pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "drim2p"
dynamic = ["version"]
description = 'A dreamy 2-photon imaging processing pipeline.'
readme = "README.md"
requires-python = ">=3.12"
license = "MIT"
keywords = ["2-photon", "two-photon", "imaging", "neuroscience", "processing"]
authors = [
  { name = "Olivier Delrée", email = "olivierdelree@protonmail.com" },
  { name = "Constantinos Eleftheriou", email = "Constantinos.Eleftheriou@ed.ac.uk" },
  { name = "Sophie Holland", email = "S.G.Holland@sms.ed.ac.uk" },
  { name = "Michelle Sanchez", email = "michelle.sr11@gmail.com" },
]
classifiers = [
  "Development Status :: 1 - Planning",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Operating System :: OS Independent",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Scientific/Engineering :: Image Processing",
  "Topic :: Scientific/Engineering :: Information Analysis",
]
dependencies = [
  "click",
  "dask",
  "duguidlab-motion-correction",  # SIMA fork
  "duguidlab-signal-separation",  # FISSA fork
  "h5py",
  "napari[pyqt6]",
  "numpy<2.0",
  "ome-types[lxml]",
  "pydantic",
]

[project.urls]
Documentation = "https://github.com/DuguidLab/drim2p#readme"
Issues = "https://github.com/DuguidLab/drim2p/issues"
Source = "https://github.com/DuguidLab/drim2p"

[project.scripts]
drim2p = "drim2p:drim2p"

[tool.hatch.version]
path = "src/drim2p/__about__.py"

[dependency-groups]
dev = [
  { include-group = "ci" },
  { include-group = "docs" },
  { include-group = "lint" },
  { include-group = "test" },
  { include-group = "types" },
]
ci = [
  "pre-commit",
]
docs = [
  "griffe-pydantic",
  "mkdocs",
  "mkdocs-caption",
  "mkdocs-click",
  "mkdocs-gen-files",
  "mkdocs-literate-nav",
  "mkdocs-material",
  "mkdocs-section-index",
  "mkdocstrings-python",
]
lint = [
  "ruff",
]
test = [
  "pytest",
  "pytest-cov",
]
types = [
  "mypy[install-types, faster-cache, reports]>=1.16",
]

[tool.hatch.envs.default]
path = ".venv"  # Use the environment provided by uv

[tool.hatch.envs.default.scripts]
ci-pc-install = "pre-commit install"
ci-pc-run = "pre-commit run"

docs-build-lax = "mkdocs build --clean"
docs-build = "docs-build-lax --strict"
docs-serve = "mkdocs serve --dev-addr localhost:8888"

lint-check = "ruff check"
lint-fix = "lint-check --fix"
lint-run = "lint-fix && ruff format {args:src/drim2p/ tests/}"

test-run-coverage = "pytest --cov=src/drim2p --cov-report=term-missing:skip-covered --cov-report=html"
test-run-coverage-browser = "test-run-coverage; open htmlcov/index.html"
test-run = "test-run-coverage --no-cov"

types-check = "mypy --install-types --non-interactive {args:src/drim2p/ tests/}"
types-report = "types-check --html-report mypy-report/"

[tool.ruff]
line-length = 88
fix = true
namespace-packages = ["scripts"]

