pyproject.toml

[build-system]
requires = [
  "setuptools >= 69",
  "setuptools_scm[toml]>=8"
]
build-backend = "setuptools.build_meta"

[project]
name = "finn-viewer"
description = "n-dimensional array viewer for cell tracking data in Python"
authors = [
    { name = "Caroline Malin-Mayor", email = "malinmayorc@janelia.hhmi.org" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: X11 Applications :: Qt",
    "Intended Audience :: Education",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: C",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Visualization",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Utilities",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX",
    "Operating System :: Unix",
    "Operating System :: MacOS",
]
requires-python = ">=3.10"
dependencies = [
    "appdirs>=1.4.4",
    "app-model>=0.3.0,<0.4.0",
    "cachey>=0.2.1",
    "certifi>=2018.1.18",
    "dask[array]>=2021.10.0",
    "imageio>=2.20,!=2.22.1",
    "jsonschema>=3.2.0",
    "lazy_loader>=0.2",
    "magicgui>=0.7.0",
    "napari-console>=0.1.1",
    "napari-plugin-engine>=0.1.9",
    "napari-svg>=0.1.8",
    "npe2>=0.7.6",
    "numpy>=1.22.2",
    "numpydoc>=0.9.2",
    "pandas>=1.3.0",
    "Pillow>=9.0",
    "pint>=0.17",
    "psutil>=5.0",
    "psygnal>=0.5.0",
    "pydantic>=1.9.0",
    "pygments>=2.6.0",
    "PyOpenGL>=3.1.0",
    "pywin32 ; platform_system == 'Windows'",
    "PyYAML>=5.1",
    "qtpy>=2.3.1",
    "scikit-image[data]>=0.19.1",
    "scipy>=1.5.4",
    "superqt>=0.6.7",
    "tifffile>=2022.7.28",
    "toolz>=0.10.0",
    "tqdm>=4.56.0",
    "typing_extensions>=4.2.0",
    "vispy>=0.14.1,<0.15",
    "wrapt>=1.11.1",
    "funtracks",
    "pyqtgraph",
    "fonticon-fontawesome6",
    "zarr<3",
]
dynamic = [
    "version",
]

[project.license]
text = "BSD 3-Clause"

[project.scripts]
finn = "finn.__main__:main"

[project.readme]
file = "README.md"
content-type = "text/markdown"

[project.urls]
Download = "https://github.com/funkelab/finn"
"Bug Tracker" = "https://github.com/funkelab/finn/issues"
"Source Code" = "https://github.com/funkelab/finn"

[project.optional-dependencies]
pyside2 = [
    "PySide2>=5.13.2,!=5.15.0 ; python_version < '3.11' and platform_machine != 'arm64'",
]
pyside6_experimental = [
    "PySide6 < 6.5 ; python_version < '3.12'"
]
pyqt6 = [
    "PyQt6 > 6.5",
    "PyQt6 != 6.6.1 ; platform_system == 'Darwin'"
]
pyside = [
    "finn-viewer[pyside2]"
]
pyqt5 = [
    "PyQt5>=5.13.2,!=5.15.0",
]
pyqt = [
    "finn-viewer[pyqt5]"
]
qt = [
    "finn-viewer[pyqt]"
]
all = [
    "finn-viewer[pyqt,optional]"
]
optional-base = [
    "zarr>=2.12.0", # needed by `builtins` (dask.array.from_zarr) to open zarr
    "napari-plugin-manager >=0.1.3, <0.2.0",
]
optional-numba = [
    "numba>=0.57.1",
    "finn-viewer[pyqt,optional]",
    "napari-plugin-manager >=0.1.0a1, <0.2.0",
]
optional = [
    "finn-viewer[optional-base,optional-numba]",
    "triangle",
    "PartSegCore-compiled-backend>=0.15.8",
]
testing = [
    "babel>=2.9.0",
    "fsspec>=2023.10.0",
    "hypothesis>=6.8.0",
    "lxml[html_clean]>5",
    "matplotlib >= 3.6.1",
    "pooch>=1.6.0",
    "coverage>7",
    "docstring_parser>=0.15",
    "pretend>=1.0.9",
    "pyautogui>=0.9.54",
    "pytest-qt>=4.3.1",
    "pytest-pretty>=1.1.0",
    "pytest>=8.1.0",
    "tensorstore>=0.1.13",
    "virtualenv>=20.17",
    "xarray>=0.16.2",
    "IPython>=7.25.0",
    "qtconsole>=4.5.1",
    "rich>=12.0.0",
    "finn-viewer[optional-base]",
]
testing_extra = [
    "torch>=1.7",
]
release = [
    "PyGithub>=1.44.1",
    "twine>=3.1.1",
    "gitpython>=3.1.0",
    "requests-cache>=0.9.2",
]
dev = [
    "ruff",
    "check-manifest>=0.42",
    "pre-commit>=2.9.0",
    "pydantic",
    "python-dotenv",
    "finn[testing]",
]
build = [
    "ruff",
    "pyqt5",
]

