pyproject.toml

# ---- Project Info and Dependencies ----

[project.urls]
Repository = "https://github.com/sichaohe/canns"
# Homepage = "https://..."
Documentation = "https://routhleck.com/canns"

[project]
name = "canns"
description = "A Python Library for Continuous Attractor Neural Networks"
authors = [
    { name="Sichao He", email="sichaohe@outlook.com" },
]
readme = "README.md"
license = "Apache-2.0"
requires-python = ">=3.11,<4.0"
dynamic = ["version"]

# https://pypi.org/classifiers/
# Adjust as needed:
classifiers = [
    # Adjust as needed:
    "Development Status :: 4 - Beta",
    # "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Typing :: Typed",
    # Include this to avoid accidentally publishing to PyPI:
    # "Private :: Do Not Upload",
]


# ---- Main dependencies ----

dependencies = [
    "brainpy[cpu]",
    "canns-lib>=0.11.0",
    "furo>=2025.7.19",
    "notebook>=7.4.4",
    "tqdm",
    "numpy>=1.24,<3",
    "numba>=0.56.0",
    "scipy>=1.9.0",
    "scikit-image>=0.19",
    "matplotlib>=3.5",
    "h5py>=3.7",
    "seaborn>=0.13.2",
    "imageio[ffmpeg]>=2.37.0",
    "textual>=7.3.0",
    "climage>=0.2.2",
    "igraph>=1.0.0",
    "leidenalg>=0.11.0",
]


# ---- Dev dependencies ----

[dependency-groups]
dev = [
    "pytest>=8.3.5",
    "pytest-sugar>=1.0.0",
    "pytest-cov>=6.0.0",
    "ruff>=0.11.9",
    "codespell>=2.4.1",
    "rich>=14.0.0",
    "basedpyright>=1.29.1",
    "funlog>=0.2.1",
    "jupyter>=1.1.1",
    "datasets>=4.4.1",
    "sphinx-copybutton>=0.5.2",
]
dev-gui = [
    "PySide6>=6.6.0",
    "pillow",
    "imageio",
    "qtawesome",
    "pytest-qt",
    "requests>=2.31.0",
]
docs = [
    "myst-parser>=4.0.1",
    "nbsphinx>=0.9.7",
    "sphinx>=8.1.3",
    "sphinx-autoapi>=3.6.0",
    "sphinx-autodoc-typehints>=3.0.1",
    "sphinx-design>=0.6.1",
    "sphinx-intl>=2.3.1",
    "sphinx-rtd-theme>=3.0.2",
    "sphinxcontrib-bibtex>=2.6.0",
]

[project.optional-dependencies]
cpu = [
    "brainpy[cpu]"
]
cuda12 = [
    "brainpy[cuda12]; platform_system == 'Linux'"
]
cuda13 = [
    "brainpy[cuda13]; platform_system == 'Linux'"
]
tpu = [
    "brainpy[tpu]; platform_system == 'Linux'"
]
gui = [
    "PySide6>=6.6.0",
    "pillow",
    "imageio",
    "qtawesome",
    "requests>=2.31.0",
]

[project.scripts]
# Add script entry points here:
canns = "canns.__main__:main"
canns-tui = "canns.pipeline.launcher:main"
canns-gallery = "canns.pipeline.gallery:main"
canns-gui = "canns.pipeline.asa_gui:main"


# ---- Build system ----

# Dynamic versioning from:
# https://github.com/ninoseki/uv-dynamic-versioning/

[build-system]
requires = ["hatchling", "uv-dynamic-versioning"]
build-backend = "hatchling.build"

[tool.hatch.version]
source = "uv-dynamic-versioning"
# Note JSON schemas don't seem to be right for tool.hatch.version.source so
# this may cause false warnings in IDEs.
# https://github.com/ninoseki/uv-dynamic-versioning/issues/21

[tool.uv-dynamic-versioning]
vcs = "git"
style = "pep440"
bump = true

[tool.hatch.build.targets.wheel]
# The source location for the package.
packages = ["src/canns"]
include = [
    "src/canns/pipeline/asa_gui/resources/**",
]

[tool.hatch.build.targets.sdist]
# Only include essential files in source distribution
include = [
    "/src",
    "/README.md",
    "/README_zh.md",
    "/LICENSE",
    "/CHANGELOG.md",
    "/CITATION.cff",
    "/pyproject.toml",
]


