pyproject.toml

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

[project]
name = "organelle-mapping"
dynamic = ["version"]
description = "Segmenting organelles"
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
keywords = []
authors = [{ name = "Larissa Heinrich", email = "heinrichl@janelia.hhmi.org" }]
classifiers = [
  "Development Status :: 4 - Beta",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: Implementation :: CPython",
  "Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
  "daisy",
  "funlib.persistence>=0.6,<0.7",
  "fibsem-tools>=7.0.5",
  "matplotlib",
  "funlib.learn.torch@git+https://git@github.com/funkelab/funlib.learn.torch.git",
  "gunpowder",
  "torch",
  "click",
  "sqlalchemy",
  "xarray",
  "xarray-datatree",
  "zarr",
  "scikit-image",
  "xarray-multiscale",
  "cellmap-schemas",
  "pydantic-zarr",
  "numcodecs",
  "neuroglancer",
  "dask",
  "tensorboardX",
  "xarray-ome-ngff",
  "monai",
  "einops",
  "pydantic",
  "scikit-learn",
  "funlib.show.neuroglancer",
  "tensorboard",
  "tems>=1.0.4",
  "torchinfo",
  "corditea@git+https://github.com/saalfeldlab/corditea.git"
]

[project.optional-dependencies]
# Opt-in "lsd-jax" LSD backend. Pulls corditea's jax extra, which installs the
# (private) lsd-jax fork. Requires SSH access to the source and a working jax.
jax = ["corditea[jax]"]

[project.urls]
Documentation = "https://github.com/saalfeldlab/organelle-mapping#readme"
Issues = "https://github.com/saalfeldlab/organelle-mapping/issues"
Source = "https://github.com/saalfeldlab/organelle-mapping"

[project.scripts]
data_prep = "organelle_mapping.data_preparation:cli"
train = "organelle_mapping.run:main"
inference = "organelle_mapping.inference:cli"
evaluate = "organelle_mapping.evaluation:cli"
postprocess = "organelle_mapping.postprocessing:cli"
sync_db = "organelle_mapping.sync_db:cli"

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

[tool.hatch.metadata]
allow-direct-references = true
source-layout = "src"

[tool.black]
target-version = ["py37"]
line-length = 120
skip-string-normalization = true

[tool.ruff]
target-version = "py37"
line-length = 120
extend-exclude = ["*.ipynb"]

[tool.ruff.lint]
select = [
  "A",
  "ARG",
  "B",
  "C",
  "DTZ",
  "E",
  "EM",
  "F",
  "FBT",
  "I",
  "ICN",
  "ISC",
  "N",
  "PLC",
  "PLE",
  "PLR",
  "PLW",
  "Q",
  "RUF",
  "S",
  "T",
  "TID",
  "UP",
  "W",
  "YTT",
]
ignore = [
  # Allow non-abstract empty methods in abstract base classes
  "B027",
  # Allow boolean positional values in function calls, like `dict.get(... True)`
  "FBT003",
  # Ignore checks for possible passwords
  "S105",
  "S106",
  "S107",
  # Ignore complexity
  "C901",
  "PLR0911",
  "PLR0912",
  "PLR0913",
  "PLR0915",
]
unfixable = [
  # Don't touch unused imports
  "F401",
]

[tool.ruff.lint.isort]
known-first-party = ["organelle_mapping"]

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

[tool.ruff.lint.per-file-ignores]
# Tests can use magic values, assertions, and relative imports
"tests/**/*" = ["PLR2004", "S101", "TID252"]
# Inference uses subprocess intentionally for worker spawning
"src/organelle_mapping/inference.py" = ["S603", "S607"]

[tool.coverage.run]
source_pkgs = ["organelle_mapping", "tests"]
branch = true
parallel = true
omit = ["src/organelle_mapping/__about__.py"]

[tool.coverage.paths]
organelle_mapping = ["src/organelle_mapping", "*/organelle-mapping/src/organelle_mapping"]
tests = ["tests", "*/organelle-mapping/tests"]

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

[tool.pixi.workspace]
channels = ["nvidia", "pytorch", "conda-forge"]
platforms = ["linux-64"]

[tool.pixi.activation.env]
MKL_NUM_THREADS = "1"
NUM_MKL_THREADS = "1"
OPENBLAS_NUM_THREADS = "1"
OPENMP_NUM_THREADS = "1"
OMP_NUM_THREADS = "1"
XLA_FLAGS = "--xla_cpu_multi_thread_eigen=false"

[tool.pixi.tasks]
test = "pytest -v"
test-cov = "coverage run -m pytest tests"
cov-report = { cmd = ["coverage combine", "coverage report"], depends-on = ["test-cov"] }
lint = "ruff check ."
format = "ruff format ."
fmt = { cmd = "ruff check --fix . && ruff format .", description = "Fix and format code" }
typecheck = "mypy --install-types --non-interactive src/organelle_mapping tests"
check-all = { depends-on = ["lint", "typecheck"], description = "Run all checks" }

[tool.pixi.dependencies]
python = "3.11.*"
xarray-datatree = "*"

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

# The override replaces corditea's requirement wholesale, so the `[jax]` extra
# must be named HERE — a bare `corditea[jax]` request elsewhere gets stripped by
# the override. This is what pulls the local corditea's lsd-jax into the dev env.
[tool.pixi.feature.local-deps.pypi-options]
dependency-overrides = { corditea = { path = "../corditea", editable = true, extras = ["jax"] } }

# Opt-in lsd-jax backend: activate organelle-mapping's own `jax` extra (which
# pulls corditea[jax] -> the private lsd-jax fork) and the CUDA jax build it
# runs on. Combine with local-deps so corditea[jax] resolves from the local
# checkout rather than public git.
[tool.pixi.feature.jax-backend.pypi-dependencies]
organelle-mapping = { path = ".", editable = true, extras = ["jax"] }
jax = { version = "*", extras = ["cuda13"] }

[tool.pixi.feature.dev.dependencies]
pytest = ">=7.3"
pytest-cov = ">=4.0"
coverage = ">=6.5"
ruff = ">=0.1.0"
mypy = ">=1.0"
black = ">=23.1.0"
jupyter = ">=1.0"
jupyterlab = ">=4.0"
ipykernel = ">=6.23"

[tool.pixi.feature.notebooks.dependencies]
jupyter = ">=1.0"
jupyterlab = ">=4.0"
ipykernel = ">=6.23"

[tool.pixi.environments]
default = { solve-group = "default" }
dev = { features = ["dev", "notebooks", "local-deps", "jax-backend"], solve-group = "dev" }