pyproject.toml

[tool.poetry]
name = "mckit-meshes"
version = "0.1.5"
description = "Python tools to work with MCNP meshtallies and weight meshes."
authors = ["dvp2015 <dmitri_portnov@yahoo.com>"]
license = "MIT"
homepage = "https://github.com/MC-kit/mckit-meshes"
repository = "https://github.com/MC-kit/mckit-meshes"
# documentation = "https://mckit-meshes.readthedocs.io
keywords = ["mesh", "weights", "variance reduction"]
readme = "README.rst"
packages = [{ include = "mckit_meshes", from = "src" }]
# Select from PyPI classifiers: https://pypi.org/classifiers/
classifiers = [
  "Development Status :: 3 - Alpha",
  "Environment :: Console",
  "Intended Audience :: Developers",
  "Intended Audience :: Science/Research",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Topic :: Scientific/Engineering :: Physics",
]

[build-system]
requires = ["poetry-core >= 1.5.2"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.scripts]
mckit-meshes = "mckit_meshes.cli.runner:mckit_meshes"

[tool.poetry.urls]
# documentation = "https://mckit-meshes.readthedocs.io"
Chnagelog = "https://github.com/MC-kit/mckit-meshes/releases"


[tool.poetry.dependencies]
python = ">=3.9,<3.13"
click = ">=8.0.1"
loguru = ">=0.6.0"
numpy = ">=1.24.2"
openpyxl = ">=3.0.9"
pandas = ">=2.0.0"
pyevtk = ">=1.4.1"
toolz = ">=0.11.2"

[tool.poetry.group.dev.dependencies]
Pygments = ">=2.10.0"
nox = ">=2022.1.7"
tomli = { version = ">=2.0.1", python = "<3.11" }

#[tool.poetry.group.profile]
#optional = true

#[tool.poetry.group.profile.dependencies]
# TODO dvp: apply yappi: https://coderzcolumn.com/tutorials/python/yappi-yet-another-python-profiler
#yappi = ">=1.3.2"

[tool.poetry.group.pre_commit.dependencies]
pre-commit = ">=2.15.0"
rstcheck = ">=6.1.2"
pydocstringformatter = ">=0.7.3"
pyupgrade = ">=3.15.0"

[tool.poetry.group.black.dependencies]
black = ">=22.8.0"

[tool.poetry.group.isort.dependencies]
isort = ">=5.9.3"

[tool.poetry.group.test.dependencies]
pytest = ">=7.1"
# pytest-cache = ">=1.0"
pytest-cov = ">=4.0"
# pytest-mock = ">=3.9"
# pytest-randomly = ">=3.12"
coverage = { version = ">=6.1.2", extras = ["toml"] }

[tool.poetry.group.coverage.dependencies]
coverage = { version = ">=6.1.2", extras = ["toml"] }

[tool.poetry.group.xdoctest.dependencies]
xdoctest = { extras = ["colors"], version = ">=0.15.10" }

[tool.poetry.group.typeguard.dependencies]
typeguard = ">=4.1.5"

[tool.poetry.group.mypy.dependencies]
mypy = ">=1.2.0"
pep8-naming = ">=0.12.1"
types-setuptools = ">=57.4.2"
numpy = ">=1.26.2"

[tool.poetry.group.flake8.dependencies]
darglint = ">=1.8.1"
flake8 = ">=6.0.0"
flake8-adjustable-complexity = ">=0.0.6"
flake8-annotations = ">=2.6.2"
flake8-annotations-coverage = ">=0.0.6"
flake8-bandit = ">=4.1.1"
flake8-bugbear = ">=23.3.23"
flake8-builtins = ">=1.5.3"
flake8-class-attributes-order = ">=0.1.3"
flake8-cognitive-complexity = ">=0.1.0"
flake8-colors = ">=0.1.9"
flake8-commas = ">=2.1.0"
flake8-comprehensions = ">=3.10.0"
flake8-docstrings = ">=1.6.0"
flake8-eradicate = ">=1.5.0"
flake8-expression-complexity = ">=0.0.11"
flake8-functions = ">=0.0.7"
flake8-import-order = ">=0.18.1"
flake8-pie = ">=0.16.0"
flake8-print = ">=5.0.0"
flake8-rst-docstrings = ">=0.2.7"
flake8-scream = ">=0.1.0"
flake8-simplify = ">=0.19.3"
flake8-use-fstring = ">=1.4"
flake8-use-pathlib = ">=0.3.0"
pylint = ">=2.15.10"
flake8-pylint = ">=0.1.3"
# TODO dvp: check/use flake8-pyprojecttoml plugin
# https://gitlab.com/durko/flake8-pyprojecttoml/-/blob/master/pyproject.toml

