pyproject.toml

[build-system]
requires = ["setuptools>=61.2"]
build-backend = "setuptools.build_meta"

# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/
[project]
name = "fwl-proteus"
version = "25.11.19"
description = "Coupled atmosphere-interior framework to simulate the temporal evolution of rocky planets"
readme = "README.md"
requires-python = ">=3.11"
authors = [
    {name="Tim Lichtenberg",         email="tim.lichtenberg@rug.nl"},
    {name="Harrison Nicholls",       email="contact@h-nicholls.space"},
    {name="Laurent Soucasse",        email="l.soucasse@esciencecenter.nl"},
    {name="Mariana Sastre",          email="m.c.villamil.sastre@rug.nl"},
    {name="Emma Postolec",           email="e.n.postolec@rug.nl"},
    {name="Flavia Pascal",           email="fpascal@astro.rug.nl"},
    {name="Ben Riegler",             email="ben.riegler@tum.de"},
    {name="Hanno Spreeuw",           email="h.spreeuw@esciencecenter.nl"},
    {name="Dan J. Bower",            email="dbower@ethz.ch"},
    {name="Mark Hammond",            email="mark.hammond@physics.ox.ac.uk"},
    {name="Stef Smeets",             email="s.smeets@esciencecenter.nl"},
    {name="Robb Calder",             email="rdc49@cam.ac.uk"},
    {name="Raymond T. Pierrehumbert",email="raymond.pierrehumbert@physics.ox.ac.uk"},
]
keywords = [
    "Astronomy",
    "Exoplanets",
    "Model-coupling",
]
license = {text = "Apache 2.0 License"}
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Astronomy",
]
dependencies = [
    "attrs",
    "cattrs",
    "fwl-janus>=24.11.05",
    "fwl-mors>=26.01.02",
    "fwl-calliope>=25.05.01",
    "fwl-zephyrus>=25.03.11",
    "fwl-aragog>=26.01.06",
    "fwl-zalmoxis>=26.01.06",
    "fwl-vulcan>=26.04.22",
    "boreas@git+https://github.com/ExoInteriors/BOREAS@0174edb",
    "cmcrameri",
    "juliacall",
    "matplotlib",
    "netCDF4",
    "numpy>=2.0.0",
    "pandas",
    "scipy",
    "pre-commit",
    "platformdirs",
    "ruff",
    "sympy",
    "astropy",
    "torch",
    "botorch",
    "gpytorch",
    "toml",
    "zenodo-get",
    "zenodo-client>=0.4.1",
    "osfclient",
    "packaging",
]

[project.urls]
homepage = "https://proteus-framework.org"
issues = "https://github.com/FormingWorlds/PROTEUS/issues"
source = "https://github.com/FormingWorlds/PROTEUS/"
documentation = "https://proteus-framework.org/proteus/"
changelog = "https://github.com/FormingWorlds/PROTEUS/releases"

[project.optional-dependencies]
develop = [
    "bump-my-version",
    # coverage[toml] enables standalone coverage tool with TOML config support (used by ratcheting script)
    # pytest-cov provides pytest integration for "pytest --cov" convenience (slightly different from CI)
    # Note: Both work independently; CI uses "coverage run -m pytest", developers can use either approach
    "coverage[toml]",
    "tomlkit>=0.11.0",
    "pillow",
    "pip-tools",
    "pytest >= 8.1",
    "pytest-cov",
    "pytest-dependency",
    "pytest-timeout",
]

docs = [
    "zensical",
    "mkdocs-material",
    "markdown-include",
    "mkdocs",
    "mkdocstrings[python]",
    "pymdown-extensions"
]

[project.scripts]
proteus = "proteus.cli:cli"

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true

[tool.setuptools.package-data]
proteus = ["juliapkg.json"]

[tool.coverage.run]
branch = true
source = ["proteus"]
omit = [
    "*/tests/*",
    "*/test_*.py",
    "*/__pycache__/*",
    "*/conftest.py",
]

[tool.pytest.ini_options]
minversion = "8.1"
addopts = [
    # Global coverage options removed from addopts.
    # CI uses "coverage run -m pytest" with [tool.coverage.*] settings.
    # For local development, use either:
    #   1. "coverage run -m pytest" (matches CI behavior, compatible with coverage ratcheting)
    #   2. "pytest --cov" (uses pytest-cov, convenient but slightly different from CI)
    # Both approaches work; choose based on preference.
    "--strict-markers",
    "--strict-config",
    "-ra",
    "--showlocals",
]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
    "unit: marks tests as unit tests",
    "smoke: marks tests as smoke tests (quick validation with real binaries, 1 timestep, low res)",
]

[tool.coverage.report]
# Coverage threshold - automatically updated by CI when coverage increases.
# See: tools/update_coverage_threshold.py and .github/workflows/ci_tests.yml.
# The ratcheting (only ever increasing or staying the same) is enforced in CI;
# do not manually decrease this value in pyproject.toml.
fail_under = 59
show_missing = true
precision = 2
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "if typing.TYPE_CHECKING:",
    "@abstractmethod",
    "@abc.abstractmethod",
]

[tool.coverage.html]
directory = "htmlcov"

[tool.proteus.coverage_fast]
# Fast CI (unit + smoke) coverage gate; ratcheted independently from full suite
# This lower bar is intended for mocked/fast tests only and will auto-increase
# when the fast suite gains coverage. Do not decrease manually.
fail_under = 44.45

[tool.ruff]
line-length = 96
target-version = "py312"
extend-exclude = ["*ipynb"]

[tool.ruff.lint]
select = [
	"F",  # Pyflakes
	"E",  # pycodestyle (error)
	"W",  # pycodestyle (warning)
    "I",    # isort
]
ignore = [
    "E501", # Line too long
    "E741", # Ambiguous variable name
]

[tool.ruff.lint.isort]
known-first-party=["proteus"]
known-third-party=["zalmoxis"]
required-imports = ["from __future__ import annotations"]

[tool.ruff.format]
quote-style = "single"
indent-style = "space"

[tool.bumpversion]
# https://callowayproject.github.io/bump-my-version/howtos/calver/
current_version = "25.11.19"
parse = """(?x)                      # Verbose mode
    (?P<release>                     # The release part
        (?:[1-9][0-9])\\.            # YY.
        (?:1[0-2]|0[1-9])\\.         # MM.
        (?:3[0-1]|[1-2][0-9]|0[1-9]) # DD
    )
    (?:\\.(?P<patch>\\d+))?         # .patch, optional
"""
serialize = ["{release}.{patch}", "{release}"]

[tool.bumpversion.parts.release]
calver_format = "{YY}.{0M}.{0D}"

[[tool.bumpversion.files]]
filename = "src/proteus/__init__.py"
search = "__version__ = '{current_version}'"
replace = "__version__ = '{new_version}'"

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = "version = \"{current_version}\""
replace = "version = \"{new_version}\""

[[tool.bumpversion.files]]
filename = "CITATION.cff"
search = "version: {current_version}"
replace = "version: {new_version}"