pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs"] # hatchling for build | hatch-vcs for versioning
build-backend = "hatchling.build" # the build backend used

[project]
name = "pynwb"
authors = [
  { name="Andrew Tritt", email="ajtritt@lbl.gov" },
  { name="Ryan Ly", email="rly@lbl.gov" },
  { name="Oliver Ruebel", email="oruebel@lbl.gov" },
  { name="Ben Dichter", email="ben.dichter@gmail.com" },
  { name="Matthew Avaylon", email="mavaylon@lbl.gov" },
  { name="Stephanie Prince", email="smprince@lbl.gov" },
]
description= "Package for working with Neurodata stored in the NWB format."
readme = "README.rst"
requires-python = ">=3.10"
license = {text = "BSD-3-Clause"}
classifiers = [
        "Programming Language :: Python",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
        "Programming Language :: Python :: 3.13",
        "Programming Language :: Python :: 3.14",
        "License :: OSI Approved :: BSD License",
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Developers",
        "Intended Audience :: Science/Research",
        "Operating System :: Microsoft :: Windows",
        "Operating System :: MacOS",
        "Operating System :: Unix",
        "Topic :: Scientific/Engineering :: Medical Science Apps."
]
dependencies = [
    "h5py>=3.6.0",
    "hdmf>=6.1.0,<7",
    "numpy>=1.24.0",
    "pandas>=1.4.0",
    "python-dateutil>=2.8.2",
    "platformdirs>=4.2.2"
]
dynamic = ["version"] # the build backend will compute the version dynamically from git tag (or a __version__)

[project.optional-dependencies]
# user-installable optional features (e.g. ``pip install pynwb[zarr]``)
zarr = [
    "hdmf-zarr>=0.11.0",
    "zarr>=2.12.0,<3",
    "numcodecs>=0.10.0,<0.16.0",  # numcodecs 0.16.0 is not compatible with zarr<3
]
termset = [
    "linkml>=1.5.0",
    "linkml-runtime>=1.5.5",
    "schemasheets>=0.4.0",
    "oaklib>=0.5.12",
]

[dependency-groups]
# development dependencies
test = [
    "codespell",
    "coverage",
    "pytest",
    "pytest-cov",
    "python-dateutil",
    "ruff",
    "tox",
]

# streaming dependencies exercised by the optional test environments. all dependencies have a lower
# bound so that the "minimum" tox envs (uv --resolution lowest-direct) resolve to sensible versions
# rather than the oldest release on PyPI.
stream = [
    "fsspec>=2023.1.0",
    "requests>=2.28.0",
    "aiohttp>=3.8.3",
]

# documentation dependencies. the gallery also needs the zarr and termset feature extras, which are
# installed alongside this group via ``pip install --group docs ".[zarr,termset]"``.
docs = [
    "matplotlib>=3.6",
    "sphinx>=4",  # improved support for docutils>=0.17
    "sphinx_rtd_theme>=1",  # <1 does not work with docutils>=0.17
    "sphinx-gallery>=0.16",
    "sphinx-copybutton>=0.5",
    "Pillow>=10.0.0",
    "dataframe_image>=0.2.3",  # used to render large dataframe as image in the sphinx gallery to improve html display
    "lxml>=4.9.3",  # used by dataframe_image when using the matplotlib backend
    "hdf5plugin>=4.0.0",
    "dandi>=0.76.5",  # 0.76.5 lifts the click<8.2 bound, allowing linkml/linkml-runtime>=1.11
    "pooch>=1.6.0",
]

[project.urls]
"Homepage" = "https://github.com/NeurodataWithoutBorders/pynwb"
"Bug Tracker" = "https://github.com/NeurodataWithoutBorders/pynwb/issues"

[project.scripts]
pynwb-validate = "pynwb.validation_cli:validation_cli"

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

[tool.hatch.build.hooks.vcs]
# this file is created/updated when the package is installed and used in
# src/pynwb/__init__.py to set `__version__` (from _version.py).
version-file = "src/pynwb/_version.py"

[tool.hatch.build.targets.sdist]
exclude = [
    ".git*",
    ".codecov.yml",
    ".readthedocs.yaml",
]

[tool.hatch.build.targets.wheel]
packages = ["src/pynwb"]
exclude = [
    ".git*",
    ".codecov.yml",
    ".readthedocs.yaml",
]

[tool.codespell]
skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,nwb-schema,./docs/_build/*,*.ipynb"
ignore-words-list = "optin,potatos,assertin"

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

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "@abstract"
]
omit = [
    "*/pynwb/_due.py",
    "*/pynwb/testing/*",
    "*/pynwb/legacy/*"
]

[tool.ruff]
lint.select = ["E", "F", "T100", "T201", "T203"]
exclude = [
  ".git",
  ".tox",
  "__pycache__",
  "build/",
  "dist/",
  "src/pynwb/nwb-schema",
  "docs/source/conf.py",
  "docs/notebooks/*",
  "src/pynwb/_due.py",
  "test.py" # remove when pytest comes along
]
line-length = 120

[tool.ruff.lint.per-file-ignores]
"tests/read_dandi/*" = ["T201"]
"docs/gallery/*" = ["E402", "T201"]
"src/*/__init__.py" = ["F401"]
"src/pynwb/_version.py" = ["T201"]
"src/pynwb/validation_cli.py" = ["T201"]
"scripts/*" = ["T201"]

# "test_gallery.py" = ["T201"] # Uncomment when test_gallery.py is created

[tool.ruff.lint.mccabe]
max-complexity = 17