pyproject.toml

[project]
name = "stingray"
dynamic = [
    "version"
]
description = "Time Series Methods For Astronomical X-ray Data"
readme = "README.rst"
authors = [
    { name = "Stingray Developers", email = "spectraltiming-stingray@googlegroups.com" }
]
license = { text = "MIT" }
requires-python = ">=3.8"
classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Scientific/Engineering :: Astronomy",
    "Topic :: Scientific/Engineering :: Physics",
]
keywords = [
    "astronomy",
    "astrophysics",
    "time series",
    "X-ray",
    "data analysis",
    "black holes",
    "neutron stars",
    "pulsars",
    "space",
    "science",
]
dependencies = [
    "numpy>=1.17",
    "astropy>=4.0",
    "scipy>=1.1.0",
    "matplotlib>=3.0,!=3.4.00",
]


[project.optional-dependencies]
test = [
    "pytest",
    "pytest-astropy",
]
test_all = [
    "astropy[test]",  # installs the [test] dependencies
    "objgraph",
    "ipython>=4.2",
    "coverage[toml]",
    "skyfield>=1.20",
    "sgp4>=2.3",
]
recommended = [
    "numba",
    "h5py",
    "pyyaml",
    "statsmodels",
    "pyfftw",
]
all = [
    "stingray[recommended]",  # installs the [recommended] dependencies
    "jplephem",
    "emcee>=3.0.0",
    "corner",
    "lightkurve",
    "pint-pulsar",
    "numcodecs",
    "xarray",
    "pyarrow",
    "pandas",
    "ultranest",
    "jax",
    "tinygp",
    "jaxns",
    "etils",
    "tensorflow_probability",
    "typing_extensions",
]
docs = [
    "tomli>=1.1.0; python_version < '3.11'",
    "jinja2==3.1.3",
    "docutils",
    "sphinx-astropy",
    "nbsphinx>=0.8.3,!=0.8.8",
    "nbconvert<7.14",
    "pandoc",
    "ipython",
    "towncrier<22.12.0",
]

[project.urls]
homepage = "https://stingray.science"
documentation = "https://docs.stingray.science"
repository = "https://github.com/stingraysoftware/stingray"

[build-system]
requires = ["setuptools",
            "setuptools_scm",
            "wheel"]

build-backend = 'setuptools.build_meta'

[tool.setuptools]
include-package-data = true
license-files = ["LICENSE.rst"]

[tool.setuptools.packages.find]
include = ["stingray*"]
exclude = ["stingray._dev*"]
namespaces = false

[tool.setuptools.package-data]
"*" = [
    "data/*",
    "*.fits",
    "*.evt",
    "*.rmf",
    "*.txt",
]
"stingray" = ["datasets/*"]

[tool.setuptools_scm]
write_to = "stingray/_version.py"

