pyproject.toml

[build-system]
requires = ["setuptools >= 64", "wheel", "setuptools_scm[toml] >= 7"]
build-backend = "setuptools.build_meta"

[project]
name = "trx-python"
dynamic = ["version"]
description = "A community-oriented file format for tractography"
readme = "README.md"
license = {text = "BSD License"}
requires-python = ">=3.11"
authors = [
    {name = "The TRX developers"}
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering",
]
dependencies = [
    "deepdiff",
    "nibabel >= 5",
    "numpy >= 1.22",
    "typer >= 0.9",
]

[project.optional-dependencies]
dev = [
    "spin >= 0.13",
    "setuptools_scm",
]
doc = [
    "matplotlib",
    "numpydoc",
    "pydata-sphinx-theme >= 0.16.1",
    "sphinx >= 8.2.0",
    "sphinx-autoapi >= 3.4.0",
    "sphinx-design",
    "sphinx-gallery",
]
style = [
    "codespell",
    "pre-commit",
    "ruff",
]
test = [
    "psutil",
    "pytest >= 7",
    "pytest-console-scripts >= 0",
    "pytest-cov",
]
all = [
    "trx-python[dev]",
    "trx-python[doc]",
    "trx-python[style]",
    "trx-python[test]",
]

[project.urls]
Homepage = "https://github.com/tee-ar-ex/trx-python"
Documentation = "https://tee-ar-ex.github.io/trx-python/"
Repository = "https://github.com/tee-ar-ex/trx-python"

[project.scripts]
trx = "trx.cli:main"
trx_concatenate_tractograms = "trx.cli:concatenate_tractograms_cmd"
trx_convert_dsi_studio = "trx.cli:convert_dsi_cmd"
trx_convert_tractogram = "trx.cli:convert_cmd"
trx_generate_from_scratch = "trx.cli:generate_cmd"
trx_manipulate_datatype = "trx.cli:manipulate_dtype_cmd"
trx_simple_compare = "trx.cli:compare_cmd"
trx_validate = "trx.cli:validate_cmd"
trx_verify_header_compatibility = "trx.cli:verify_header_cmd"
trx_visualize_overlap = "trx.cli:visualize_cmd"
trx_info = "trx.cli:info_cmd"

[tool.setuptools]
packages = ["trx"]
include-package-data = true

[tool.setuptools_scm]
write_to = "trx/_version.py"
fallback_version = "0.0"
local_scheme = "no-local-version"

[tool.codespell]
ignore-words-list = "astroid"

[tool.spin]
package = "trx"

[tool.spin.commands]
"Setup" = [".spin/cmds.py:setup"]
"Build" = ["spin.cmds.pip.install"]
"Test" = [".spin/cmds.py:test", ".spin/cmds.py:lint"]
"Docs" = [".spin/cmds.py:docs"]
"Clean" = [".spin/cmds.py:clean"]

[tool.numpydoc_validation]
checks = [
    "all",   # report on all checks, except the below
    # These we we ignore:
    "GL01",  # Docstring should start in the line immediately after the quotes
    "GL02",  # Closing quotes on own line (doesn't work on Python 3.13 anyway)
    "EX01",
    "EX02",  # examples failed (we test them separately)
    "ES01",  # no extended summary
    "SA01",  # no see also
    "YD01",  # no yields section
    "SA04",  # no description in See Also
    "PR04",  # Parameter "shape (n_channels" has no type
    "RT02",  # The first line of the Returns section should
]
# remember to use single quotes for regex in TOML
exclude = [  # don't report on objects that match any of these regex
    '\.undocumented_method$',
    '\.__repr__$',
    '\.__str__$',
    '\.__len__$',
    '\.__getitem__$',
    '\.__deepcopy__$',
]
exclude_files = [ # don't process filepaths that match these regex
    '^trx/tests/.*',
    '^module/gui.*',
    '^examples/.*',
]
override_SS05 = [  # override SS05 to allow docstrings starting with these words
    '^Process ',
    '^Assess ',
    '^Access ',
]