-
Notifications
You must be signed in to change notification settings - Fork 2
/
pyproject.toml
142 lines (121 loc) · 3.05 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
139
140
141
[tool.poetry]
name = "structural-bioinformatics"
version = "0.1.0"
description = "Teaching materials for the course: Structural Bioinformatics"
authors = ["Yerko Escalona <[email protected]>"]
readme = "README.md"
license = "CC BY-NC-SA 4.0"
package-mode = false
[tool.poetry.dependencies]
python = "~3.10"
biopandas = "0.4.1"
ipykernel = "^6.29.5"
jupyter = "1.1.1"
matplotlib = "3.9.2"
MDAnalysis = "2.7.0"
mdtraj = "1.10.0"
nglview = "3.1.2"
numpy = "1.26.4"
OpenMM = "8.2.0"
pandas = "2.2.2"
py3dmol = "2.4.0"
pypdb = "2.4"
rdkit = "2024.3.5"
scipy = "1.13.1"
tqdm = "4.66.6"
tensorflow = "^2.18.0"
jax = "^0.4.35"
dm-tree = "^0.1.8"
biopython = "^1.84"
dm-haiku = "^0.0.13"
absl-py = "^2.1.0"
jmp = "^0.0.4"
ml-collections = "^0.1.1"
tabulate = "^0.9.0"
six = "^1.16.0"
[tool.poetry.group.dev.dependencies]
ruff = "^0.7.1"
pytest = "^8.3.3"
pre-commit = "^4.0.1"
poetry-plugin-export = "^1.8.0"
nbstripout = "^0.8.0"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.ruff]
# Exclude a variety of commonly ignored directories.
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".git-rewrite",
".hg",
".ipynb_checkpoints",
".mypy_cache",
".nox",
".pants.d",
".pyenv",
".pytest_cache",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
".vscode",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"site-packages",
"venv",
]
# Same as Black.
line-length = 88
indent-width = 4
# Set target Python version to 3.10
target-version = "py310"
[tool.ruff.lint]
# Enable Pyflakes (`F`), a subset of pycodestyle (`E`), and docstring checks (`D`).
select = [
"E4", # Import related errors
"E7", # Indentation errors
"E9", # Hanging indentation
"F", # Pyflakes
"D" # Docstring checks
]
ignore = []
# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []
# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
[tool.ruff.per-file-ignores]
"**/*.ipynb" = [
"F811", # redefinition of unused variable
]
[tool.ruff.lint.pydocstyle]
convention = "google" # Accepts: "google", "numpy", or "pep257".
[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"
# Like Black, indent with spaces, rather than tabs.
indent-style = "space"
# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false
# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"
# Enable auto-formatting of code examples in docstrings. Markdown,
# reStructuredText code/literal blocks and doctests are all supported.
#
# This is currently disabled by default, but it is planned for this
# to be opt-out in the future.
docstring-code-format = false
# Set the line length limit used when formatting code snippets in
# docstrings.
#
# This only has an effect when the `docstring-code-format` setting is
# enabled.
docstring-code-line-length = "dynamic"