[tool.pytest.ini_options]
minversion = 7.0
testpaths = [
    "stingray",
    "docs",
]
norecursedirs = [
    "docs[\\/]_build",
    "docs[\\/]generated",
]
astropy_header = true
doctest_plus = "enabled"
text_file_format = "rst"
remote_data_strict = true
addopts = "--color=yes --doctest-rst"
filterwarnings = [
    "error",
    "ignore:Unrecognized parfile line:UserWarning",
    "ignore:.*:ResourceWarning",
    "ignore:distutils Version classes are deprecated.:DeprecationWarning",
    "ignore:unclosed .ssl.SSLSocket:ResourceWarning",
    "ignore:.*set self.value directly:DeprecationWarning",
    "ignore:On Windows, the size of an integer is 32 bits:UserWarning",
    "ignore:.*Number of segments used in averaging.*:UserWarning",
    "ignore:.*:astropy.units.core.UnitsWarning",
    "ignore:.*cannot be added to FITS Header:astropy.utils.exceptions.AstropyUserWarning",
    "ignore:The recommended numba package is not installed:UserWarning",
    "ignore:More than 20 figures have been opened.:RuntimeWarning",
    "ignore:This platform does not support:RuntimeWarning",
    "ignore:Some error bars in the Averaged:UserWarning",
    "ignore:n_ave is below 30:UserWarning",
    "ignore:pyfftw not installed:UserWarning",
    "ignore:SIMON says. Errorbars on cross spectra are not thoroughly tested.:UserWarning",
    "ignore:SIMON says. Stingray only uses poisson err_dist at the moment.:UserWarning",
    "ignore:SIMON says. Looks like your lightcurve:UserWarning",
    "ignore:Matplotlib is currently using agg, which is a:UserWarning",
    "ignore:Using or importing the ABCs from 'collections':DeprecationWarning",
    "ignore:unclosed file:ResourceWarning",
    "ignore:numpy.ufunc size changed:RuntimeWarning",
    "ignore:numpy.ndarray size changed:RuntimeWarning",
    "ignore:invalid value encountered:RuntimeWarning",
    "ignore:divide by zero encountered:RuntimeWarning",
    "ignore:underflow encountered:RuntimeWarning",
    "ignore:overflow encountered:RuntimeWarning",
    "ignore:table path was not set via the path= argument; using default path:UserWarning",
    "ignore:Large Datasets may not be processed efficiently:UserWarning",
    "ignore:.*is a deprecated alias for:DeprecationWarning",
    "ignore:.*HIERARCH card will be created.*:",
    "ignore:.*FigureCanvasAgg is non-interactive.*:UserWarning",
    "ignore:.*jax.* deprecated:DeprecationWarning:",
    "ignore:.*Converting to lower precision.*:UserWarning",
    "ignore:.*is_categorical_dtype is deprecated.*:DeprecationWarning",
    "ignore:.*datetime.datetime.utcfromtimestamp.*:DeprecationWarning",
    "ignore:.*__array_wrap__ must accept context and return_scalar arguments:DeprecationWarning",
    "ignore:.*Pyarrow:",
    "ignore:.*Creating an ndarray from ragged nested sequences:",

]

[tool.towncrier]
    package = "stingray"
    filename = "CHANGELOG.rst"
    directory = "docs/changes/"
    issue_format = "`#{issue} <https://github.com/StingraySoftware/stingray/pull/{issue}>`__"
    title_format = "v{version} ({project_date})"
    underlines = "-^"

    [[tool.towncrier.type]]
        directory = "breaking"
        name = "Breaking Changes"
        showcontent = true

    [[tool.towncrier.type]]
      directory = "deprecation"
      name = "Deprecations"
      showcontent = true

    [[tool.towncrier.type]]
      directory = "removal"
      name = "Removals"
      showcontent = true

    [[tool.towncrier.type]]
      directory = "feature"
      name = "New Features"
      showcontent = true

    [[tool.towncrier.type]]
      directory = "bugfix"
      name = "Bug Fixes"
      showcontent = true

    [[tool.towncrier.type]]
      directory = "doc"
      name = "Documentation"
      showcontent = true

    [[tool.towncrier.type]]
      directory = "trivial"
      name = "Internal Changes"
      showcontent = true

[tool.black]
line-length = 100

[tool.coverage]

    [tool.coverage.run]
        omit = [
            "stingray/_astropy_init*",
            "stingray/conftest.py",
            "stingray/*setup_package*",
            "stingray/tests/*",
            "stingray/*/tests/*",
            "stingray/extern/*",
            "stingray/version*",
            "*/stingray/_astropy_init*",
            "*/stingray/conftest.py",
            "*/stingray/*setup_package*",
            "*/stingray/tests/*",
            "*/stingray/*/tests/*",
            "*/stingray/extern/*",
            "*/stingray/version*",
        ]

    [tool.coverage.report]
        exclude_lines = [
            # Have to re-enable the standard pragma
            "pragma: no cover",
            # Don't complain about packages we have installed
            "except ImportError",
            # Don't complain if tests don't hit defensive assertion code:
            "raise AssertionError",
            "raise NotImplementedError",
            # Don't complain about script hooks
            "'def main(.*):'",
            # Ignore branches that don't pertain to this version of Python
            "pragma: py{ignore_python_version}",
            # Don't complain about IPython completion helper
            "def _ipython_key_completions_",
        ]

[tool.flake8]
max-line-length = 100
exclude = ".git,__pycache__,docs/source/conf.py,old,build,dist,*.egg-info"
extend-ignore = "E203, W503, W605"

[tool.pycodestyle]
max-line-length = 100
exclude = ".git,__pycache__,docs/source/conf.py,old,build,dist,*.egg-info"