pyproject.toml

[build-system]
requires = ["setuptools>=64"]
build-backend = "setuptools.build_meta"

[project]
name = "neuroconv"
version = "0.6.2"
description = "Convert data from proprietary formats to NWB format."
readme = "README.md"
authors = [
    { name = "Cody Baker" },
    { name = "Szonja Weigl" },
    { name = "Heberto Mayorquin" },
    { name = "Paul Adkisson" },
    { name = "Luiz Tauffer" },
    { name = "Ben Dichter", email = "ben.dichter@catalystneuro.com" },
]
urls = { "Homepage" = "https://github.com/catalystneuro/neuroconv" }
license = { file = "license.txt" }
keywords = ["nwb"]
classifiers = [
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Operating System :: POSIX :: Linux",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: MacOS",
    "License :: OSI Approved :: BSD License",

]
requires-python = ">=3.9"
dependencies = [
    "numpy>=1.22.0, <2.0.0; python_version <= '3.11'",
    "numpy>=1.26.0, <2.0.0; python_version >= '3.12'",
    "jsonschema>=3.2.0",
    "PyYAML>=5.4",
    "scipy>=1.4.1",
    "h5py>=3.9.0",
    "hdmf>=3.13.0",
    "hdmf_zarr>=0.7.0",
    "pynwb>=2.7.0",
    "pydantic>=2.0.0",
    "typing_extensions>=4.1.0",
    "psutil>=5.8.0",
    "tqdm>=4.60.0",
    "pandas",
    "parse>=1.20.0",
    "click",
    "docstring-parser",
    "packaging"  # Issue 903
]


[project.optional-dependencies]
test = [
    "pytest",
    "pytest-cov",
    "ndx-events>=0.2.0",  # for special tests to ensure load_namespaces is set to allow NWBFile load at all times
    "parameterized>=0.8.1",
    "ndx-miniscope",
    "spikeinterface[qualitymetrics]>=0.101.0",
    "zarr<2.18.0",  # Error with Blosc (read-only during decode) in numcodecs on May 7; check later if resolved
    "pytest-xdist"
]

docs = [
    "Jinja2<3.1",
    "Sphinx==5.1.1",
    "sphinx_rtd_theme==1.0.0",
    "readthedocs-sphinx-search==0.1.2",
    "sphinx-toggleprompt==0.2.0",
    "sphinx-copybutton==0.5.0",
    "roiextractors",  # Needed for the API documentation
    "spikeinterface>=0.101.0",  # Needed for the API documentation
    "pydata_sphinx_theme==0.12.0"
]
dandi = ["dandi>=0.58.1"]
compressors = ["hdf5plugin"]
aws = ["boto3"]

[tool.setuptools.packages.find]
where = ["src"]


[project.scripts]
neuroconv = "neuroconv.tools.yaml_conversion_specification._yaml_conversion_specification:run_conversion_from_yaml_cli"


[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra --doctest-glob='*.rst'"
testpaths = ["docs/conversion_examples_gallery/", "tests"]
doctest_optionflags = "ELLIPSIS"


[tool.black]
line-length = 120
target-version = ['py38', 'py39', 'py310']
include = '\.pyi?$'
extend-exclude = '''
/(
  \.toml
  |\.yml
  |\.txt
  |\.sh
  |\.git
  |\.ini
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''


[tool.ruff]

[tool.ruff.lint]
select = [
    "F401",  # Unused import
    "I",  # All isort rules
    "D101",  # Missing docstring in public class
    "D103",  # Missing docstring in public function
]
fixable = ["ALL"]

[tool.ruff.lint.per-file-ignores]
"**__init__.py" = ["F401", "I"]
"tests/**" = ["D"] # We are not enforcing docstrings in tests
"src/neuroconv/tools/testing/data_interface_mixins.py" = ["D"]  # We are not enforcing docstrings in the interface mixings
"docs/conf.py" = ["D"]  # We are not enforcing docstrings in the conf.py file
"docs/conversion_examples_gallery/conftest.py" = ["D"]  # We are not enforcing docstrings in the conversion examples

[tool.ruff.lint.isort]
relative-imports-order = "closest-to-furthest"
known-first-party = ["neuroconv"]


[tool.codespell]
skip = '.git*,*.pdf,*.css'
check-hidden = true
ignore-words-list = 'assertin'