pyproject.toml

[tool.poetry]
name = "atomea"
version = "0.0.0"
description = "Extensible schema for atomistic data and calculations."
authors = [
    "OASCI <us@oasci.org>",
]
license = "Apache-2.0"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
loguru = "^0.7.2"
pydantic = "^2.7.1"
pyyaml = "^6.0.1"
numpy = "^1.26.2"

[tool.poetry.group.storage.dependencies]
zarr = "^2.16.1"

[tool.poetry.group.sim.dependencies]
mdanalysis = "^2.6.1"

[tool.poetry.group.dev.dependencies]
black = "^23.9.0"
isort = "^5.12.0"
pre-commit = "^3.4.0"
mypy = "^1.5.1"
mypy-extensions = "^1.0.0"
bump-my-version = "^0.11.0"
poetry-dynamic-versioning = "^1.3.0"
requests = "^2.31.0"
ruff = "^0.4.5"
types-pyyaml = "^6.0.12.20240311"
twine = "^5.1.0"
pylint = "^3.2.2"

[tool.poetry.group.test.dependencies]
pytest = "^7.4.2"
pytest-cov = "^4.1.0"
pytest-html = "^4.0.1"
coverage = "^7.3.1"
colorama = "^0.4.6"

[tool.poetry.group.docs.dependencies]
mkdocs = "^1.5.3"
mkdocs-material = "^9.4.7"
material-plausible-plugin = "^0.2.0"
pymdown-extensions = "^10.3.1"
mkdocs-table-reader-plugin = "^2.0.3"
mkdocstrings = "^0.25.2"
mkdocstrings-python = "^1.10.9"
griffe = "^1.2.0"
mkdocs-gen-files = "^0.5.0"
mkdocs-awesome-pages-plugin = "^2.9.2"

[tool.bumpversion]
current_version = "0.0.0"
tag = true
commit = true

[[tool.bumpversion.files]]
filename = "CHANGELOG.md"
no_regex = false
search = "\\[Unreleased\\]"
replace = "[Unreleased]\n\n## [{new_version}] - {now:%Y-%m-%d}"

[tool.poetry-dynamic-versioning]
enable = true
vcs = "git"
format-jinja = "{%- if distance == 0 -%}{{ serialize_pep440(base) }}{%- else -%}{{ serialize_pep440(base, post=distance) }}{%- endif -%}"

[tool.poetry-dynamic-versioning.substitution]
patterns = [
    "(^__version__\\s*(?::.*?)?=\\s*['\"])[^'\"]*(['\"])",
]

[tool.ruff]
target-version = "py312"
line-length = 88
indent-width = 4
exclude = [
    ".git",
    ".hg",
    ".mypy_cache",
    ".tox",
    ".venv",
    "_build",
    "buck-out",
    "build",
    "dist",
    "env",
    "venv",
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
docstring-code-format = true
docstring-code-line-length = "dynamic"

[tool.pylint.messages_control]
good-names = [
    "i",
    "j",
    "e",
    "ex",
]
ignore = [
    "CVS",
    "_version.py",
    "conf.py",
]
disable = [
    "R0913",
]

[tool.isort]
py_version = 312
line_length = 88
known_typing = [
    "typing",
    "types",
    "typing_extensions",
    "mypy",
    "mypy_extensions",
]
sections = [
    "FUTURE",
    "TYPING",
    "STDLIB",
    "THIRDPARTY",
    "FIRSTPARTY",
    "LOCALFOLDER",
]
profile = "black"
include_trailing_comma = true
multi_line_output = 3
indent = 4
color_output = true

[tool.black]
target-version = [
    "py312",
]
line-length = 88
color = true

[tool.mypy]
python_version = "3.12"
pretty = true
show_traceback = true
color_output = true
allow_redefinition = false
check_untyped_defs = true
disallow_any_generics = true
disallow_incomplete_defs = true
ignore_missing_imports = true
implicit_reexport = false
no_implicit_optional = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
strict_equality = true
strict_optional = true
warn_no_return = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
warn_unused_ignores = true