[project.entry-points.pytest11]
finn = "finn.utils._testsupport"

[project.entry-points."finn.manifest"]
finn_builtins = "finn_builtins:builtins.yaml"

[tool.setuptools]
zip-safe = false
include-package-data = true
license-files = [
    "LICENSE",
]

[tool.setuptools.packages.find]
namespaces = false

[tool.setuptools.package-data]
"*" = [
    "*.pyi",
]
finn_builtins = [
    "builtins.yaml",
]


[tool.setuptools_scm]
write_to = "finn/_version.py"

[tool.check-manifest]
ignore = [
  ".cirrus.yml",
  ".pre-commit-config.yaml",
  "asv.conf.json",
  "codecov.yml",
  "Makefile",
  "finn/_version.py",  # added during build by setuptools_scm
  "tools/minreq.py",
  "tox.ini",
  "finn/_qt/qt_resources/_qt_resources_*.py",
  "*.pyi",  # added by make typestubs
  "binder/*",
  ".env_sample",
  ".devcontainer/*",
  "finn/resources/icons/_themes/*/*.svg"
]

[tool.ruff]
line-length = 90
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*",
]

fix = true

[tool.ruff.format]
quote-style = "single"

[tool.ruff.lint]
select = [
    "E", "F", "W", #flake8
    "UP", # pyupgrade
    "I", # isort
    "YTT", #flake8-2020
    "TC", # flake8-type-checing
    "BLE", # flake8-blind-exception
    "B", # flake8-bugbear
    "A", # flake8-builtins
    "C4", # flake8-comprehensions
    "ISC", # flake8-implicit-str-concat
    "G", # flake8-logging-format
    "PIE", # flake8-pie
    "COM", # flake8-commas
    "SIM", # flake8-simplify
    "INP", # flake8-no-pep420
    "PYI", # flake8-pyi
    "Q", # flake8-quotes
    "RSE", # flake8-raise
    "RET", # flake8-return
    "TID",  # flake8-tidy-imports # replace absolutify import
    "TRY", # tryceratops
    "ICN", # flake8-import-conventions
    "RUF", # ruff specyfic rules
    "NPY201", # checks compatibility with numpy version 2.0
    "ASYNC", # flake8-async
    "EXE", # flake8-executable
    "FA", # flake8-future-annotations
    "LOG", # flake8-logging
    "SLOT", # flake8-slots
    "PT", # flake8-pytest-style
    "T20", # flake8-print
]
ignore = [
    # "E501", 
    "TC001", "TC002", "TC003",
    "A003", # flake8-builtins - we have class attributes violating these rule
    "COM812", # flake8-commas - we don't like adding comma on single line of arguments
    "COM819", # conflicts with ruff-format
    "SIM117", # flake8-simplify - we some of merged with statements are not looking great with black, reanble after drop python 3.9
    "RET504", # not fixed yet https://github.com/charliermarsh/ruff/issues/2950
    "TRY003", # require implement multiple exception class
    "RUF005", # problem with numpy compatybility, see https://github.com/charliermarsh/ruff/issues/2142#issuecomment-1451038741
    "B028", # need to be fixed
    "PYI015", # it produces bad looking files (@jni opinion)
    "W191", "Q000", "Q001", "Q002", "Q003", "ISC001", # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
]

