pyproject.toml

[tool.poetry]
name = "xpypact"
version = "0.12.3"
description = "\"Python workflow framework for FISPACT.\""
authors = ["dvp <dmitri_portnov@yahoo.com>"]
license = "MIT"
homepage = "https://github.com/MC-kit/xpypact"
repository = "https://github.com/MC-kit/xpypact"
documentation = "https://xpypact.readthedocs.io"
keywords = [
  "element",
  "nuclide",
  "isotope",
  "abundance",
  "FISPACT",
  "activation",
  "duckdb",
  "polars",
]
readme = "README.rst"
packages = [{ include = "xpypact", 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",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering :: Physics",
]

[build-system]
requires = ["poetry-core >= 1.8.3"]
build-backend = "poetry.core.masonry.api"

# [tool.poetry.scripts]
# xpypact = "xpypact.cli.runner:xpypact"

[tool.poetry.urls]
documentation = "https://xpypact.readthedocs.io"
Changelog = "https://github.com/MC-kit/xpypact/releases"


[tool.poetry.dependencies]
python = ">=3.10,<3.14"
duckdb = ">=1.0.0"
mckit-nuclides = ">=0.3.2"
multipledispatch = ">=0.6.0"
numpy = ">=2.0"
polars = {version = ">=1.12.0", extras = ["all"]}
pyarrow = ">=18.0.0"
rich = ">=13.7.0"
msgspec = {git = "https://github.com/jcrist/msgspec.git", rev = "main"}  # TODO: switch back to PyPI on update to Python 3.13

[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"
sqlfluff = ">=2.3.2"
pyupgrade = ">=3.15.0"

[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"] }
xdoctest = { extras = ["colors"], version = ">=0.15.10" }
pytest-benchmark = ">=4.0.0"

[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.docs.dependencies]
sphinx = ">=6.1.3"
sphinx-autodoc-typehints = ">=1.19.5"

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

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

[tool.poetry.group.analysis]
optional = true

[tool.poetry.group.analysis.dependencies]
jupysql = ">=0.10.9"
jupyterlab = ">=4.0.12"
jupytext = ">=1.16.1"
matplotlib = ">=3.7.1"
xlsxwriter = "^3.1.9"
xlsx2csv = "^0.8.2"


[tool.pytest.ini_options]
minversion = "6.2"
cache_dir = '.cache/pytest'
norecursedirs = '''
*.egg-info
.*
build
data
dist
docs/_build
docs/examples
htmlcov
notebooks
tools
wrk
'''
python_functions = "test_*  profile_*"
addopts = '''
-ra
-q
--tb=short
--doctest-modules
--strict-markers
--ignore setup.py
--failed-first
--xdoctest
'''
doctest_optionflags = "ELLIPSIS NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL ALLOW_UNICODE ALLOW_BYTES"
testpaths = ["tests", "src"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
# 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',
    # pandas 2.1.4 at python 3.12
    'ignore:.*datetime.datetime.utcfromtimestamp\(\) is deprecated:DeprecationWarning',
    # openpyxl 3.1.2 qt python 3.12
    'ignore:.*datetime.datetime.utcnow\(\):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 = ["*_tab.py", "**/__init__.py"]

[tool.coverage.report]
show_missing = true
skip_covered = true
fail_under = 100
omit = ["*_tab.py", "**/__init__.py", "**/types.py"]
# 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 = "3.12"
strict = true
follow_imports = "silent"
disallow_untyped_defs = true
files = "src/**/*.py"
plugins = ["numpy.typing.mypy_plugin"]

[[tool.mypy.overrides]]
module = [
    "IPython.core.magic",
    "IPython.core.magic_arguments",
    "click",
    "click.testing",
    "dask.*",
    "duckdb",
    "loguru",
    "mckit_nuclides.*",
    "msgspec",
    "multipledispatch",
    "nox",
    "numpy.testing",
    "pandas",
    "polars",
    "pytest",
    "scipy.constants",
    "scipy.sparse",
    "tomli",
    "tomllib",
    "xdoctest",
]
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 `ruff format` responsibility
]

[tool.ruff]
target-version = "py310"

line-length = 100

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

# show source code snippets when reporting violations
output-format = "concise"

src = ["src", "tests"]

exclude = [
    "*.egg-info",
    ".cache",
    "__pycache__",
    "adhoc",
    "docs/source/conf.py",
    "notebooks",
    "wrk",
]

