pyproject.toml

[project]
name = "hendrics"
dynamic = [
    "version"
]
description = "High ENergy Data Reduction Interface from the Command Shell"
readme = "README.rst"
authors = [
    { name = "Matteo Bachetti", email = "matteo@matteobachetti.it" }
]
license = { text = "3-clause BSD" }
requires-python = ">=3.9"
classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: C",
    "Programming Language :: Cython",
    "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,!=3.8.0",
    "stingray>=2.2.3",
    "tqdm",
    "pyyaml"
]


[project.optional-dependencies]
test = [
    "pytest",
    "pytest-astropy",
]
test_all = [
    "h5py",
    "pandas",
    "pint-pulsar",
    "imageio",
    "numba",
    "netcdf4==1.7.0",
    "scikit-image",
    "statsmodels"
]
recommended = [
    "numba",
    "h5py",
    "pyyaml",
    "statsmodels",
    "pyfftw",
]
all = [
    "hendrics[recommended]",
    "pandas",
    "pint-pulsar",
    "imageio",
    "netcdf4==1.7.0",
    "scikit-image",
    "statsmodels"
]
docs = [
    "tomli>=1.1.0; python_version < '3.11'",
    "jinja2==3.1.3",
    "docutils",
    "sphinx-astropy",
    "sphinx-toolbox",
    "nbsphinx>=0.8.3,!=0.8.8",
    "nbconvert<7.14",
    "pandoc",
    "ipython",
    "towncrier<22.12.0",
]

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


[project.scripts]
HEN2xspec = "hendrics.save_as_xspec:main"
HENaccelsearch = "hendrics.efsearch:main_accelsearch"
HENbaseline = "hendrics.lcurve:baseline_main"
HENbinary = "hendrics.binary:main_presto"
HENcalibrate = "hendrics.calibrate:main"
HENcolors = "hendrics.colors:main"
HENcreategti = "hendrics.create_gti:main"
HENdeorbit = "hendrics.fold:main_deorbit"
HENdumpdyn = "hendrics.fspec:dumpdyn_main"
HENefsearch = "hendrics.efsearch:main_efsearch"
HENexcvar = "hendrics.exvar:main"
HENexposure = "hendrics.exposure:main"
HENfake = "hendrics.fake:main"
HENfiltevents = "hendrics.io:main_filter_events"
HENfold = "hendrics.fold:main_fold"
HENfspec = "hendrics.fspec:main"
HENjoinevents = "hendrics.read_events:main_join"
HENlags = "hendrics.timelags:main"
HENlcurve = "hendrics.lcurve:main"
HENmodel = "hendrics.modeling:main_model"
HENphaseogram = "hendrics.phaseogram:main_phaseogram"
HENphasetag = "hendrics.phasetag:main_phasetag"
HENplot = "hendrics.plot:main"
HENpowercolors = "hendrics.power_colors:main"
HENreadevents = "hendrics.read_events:main"
HENreadfile = "hendrics.io:main"
HENrebin = "hendrics.rebin:main"
HENscramble = "hendrics.fake:main_scramble"
HENscrunchlc = "hendrics.lcurve:scrunch_main"
HENsplitevents = "hendrics.read_events:main_splitevents"
HENsumfspec = "hendrics.sum_fspec:main"
HENvarenergy = "hendrics.varenergy:main"
HENz2vspf = "hendrics.efsearch:main_z2vspf"
HENzsearch = "hendrics.efsearch:main_zsearch"

[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 = ["hendrics*"]
exclude = ["hendrics._dev*"]
namespaces = false

[tool.setuptools.package-data]
"*" = [
    "data/*",
    "*.fits",
    "*.evt",
    "*.rmf",
]
"hendrics.compat" = ["datasets/*"]
"hendrics.tests" = ["data/*"]