[tool.ruff.lint.per-file-ignores]
"finn/_vispy/__init__.py" = ["E402"]
"**/_tests/*.py" = ["B011", "INP001", "TRY301", "B018", "RUF012"]
"finn/utils/_testsupport.py" = ["B011"]
"tools/validate_strings.py" = ["F401"]
"tools/**" = ["INP001", "T20"]
"examples/**" = ["ICN001", "INP001", "T20"]
"**/vendored/**" = ["TID"]
"finn/benchmarks/**" = ["RUF012", "TID252"]

[tool.ruff.lint.flake8-builtins]
builtins-allowed-modules = ["io", "types", "threading"]

[tool.ruff.lint.pyupgrade]
keep-runtime-typing = true

[tool.ruff.lint.flake8-quotes]
docstring-quotes = "double"
inline-quotes = "single"
multiline-quotes = "double"

[tool.ruff.lint.flake8-tidy-imports]
# Disallow all relative imports.
ban-relative-imports = "all"

[tool.ruff.lint.isort]
known-first-party=['finn']
combine-as-imports = true

[tool.ruff.lint.flake8-import-conventions]
[tool.ruff.lint.flake8-import-conventions.extend-aliases]
# Declare a custom alias for the `matplotlib` module.
"dask.array" = "da"
xarray = "xr"

[tool.pytest.ini_options]
# These follow standard library warnings filters syntax.  See more here:
# https://docs.python.org/3/library/warnings.html#describing-warning-filters
addopts = ["--maxfail=5",  "--durations=10",  "-ra", "--strict-markers", "--strict-config"]
console_output_style = "count"
minversion = "8"
# log_cli_level = "INFO"
xfail_strict = true
testpaths = ["finn", "finn_builtins"]


# NOTE: only put things that will never change in here.
# napari deprecation and future warnings should NOT go in here.
# instead... assert the warning with `pytest.warns()` in the relevant test,
# That way we can clean them up when no longer necessary
filterwarnings = [
  "error:::finn", # turn warnings from finn into errors
  "error:::test_.*", # turn warnings in our own tests into errors
  "default:::finn.+vendored.+",  # just print warnings inside vendored modules
  "ignore::DeprecationWarning:shibokensupport",
  "ignore::DeprecationWarning:ipykernel",
  "ignore::DeprecationWarning:tensorstore",
  "ignore:Accessing zmq Socket:DeprecationWarning:jupyter_client",
  "ignore:pythonw executable not found:UserWarning:",
  "ignore:data shape .* exceeds GL_MAX_TEXTURE_SIZE:UserWarning",
  "ignore:For best performance with Dask arrays in napari:UserWarning:",
  "ignore:numpy.ufunc size changed:RuntimeWarning",
  "ignore:Multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed",
  "ignore:Alternative shading modes are only available in 3D, defaulting to none",
  "ignore:distutils Version classes are deprecated::",
  "ignore:There is no current event loop:DeprecationWarning:",
  "ignore:(?s).*Pyarrow will become a required dependency of pandas:DeprecationWarning",  # pandas pyarrow (pandas<3.0),
  # TODO: remove once xarray is updated to avoid this warning
  # https://github.com/pydata/xarray/blame/b1f3fea467f9387ed35c221205a70524f4caa18b/pyproject.toml#L333-L334
  # https://github.com/pydata/xarray/pull/8939
  "ignore:__array__ implementation doesn't accept a copy keyword, so passing copy=False failed.",
  "ignore:pkg_resources is deprecated",
  "ignore:Deprecated call to `pkg_resources.declare_namespace",
  "ignore:Use Group.create_array instead."
]
markers = [
    "examples: Test of examples",
    "disable_qthread_start: Disable thread start in this Test",
    "disable_qthread_pool_start: Disable strarting QRunnable using QThreadPool start in this Test",
    "disable_qtimer_start: Disable timer start in this Test",
    "disable_qanimation_start: Disable animation start in this Test",
    "enable_console: Don't mock the IPython console (in QtConsole) in this Test",
    # mark slow tests, so they can be skipped using: pytest -m "not slow"
    "slow: mark a test as slow",
    "key_bindings: Test of keybindings",
]

