]
requires = [
    "setuptools",
    "setuptools-scm",
    "wheel"
]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src/python"]

[tool.setuptools]
package-dir = {"" = "src/python"}

[tool.mypy]
ignore_missing_imports = true

[tool.pylint.'MASTER']
init-hook = "import sys; sys.path.append('src/python')"
disable = ["duplicate-code"]

[tool.pixi.project]
name = "ensembl-genes"
channels = ["pypi"]

[tool.pylint."MESSAGES CONTROL"]
disable = ["import-error"]

[tool.pylint."DESIGN"]
max-positional-arguments = 20