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

[tool.pytest.ini_options]
minversion = 7.0
testpaths = [
    "hendrics",
    "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::DeprecationWarning",
    "error:.*Casting complex values:",
    "ignore:.*ERFA function:",
    "ignore:.*data are not sorted. :UserWarning:stingray",
    "ignore:.*extended precision floating-point:RuntimeWarning:pint",
    "ignore:.*pyfftw not installed:UserWarning",
    "ignore:`product` is deprecated as of NumPy 1.25.0:DeprecationWarning",
    "ignore:.*n_ave is below 30:UserWarning",
    "ignore:.*Some error bars in the Averaged Crossspectrum:UserWarning",
    "ignore:.*This platform does not support extended precision.*:RuntimeWarning:pint",
    "ignore:.*function is deprecated. Set self.value.*:DeprecationWarning:pint",
    "ignore:.*distutils Version classes are deprecated.*:DeprecationWarning:astropy",
    "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:elementwise == comparison failed and returning scalar instead:FutureWarning:astropy",
    "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:Beware! For cpds and derivatives, I assume that:UserWarning",
    "ignore:SIMON says. Lightcurves have different statistics:UserWarning",
    "ignore: SIMON says. Coherence is not ideal:UserWarning",
    "ignore:SIMON says. The excess variance in the:UserWarning",
    "ignore:SIMON says. Number of segments used in averaging:UserWarning",
    "ignore:.*deprecated alias for.*:DeprecationWarning",
    "ignore:.*namespace is deprecated.*:DeprecationWarning",
    "ignore:.*Matplotlib 3.8",
]

[tool.towncrier]
    package = "hendrics"
    filename = "CHANGELOG.rst"
    directory = "docs/changes/"
    issue_format = "`#{issue} <https://github.com/StingraySoftware/hendrics/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.coverage]

    [tool.coverage.run]
        omit = [
            "hendrics/_astropy_init*",
            "hendrics/conftest.py",
            "hendrics/*setup_package*",
            "hendrics/tests/*",
            "hendrics/compat/*",
            "hendrics/*/tests/*",
            "hendrics/extern/*",
            "hendrics/version*",
            "hendrics/_version*",
            "*/hendrics/_astropy_init*",
            "*/hendrics/conftest.py",
            "*/hendrics/*setup_package*",
            "*/hendrics/tests/*",
            "*/hendrics/*/tests/*",
            "*/hendrics/extern/*",
            "*/hendrics/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.ruff]
lint.select = ["ALL"]
line-length = 100
exclude=[
    "notebooks/*.ipynb",
    "*.svg",
    "docs/conf.py",
    "docs/scripts/cli.rst",
    "_astropy_init.py",
    "__init__.py",
    "compatibility.py",
]
lint.ignore = [  # NOTE: non-permanent exclusions should be added to `.ruff.toml` instead.

    # flake8-builtins (A) : shadowing a Python built-in.
    # New ones should be avoided and is up to maintainers to enforce.
    "A00",

    # flake8-annotations (ANN)
    "ANN101",  # No annotation for `self`.
    "ANN102",  # No annotation for `cls`.

    # flake8-bugbear (B)
    "B008",  # FunctionCallArgumentDefault

    # flake8-commas (COM)
    "COM812",  # TrailingCommaMissing
    "COM819",  # TrailingCommaProhibited

    # pydocstyle (D)
    # Missing Docstrings
    "D102",  # Missing docstring in public method. Don't check b/c docstring inheritance.
    "D105",  # Missing docstring in magic method. Don't check b/c class docstring.
    # Whitespace Issues
    "D200",  # FitsOnOneLine
    # Docstring Content Issues
    "D410",  # BlankLineAfterSection. Using D412 instead.
    "D400",  # EndsInPeriod.  NOTE: might want to revisit this.