[tool.mypy]
files = "finn"
# This file triggers an internal mypy error, so exclude collection
# TODO: fix this
exclude = "finn/utils/events/_tests/test_evented_model\\.py"
plugins =  "numpy.typing.mypy_plugin, pydantic.mypy"
ignore_missing_imports = true
hide_error_codes = false
warn_redundant_casts = true
disallow_incomplete_defs = true
disallow_untyped_calls = true
disallow_untyped_defs = true
warn_unused_ignores = true
check_untyped_defs = true
no_implicit_optional = true
disable_error_code = [
  # See discussion at https://github.com/python/mypy/issues/2427;
  # mypy cannot run type checking on method assignment, but we use
  # that in several places, so ignore the error
  'method-assign'
]
# see `$ qtpy mypy-args` and qtpy readme. This will be used by `tox -e mypy`
# to properly infer with PyQt6 installed
always_false=['PYSIDE6', 'PYSIDE2', 'PYQT5']
always_true=['PYQT6']


# gloabl ignore error
[[tool.mypy.overrides]]
module = [
  '*._tests.*',
  '*.experimental.*',
  '*._vendor.*',
  '*.benchmarks.*',
  'finn_builtins.*'
]
ignore_errors = true




# individual ignore error
# we should strive to remove those
# See https://github.com/napari/napari/issues/2751
# you can regenerate this list with the following command \047 is single quote.
# mypy napari | cut -f1 -d: | sort | uniq  | tr '/' '.'  | sed 's/\.py//' | awk '{ print "    \047" $0 "\047," }'
[[tool.mypy.overrides]]
module = [
    'finn._qt.code_syntax_highlight',
    'finn._qt.containers._base_item_model',
    'finn._qt.containers._base_item_view',
    'finn._qt.containers._layer_delegate',
    'finn._qt.containers.qt_axis_model',
    'finn._qt.containers.qt_layer_model',
    'finn._qt.containers.qt_list_model',
    'finn._qt.containers.qt_list_view',
    'finn._qt.containers.qt_tree_model',
    'finn._qt.containers.qt_tree_view',
    'finn._qt.dialogs.confirm_close_dialog',
    'finn._qt.dialogs.preferences_dialog',
    'finn._qt.dialogs.qt_about',
    'finn._qt.dialogs.qt_activity_dialog',
    'finn._qt.dialogs.qt_modal',
    'finn._qt.dialogs.qt_notification',
    'finn._qt.dialogs.qt_package_installer',
    'finn._qt.dialogs.qt_plugin_dialog',
    'finn._qt.dialogs.qt_plugin_report',
    'finn._qt.dialogs.qt_reader_dialog',
    'finn._qt.dialogs.screenshot_dialog',
    'finn._qt.experimental.qt_chunk_receiver',
    'finn._qt.experimental.qt_poll',
    'finn._qt.layer_controls.qt_colormap_combobox',
    'finn._qt.layer_controls.qt_image_controls',
    'finn._qt.layer_controls.qt_image_controls_base',
    'finn._qt.layer_controls.qt_labels_controls',
    'finn._qt.layer_controls.qt_layer_controls_base',
    'finn._qt.layer_controls.qt_layer_controls_container',
    'finn._qt.layer_controls.qt_points_controls',
    'finn._qt.layer_controls.qt_shapes_controls',
    'finn._qt.layer_controls.qt_surface_controls',
    'finn._qt.layer_controls.qt_tracks_controls',
    'finn._qt.layer_controls.qt_vectors_controls',
    'finn._qt.menus._util',
