-
Notifications
You must be signed in to change notification settings - Fork 1
/
pyproject.toml
138 lines (127 loc) · 3.36 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
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
name = "single_translator_VAE"
version = "0.0.1"
description = "Single-cell and single-nucleus RNA-sequencing translation with VAE"
readme = "README.md"
requires-python = ">=3.9"
license = {file = "LICENSE"}
authors = [
{name = "Adriana Ivich"},
]
maintainers = [
{name = "Adriana Ivich", email = "[email protected]"},
]
urls.Documentation = "https://single_translator_VAE.readthedocs.io/"
urls.Source = "https://github.com/ivichadriana/single_translator_VAE"
urls.Home-page = "https://github.com/ivichadriana/single_translator_VAE"
dependencies = [
"anndata",
"session-info",
"scvi",
"scvi-tools",
"scanpy",
"openTSNE"
]
[project.optional-dependencies]
dev = [
"pre-commit",
"twine>=4.0.2",
]
doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4",
"sphinx-book-theme>=1.0.0",
"myst-nb",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
# For notebooks
"ipykernel",
"ipython",
"sphinx-copybutton",
"pandas",
]
test = [
"pytest",
"coverage",
]
[tool.hatch.build.targets.wheel]
packages = ['src/single_translator_VAE']
[tool.coverage.run]
source = ["single_translator_VAE"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
[tool.ruff]
line-length = 120
src = ["src"]
extend-include = ["*.ipynb"]
[tool.ruff.format]
docstring-code-format = true
[tool.ruff.lint]
select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"RUF100", # Report unused noqa directives
]
ignore = [
# line too long -> we accept long comment lines; formatter gets rid of long code lines
"E501",
# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
"E731",
# allow I, O, l as variable names -> I is the identity matrix
"E741",
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __magic__ methods are are often self-explanatory, allow missing docstrings
"D105",
# first line should end with a period [Bug: doesn't work with single-line docstrings]
"D400",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
[tool.cruft]
skip = [
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks/example.ipynb",
]