[tool.poetry.group.docs.dependencies]
sphinx = ">=6.1.3"
sphinx-autodoc-typehints = ">=1.19.5"
sphinx-click = ">=4.4.0"

[tool.poetry.group.docs_auto.dependencies]
sphinx-autobuild = ">=2021.3.14"


[tool.poetry.group.pylsp.dependencies]
pylsp-mypy = ">=0.6.6"
pyls-isort = ">=0.2.2"
python-lsp-black = ">=1.2.1"
pyls-memestra = ">=0.0.16"
pylsp-rope = ">=0.1.11"
ruff-lsp = ">=0.0.35"

[tool.poetry.group.ruff.dependencies]
ruff = ">=0.0.259"

[tool.isort]
atomic = true
ensure_newline_before_comments = true
known_first_party = "mckit_meshes"
known_third_party = "mpl_toolkits,matplotlib,numpy,scipy"
known_typing = "typing,types,typing_extensions,mypy,mypy_extensions"
sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
default_section = "FIRSTPARTY"
use_parentheses = true
multi_line_output = 3
line_length = 100
include_trailing_comma = true
lines_between_types = 1
skip_gitignore = true
skip_glob = ["*-example.py"]


# NOTE: you have to use single-quoted strings in TOML for regular expressions.
# It's the equivalent of r-strings in Python.  Multiline strings are treated as
# verbose regular expressions by Black.  Use [ ] to denote a significant space
# character.

[tool.black]
line-length = 100
include = '''
(
    \.pyi?$
)
'''
exclude = '''
(
    \.eggs
  | \.git
  | \.mypy_cache
  | \.pytest_cache
  | \.nox
  | \.venv
  | \.idea
  | _build
  | build
  | build_configs
  | dist
  | 3rd-party
  | data
  | htmlcov
  | \.egg-info
  | _tab\.py$
  | notebooks
  | wrk
)
'''

[tool.pytest.ini_options]
minversion = "6.0"
norecursedirs = ".* build dist *.egg-info data htmlcov notebooks tools wrk"
python_functions = "test_*  profile_*"
addopts = "-ra -q --tb=short --doctest-modules --strict-markers --ignore setup.py --failed-first"
doctest_optionflags = "NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL ALLOW_UNICODE ALLOW_BYTES"
testpaths = ["tests"]
markers = ["slow: too slow tests"]
# xfail tests that pass should fail the test suite
xfail_strict = true
filterwarnings = [
  "error",
  'ignore:Implementing implicit namespace packages \(as specified in PEP 420\) is preferred to `pkg_resources.declare_namespace`',
  "ignore:.*not typechecking multipledispatch.dispatcher.*UserWarning",
  'ignore:.*io.FileIO \[closed\]',
  'ignore:.*Deprecated call to `pkg_resources.declare_namespace',
  'ignore:.*Implicit None on return values:DeprecationWarning',
]
log_format = "%(asctime)s %(levelname)s %(message)s"
log_date_format = "%Y-%m-%d %H:%M:%S"

[tool.xdoctest]
quiet = true
options = ""

[tool.coverage.paths]
source = ["src", ".nox/*/site-packages"]

[tool.coverage.run]
branch = true
source = ["src"]
omit = ["*/plotting/*"]

[tool.coverage.report]
show_missing = true
skip_covered = true
fail_under = 80     # TODO dvp: increase limit to 100 with code maturing
# Regexes for lines to exclude from consideration
exclude_lines = [
  # Have to re-enable the standard pragma
  "pragma: no cover",
  # Don't complain about missing debug-only code:
  "def __repr__",
  "if self.debug",
  # Don't complain if tests don't hit defensive assertion code:
  "raise AssertionError",
  "raise NotImplementedError",
  # Don't complain if non-runnable code isn't run:
  "if 0:",
  "if __name__ == .__main__.:",
  "if TYPE_CHECKING:",
]
ignore_errors = true
sort = "Cover"


# MyPy config
# See https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file
#     https://dev.to/tusharsadhwani/the-comprehensive-guide-to-mypy-561m
[tool.mypy]
python_version = "3.11"
# strict = true     # TODO dvp: uncomment this to get strict control
follow_imports = "silent"
# namespace_packages = true
warn_return_any = true
warn_unused_configs = true
show_error_codes = true
show_error_context = true
error_summary = true
warn_redundant_casts = true
warn_unreachable = true
warn_unused_ignores = true
files = "src/mckit_meshes/**/*.py"
plugins = ["numpy.typing.mypy_plugin"]