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

[tool.ruff.lint]
preview = true

select = [
  "ERA",     # Disallow commented out code
  "YTT",     # Prevent misuse of `sys.version`
  "ANN",     # Force function annotations
  "S",       # Security testing (flake8-bandit)
  "BLE",     # Disallow blind except
  "B",       # Catch common sources of bugs
  "A",       # Disallow shadowing builtins
  "COM818",  # Trailing comma rules
  "C4",      # Ensure correct comprehensions
  "CPY",     # Force a copyright notice at the top of files
  "DTZ",     # Disallow naive datetime
  "T10",     # Disallow debugger traces
  "EM",      # Disallow strings inside exception constructors
  "EXE",     # Validate shebangs
  "FIX",     # Remind about FIXMEs
  "FA",      # Ensure proper usage of `from __future__ import annotations`
  "ISC",     # Ensure good practice for implicit string concatenation
  "ICN",     # Force using conventional aliases for popular packages
  "LOG",     # Ensure good practice for logging
  "G",       # Ensure good practice for log formatting
  "INP",     # Disallow namespace packages
  "PIE",     # Miscellaenous linting (flake8-pie)
  "T20",     # Disallow print statements
  "PT",      # Ensure good practice for pytest-based tests
  "Q",       # Enforce double quotes style
  "RSE",     # Disallow empty parentheses after exceptions
  "RET",     # Ensure proper return values
  "SLF",     # Disallow use of private members
  "SIM",     # Ensure code is simplified
  "TID253",  # Disallow banned imports at the module level
  "TD",      # Ensure proper use of TODOs
  "TC",      # Ensure proper typing imports and forward references
  "ARG",     # Disallow unused arguments
  "PTH",     # Ensure `pathlib` functions are used where possible
  "FLY",     # Favour f-strings to `str.join`
  "I",       # Ensure properly sorted imports
  "NPY",     # Disallow use of deprecated NumPy functions and type aliases
  "N",       # Ensure PEP 8 naming conventions
  "PERF",    # Disallow performance anti-patterns
  "E", "W",  # Ensure proper adherence to PEP 8
  "DOC",     # Ensure proper docstrings information
  "D",       # Ensure proper docstrings style
  "F",       # Miscellaenous linting (Pyflakes)
  "PGH",     # Disallow blanket `noqa` and `type: ignore`, and invalid mock access
  "PL",      # Pylint checks
  "UP",      # Ensure use of up-to-date syntax
  "FURB",    # Ensure use of up-to-date syntax
  "RUF",     # Miscellaneous linting (Ruff)
  "TRY",     # Ensure good practice for exception handling
]

ignore = [
  "ANN401",                # Allow `Any` function parameter
  "FIX002",                # Allow unsolved TODOs
  "G001", "G002", "G004",  # Allow formatted strings inside logging calls
  "RET505", "RET506",      # Avoid false posiives (especially with `if-elif` where the `if` returns or raises)
  "TD002", "TD003",        # Don't enforce including an author or issue with TODOs
  "TC003",                 # Don't force the use of `if TYPE_CHECKING` blocks
  "D100", "D104",          # Allow undocumented modules and packages
  "D107",                  # Don't force a documented `__init__` since we document it at the class level
  # Allow too many branches, arguments, locals, statements, and positional arguments
  "PLR0912", "PLR0913", "PLR0914", "PLR0915", "PLR0917",
]

unfixable = [
  "B905",  # Force programmer to decide which strictness to use with `builtins.zip`
]

[tool.ruff.lint.flake8-copyright]
notice-rgx = "(?i)SPDX-FileCopyrightText: © ?\\d{4}"

[tool.ruff.lint.flake8-tidy-imports]
banned-module-level-imports = [
  "fissa",
  "ome_types",
  "sima",
]

[tool.ruff.lint.isort]
force-single-line = true

[tool.ruff.lint.pydocstyle]
convention = "google"

# `mypy` config
[tool.mypy]
strict = true
pretty = true
allow_redefinition_new = true
local_partial_types = true  # Necessary when allow_redefinition_new is enabled
allow_redefinition = true
warn_unreachable = true
show_error_code_links = true
untyped_calls_exclude = [
  "dask.array"
]

[[tool.mypy.overrides]]
module = [
  "h5py.*",
  "fissa.*",
  "napari.*",
  "sima.*",
]
ignore_missing_imports = true

[tool.basedpyright]
reportImplicitStringConcatenation = false # Avoid nesting implicit concatenation of string in function calls

# `coverage` config
[tool.coverage.run]
source_pkgs = ["drim2p", "tests"]
branch = true
parallel = true
omit = [
  "src/drim2p/__about__.py",
]

[tool.coverage.paths]
drim2p = ["src/drim2p", "*/drim2p/src/drim2p"]
tests = ["tests", "*/drim2p/tests"]

[tool.coverage.report]
exclude_lines = [
  "no cov",
  "if __name__ == .__main__.:",
  "if TYPE_CHECKING:",
]