pyproject.toml

[project]
name = "napari-mcp"
dynamic = ["version"]
description = "MCP server for remote control of napari viewers via Model Context Protocol"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "BSD-3-Clause" }
authors = [{ name = "Ilan Theodoro", email = "ilan.silva@czbiohub.org" }]
maintainers = [{ name = "Ilan Theodoro", email = "ilan.silva@czbiohub.org" }]
keywords = ["napari", "mcp", "microscopy", "image-analysis", "ai", "claude"]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Framework :: napari",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: BSD License",
  "Operating System :: OS Independent",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Topic :: Scientific/Engineering :: Image Processing",
  "Topic :: Scientific/Engineering :: Visualization",
  "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
  "fastmcp>=2.10.3",
  "napari>=0.5.5",
  "qtpy>=2.4.1",
  "Pillow>=10.3.0",
  "imageio>=2.34.0",
  "numpy>=1.26.0",
  "typer>=0.9.0",
  "rich>=13.0.0",
  "toml>=0.10.2",
  'tomli>=2.0; python_version < "3.11"',
]

[project.urls]
Homepage = "https://github.com/royerlab/napari-mcp"
Repository = "https://github.com/royerlab/napari-mcp"
Documentation = "https://royerlab.github.io/napari-mcp/"
"Bug Tracker" = "https://github.com/royerlab/napari-mcp/issues"

[project.optional-dependencies]
dev = [
  "ruff>=0.12.10",
  "mypy>=1.17.0",
  "types-toml>=0.10.8.20240310",
  "types-Pillow>=10.0.0",
  "pre-commit>=4.3.0",
  "bandit>=1.8.6",
]
all = ["napari-mcp[dev]"]

[project.scripts]
napari-mcp = "napari_mcp.server:main"
napari-mcp-install = "napari_mcp.cli.main:app"

[project.entry-points."napari.manifest"]
napari-mcp = "napari_mcp:napari.yaml"

[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8.0", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
napari_mcp = ["napari.yaml"]

[tool.setuptools_scm]
write_to = "src/napari_mcp/_version.py"
fallback_version = "0.0.1"
version_scheme = "guess-next-dev"
local_scheme = "node-and-date"
# Accept SemVer tags, including pre-release/build metadata (e.g., v1.2.3, v1.2.3-alpha.1, 1.2.3+build)
tag_regex = "^(?P<prefix>v)?(?P<version>\\d+\\.\\d+\\.\\d+(?:-[0-9A-Za-z.-]+)?(?:\\+[0-9A-Za-z.-]+)?)$"

[tool.pytest.ini_options]
addopts = [
  "-q",
  "-p napari",
  "--strict-markers",
  "--tb=short",
  "--cov-config=.coveragerc",
  "-p no:cacheprovider",      # Disable cache for better isolation
]
asyncio_mode = "auto"
asyncio_default_fixture_loop_scope = "function"
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
markers = [
  "realgui: marks tests that require a real napari GUI session (deselect with -m 'not realgui')",
  "slow: marks tests as slow (deselect with -m 'not slow')",
  "integration: marks integration tests",
  "unit: marks unit tests",
  "smoke: marks smoke tests for quick validation",
  "isolated: marks tests that must run in complete isolation",
  "benchmark: marks performance benchmark tests",
]
filterwarnings = [
  "ignore::DeprecationWarning:napari.*",
  "ignore::DeprecationWarning:vispy.*",
  "ignore::DeprecationWarning:qtpy.*",
  "ignore::PendingDeprecationWarning:napari.*",
]
# Test isolation settings
junit_family = "xunit2"

[tool.ruff]
line-length = 88
target-version = "py310"
exclude = [
  ".bzr",
  ".direnv",
  ".eggs",
  ".git",
  ".mypy_cache",
  ".pants.d",
  ".ruff_cache",
  ".svn",
  ".tox",
  ".venv",
  "__pypackages__",
  "_build",
  "buck-out",
  "build",
  "dist",
  "node_modules",
  "venv",
  "*vendored*",
  "*_vendor*",
  "*_version.py",
]
fix = true

[tool.ruff.lint]
select = [
  "E",   # pycodestyle errors
  "W",   # pycodestyle warnings
  "F",   # pyflakes
  "I",   # isort
  "B",   # flake8-bugbear
  "C4",  # flake8-comprehensions
  "UP",  # pyupgrade
  "SIM", # flake8-simplify
  "TCH", # flake8-type-checking
  "TID", # flake8-tidy-imports
  "Q",   # flake8-quotes
  "S",   # bandit
  "D",   # pydocstyle
  "BLE", # flake8-blind-exception
  "A",   # flake8-builtins
  "ISC", # flake8-implicit-str-concat
  "G",   # flake8-logging-format
  "PIE", # flake8-pie
]
ignore = [
  "E501",   # line too long - handled by ruff format
  "BLE001", # blind except - needed for robust error handling in server code
  "S101",   # assert detected - allow in tests
  "S110",   # try-except-pass - acceptable for best-effort operations
  "SIM105", # contextlib.suppress - prefer explicit try/except for clarity
  "TCH003", # typing-only imports - not critical for functionality
  "D401",   # imperative mood - not critical for functionality
  "E402",   # module import not at top - needed for conditional imports
  "UP006",  # type annotation - magicgui requires runtime type annotation
  "UP007",  # type annotation - magicgui requires runtime type annotation
]

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

[tool.ruff.lint.per-file-ignores]
"tests/**" = [
  "S101",
  "S106",
  "S311",
  "D",
] # Allow asserts, hardcoded passwords, random, and skip docstrings in tests
"src/napari_mcp/server.py" = ["S102", "S307", "A002"]  # exec/eval needed for MCP execute_code; format param
"src/napari_mcp/bridge_server.py" = ["S102", "S307"]  # exec/eval needed for MCP execute_code
"src/napari_mcp/_helpers.py" = ["S102", "S307"]  # exec/eval needed for run_code helper
"src/napari_mcp/cli/install/utils.py" = ["S603", "S607"]  # subprocess needed for python detection
"src/napari_mcp/cli/install/codex_cli.py" = ["S603", "S607"]  # subprocess needed for codex

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

[dependency-groups]
dev = [
    "ruff>=0.12.10",
    "types-toml>=0.10.8.20240310",
]
testing = [
  "pytest>=8.4.0",
  "pytest-asyncio>=0.23.0",
  "pytest-cov>=4.0.0",
  "pytest-qt>=4.0.0",
  "pytest-xdist>=3.5.0",
  "pytest-timeout>=2.2.0",
  "pytest-benchmark>=4.0.0",
  "pytest-mock>=3.12.0",
  "pytest-random-order>=1.1.0",
  "pytest-forked>=1.6.0",
  "hypothesis>=6.100.0",
  "napari[testing,pyqt6]",
]

[tool.pixi.workspace]
channels = ["conda-forge"]
platforms = ["osx-arm64"]

[tool.pixi.pypi-dependencies]
napari-mcp = { path = ".", editable = true }

[tool.pixi.environments]
default = { solve-group = "default" }
all = { features = ["all", "dev", "testing"], solve-group = "default" }
dev = { features = ["dev"], solve-group = "default" }
testing = { features = ["testing"], solve-group = "default" }

[tool.pixi.tasks]