pyproject.toml

[build-system]
requires = ["setuptools", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "firecrown"
authors = [
    { name = "DESCs Firecrown Developers" },
]
description = "DESC Cosmology Likelihood Framework"
requires-python = ">=3.11"
license-files = ["LICENSE"]
dependencies = [
    "astropy",
    "cobaya",
    "cosmosis",
    "lsstdesc-crow",
    "fitsio",
    "numcosmo_py",
    "numpy",
    "pandas",
    "pyccl",
    "pydantic",
    "pyyaml",
    "rich",
    "sacc",
    "scipy",
    "typer",
]
dynamic = ["version", "readme"]

[tool.setuptools_scm]
version_scheme = "guess-next-dev"
local_scheme = "dirty-tag"
tag_regex = "^(?:v)?(?P<version>[0-9]+\\.[0-9]+\\.[0-9]+(a[0-9]+)?)$"

[tool.setuptools_scm.scm.git]
describe_command = [
    "git", "describe", "--dirty", "--tags", "--long", "--abbrev=40", "--match",
    "v*"
]

[tool.setuptools.dynamic]
readme = { file = "README.md", content-type = "text/markdown" }

[project.urls]
Homepage = "https://github.com/LSSTDESC/firecrown"

[tool.setuptools.packages.find]
include = ["firecrown*"]
exclude = ["examples*", "tests*", "tutorial*", "docs*"]

[project.scripts]
firecrown = "firecrown.app:app"
firecrown-link-checker = "firecrown.fctools.link_checker:app"

# Coverage configuration
[tool.coverage.run]
branch = true
parallel = true
concurrency = ["multiprocessing"]
source = ["firecrown"]

[tool.coverage.report]
exclude_also = [
   # Don't complain about unreachable code
   '^ +assert_never\(.*?\)$',
   '^ +case _ as unreachable.*:$',
]

# Ruff configuration - replaces flake8 and pylint (black still used for formatting)
[tool.ruff]
line-length = 88
target-version = "py311"

[tool.ruff.lint]
# Enable rules equivalent to flake8 + pylint + additional useful rules
select = [
    # Pycodestyle (replaces flake8 E/W)
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    
    # Pyflakes (replaces flake8 F)
    "F",      # Pyflakes
    
    # mccabe (replaces flake8 complexity)
    "C90",    # mccabe complexity
    
    # isort (import sorting)
    "I",      # isort
    
    # pydocstyle (docstring checks, replaces some pylint docstring rules)
    "D",      # pydocstyle
    
    # pyupgrade (modernize Python code)
    "UP",     # pyupgrade
    
    # pylint-like rules
    "PL",     # Pylint
    
    # Additional useful rules
    "B",      # flake8-bugbear (bug and design problems)
    "A",      # flake8-builtins (builtin shadowing)
    "C4",     # flake8-comprehensions
    "DTZ",    # flake8-datetimez
    "T10",    # flake8-debugger
    "DJ",     # flake8-django
    "EM",     # flake8-errmsg
    "EXE",    # flake8-executable
    "FA",     # flake8-future-annotations
    "ICN",    # flake8-import-conventions
    "G",      # flake8-logging-format
    "INP",    # flake8-no-pep420
    "PIE",    # flake8-pie
    "T20",    # flake8-print
    "PYI",    # flake8-pyi
    "PT",     # flake8-pytest-style
    "RSE",    # flake8-raise
    "RET",    # flake8-return
    "SLF",    # flake8-self
    "SLOT",   # flake8-slots
    "SIM",    # flake8-simplify
    "TID",    # flake8-tidy-imports
    "TCH",    # flake8-type-checking
    "INT",    # flake8-gettext
    "ARG",    # flake8-unused-arguments
    "PTH",    # flake8-use-pathlib
    "TD",     # flake8-todos
    "FIX",    # flake8-fixme
    "ERA",    # eradicate (commented-out code)
    "PD",     # pandas-vet
    "PGH",    # pygrep-hooks
    "NPY",    # NumPy-specific rules
    "RUF",    # Ruff-specific rules
]

# Ignore rules to match existing flake8/pylint configuration
ignore = [
    # Docstring rules that flake8 ignores
    "D107",   # Missing docstring in __init__ (matches flake8 ignore)
    "D401",   # First line should be imperative (matches flake8 ignore)  
    "D402",   # First line should not be signature (matches flake8 ignore)
    
    # Additional common ignores for scientific code
    "PLR0913", # Too many arguments (scientific functions often need many params)
    "PLR0915", # Too many statements (complex scientific calculations)
    "PLR2004", # Magic value (scientific constants are common)
    "C901",    # Too complex (use max-complexity setting instead)
    
    # Import rules that may be too strict for scientific packages
    "F403",    # Star imports (common in scientific packages)
    "F405",    # Name may be undefined from star imports
    
