img-embed-td/pyproject.toml at main · royerlab/img-embed-td · GitHub

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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "img-embed-td"
dynamic = ["version"]
authors = [
    { name = "Ilan Theodoro", email = "ilan.silva@czbiohub.org" },
    { name = "Jordao Bragantini", email = "jordao.bragantini@czbiohub.org" },
]
description = "Image embedding utilities for tracksdata"
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "click>=8.3.0",
    "cmap>=0.6.2",
    "einops>=0.8.1",
    "torch>=2.9.0",
    "torchvision>=0.24.0",
    "tracksdata",
    "transformers>=4.57.1",
]
license = "BSD-3-Clause"

[project.optional-dependencies]
test = [
  "spatial-graph",
  "pytest>=7.0",
  "pytest-cov",
  "pytest-html",
]

[project.urls]
Documentation = "https://github.com/royerlab/img-embed-td#readme"
Issues = "https://github.com/royerlab/img-embed-td/issues"
Source = "https://github.com/royerlab/img-embed-td"

[project.scripts]
img-embed-td = "img_embed_td.cli:main"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.hooks.vcs]
version-file = "src/img_embed_td/__about__.py"

# https://docs.astral.sh/ruff
[tool.ruff]
target-version = "py310"
src = ["src"]
line-length = 120

# https://docs.astral.sh/ruff/rules
[tool.ruff.lint]
pydocstyle = { convention = "numpy" }
ignore = ["E712"]
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D417", # Missing argument descriptions in Docstrings
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
    "TID",  # flake8-tidy-imports
]

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]

# https://docs.astral.sh/ruff/formatter/
[tool.ruff.format]
docstring-code-format = true
skip-magic-trailing-comma = false # default is false

# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
show_missing = true
skip_covered = true
exclude_lines = [
    "@njit",  # numba is not supported by coverage
    "@jitclass",
    "@overload",
    "pragma: no cover", # Have to re-enable the standard pragma
    "def __repr__", # Don't complain about missing debug-only code:
    "raise AssertionError",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",  # Ignore type checking
    "if __name__ == .__main__.:", # Don't complain if non-runnable code isn't run:
    "@(abc.)?abstractmethod", # Don't complain about abstract methods, they aren't run:
    "def .*: \\.\\.\\.$",  # Exclude function headers that end with "..." (type stubs)
    "raise ValueError",
]

[tool.coverage.run]
source = ["src"]
branch = true
parallel = true
omit = [
  "src/img_embed_td/__about__.py",
  "src/img_embed_td/conftest.py",
  "**/_test/*.py",
]