pyproject.toml

[build-system]
build-backend = "setuptools.build_meta"
requires = [ "setuptools>=77", "setuptools-scm>=8" ]

[project]
name = "cytodataframe"
description = """\
  An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation \
  masks.\
  """
readme = "README.md"
license = "BSD-3-Clause"
authors = [ { name = "Way Science Community" } ]
requires-python = ">=3.11,<3.14"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
]
dynamic = [ "version" ]
# ipyvolume, matplotlib, and pywavelets are intentionally dropped from core
# dependencies here: 3D rendering already moved to pyvista/trame (see
# optional-dependencies.viz3d below) before this change, leaving these three
# as dead weight - none are imported anywhere in src/. nest-asyncio2 moved to
# optional-dependencies.viz3d instead of being dropped: pyvista's trame
# notebook backend imports it directly to launch without an explicit
# `await`, and silently falls back to a static (non-interactive) render with
# a UserWarning when it is missing.
dependencies = [
  "imagecodecs>=2024.9.22,<2027",
  "imageio>=2.37,<3",
  "ipython>=8.12.3,<10",
  "ipywidgets>=8.1.7,<9",
  "opencv-python>=4.10.0.84,<6",
  "pandas>=2.2.2,<4",
  "polars>=1,<3",
  "pyarrow>=16",
  "scikit-image>0.19.3",
]
optional-dependencies.all = [
  "cytodataframe[ome,viz3d]",
]
# Optional feature stacks. Install with e.g. `pip install cytodataframe[viz3d,ome]`.
# These are imported lazily, so the core package imports fine without them.
optional-dependencies.ome = [
  # OME-Arrow image read/write/embedding (to_ome_parquet, OME-Arrow columns).
  "ome-arrow>=0.0.3,<0.1.1",
]
optional-dependencies.viz3d = [
  # Interactive 3D volume rendering (trame/pyvista views in notebooks).
  # nest-asyncio2 lets pyvista launch its notebook trame server without an
  # explicit `await`; without it, 3D views silently fall back to a static
  # render.
  "nest-asyncio2>=1.7,<2",
  "pyvista>=0.46.4",
  "trame>=3.12",
  "trame-vtk>=2.10",
  "trame-vuetify>=3.1",
]

[dependency-groups]
dev = [
  "black>=24.10,<27",
  "cosmicqc>=1.0.1; python_version<'3.13' and python_version>='3.10'",
  "coverage>=7.6,<8",
  "duckdb>=1.1.3,<2",
  "httpcore>=0.18,<1.1",
  "hypothesis>=6,<7",
  "isort>=5.13.2,<10",
  "jupyterlab>=4.3,<5",
  "jupyterlab-code-formatter>=3.0.2,<4",
  "jupytext>=1.16.4,<2",
  # optional-feature stacks needed to exercise the full test suite
  "nest-asyncio2>=1.7,<2",
  "ome-arrow>=0.0.3,<0.1.1",
  "poethepoet>=0.37,<0.49",
  "pytest>=8.3.3,<10",
  "pytest-cov>=5,<8",
  "pyvista>=0.46.4",
  "sqlalchemy>=1.3.6,<3",
  "trame>=3.12",
  "trame-vtk>=2.10",
  "trame-vuetify>=3.1",
]
docs = [
  "dunamai>=1.22,<2",
  "myst-nb>=1.1.2,<2",
  "myst-parser>=3,<6",
  "pydata-sphinx-theme>=0.16,<0.24",
  "sphinx>=9,<9.1",
  "sphinx-multiversion",
]

[tool.setuptools]
packages.find.where = [ "src" ]
package-dir = { "" = "src" }

[tool.setuptools_scm]
version_file = "src/cytodataframe/_version.py"
version_scheme = "no-guess-dev"
local_scheme = "no-local-version"
root = "."

[tool.uv]
default-groups = [
  "dev",
  "docs",
]
sources.sphinx-multiversion = { git = "https://github.com/J-RN/sphinx-multiversion", rev = "a77f0c862dace3a62c18fc866da60ef7dde3873d" }

[tool.ruff]
target-version = "py311"
line-length = 88
fix = true
lint.select = [
  # flake8-builtins
  "A",
  # flake8-annotations
  "ANN",
  # flake8-comprehensions
  "C4",
  # mccabe
  "C90",
  # pycodestyle
  "E",
  # pyflakes
  "F",
  # isort
  "I",
  # pylint
  "PL",
  # ruff
  "RUF",
  # flake8-simplify
  "SIM",
  "W",
]
# Ignore `E402` and `F401` (unused imports) in all `__init__.py` files
lint.per-file-ignores."__init__.py" = [ "E402", "F401" ]
lint.per-file-ignores."docs/src/examples/*.py" = [ "E402", "E501" ]
lint.per-file-ignores."src/cytodataframe/*.py" = [ "ANN401", "PLC0415" ]
lint.per-file-ignores."src/cytodataframe/image.py" = [ "PLR2004" ]
# ignore typing rules for tests
lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004", "SIM105" ]

# specify where version replacement is performed
[tool.bandit]
exclude_dirs = [ "tests" ]

[tool.pytest]
ini_options.addopts = "--cov=src/cytodataframe --cov-report=term-missing:skip-covered --no-cov-on-fail"

[tool.coverage]
# settings to avoid errors with cv2 and coverage
# see here for more: https://github.com/nedbat/coveragepy/issues/1653
run.omit = [
  "config-3.py",
  "config.py",
]

[tool.jupytext]
formats = "ipynb,py:light"

[tool.poe]
# note: quarto commands below expect quarto installed on the local system.
# see here for more information: https://quarto.org/docs/download/
tasks.poster-preview.shell = """
quarto preview \
  docs/presentations/2025-sbi2/poster.qmd
"""
tasks.poster-render.shell = """\
  quarto render \\\n  docs/presentations/2025-sbi2/poster.qmd\n  mv \
  docs/presentations/2025-sbi2/cytodataframe-2025-poster.pdf \\\n  docs/src/_static/cytodataframe-2025-poster.pdf\n\
  """