[[tool.mypy.overrides]]
module = [
  "click",
  "click.testing",
  "loguru",
  "importlib_metadata",
  "multipledispatch",
  "nox",
  "numpy.testing",
  "pandas",
  "pytest",
  "scipy.constants",
  "tomli",
  "tomllib",
]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["tomllib", "tomli"]
allow_redefinition = true
disable_error_code = "no-redef"

[tool.check-manifest]
ignore = ["tests/*", "tools/*", "*.yaml", "noxfile.py"]

[tool.ipdb]
# For debugging in jupyterlab and ipython
# see https://github.com/gotcha/ipdb
context = 5

[tool.tryceratops]
include = ["src"]
experimental = true

[tool.pydocstringformatter]
write = true
style = "pep257"
exclude = ["tools/**", "src/**/*_parser.py", "src/**/*_tab.py"]
strip-whitespaces = true
max-line-length = 100
summary-quotes-same-line = true


[tool.pylint]
good-names-rgxs = ["."] # a single character variable is okay
logging-format-style = "new" # use {} in logging messages
deprecated-modules = ["six"]
extension-pkg-allow-list = ["duckdb"]
disable = [
  "wrong-import-order", # this is `isort` responsibility
]


[tool.ruff]
target-version = "py38"
#see full list: https://beta.ruff.rs/docs/rules/#pyflakes-f
#or run 'ruff linter' to see a brief list
select = [
  "A",   # flake8-builtins
  "ANN", # flake8-annotations
  "ARG", # flake8-unused-arguments
  "B",   # flake8-bugbear
  "BLE", # flake8-blind-except
  "C4",  # flake8-comprehensions
  "C90", # mccabe
  "COM", # flake8-commas
  "DJ",  # flake8-django
  "D",   # pydocstyle
  "DTZ", # flake8-datetimez
  "EM",  # flake8-errmsg
  "ERA", # eradicate
  "E",   # pycodestyle
  "EXE", # flake8-executable
  "FBT", # flake8-boolean-trap  https://adamj.eu/tech/2021/07/10/python-type-hints-how-to-avoid-the-boolean-trap
  "F",   # Pyflakes
  "G",   # flake8-logging-format
  "ICN", # flake8-import-conventions
  "I",   # isort
  "INP", # flake8-no-pep420
  "ISC", # flake8-implicit-str-concat
  "N",   # pep8-naming
  "NPY", # NumPy-specific rules
  "PD",  # pandas-vet
  "PGH", # pygrep-hooks
  "PIE", # flake8-pie
  "PL",  # Pylint
  "PT",  # flake8-pytest-style
  "PTH", # flake8-use-pathlib
  "PYI", # flake8-pyi
  "Q",   # flake8-quotes
  "RET", # flake8-return
  "RSE", # flake8-raise
  "RUF", # Ruff-specific rules
  "S",   # flake8-bandit
  "SIM", # flake8-simplify
  "SLF", # flake8-self
  "T10", # flake8-debugger
  "T20", # flake8-print
  "TCH", # flake8-type-checking
  "TID", # flake8-tidy-imports
  "TRY", # tryceratops
  "UP",  # pyupgrade
  "W",   # pycodestyle 2
  "YTT", # flake8-2020
]

# Ignore rules that currently fail on the codebase
ignore = [
  "ANN001", # ANN001 Missing type annotation for function argument: doesn't allow to use functools dispatching
  "ANN002", # ANN002 Missing type annotation for *drop_items: ... as above
  "ANN101", # ANN101 Missing type annotation for self in method
  "ANN102", # ANN102 Missing type annotation for cls in classmethod
  "ANN201", # Missing return type annotation for public function `mesh2com`
  "ANN202", # ANN202 Missing return type annotation for protected function: ... dispatching
  "ANN204", # ANN204 Missing return type annotation for special method

  # "ARG001", # Unused function argument: `expected`

  "B905", # B905 `zip()` without an explicit `strict=` parameter - ignore while support 3.8, 3.9

  # "C812",   # C812 Missing trailing comma: black compatibility
  "C901", # too complex - ...

  "D100", # Missing docstring in public module
  "D101", # Missing docstring in public class
  "D102", # Missing docstring in public method
  "D103", # Missing docstring in public function
  "D105", # D105 Missing docstring in magic method (__hash__, __eq__)
  "D104", # Missing docstring in public package
  "D106", # Missing docstring in public nested class
  "D107", # Missing docstring in __init__
  # "D417",   # Missing argument descriptions in the docstring: `config`, `ebins`, - TODO


