pyproject.toml

[build-system]
requires = [
    "setuptools>=64",
    "setuptools_scm>=8"
]
build-backend = "setuptools.build_meta"

[project]
name = "ArchNGV"
description = "NGV architecture modules"
readme = "README.md"
requires-python = ">=3.9"
license = { file = "LICENSE.txt" }
authors = [
  { name = "Blue Brain Project, EPFL" },
]
dependencies = [
  "numpy>=1.22",
  "h5py>=3.1.0",
  "scipy>=1.5.0",
  # 0.1.21 supports resolution of ngv populations extra files
  "libsonata>=0.1.21",
  "bluepysnap>=1.0",
  "cached-property>=1.5",
  "voxcell>=3.0.0",
  "vascpy>=0.1.0",
  # 3.17.1 is available in spack.
  # Update to a higher version in spack after checking that py-atlas-building-tools works
  "trimesh>=3.17.1",  # Method Trimesh:subdivide_loop is needed
  # trimesh soft dependency for using marching cubes
  "scikit-image>=0.18",
  # requests module pin urrlib3 in recent versions
  # see https://github.com/psf/requests/issues/6432
  "urllib3>=1.21.1,<1.27; python_version <= '3.8'",
]
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Intended Audience :: Education",
  "Intended Audience :: Science/Research",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dynamic = ["version"]

[project.optional-dependencies]
docs = [
  "sphinx-bluebrain-theme"
]
all = [
  "ngv-ctools>=1.0.0",
  "Click>=7.0",
  "numpy-stl>=2.10",
  "openmesh>=1.1.2",
  "pyyaml>=5.0",
  "pandas>=1.1.0",
  "multivoro",
  "MorphIO>=3.2.0",
  "morph-tool>=2.4.0",
  "snakemake>=5.0.0",
  "tmd>=2.0.11",
  "NeuroTS>=3.4.0",
  "diameter-synthesis>=0.5.4",
  "dask[distributed,bag]>=2022.04.1",
  "dask_mpi>=2.0",
  "brain-indexer>=3.0.0",
  "atlas-commons>=0.1.4",
  "meshio>=5.3.4",
]

[project.urls]
Homepage = "https://github.com/BlueBrain/ArchNGV"
Repository = "https://github.com/BlueBrain/ArchNGV"
Issues = "https://github.com/BlueBrain/ArchNGV/issues"
Tracker = "https://github.com/BlueBrain/ArchNGV/issues"

[project.scripts]
ngv = "archngv.app.__main__:app"

[tool.setuptools.packages.find]
include = ["archngv"]
namespaces = false

[tool.setuptools_scm]
local_scheme = "no-local-version"

[tool.black]
line-length = 100
target-version = [
    'py39',
    'py310',    
    'py311',    
    'py312',    
]
include = '''
^/(
      archngv/.*\.py
    | tests/.*\.py
    | doc/source/conf\.py
    | setup\.py
)$
'''

[tool.isort]
profile = "black"
line_length = 100

[tool.pylint.messages_control]
disable = [
    "invalid-name",
    "too-few-public-methods",
    "too-many-public-methods",
    "fixme",
    "superfluous-parens",
    "import-outside-toplevel",
    "unsubscriptable-object",
    "unsupported-assignment-operation",
    "unnecessary-lambda-assignment",
    "unbalanced-tuple-unpacking",
    "unspecified-encoding",
    "consider-using-f-string",
    "use-yield-from"
]

[tool.pylint.format]
# Regexp for a line that is allowed to be longer than the limit.
ignore-long-lines = '\bhttps?://\S'
# Maximum number of characters on a single line.
max-line-length = 100

[tool.pylint.design]
# Maximum number of arguments for function / method
max-args = 8
# Argument names that match this expression will be ignored. Default to name
# with leading underscore
ignored-argument-names = '_.*'
# Maximum number of locals for function / method body
max-locals = 30
# Maximum number of return / yield for function / method body
max-returns = 6
# Maximum number of branch for function / method body
max-branches = 12
# Maximum number of statements in function / method body
max-statements = 50
# Maximum number of parents for a class (see R0901).
max-parents = 7
# Maximum number of attributes for a class (see R0902).
max-attributes = 40
# Minimum number of public methods for a class (see R0903).
min-public-methods = 0
# Maximum number of public methods for a class (see R0904).
max-public-methods = 60

[tool.pylint.similarities]
# Minimum lines number of a similarity.
min-similarity-lines = 25
# Ignore comments when computing similarities.
ignore-comments = 'yes'
# Ignore docstrings when computing similarities.
ignore-docstrings = 'yes'

[tool.pylint.typecheck]
# List of classes names for which member attributes should not be checked
# (useful for classes with attributes dynamically set).

ignored-modules = [
    "tns",
    "numpy",
    "numpy.*",
    "scipy.stats",
    "scipy.spatial",
]

#as of numpy 1.8.0, name resolution seems to be a problem.  Ignore lookups in numpy
ignored-classes = ["numpy"]

extension-pkg-allow-list=[
    "cKDTree",
    "libsonata",
    "morphio",
    "ngv_ctools",
    "numpy",
    "openmesh",
    "scipy",
    "spatial_index",
]