ClayCode/pyproject.toml at main · sarahvs99/ClayCode · 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
[project]
name = "ClayCode"
version = "0.1.1"
description = "A python package for building clay models and analysing MD simulation data of clay systems"
authors = [{ name = "Hannah Pollak", email = "h.pollak@sms.ed.ac.uk" }]
license = { file = "LICENSE" }
readme = "README.md"
requires-python = "==3.10"
dependencies = ['matplotlib>=3.6.2',
    'mdanalysis>=2.5',
    'numpy~=1.23.5',
    'pandas~=1.5.2',
    'pyyaml>=6',
    'scipy>=1.11',
    'tqdm~=4.66.1',
    'parmed>=4.1',
    'nocasedict',
    'zarr~=2.16',
    'dask~=2023.10',
    'caseless-dictionary==1.0.3',
    'importlib_resources>=6.0',
    'numba>=0.57',
    'nglview>=3.0',
    'unicodeit',
    'seaborn',
    'scikit-learn',]
classifiers = ["Programming Language :: Python :: 3",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent"]

[project.scripts]
ClayCode = "ClayCode:__main__.run"
ClayCodeTests = "ClayCodeTests:__main__"

[tool.setuptools.packages.find]
namespaces = true
where = ['package', 'tests']

[tool.setuptools]
include-package-data = true

[tool.setuptools.package-data]
"ClayCode.data" = ['*/FF/*.ff/*.itp',
    '*/FF/*.itp', '*/MDP/*.mdp', '*/UCS/*/*.itp', '*/UCS/*/*.gro',
    '*/UCS/*/*.top', '*/CLAYS/*/*/*/*.gro', '*/CLAYS/*/*/*/*.top',
    '*/UCS/*.csv', '*/UCS/*.yaml']
"ClayCode.builder.config" = ['defaults.yaml']
"ClayCodeTests.builder" = ['data/*.yaml', 'data/*.csv']
"ClayCode.siminp.config" = ["defaults.yaml"]
"ClayCode.siminp.scripts" = ["*.sh"]
"ClayCode.addmols.config" = ["defaults.yaml", "addtypes.yaml"]
"ClayCode.analysis.data" = ['peaks_edges/*.p']
"ClayCode.analysis.config" = ['defaults.yaml']
"Tutorial" = ['*.yaml', '*.csv', '*.gro', '*.top', '*.itp', '*.mdp', '*.sh']

[project.urls]
"Homepage" = "https://github.com/Erastova-group/ClayCode.git"

[build-system]
requires = ["setuptools>=68"]
build-backend = "setuptools.build_meta"

[tool.black]
line-length = 79
include = '.pyi?$'
exclude = '''
/(
    .git
    | .hg
    | .mypy_cache
    | .tox
    | .venv
    | _build
    | buck-out
    | build
    | dist
)/
'''

[tool.isort]
profile = 'black'
line_length = 79
multi_line_output = 3
include_trailing_comma = 'True'
ensure_newline_before_comments = 'True'
use_parentheses = 'True'

[project.optional-dependencies]
test = ["pytest>=6.0",
    "pytest-xdist>=2.5",
    "pytest-cov>=3.0",
]
[tool.dev-dependencies]
    black = ">=23.9.1"
    flake8 = ">=3.9.2"
    isort = ">=5.9.3"
    mypy = ">=0.910"
    pylint = ">=2.11.1"
    pytest = ">=6.0"
    pytest-xdist = ">=2.5"
    pytest-cov = ">=3.0"

[tool.pytest.ini_options]
addopts = ["--import-mode=importlib", "-p no:cacheprovider"]
minversion = "6.0"
pythonpath= "src"
testpaths = ["ClayCodeTests",
]
python_files = ["test_*.py", "*_test.py", "test.py"]
log_cli = "true"
log_level = "INFO"