  # "E203",   # E203: Whitespace before ‘:'
  # "E401",  # Multiple imports on one line
  "E402", # Module level import not at top of file
  "E501", # Line too long (<LENGTH> > 100 characters)
  # "E701",  # Multiple statements on one line (colon)
  # "E702",  # Multiple statements on one line (semicolon)
  # "E703",  # Statement ends with an unnecessary semicolon
  # "E704",  # Multiple statements on one line (def)
  # "E711",  # Comparison to `None` should be `cond is not None`
  # "E712",  # Comparison to `<BOOL>` should be `cond is <BOOL>`
  # "E713",  # Test for membership should be `not in`
  # "E714",  # Test for object identity should be `is not`
  # "E721",  # Do not compare types, use `isinstance()`
  # "E722",  # Do not use bare `except`
  # "E731",  # Do not assign a `lambda` expression, use a `def`
  # "E741",  # Ambiguous variable name: `<VARIABLE>`
  # "E743",  # Ambiguous function name: `<FUNCTION>`

  "EM101", # Exception must not use a string literal, assign to variable first
  "EM102", # Exception must not use an f-string literal, assign to variable first

  # "N803",    # Argument name `R` should be lowercase
  # "N806",    # Variable `D` in function should be lowercase

  # "F401",  # `<TYPE>` imported but unused
  # "F403",  # `from <MODULE> import *` used; unable to detect undefined names
  # "F405",  # `<TYPE>` may be undefined, or defined from star imports: `<MODULE>`
  # "F523",  # `.format` call has unused arguments at position(s): <INDEX>
  # "F601",  # Dictionary key literal `'<KEY>'` repeated
  # "F811",  # Redefinition of unused `<VARIABLE>` from line <LINE>
  # "F821",  # Undefined name `VARIABLE`
  # "F823",  # Local variable `VARIABLE` referenced before assignment
  # "F841",  # Local variable `VARIABLE` is assigned to but never used

  "FBT001", # Boolean positional arg in function definition (TODO!)
  "FBT002", # Boolean default value in function definition (TODO!)
  "FBT003", # Boolean positional value in function call

  "I001", # import order is controlled by isort
  # "I101",
  # "I201",
  # "I202",
  # "INP001",  # File `tools/clear-prev-dist-info.py` is part of an implicit namespace package.

  # ignore some questionable pandas-vet warnings
  # "PD005", # use operator instead of method
  # "PD008", # We use at() to access single values
  # "PD009", # And we use iat()

  "PLE1205", # logging-too-many-args - with use logure with '{' style of placeholders

  "PLR0912", # Too many branches (15 > 12)
  "PLR0913", # Too many arguments to function call (6 > 5)
  "PLR0915", # Too many statements (65 > 50)
  "PLR2004", # magic number - don't want declare 0.0 as constant
  # "PLR5501", # Consider using `elif` instead of `else` then `if` to remove one indentation level

  "PT019", # Fixture `_bin` without value is injected as parameter (false positive?)

  "S101", # Use of `assert` detected
  # "S301",    # `pickle` and modules that wrap... - TODO - use sql instead of pickle

  "SLF001", # Private member accessed: `_geometry_spec`

  # "TCH001",  # Move application import `mckit.utils.named` into a type-checking block

  "TRY003", #  Avoid specifying long messages outside the exception class

  # "W503",  # Line break before binary operator: for compatibility with black settings
]

# Same as Black.
line-length = 100

# show an enumeration of all autofixed lint violations
show-fixes = true

# show source code snippets when reporting violations
show-source = true

src = ["src", "tests"]

# Allow unused variables when underscore-prefixed.
# dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
dummy-variable-rgx = "^_$"
exclude = [
  "docs/source/conf.py",
  "__pycache__",
  "adhoc",
  "wrk",
  "*.egg-info",
  ".cache",
  "notebooks/dvp/*.py",
]
# Assume Python 3.10.
# target-version = "py310"

[tool.ruff.per-file-ignores]
"__init__.py" = ["E402"]
"benchmarks/*" = ["S101"]
"noxfile.py" = ["ANN"]
"tests/*" = ["ANN", "D100", "D101", "D102", "D103", "D104", "PLR2004", "S101"]
"tools/*" = ["T201", "INP001", "S603", "S607"]

[tool.ruff.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 15

[tool.ruff.flake8-annotations]
mypy-init-return = true # skip return type for __init__() methods

[tool.ruff.flake8-type-checking]
strict = true

[tool.ruff.isort]
known-first-party = ["src"]
known-third-party = ["mpl_toolkits", "matplotlib", "numpy", "scipy"]
required-imports = ["from __future__ import annotations"]


[tool.ruff.flake8-pytest-style]
parametrize-names-type = "csv"

[tool.ruff.pydocstyle]
convention = "google" # Use Google-style docstrings.