    # pycodestyle (E, W)
    "E711",  # NoneComparison  (see unfixable)
    "E741",  # AmbiguousVariableName. Physics variables are often poor code variables

    # flake8-fixme (FIX)
    "FIX002",  # Line contains TODO | notes for improvements are OK iff the code works

    # ISC001 shouldn't be used with ruff format
    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
    "ISC001",

    # pep8-naming (N)
    "N803",  # invalid-argument-name. Physics variables are often poor code variables
    "N806",  # non-lowercase-variable-in-function. Physics variables are often poor code variables

    # pandas-vet (PD)
    "PD",

    "PGH004", # noqa

    # pylint (PLR and PLW)
    "PLR1730", # if-stmt-min-max (not always clearer, and sometimes slower)
    "PLW0642", # self-or-cls-assignment (occasionally desirable, very rarely a mistake)

    # flake8-use-pathlib (PTH)
    "PTH123", # builtin-open (not worth creating a Path object, builtin open is fine)
    "PTH118", # os.path.join is fine
    "PTH207", # standard glob is fine
    "PTH120", # os.path.dirname is fine
    "PTH110", # os.path.exists is fine
    "PTH100", # os.path.abspath is fine
    "PTH122", # os.path.splitext is fine
    "PTH119", # os.path.basename is fine
    "PTH109", # os.getcwd is fine
    "PTH108", # os.unlink is fine
    "PTH103", # os.makedirs is fine

    # flake8-simplify (SIM)
    "SIM103", # needless-bool (cannot be safely applied in all contexts (np.True_ is not True))

    # flake8-self (SLF)
    "SLF001", # private member access

    # flake8-todos (TD)
    "TD002",  # Missing author in TODO

    # flake8-return (RET)
    # RET can sometimes help find places where refactoring is very helpful,
    # but enforcing it everywhere might create undesirable churn
    "RET505",  # superfluous-else-return
    "RET506",  # superfluous-else-raise

    # Ruff-specific rules (RUF)
    "RUF005",  # unpack-instead-of-concatenating-to-collection-literal -- it's not clearly faster.
]

[tool.ruff.lint.extend-per-file-ignores]
"setup.py" = ["INP001"]  # Part of configuration, not a package.
".github/workflows/*.py" = ["INP001"]
"notebooks/*.py" = ["INP001"]

"test_*.py" = [
    "ANN201",  # Public function without return type annotation
    "B018",  # UselessExpression
    "D",  # pydocstyle
    "S101",  # Use of assert detected
]
".pyinstaller/*.py" = ["INP001"]  # Not a package.
"conftest.py" = ["INP001"]  # Part of configuration, not a package.
"docs/*.py" = [
    "INP001",  # implicit-namespace-package. The examples are not a package.
]

[tool.ruff.lint.flake8-annotations]
ignore-fully-untyped = true
mypy-init-return = true

[tool.ruff.lint.flake8-comprehensions]
allow-dict-calls-with-keyword-arguments = true

[tool.ruff.lint.flake8-type-checking]
exempt-modules = []

[tool.ruff.lint.isort]
known-first-party = ["astropy", "extension_helpers"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.codespell]
skip = """
    *.cff,
    */data/*,
    *extern/*,
    hendrics/CITATION,
    docs/credits.rst,
    *_lextab.py,
    *_parsetab.py,
    *.svg,
    docs/scripts/cli.rst,
    *.ipynb,
    pyproject.toml,
"""
# The following list of words for codespell to ignore may contain some
# misspellings that should be revisited and fixed in the future.
ignore-words-list = """
    aas,
    ans,
    bu,
    bubu,
    clen,
    coo,
    datas,
    ded,
    dum,
    fo,
    hel,
    lightyear,
    livetime,
    livetimes,
    lond,
    nax,
    nd,
    ned,
    nin,
    numer,
    observ,
    precess,
    precessed,
    precesses,
    precessing,
    pres,
    som,
    splitted,
    stil,
    te,
    wirth,
"""

[tool.docformatter]
    # The ``summaries`` are not (yet) 75 characters because the summary lines can't be
    # automatically wrapped and must be re-written, which should be done at some point.
    recursive = true
    wrap-summaries = 1000
    wrap-descriptions = 75
    black = true
    syntax = "numpy"