    'finn._qt.menus.debug_menu',
    'finn._qt.menus.file_menu',
    'finn._qt.perf.qt_event_tracing',
    'finn._qt.perf.qt_performance',
    'finn._qt.qt_event_filters',
    'finn._qt.qt_event_loop',
    'finn._qt.qt_main_window',
    'finn._qt.qt_resources._svg',
    'finn._qt.qt_viewer',
    'finn._qt.qthreading',
    'finn._qt.utils',
    'finn._qt.widgets._slider_compat',
    'finn._qt.widgets.qt_color_swatch',
    'finn._qt.widgets.qt_dict_table',
    'finn._qt.widgets.qt_dims',
    'finn._qt.widgets.qt_dims_slider',
    'finn._qt.widgets.qt_dims_sorter',
    'finn._qt.widgets.qt_extension2reader',
    'finn._qt.widgets.qt_font_size',
    'finn._qt.widgets.qt_highlight_preview',
    'finn._qt.widgets.qt_keyboard_settings',
    'finn._qt.widgets.qt_message_popup',
    'finn._qt.widgets.qt_mode_buttons',
    'finn._qt.widgets.qt_plugin_sorter',
    'finn._qt.widgets.qt_progress_bar',
    'finn._qt.widgets.qt_range_slider_popup',
    'finn._qt.widgets.qt_scrollbar',
    'finn._qt.widgets.qt_size_preview',
    'finn._qt.widgets.qt_spinbox',
    'finn._qt.widgets.qt_splash_screen',
    'finn._qt.widgets.qt_theme_sample',
    'finn._qt.widgets.qt_tooltip',
    'finn._qt.widgets.qt_viewer_buttons',
    'finn._qt.widgets.qt_viewer_dock_widget',
    'finn._qt.widgets.qt_viewer_status_bar',
    'finn._qt.widgets.qt_welcome',
    'finn._vispy.canvas',
    'finn._vispy.experimental.texture_atlas',
    'finn._vispy.experimental.tile_set',
    'finn._vispy.experimental.tiled_image_visual',
    'finn._vispy.experimental.vispy_tiled_image_layer',
    'finn._vispy.overlays.base',
    'finn._vispy.utils.cursor',
    'finn.components.layerlist',
    'finn.layers._layer_actions',
    'finn.layers._multiscale_data',
    'finn.layers.intensity_mixin',
    'finn.layers.points._points_key_bindings',
    'finn.layers.points._points_utils',
    'finn.layers.points.points',
    'finn.layers.shapes._shapes_mouse_bindings',
    'finn.layers.shapes.shapes',
    'finn.layers.utils.color_encoding',
    'finn.layers.utils.color_manager',
    'finn.layers.utils.stack_utils',
    'finn.layers.utils.string_encoding',
    'finn.layers.utils.style_encoding',
    'finn.layers.utils.text_manager',
    'finn.utils._magicgui',
    'finn.utils._testsupport',
    'finn.utils._tracebacks',
    'finn.utils.action_manager',
    'finn.utils.events.containers._evented_dict',
    'finn.utils.events.containers._evented_list',
    'finn.utils.events.containers._nested_list',
    'finn.utils.events.custom_types',
    'finn.utils.events.debugging',
    'finn.utils.events.event',
    'finn.utils.events.evented_model',
    'finn.utils.interactions',
    'finn.utils.key_bindings',
    'finn.utils.mouse_bindings',
    'finn.utils.progress',
    'finn.utils.shortcuts',
    'finn.utils.stubgen',
    'finn.utils.transforms.transforms',
    'finn.utils.tree.group',
    'finn.view_layers',
    'finn._app_model.injection._processors',
]
ignore_errors = true