[tool.pytest.ini_options]
norecursedirs = [
    "atomea",
    "*.egg",
    ".eggs",
    "dist",
    "build",
    "docs",
    ".tox",
    ".git",
    "__pycache__",
]
doctest_optionflags = [
    "NUMBER",
    "NORMALIZE_WHITESPACE",
    "IGNORE_EXCEPTION_DETAIL",
]
addopts = [
    "--strict-markers",
    "--tb=short",
    "--doctest-modules",
    "--doctest-continue-on-failure",
]

[tool.coverage.run]
source = [
    "tests",
]

[build-system]
requires = [
    "poetry-core>=1.0.0",
    "poetry-dynamic-versioning>=1.0.0,<2.0.0",
]
build-backend = "poetry_dynamic_versioning.backend"

[coverage.paths]
source = "atomea"

[coverage.run]
branch = true

[coverage.report]
fail_under = 50
show_missing = true

["tool.poetry.group.conda.dependencies"]
appdirs = "^1.4.4"
"backports.tarfile" = "^1.0.0"
Brotli = "^1.1.0"
build = "^1.2.1"
CacheControl = "^0.14.0"
cachy = "^0.3.0"
certifi = "^2024.6.2"
cffi = "^1.16.0"
cfgv = "^3.3.1"
charset-normalizer = "^3.3.2"
cleo = "^2.1.0"
click = "^8.1.7"
click-default-group = "^1.2.4"
clikit = "^0.6.2"
colorama = "^0.4.6"
conda_lock = "^2.5.7"
conda_poetry_liaison = "^0.1.2"
crashtest = "^0.4.1"
cryptography = "^42.0.8"
distlib = "^0.3.8"
dulwich = "^0.21.7"
ensureconda = "^1.4.4"
fastjsonschema = "^2.19.1"
filelock = "^3.15.0"
gitdb = "^4.0.11"
GitPython = "^3.1.43"
html5lib = "^1.1"
identify = "^2.5.36"
idna = "^3.7"
importlib_metadata = "^7.1.0"
importlib_resources = "^6.4.0"
installer = "^0.7.0"
"jaraco.classes" = "^3.4.0"
"jaraco.context" = "^5.3.0"
"jaraco.functools" = "^4.0.0"
jeepney = "^0.8.0"
Jinja2 = "^3.1.4"
keyring = "^24.3.1"
MarkupSafe = "^2.1.5"
more-itertools = "^10.3.0"
msgpack = "^1.0.8"
nodeenv = "^1.9.1"
numpy = "^1.26.4"
packaging = "^24.1"
pastel = "^0.2.1"
pexpect = "^4.9.0"
pip = "^24.0"
pkginfo = "^1.11.1"
platformdirs = "^4.2.2"
poetry = "^1.8.3"
poetry-core = "^1.9.0"
poetry-plugin-export = "^1.8.0"
pre_commit = "^3.7.1"
ptyprocess = "^0.7.0"
pycparser = "^2.22"
pydantic = "^2.7.4"
pydantic_core = "^2.18.4"
pylev = "^1.4.0"
pyproject_hooks = "^1.1.0"
PySocks = "^1.7.1"
PyYAML = "^6.0.1"
rapidfuzz = "^3.9.3"
requests = "^2.32.3"
requests-toolbelt = "^1.0.0"
"ruamel.yaml" = "^0.18.6"
"ruamel.yaml.clib" = "^0.2.8"
SecretStorage = "^3.3.3"
setuptools = "^70.0.0"
shellingham = "^1.5.4"
six = "^1.16.0"
smmap = "^5.0.0"
tomli = "^2.0.1"
tomli_w = "^1.0.0"
tomlkit = "^0.12.5"
toolz = "^0.12.1"
trove-classifiers = "^2024.5.22"
typing_extensions = "^4.12.2"
ukkonen = "^1.0.1"
urllib3 = "^1.26.18"
virtualenv = "^20.26.2"
webencodings = "^0.5.1"
wheel = "^0.43.0"
zipp = "^3.19.2"