pyproject.toml

# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.

# Regarding pyproject.toml see
# - PEP 517 project metadata https://www.python.org/dev/peps/pep-0517
# - PEP 518 project metadata https://www.python.org/dev/peps/pep-0518
# - PEP 621 project metadata https://www.python.org/dev/peps/pep-0621

[tool.setuptools_scm]
write_to = "src/sisl/_version.py"
version_file = "src/sisl/_version.py"
fallback_version = "0.15.2"

# First we define the build-system which we will probably alter the most
[build-system]
requires = [
    "setuptools_scm[toml]>=6.2",
    "scikit-build-core[pyproject]>=0.8",
    "Cython>=3",
    "numpy>=2.0.0rc1"
]
build-backend = "scikit_build_core.build"

# Top most items are probably changed the most
[project]
requires-python = ">=3.9"

name = "sisl"
description = "Manipulation and post-processing of DFT output and creating tight-binding models for NEGF transport"
readme = "README.md"
license = {text = "MPL-2.0"}
keywords = [
    "tight-binding",
    "DFT",
    "LCAO",
    "NEGF",
    "physics"
]

# Our dependencies should pretty much follow EOL python releases
# However, the exception is currently that numpy.typing.NDArray
# is currently (as of August 2024) required in some dependency
# packages (PIL).
# So this time around we will be taking a bit more recent one.
# Otherwise, the chosen versions should be something like:
# See when the currently oldest LIVE Python version was first released.
# E.g. 3.9 was released 2020-10-05.
# Now all dependencies that were released around the same time should be the
# lower bound of dependencies.
dependencies = [
    # We need npt.NDArray
    "numpy>=1.21",
    "scipy>=1.6",
    # I can't get it to work on py311 with older versions
    "pyparsing>=2.2.1",
    # xarray fixes get_loc in 0.21
    "xarray>=0.21",
]

authors = [
    {name = "Nick Papior", email = "nickpapior@gmail.com"},
    {name = "Pol Febrer"}
]
maintainers = [{name="sisl developers"}]

classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)",
    "Programming Language :: C",
    "Programming Language :: Fortran",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Software Development",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Physics",
    "Operating System :: OS Independent",
]

# We purposefully get the version dynamically
dynamic = ["version"]



[tool.scikit-build]
# Consider adding
# minimum-version to choose the fallback mechanism in scikit-build-core
wheel.packages = ["src/sisl", "src/sisl_toolbox"]

# required for dynamic metadata
experimental = true

metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"

# define a consistent build directory
build-dir = "build/{wheel_tag}"

# cmake and ninja stuff
cmake.verbose = true
cmake.version = ">=3.20"

# source configuration
sdist.reproducible = true
sdist.include = ["src/sisl/_version.py", "*/CMakeLists.txt"]

wheel.expand-macos-universal-tags = true


[project.scripts]
sgeom = "sisl._core.geometry:sgeom"
sgrid = "sisl._core.grid:sgrid"
sdata = "sisl.utils._sisl_cmd:sisl_cmd"
stoolbox = "sisl_toolbox.cli:stoolbox_cli"


[project.urls]
# See here for which are allowed:
#  https://github.com/pypi/warehouse/blob/main/warehouse/templates/packaging/detail.html
Homepage = "https://zerothi.github.io/sisl"
Releases = "https://github.com/zerothi/sisl/releases"
Documentation = "https://zerothi.github.io/sisl"
Source = "https://github.com/zerothi/sisl"
Tracker = "https://github.com/zerothi/sisl/issues"
Discussions = "https://github.com/zerothi/sisl/discussions"
Changelog = "https://zerothi.github.io/sisl/changelog/index.html"
Chat = "https://discord.gg/5XnFXFdkv2"