# ---- Settings ----

[tool.ruff]
# Set as desired, typically 88 (black standard) or 100 (wide).
line-length = 100

[tool.ruff.lint]
select = [
    # See: https://docs.astral.sh/ruff/rules/
    # Basic list from: https://docs.astral.sh/ruff/linter/#rule-selection
    "E", # https://docs.astral.sh/ruff/rules/#error-e
    "F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
    "UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
    "B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
    "I", # https://docs.astral.sh/ruff/rules/#isort-i
    # Other possibilities:
    # "D" # https://docs.astral.sh/ruff/rules/#pydocstyle-d
    # "Q" # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
    # "COM" # https://docs.astral.sh/ruff/rules/#flake8-commas-com
    # "SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim

]
ignore = [
    # Disable some rules that are overly pedantic. Add/remove as desired:
    "E501", # https://docs.astral.sh/ruff/rules/line-too-long/
    "E402", # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/
    "E731", # https://docs.astral.sh/ruff/rules/lambda-assignment/
    # We use both ruff formatter and linter so some rules should always be disabled.
    # See: https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
    "W191", # https://docs.astral.sh/ruff/rules/tab-indentation/
    "E111", # https://docs.astral.sh/ruff/rules/indentation-with-invalid-multiple/
    "E114", # https://docs.astral.sh/ruff/rules/indentation-with-invalid-multiple-comment/
    "E117", # https://docs.astral.sh/ruff/rules/over-indented/
    "D206", # https://docs.astral.sh/ruff/rules/docstring-tab-indentation/
    "D300", # https://docs.astral.sh/ruff/rules/triple-single-quotes/
    "Q000", # https://docs.astral.sh/ruff/rules/bad-quotes-inline-string/
    "Q001", # https://docs.astral.sh/ruff/rules/bad-quotes-multiline-string/
    "Q002", # https://docs.astral.sh/ruff/rules/bad-quotes-docstring/
    "Q003", # https://docs.astral.sh/ruff/rules/avoidable-escaped-quote/
    "COM812", # https://docs.astral.sh/ruff/rules/missing-trailing-comma/
    "COM819", # https://docs.astral.sh/ruff/rules/prohibited-trailing-comma/
    "ISC002", # https://docs.astral.sh/ruff/rules/multi-line-implicit-string-concatenation/
]

[tool.basedpyright]
# BasedPyright currently seems like the best type checker option, much faster
# than mypy and with a good extension for VSCode/Cursor.
# https://marketplace.visualstudio.com/items?itemName=detachhead.basedpyright
# https://docs.basedpyright.com/latest/configuration/config-files/#sample-pyprojecttoml-file
include = ["src"]
#exclude = [ ... ]
#include = ["src", "tests", "devtools"]
# By default BasedPyright is very strict, so you almost certainly want to disable
# some of the rules.
# First, these turn off warnings about (yes) how you ignore warnings:
reportIgnoreCommentWithoutRule = false
reportUnnecessaryTypeIgnoreComment = false
# A few typically noisy warnings are next.
# How many you enable is up to you. The first few are off by default, but you can
# comment/uncomment these as desired:
reportMissingTypeStubs = false
reportUnusedCallResult = false
reportAny = false
reportExplicitAny = false
reportImplicitStringConcatenation = false
reportUnreachable = false
# reportPrivateImportUsage = false
# reportPrivateLocalImportUsage = false
# reportMissingImports = false
# reportUnnecessaryIsInstance = false
reportArgumentType = false
reportGeneralTypeIssues = false
reportUnknownArgumentType = false
reportUnknownVariableType = false
reportOperatorIssue = false


[tool.codespell]
# Add here as needed:
# ignore-words-list = "foo,bar"
# skip = "foo.py,bar.py"

[tool.pytest.ini_options]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
testpaths = [
    "tests",
]
norecursedirs = []
filterwarnings = []
addopts = "--assert=plain -ra"
markers = [
    "integration: tests that exercise multi-module flows or external dependencies",
    "visualization: tests that generate plots or graphics",
    "slow: tests that are notably slower than unit tests",
]

[tool.coverage.run]
branch = true
source = ["canns"]

[tool.coverage.report]
skip_covered = true
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
]