    # Rules that may conflict with black formatting or are too strict
    "COM812",  # Trailing comma missing (conflicts with black)
    "COM819",  # Trailing comma prohibited (conflicts with black)
    "ISC001",  # Implicitly concatenated string literals (can conflict with formatter)
    "Q000",    # Double quotes found but single quotes preferred
    "Q001",    # Single quotes found but double quotes preferred
    "Q002",    # Docstring should use double quotes
    "Q003",    # Docstring should use single quotes
]

# Set complexity limit to match pylint
mccabe.max-complexity = 10

[tool.ruff.lint.per-file-ignores]
# Test files don't need docstrings and can be more flexible
"tests/**/*.py" = [
    "D100",    # Missing docstring in public module
    "D102",    # Missing docstring in public method
    "D103",    # Missing docstring in public function
    "D104",    # Missing docstring in public package
    "D200",    # One-line docstring should fit on one line
    "D202",    # No blank lines allowed after function docstring
    "D205",    # 1 blank line required between summary and description
    "D209",    # Multi-line docstring closing quotes should be on separate line
    "D212",    # Multi-line docstring summary should start at the first line
    "D213",    # Multi-line docstring summary should start at the second line
    "D400",    # First line should end with a period
    "PLR2004", # Magic values OK in tests
    "S101",    # Use of assert OK in tests
    "ARG001",  # Unused function arguments OK in tests/fixtures
    "PLR0913", # Too many arguments OK in test functions
]

# Examples can have less strict rules
"examples/**/*.py" = [
    "D100", "D102", "D103", "D104",  # Docstring requirements relaxed
    "PLR0913",  # Too many arguments
    "PLR0915",  # Too many statements  
    "E501",     # Line too long (matches existing per-file ignore)
    "T201",     # Print statements OK in examples
    "PLR2004",  # Magic values OK in examples
    "INP001",   # Implicit namespace packages OK
]

# Allow specific patterns in different directories
"pylint_plugins/**/*.py" = [
    "PLR0913",  # Many arguments OK for plugins
]

# Command-line utilities in fctools legitimately use print() for user output
"firecrown/fctools/**/*.py" = [
    "T201",     # Print statements OK in CLI tools (coverage_summary, print_code, etc.)
]

[tool.ruff.lint.pydocstyle]
# Use Google docstring convention (common in scientific Python)
convention = "google"

[tool.ruff.lint.isort]
# Group imports properly for scientific packages
known-first-party = ["firecrown"]
known-third-party = ["numpy", "scipy", "pandas", "matplotlib", "astropy", "pyccl", "sacc", "cosmosis", "cobaya"]

# Black configuration - keep existing formatting tool
[tool.black]
line-length = 88
target-version = ['py311']
extend-exclude = 'examples/srd_sn/sndata'

# Pyright configuration - runs alongside mypy without conflicts
[tool.pyright]
# Include all main source directories
include = ["firecrown", "tests", "examples"]

# Exclude common non-source directories
exclude = [
    "**/node_modules",
    "**/__pycache__",
    "**/.pytest_cache",
    "**/build",
    "**/dist",
    "docs/_build",
    ".git"
]

# Python version (should match your target)
pythonVersion = "3.11"

# Type checking configuration
typeCheckingMode = "off"  # Can be "off", "basic", or "strict"

# Enable useful warnings
reportMissingImports = true
reportMissingTypeStubs = false  # Don't warn about missing stubs for third-party packages
reportUnusedImport = true
reportUnusedClass = true
reportUnusedFunction = true
reportUnusedVariable = true
reportDuplicateImport = true

# Scientific computing specific settings
reportMissingParameterType = false  # NumPy/SciPy often have complex signatures
reportUnknownParameterType = false  # Allow flexibility with scientific libraries
reportUnknownMemberType = false     # NumPy arrays have dynamic typing

# Allow flexibility for scientific computing patterns
reportGeneralTypeIssues = false
reportOptionalMemberAccess = true
reportOptionalSubscript = true
reportPrivateImportUsage = false    # Scientific packages often use private imports

# Disable false positives common in scientific computing
reportOperatorIssue = false         # PyCC/CCL Pk2D objects support operators despite type annotations
reportUnknownArgumentType = false   # Scientific libraries often have dynamic argument types
reportUnknownVariableType = false   # NumPy/SciPy operations create dynamic types

# Performance - don't analyze every possible path
reportUnnecessaryIsInstance = false
reportUnnecessaryCast = false

# Mypy configuration
[tool.mypy]
ignore_missing_imports = true
check_untyped_defs = true
exclude = "build|docs|.venv|venv|examples/srd_sn/sndata"
warn_unused_configs = true
warn_redundant_casts = true
warn_unused_ignores = true
no_implicit_optional = true
strict_equality = true
extra_checks = true
disallow_subclassing_any = true
disallow_untyped_decorators = true
explicit_package_bases = true
# disallow_any_generics = true

[[tool.mypy.overrides]]
module = "firecrown.connector.cobaya.*"
disallow_subclassing_any = false