[[tool.mypy.overrides]]
module = [
    "finn.settings",
    "finn.settings._yaml",
    "finn.plugins.exceptions",
    "finn._app_model.actions._toggle_action",
    "finn._vispy.filters.tracks",
    "finn._vispy.utils.text",
    "finn._vispy.utils.visual",
    "finn._vispy.visuals.clipping_planes_mixin",
    "finn._vispy.visuals.markers",
    "finn._vispy.visuals.surface",
    "finn.layers.shapes._shapes_models.path",
    "finn.layers.shapes._shapes_models.polygon",
    "finn.layers.shapes._shapes_models._polygon_base",
    "finn.layers.shapes._shapes_models.ellipse",
    "finn.layers.shapes._shapes_models.line",
    "finn.layers.shapes._shapes_models.rectangle",
    "finn.layers.shapes._shapes_models.shape",
    "finn.resources._icons",
    "finn.utils.color",
    "finn.utils.events.containers._dict",
    "finn.utils.events.event_utils",
    "finn.utils.migrations",
    "finn.utils.validators",
    "finn.window"
]
disallow_incomplete_defs = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn._event_loop",
    "finn._vispy.utils.quaternion",
    "finn._vispy.visuals.bounding_box",
    "finn._vispy.visuals.image",
    "finn._vispy.visuals.interaction_box",
    "finn._vispy.visuals.points",
    "finn._vispy.visuals.scale_bar",
    "finn.components._layer_slicer",
    "finn.components._viewer_mouse_bindings",
    "finn.components.overlays.base",
    "finn.components.overlays.interaction_box",
    "finn.utils.colormaps.categorical_colormap_utils",
]
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn.components.viewer_model",
    "finn.settings._fields",
    "finn.settings._migrations",
    "finn.settings._base",
    "finn.types",
    "finn.plugins._npe2",
    "finn.settings._napari_settings",
    "finn.plugins._plugin_manager",
    "finn.plugins.utils",
    "finn._qt._qapp_model.qactions._file",
    "finn._qt._qapp_model.qactions._help",
    "finn._qt._qapp_model.qactions._view",
    "finn._vispy.camera",
    "finn._vispy.layers.image",
    "finn._vispy.layers.scalar_field",
    "finn._vispy.layers.tracks",
    "finn._vispy.layers.vectors",
    "finn._vispy.overlays.axes",
    "finn._vispy.overlays.interaction_box",
    "finn._vispy.overlays.labels_polygon",
    "finn._vispy.overlays.scale_bar",
    "finn._vispy.overlays.text",
    "finn.layers.labels._labels_key_bindings",
    "finn.layers.utils._slice_input",
    "finn.utils._register",
    "finn.utils.colormaps.categorical_colormap",
    "finn.utils.colormaps.standardize_color",
    "finn.utils.geometry",
    "finn.utils.io",
    "finn.utils.notebook_display",
    "finn.utils.transforms.transform_utils",
    "finn.utils.translations",
    "finn.utils.tree.node",
    "finn.viewer",
    "finn.layers.shapes._shape_list",
    "finn.layers.vectors.vectors",
]
disallow_incomplete_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn.plugins",
    "finn._vispy.layers.base",
    "finn._vispy.visuals.axes",
    "finn.layers.labels._labels_mouse_bindings",
    "finn.layers.utils.color_manager_utils",
    "finn.utils.colormaps.vendored._cm",
    "finn.utils.colormaps.vendored.cm",
    "finn.utils.status_messages",
    "finn.layers.shapes._shapes_utils"
]
disallow_untyped_calls = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn._app_model._app",
    "finn.utils.theme",
]
disallow_incomplete_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false
warn_unused_ignores = false

[[tool.mypy.overrides]]
module = [
    "finn._app_model.context._context",
    "finn._qt.containers._factory"
]
disallow_incomplete_defs = false
disallow_untyped_defs = false
warn_unused_ignores = false

