pyproject.toml

# lsqfitgp/pyproject.toml
#
# Copyright (c) 2023, 2024, Giacomo Petrillo
#
# This file is part of lsqfitgp.
#
# lsqfitgp is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# lsqfitgp is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with lsqfitgp.  If not, see <http://www.gnu.org/licenses/>.

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[project]
name = "lsqfitgp"
authors = [
  { name="Giacomo Petrillo", email="info@giacomopetrillo.com" },
]
description = "A general purpose Gaussian process regression module"
readme = "README.md"
requires-python = ">=3.9" # oldest supported by jax 0.4.26
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Development Status :: 3 - Alpha",
    "Operating System :: MacOS",
    "Operating System :: POSIX :: Linux",
]
dependencies = [
    'numpy>=1.22', # oldest supported by jax 0.4.26
    'scipy>=1.10', # oldest supported by jax 0.4.26 and without quirky bugs
    'jax>=0.4.26', # first that fixes polygamma & zeta fp64
    'jaxlib>=0.4.26',
    'gvar>=12.0', # first with custom formatting
]
dynamic = ["version"]

[tool.setuptools.dynamic]
version = {attr = "lsqfitgp.__version__"}

[tool.setuptools.packages.find]
where = ["src"]
namespaces = false

[project.urls]
"Homepage" = "https://github.com/Gattocrucco/lsqfitgp"
"Bug Tracker" = "https://github.com/Gattocrucco/lsqfitgp/issues"

[project.optional-dependencies]

dev = [ # to work locally on lsqfitgp
    "numpy",
    "scipy",
    "matplotlib",
    "gvar",
    "lsqfit",
    "jax",
    "jaxlib",
    "sphinx",
    "myst-parser",
    "numpydoc",
    "pytest",
    "coverage[toml]",
    "twine",
    "ipython",
    "mpmath",
    "pandas",
    "polars[pyarrow]",
    "build",
    "statsmodels",
    "tqdm",
    "tabulate",
    "appnope",
]

tests = [ # to run the unit tests on CI
    "numpy",
    "scipy",
    "gvar",
    "jax",
    "jaxlib",
    "pytest",
    "coverage[toml]",
    "mpmath",
    "pandas",
    "polars[pyarrow]",
    "statsmodels",
]

tests-old = [ # to run the unit tests on CI, with minimum supported dependencies
    "numpy==1.22",
    "scipy==1.10",
    "gvar==12.0",
    "jax==0.4.26",
    "jaxlib==0.4.26",
    "pytest",
    "coverage[toml]",
    "mpmath",
    "pandas<1.5",
    "polars==1.0.0",
    "pyarrow==10.0.1",
    "statsmodels",
]
# TODO can I restrict tests-old to the pins, and use [tests,tests-old]?

docs = [ # to run examples, documentation code, and build documentation on CI
    "numpy",
    "scipy",
    "matplotlib",
    "gvar",
    "lsqfit",
    "jax",
    "jaxlib",
    "sphinx",
    "myst-parser",
    "numpydoc",
    "coverage[toml]",
    "polars",
    "pandas",
    "statsmodels",
    "pyarrow",
    "tqdm",
    "tabulate",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
filterwarnings = [
    'ignore:JAX on Mac ARM machines',
    'ignore:the imp module is deprecated',
    'ignore:k >= N for N \* N square matrix',
    'ignore:Passing None has been deprecated',
    'ignore:minimization failed. Desired error not necessarily achieved due to precision loss\.',
    'ignore:in the future the `\.dtype` attribute of a given datatype object must be a valid dtype instance\. `data_type\.dtype` may need to be coerced using `np\.dtype\(data_type\.dtype\)`\. \(Deprecated NumPy 1\.20\)',
    'ignore:The problem size .+? minus the constraints size .+? is too small',
]
addopts = [
    "-r xXfE",
    "--pdbcls=IPython.terminal.debugger:TerminalPdb",
    "--durations=3",
]

# I wanted to use `--import-mode=importlib`, but it breaks importing submodules,
# in particular `from . import util`.

[tool.coverage.run]
branch = true
source = ["lsqfitgp"]

[tool.coverage.report]
show_missing = true

[tool.coverage.html]
show_contexts = true

[tool.coverage.paths]
# the first path in each list must be the source directory in the machine that's
# generating the coverage report

github = [
    '/home/runner/work/lsqfitgp/lsqfitgp/src/lsqfitgp/',
    '/Users/runner/work/lsqfitgp/lsqfitgp/src/lsqfitgp/',
    'D:\a\lsqfitgp\lsqfitgp\src\lsqfitgp\',
    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/lsqfitgp/',
    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/lsqfitgp/',
    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/lsqfitgp/',
    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\lsqfitgp\',
]

local = [
    'src/lsqfitgp/',
    '/home/runner/work/lsqfitgp/lsqfitgp/src/lsqfitgp/',
    '/Users/runner/work/lsqfitgp/lsqfitgp/src/lsqfitgp/',
    'D:\a\lsqfitgp\lsqfitgp\src\lsqfitgp\',
    '/Library/Frameworks/Python.framework/Versions/*/lib/python*/site-packages/lsqfitgp/',
    '/Users/runner/hostedtoolcache/Python/*/*/lib/python*/site-packages/lsqfitgp/',
    '/opt/hostedtoolcache/Python/*/*/lib/python*/site-packages/lsqfitgp/',
    'C:\hostedtoolcache\windows\Python\*\*\Lib\site-packages\lsqfitgp\',
]