Bayesian/pyproject.toml at main · JETSCAPE/Bayesian · GitHub

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[build-system]
# pdm
requires = ["wheel" , "pdm-pep517"]
build-backend = "pdm.pep517.api"
# hatch
#requires = ["hatchling"]
#build-backend = "hatchling.build"

[project]
name = "jetscape-bayesian"
description = "Analysis pipeline to implement Bayesian inference in high-energy physics "
license = {text = "BSD-3-Clause"}
requires-python = ">=3.10"
authors = [
  { name = "Raymond Ehlers", email = "raymond.ehlers@cern.ch" },
  { name = "Luna (Yi) Chen", email = "chen.yi.first@gmail.com" },
  { name = "Christal Martin", email = "cbaillar@vols.utk.edu" },
  { name = "Cameron Parker", email = "cameron.parker@tamu.edu" },
]
dynamic = ["version"]
dependencies = [
    # Data analysis and plotting
    "matplotlib >=3.5.2",
    "numpy >=1.22.4",
    "pandas >=1.4.2",
    "pyyaml >=6.0",
    "seaborn >=0.11.2",
    "silx >=1.0.0",
    # Emulator training
    # "gpflow >=2.5.2",
    "pymc >=4.0.0",
    "scikit-learn >=1.1.1",
    "emcee>=3.1.4",
    "rich>=13.4.2",
    "attrs>=23.1.0",
    "statsmodels>=0.14.0",
]

[project.optional-dependencies]
test = [
    "pytest >=6.2.4",
    "pytest-cov >=3",
    "pytest-sugar >=0.9.5",
]
dev = [
    "ruff >=0.0.209",
    "mypy>=1.13.0",
    "ipython >=8.0",
    "ipykernel >=6.15.1",
    "pytest >=7.4.0",
    "pocoMC >=1.2.2",
    "ipython>=8.37.0",
]

[tool.hatch]
version.path = "src/bayesian/__init__.py"

[tool.pdm]
version = { source = "file", path = "src/bayesian/__init__.py" }

[tool.black]
line-length = 120

[tool.mypy]
files = ["src", "tests"]
python_version = "3.10"
warn_unused_configs = true
strict = true
show_error_codes = true
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
warn_unreachable = true
no_implicit_reexport = false
disallow_untyped_defs = false
disallow_incomplete_defs = false
exclude = [".venv*"]

[[tool.mypy.overrides]]
module = [
    "sklearn",
    "sklearn.decompoistion",
    "sklearn.gaussian_process",
    "sklearn.preprocessing",
]
ignore_missing_imports = true

[tool.ruff]
exclude = [
    '.git',
    '.env',
    '.env3',
    '.venv',
    '.venv*',
    'env',
    '__pycache__',
    'bak',
    'build',
    'dist',
]
line-length = 120

[tool.ruff.lint]
select = [
    "E", "F", "W", # flake8
    "C901",        # mccabe
    "B", "B904",   # flake8-bugbear
    "I",           # isort
    "ARG",         # flake8-unused-arguments
    "C4",          # flake8-comprehensions
    "EM",          # flake8-errmsg
    "EXE",         # flake8-executable
    "ICN",         # flake8-import-conventions
    "ISC",         # flake8-implicit-str-concat
    "NPY",         # NumPy specific rules
    "PGH",         # pygrep-hooks
    "PIE",         # flake8-pie
    "PL",          # pylint
    "PT",          # flake8-pytest-style
    "PTH",         # flake8-use-pathlib
    "RET",         # flake8-return
    "RUF",         # Ruff-specific
    "SIM",         # flake8-simplify
    "T20",         # flake8-print
    "TID251",      # flake8-tidy-imports
    "UP",          # pyupgrade
    "YTT",         # flake8-2020
]
extend-ignore = [
    "E501",
    "E722",
    "RUF001",  # Unicode chars
    "PLR",
    "ISC003",  # Force string to be implicitly concatenated. However, I find this structure to be useful for better
               # readability due to consistent spacing with plotting labels.
]
unfixable = [
    "T20",      # flake8-print
    "F841",     # Removes unused variables
]
# Allow for characters that could be confused (per ruff)
allowed-confusables = ["σ", "ρ", "×"]

[tool.ruff.lint.mccabe]
max-complexity = 12

[tool.ruff.lint.isort]
known-first-party = []

[tool.pylint]
master.py-version = "3.10"
master.ignore-paths= []
reports.output-format = "colorized"
similarities.ignore-imports = "yes"
messages_control.disable = [
  "design",
  "fixme",
  "line-too-long",
  "wrong-import-position",
]

[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = ["error"]
log_cli_level = "INFO"
testpaths = [
  "tests",
]

[tool.check-manifest]
ignore = [
  ".github/**",
  "docs/**",
  ".pre-commit-config.yaml",
  ".readthedocs.yml",
  "noxfile.py",
]