poli/pyproject.toml at dev · MachineLearningLifeScience/poli · 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
[build-system]
requires = ["setuptools<=68"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
license-files = []

[project]
name = "poli-core"
version = "1.3.1"
description = "poli, a library of discrete objective functions"
readme = "README.md"
authors = [{name="Miguel González-Duque", email="miguelgondu@gmail.com"}, {name="Simon Bartels", email="bartels@di.ku.dk"}]
license = {file = "LICENSE"}
classifiers = [
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Intended Audience :: Education",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Development Status :: 3 - Alpha",
    "Operating System :: MacOS",
    "Operating System :: Unix",
]
keywords = ["optimization", "molecular", "discrete", "proteins"]
dependencies = [
    "numpy",
    "rdkit",
    "selfies"
]
requires-python = ">=3.9"

[project.optional-dependencies]
foldx = [
    "biopython",
    "python-levenshtein",
    "pdb-tools",
]
protein = [
    "biopython",
    "python-levenshtein",
    "pdb-tools",
]
dms = [
    "pandas",
]
ehrlich = [
    "pytorch-holo",
    "botorch<=0.13.0",
]
ehrlichholo = [
    "pytorch-holo",
]
dockstring = [
    "dockstring"
]
rmf = [
    "scipy",
]
rosetta_energy = [
    "biopython",
    "pyrosetta-installer",
]
dev = ["black", "tox", "pytest", "bump-my-version", "pre-commit", "pyright"]
docs = ["sphinx", "furo"]

[project.urls]
Homepage = "https://github.com/MachineLearningLifeScience/poli"

[tool.pytest.ini_options]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "poli__lambo: marks tests that run in the poli__lambo environment",
    "poli__dockstring: marks tests that run in the poli__dockstring environment",
    "poli__tdc: marks tests that run in the poli__tdc environment",
    "poli__protein: marks tests that run in the poli__protein environment",
    "poli__rasp: marks tests that run in the poli__rasp environment",
    "poli__rmf: marks tests that run in poli__rmf environment",
    "poli__rosetta_energy: marks tests that run in poli__rosetta_energy",
    "poli__ehrlich_holo: marks tests that run in poli__ehrlich_holo environment",
    "poli__dms: marks tests that run in poli__dms environment",
    "isolation: marks tests that require isolation of the black box function",
    "unmarked: All other tests, which usually run in the base environment",
]

[tool.pyright]
include = ["src/poli"]
exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas", "examples", "src/poli/tests"]
reportIncompatibleMethodOverride = "none"

[tool.isort]
profile = "black"

[tool.ruff]
exclude = ["src/poli/core/util/proteins/rasp/inner_rasp", "src/poli/objective_repository/gfp_cbas"]

[tool.bumpversion]
current_version = "1.2.0"
parse = """(?x)
    (?P<major>0|[1-9]\\d*)\\.
    (?P<minor>0|[1-9]\\d*)\\.
    (?P<patch>0|[1-9]\\d*)
    (?:
        .                             # dash separator for pre-release section
        (?P<pre_l>[a-zA-Z-]+)         # pre-release label
        (?P<pre_n>0|[1-9]\\d*)        # pre-release version number
    )?                                # pre-release section is optional
"""
serialize = [
    "{major}.{minor}.{patch}.{pre_l}{pre_n}",
    "{major}.{minor}.{patch}",
]
search = 'current_version = "{current_version}"'
replace = 'current_version = "{new_version}"'
regex = false
ignore_missing_version = false
ignore_missing_files = false
tag = false
sign_tags = false
tag_name = "v{new_version}"
tag_message = "Bump version: {current_version} → {new_version}"
allow_dirty = false
commit = false
message = "Bump version: {current_version} → {new_version}"
commit_args = ""

[tool.bumpversion.parts.pre_l]
values = ["dev"]

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'

[[tool.bumpversion.files]]
filename = "src/poli/__init__.py"
search = '__version__ = "{current_version}"'
replace = '__version__ = "{new_version}"'

[[tool.bumpversion.files]]
filename = "setup.cfg"
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'

[[tool.bumpversion.files]]
filename = "CITATION.cff"
search = 'version: {current_version}'
replace = 'version: {new_version}'

[dependency-groups]
dev = [
    "pre-commit>=4.2.0",
    "pyright>=1.1.403",
    "pytest>=8.4.0",
    "ruff>=0.12.3",
]