[[tool.mypy.overrides]]
module = [
    "finn._qt.menus.plugins_menu",
    "finn._vispy.layers.labels",
    "finn._vispy.layers.points",
    "finn._vispy.layers.shapes",
    "finn._vispy.layers.surface",
    "finn.components._viewer_key_bindings",
    "finn.layers.labels.labels",
    "finn.layers.surface.surface",
    "finn.layers.tracks.tracks",
    "finn.layers.utils.layer_utils",
    "finn.utils._dtype",
    "finn.utils.colormaps.colormap_utils",
    "finn.utils.misc",
]
check_untyped_defs = false
disallow_incomplete_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn.components.camera",
    "finn.components.dims",
    "finn.conftest",
    "finn.layers.labels._labels_utils",
    "finn.layers.points._points_mouse_bindings",
    "finn.utils.colormaps.colormap",
    "finn.utils.notifications",
]
check_untyped_defs = false
disallow_incomplete_defs = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn.utils.events.containers._typed",
]
check_untyped_defs = false
disallow_incomplete_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false
warn_unused_ignores = false

[[tool.mypy.overrides]]
module = [
    "finn.__main__",
    "finn.utils.colormaps.vendored.colors",
    "finn.layers.image.image",
    "finn.layers._scalar_field.scalar_field",
]
check_untyped_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn._app_model.context._layerlist_context",
    "finn.components.overlays.labels_polygon",
    "finn.plugins.io",
    "finn.utils.colormaps.vendored._cm_listed"
]
disallow_untyped_calls = false

[[tool.mypy.overrides]]
module = [
    "finn._qt.containers.qt_layer_list",
    "finn.layers.base.base"
]
check_untyped_defs = false
disallow_untyped_calls = false
disallow_untyped_defs = false
warn_unused_ignores = false

[[tool.mypy.overrides]]
module = [
    "finn._vispy.overlays.bounding_box",
    "finn._vispy.overlays.brush_circle",
    "finn.utils._test_utils",
]
check_untyped_defs = false
disallow_untyped_defs = false

[[tool.mypy.overrides]]
module = [
    "finn._pydantic_compat",
]
ignore_errors = true


[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "if typing.TYPE_CHECKING:",
    "raise NotImplementedError()",
    "except ImportError:",
    "^ +\\.\\.\\.$",
]

[tool.coverage.run]
omit = [
    "*/_vendor/*",
    "*/_version.py",
    "*/benchmarks/*",
    "finn/utils/indexing.py",
    "**/add_layer.py_tmpl"
]
source = [
    "finn",
    "finn_builtins",
]

[tool.coverage.paths]
source = [
    "finn/",
]
builtins = [
    "finn_builtins/",
]

[tool.importlinter]
root_package = "finn"
include_external_packages = true

[[tool.importlinter.contracts]]
name = "Forbid import PyQt and PySide"
type = "forbidden"
source_modules = "finn"
forbidden_modules = ["PyQt5", "PySide2", "PyQt6", "PySide6"]
ignore_imports = [
    "finn._qt -> PySide2",
    "finn.plugins._npe2 -> finn._qt._qplugins",
]

[[tool.importlinter.contracts]]
name = "Block import from qt module in finn.layers"
type = "layers"
layers = ["finn.qt","finn.layers"]
ignore_imports = [
    "finn.plugins._npe2 -> finn._qt._qplugins",
    # TODO: remove once npe1 deprecated
    "finn._qt.qt_main_window -> finn._qt._qplugins",
]

[[tool.importlinter.contracts]]
name = "Block import from qt module in finn.components"
type = "layers"
layers = ["finn.qt","finn.components"]
ignore_imports = [
    "finn.plugins._npe2 -> finn._qt._qplugins",
    # TODO: remove once npe1 deprecated
    "finn._qt.qt_main_window -> finn._qt._qplugins",
]