[tool.ruff.lint]
#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
    "AIR", # Airflow https://airflow.apache.org/docs/apache-airflow/stable/index.html
    "ARG", # flake8-unused-arguments
    "ASYNC", # flake8-async
    "B", # flake8-bugbear
    "BLE", # flake8-blind-except
    "C4", # flake8-comprehensions
    "C90", # mccabe
    "COM", # flake8-commas
    "D", # pydocstyle
    "DJ", # flake8-django
    "DTZ", # flake8-datetimez
    "E", # pycodestyle
    "EM", # flake8-errmsg
    "ERA", # eradicate
    "EXE", # flake8-executable
    "F", # Pyflakes
    "FA", # flake8-future-annotations
    "FBT", # flake8-boolean-trap  https://adamj.eu/tech/2021/07/10/python-type-hints-how-to-avoid-the-boolean-trap
    "FIX", # flake8-fixme
    "FLY", # flynt
    "FURB", # refurb
    "G", # flake8-logging-format
    "I", # isort
    "ICN", # flake8-import-conventions
    "INP", # flake8-no-pep420
    "INT", # flake8-gettext
    "ISC", # flake8-implicit-str-concat
    "LOG", # flake8-log
    "N", # pep8-naming
    "NPY", # NumPy-specific rules
    "PD", # pandas-vet
    "PERF", # Perflint
    "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
    "SLOT", # flake8-slot
    "T10", # flake8-debugger
    "T20", # flake8-print
    "TD", # flake8-todos
    "TCH", # flake8-type-checking
    "TID", # flake8-tidy-imports
    "TRY", # tryceratops
    "UP", # pyupgrade
    "W", # pycodestyle 2
    "YTT", # flake8-2020
]

#warning: The isort option `isort.split-on-trailing-comma` is incompatible with the formatter `format.skip-magic-trailing-comma=true` option. To avoid unexpected behavior, we recommend either setting `isort.split-on-trailing-comma=false` or `format.skip-magic-trailing-comma=false`.

# 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 3.9

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

    "COM812", # may cause conflicts when used with the ruff formatter

    # "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",
    # "I101",
    # "I201",
    # "I202",
    # "INP001",  # File `tools/clear-prev-dist-info.py` is part of an implicit namespace package.
    "ISC001", # may cause conflicts when used with the ruff formatter

    # 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 - we use loguru 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`

    "TD", # TODO @dvp: revise TODOs and move actual to issues
    "FIX", # -- the same as above
    # "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
]


[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402"]
"src/xpypact/fluxes.py" = ["F811"]
"benchmarks/*" = ["S101"]
"noxfile.py" = ["ANN"]
"tests/*" = ["ANN", "D100", "D101", "D102", "D103", "D104", "PLR2004", "S101"]
"src/xpypact/inventory.py" = ["F811"]
"src/xpypact/data_arrays.py" = ["ANN401", "PD011"]
"src/xpypact/utils/resource.py" = ["ANN202"]
"tools/*" = ["T201", "INP001", "S603", "S607"]
"docs/source/conf.py" = ["A001", "D100", "ERA001", "INP001"]

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

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

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

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

[tool.ruff.lint.isort]
known-first-party = ["src"]
known-third-party = ["mpl_toolkits", "matplotlib", "numpy", "scipy", "loguru", "tqdm", "dotenv"]
default-section = "third-party"
lines-between-types = 1
required-imports = ["from __future__ import annotations"]
case-sensitive = true
section-order = [
    "future",
    "typing",
    "standard-library",
    "third-party",
    "first-party",
    "local-folder",
    "testing"
]



[tool.ruff.lint.isort.sections]
"typing" = ["typing", "typing_extension"]
"testing" = ["tests"]

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

[tool.ruff.format]
docstring-code-format = true

[tool.sqlfluff.core]
dialect = "duckdb"
sql_file_exts = ".sql,.dml,.ddl"
max_line_length = 120

[tool.sqlfluff.indentation]
# While implicit indents are not enabled by default. Many of the
# SQLFluff maintainers do use them in their projects.
allow_implicit_indents = true

# The default configuration for aliasing rules is "consistent"
# which will auto-detect the setting from the rest of the file. This
# is less desirable in a new project and you may find this (slightly
# more strict) setting more useful.
[tool.sqlfluff.rules.aliasing.table]
aliasing = "explicit"

[tool.sqlfluff.rules.aliasing.column]
aliasing = "explicit"

[tool.sqlfluff.rules.aliasing.length]
min_alias_length = 3

# The default configuration for capitalisation rules is "consistent"
# which will auto-detect the setting from the rest of the file. This
# is less desirable in a new project and you may find this (slightly
# more strict) setting more useful.
# Typically, we find users rely on syntax highlighting rather than
# capitalisation to distinguish between keywords and identifiers.
# Clearly, if your organisation has already settled on uppercase
# formatting for any of these syntax elements then set them to "upper".
# See https://stackoverflow.com/questions/608196/why-should-i-capitalize-my-sql-keywords-is-there-a-good-reason
[tool.sqlfluff.rules.capitalisation.keywords]
capitalisation_policy = "lower"
[tool.sqlfluff.rules.capitalisation.identifiers]
capitalisation_policy = "lower"
[tool.sqlfluff.rules.capitalisation.functions]
extended_capitalisation_policy = "lower"
[tool.sqlfluff.rules.capitalisation.literals]
capitalisation_policy = "lower"
[tool.sqlfluff.rules.capitalisation.types]
extended_capitalisation_policy = "lower"

[tool.jupytext]
# https://jupytext.readthedocs.io/en/latest/config.html
# Pair ipynb notebooks to py:percent text notebooks
formats = "ipynb,md,py:percent"