Repository navigation
Expand file tree
/
Copy pathpyproject.toml
More file actions
102 lines (91 loc) · 3.72 KB
/
Copy pathpyproject.toml
File metadata and controls
102 lines (91 loc) · 3.72 KB
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
[project]
name = "atomweaver"
version = "0.1.0"
description = "AtomWeaver: multi-component flow-matching all-atom peptide side-chain design."
readme = "README.md"
requires-python = ">=3.11"
license = { text = "AGPL-3.0-or-later" }
classifiers = [
"License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
]
# Versions below are floors; the staging build was tested on the exact versions noted in comments.
dependencies = [
"torch>=2.2", # tested: 2.10.0
"numpy>=1.24", # tested: 2.4.1
"scipy>=1.10", # tested: 1.17.0
"scikit-learn>=1.3", # tested: 1.8.0
"joblib>=1.3", # tested: 1.5.3
"typer>=0.12", # tested: 0.21.1
]
[project.optional-dependencies]
dev = ["pytest>=9.1", "ruff>=0.16"]
[build-system]
requires = ["setuptools>=68"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
packages = ["atomweaver", "atomweaver.joint_diffusion"]
[tool.ruff]
line-length = 120
target-version = "py311"
[tool.ruff.lint]
select = [
"F", # pyflakes
"I", # isort
"E", # pycodestyle error
"N", # pep8-naming
"D", # pydocstyle
"B", # flake8-bugbear
"A", # flake8-builtins
"COM", # flake8-commas
"C4", # flake8-comprehensions
"T10", # flake8-debugger
"EM", # flake8-errmsg
"FA", # flake8-future-annotations
"ISC", # flake8-implicit-str-concat
"LOG", # flake8-logging
"G", # flake8-logging-format
"INP", # flake8-no-pep420
"PIE", # flake8-pie
"PT", # flake8-pytest-style
"Q", # flake8-quotes
"RSE", # flake8-raise
"RET", # flake8-return
"SIM", # flake8-simplify
"TC", # flake8-type-checking
"ARG", # flake8-unused-arguments
"PTH", # flake8-use-pathlib
"PD", # pandas-vet
"PLC", # pylint conventions
"PLE", # pylint errors
"NPY", # NumPy-specific rules
"PERF", # perflint
"FURB", # refurb
"RUF", # ruff-specific rules
]
# Local imports avoid model/data import cycles; unused unpacked dimensions follow F841 conventions.
ignore = ["COM812", "D200", "D401", "EM101", "EM102", "PD010", "PTH123", "PLC0415", "RUF059"]
exclude = ["./docs/*"]
pydocstyle.convention = "numpy"
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F403"]
# CLI and utility scripts: matrix/dimension notation (B, L, K, R), Typer-idiom option defaults, long
# explanatory comments, and other deliberate conventions in this code. Correctness rules stay on.
"./scripts/*" = [
"INP001", "D103", "SIM105",
"N803", "N806", "N816", "N802", "N812", "ARG001", "ARG002", "B008", "C408", "RUF001", "RUF002",
"RUF003", "RUF005", "D100", "D102", "D105", "D205", "D301", "D400", "E501", "E741", "E402", "F841",
"SIM102", "SIM108", "SIM115", "SIM118", "SIM210", "SIM401", "RUF013", "RUF015", "PERF102", "PERF401",
"RET504", "B007", "B904", "PD011", "PTH100", "PTH103", "PTH105", "PTH108", "PTH110", "PTH118", "PTH119",
"PTH120", "PTH207", "RUF100",
]
# Model package: matrix/dimension notation (B, L, K, R, x_T) per the ML literature, Angstrom/mu in
# prose, narrative multi-paragraph docstrings, and long trailing explanatory comments. Correctness
# rules (F821 undefined name, F811 redefinition) stay on everywhere.
"./atomweaver/joint_diffusion/*" = [
"N803", "N806", "N816", "ARG001", "ARG002", "B008", "RUF001", "RUF002", "RUF003", "D100", "D102", "D105",
"D205", "D301", "D400", "E501", "E741", "E402", "F841", "SIM102", "SIM108", "SIM115", "SIM118", "SIM210",
"SIM401", "RUF013", "RUF015", "PERF102", "PERF401", "RET504", "B007", "B904", "PD011", "PTH100", "PTH103",
"PTH105", "PTH108", "PTH110", "PTH118", "PTH119", "PTH120", "PTH207", "RUF100",
]
[tool.ruff.format]
docstring-code-format = true