[project.optional-dependencies]

analysis = [
    "netCDF4",
    "tqdm>=4.36.0",
]

viz = [
    "nodify",
    "netCDF4",
    "dill >= 0.3.2",
    "pathos",
    "scikit-image",
    "plotly",
    "matplotlib",
    "ase",
]

viz-plotly = [
    "nodify",
    "netCDF4",
    "dill >= 0.3.2",
    "pathos",
    "scikit-image",
    "plotly",
]

viz-matplotlib = [
    "nodify",
    "netCDF4",
    "dill >= 0.3.2",
    "pathos",
    "scikit-image",
    "matplotlib",
]

viz-blender = [
    "nodify",
    "netCDF4",
    "dill >= 0.3.2",
    "pathos",
    "scikit-image",
]

viz-ase = [
    "netCDF4",
    "dill >= 0.3.2",
    "pathos",
    "scikit-image",
    "ase",
]

test = [
    "pytest>=7",
    "coverage[toml]",
    "pytest-cov",
    "pytest-env",
    "pytest-faulthandler",
]

docs = [
    "sphinx<8",
    "nbsphinx",
    "sphinx-rtd-theme",
    "sphinx-design",
    "sphinx-gallery",
    "sphinx-copybutton",
    "sphinx-togglebutton",
    "sphinx-inline-tabs",
    "sphinxcontrib-bibtex",
    "sphinxext-rediraffe",
    "importlib-metadata",
    "ipykernel",
    "ipywidgets",
    "jupyterlab-widgets",
    "kaleido",
    "pytz",
    # Visualizing nodes
    "networkx",
    "pyvis",
    "pybtex",
    "pandoc",
]


[tool.pytest.ini_options]
testpaths = [
    "src"
]
markers = [
    "slow: mark a test as slow",
]

addopts = "-rXs --durations=20"

[tool.coverage.run]
source_pkgs = [
    "sisl",
    "sisl_toolbox",
]
omit = [
    "*/conftest.py",
]

[tool.coverage.report]
include_namespace_packages = true
exclude_also = [
    "raise NotImplementedError",
]
exclude_lines = [
  "@overload",
  'if __name__ == "__main":',
  "if TYPE_CHECKING:",
]

[tool.pylint]
[tool.pylint.master]
jobs = 6
ignore-paths = [
   ".*/tests/.*.py"
]

ignore-patterns = [
   "conftest.py",
   # This is autogenerated, but may be present
   "_version.py"
]

# Do not create false-positives for Cython extensions
extension-pkg-allow-list = [
   "sisl._math_small",
   "sisl._indices",
   "sisl._core._lattice",
   "sisl.io.siesta._siesta",
   "sisl.physics._bloch",
   "sisl.physics._matrix_k",
   "sisl.physics._matrix_dk",
   "sisl.physics._matrix_ddk",

   # external packages required
   "numpy",
   "scipy"
]


[tool.pylint.format]
# Currently no formatting rules

[tool.pylint.messages_control]
max-line-length = 110

disable = [
    "invalid-name",
    "missing-module-docstring",
    "redefined-builtin"
]



[tool.tox]

legacy_tox_ini = """
[tox]
minversion = 3.3.0
envlist = py39,py310,py311,py312
isolated_build = True

[testenv]
setenv =
    SISL_NUM_PROCS=1
deps = -rdocs/requirements.txt
commands = pytest -s -rXs {posargs}
"""


[tool.isort]
# how should sorting be done
profile = "black"
sections = ['FUTURE', 'STDLIB', 'THIRDPARTY', 'FIRSTPARTY', 'LOCALFOLDER']
known_first_party = ["sisl_toolbox", "sisl"]
line_length = 88
overwrite_in_place = true
extend_skip = ["src/sisl/__init__.py", "src/sisl/_version.py"]
extend_skip_glob = ["files/*", "*/.*"]
multi_line_output = "VERTICAL_HANGING_INDENT"

[tool.black]
line-length = 88
target-version = ["py39", "py310", "py311", "py312"]
extend-exclude = """
(
 ^/files/*
 | /\\..*
 | .*/\\..*
)
"""


[tool.numpydoc_validation]
checks = ["all", "EX01", "SA01", "ES01"]
exclude = [
    '^conf\.',
]