pyproject.toml

# ╔═══════════════╗
# ║ build / meta  ║
# ╚═══════════════╝
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "dapper"
dynamic = ["version"]
description = "DAPPER benchmarks the performance of data assimilation (DA) methods."
readme = "README.md"
license = { text = "MIT" }
authors = [{ name = "Patrick N. Raanes", email = "patrick.n.raanes@gmail.com" }]
requires-python = ">=3.12"
keywords = [
  "data-assimilation",
  "enkf",
  "kalman-filtering",
  "state-estimation",
  "particle-filter",
  "bayesian-methods",
  "bayesian-filter",
  "chaos",
]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Mathematics",
  "Programming Language :: Python :: 3",
  "Operating System :: OS Independent",
]
dependencies = [
  "scipy>=1.14",
  "numpy~=2.0",
  "matplotlib>=3.10",
  "pyyaml>=6.0.2",
  "notebook~=6.5",        # Colab uses 6.5.7
  "setuptools>=65.5.0",   # Appears necessary when installing with uv?
  "mpl-tools==0.4.1",
  "tqdm~=4.67",
  "colorama~=0.4.1",
  "tabulate>=0.9",
  "pathos~=0.3",
  "dill==0.3.8",          # NB: use same version on remote computing servers (due to serialisation)
  "threadpoolctl>=3.0.0",
  "ipywidgets>=8.1.8",    # tqdm.auto needs this to be installed
]

[project.optional-dependencies]
Qt = ["PyQt5", "qtpy"]
debug = ["line_profiler", "pre-commit", "ipython>=7.34", "ipdb"]
test = ["pytest", "pytest-cov", "pytest-timeout"]
lint = ["ruff", "ty"]
doc = [
  "mkdocs-material",
  "mkdocstrings",
  "mkdocstrings-python",
  "mkdocs-gen-files",
  "mkdocs-literate-nav",
  "mkdocs-section-index",
  "mkdocs-glightbox",
  "mkdocs-jupyter",
  "pybtex",
  "jupytext",
]
dev = ["dapper[debug,test,lint,doc]"]

[project.urls]
Documentation = "https://nansencenter.github.io/DAPPER/"
Source = "https://github.com/nansencenter/DAPPER"
Tracker = "https://github.com/nansencenter/DAPPER/issues"

[tool.hatch.version]
path = "dapper/__init__.py"

[tool.hatch.build.targets.wheel]
packages = ["dapper"]


# ╔═══════╗
# ║ tests ║
# ╚═══════╝
[tool.pytest.ini_options]
minversion = "6.0"
# Since `--doctest-modules` requires specifying `dapper`,
# it means pytest won't discover `test` dir on its own.
# So to run all tests, do `pytest tests`.
addopts = """
    --ignore=tests/test_plotting_interactive.py
    --ignore=tests/test_demos.py
--doctest-modules dapper
    --ignore-glob=**/QG/*
    --ignore-glob=**/magic.py
    --ignore-glob=**/autoscaler.py
    --ignore-glob=**/demo.py
    --ignore-glob=**/illust_*.py
    --ignore-glob=dapper/mods/KS/compare_schemes.py
    --ignore=dapper/mods/explore_props.py
"""
# mpl uses distutils (deprecated in python>=3.10).
# The warning only prints via pytest.
# Silence until mpl is upgraded (when Colab does so).
# dill 0.3.8 accesses numpy.core (deprecated in numpy>=2.0); pinned for remote server compat.
filterwarnings = [
  'ignore:distutils:DeprecationWarning',
  'ignore:numpy.core is deprecated:DeprecationWarning',
]

[tool.coverage.run]
branch = true       # stricter
source = ["dapper"]
#omit = ["bad_file.py"]

[tool.coverage.report]
ignore_errors = true
exclude_lines = [
  "pragma: no cover",
  "def __repr__",
  "if self.debug",
  "raise AssertionError",
  "raise NotImplementedError",
  "if 0:",
  "if __name__ == .__main__.:",
]

# ╔════╗
# ║ ty ║
# ╚════╝
[tool.ty.src]
exclude = [
  "tests",
  "build",
  "docs",
  "site",
  "dapper/mods",
  "scripts",
  "dapper/tools/remote/autoscaler.py",
]

[tool.ty.rules]
invalid-method-override = "ignore"
too-many-positional-arguments = "ignore"


# ╔══════╗
# ║ ruff ║
# ╚══════╝
[tool.ruff]
# Exclude a variety of commonly ignored directories.
exclude = [
  "scripts",
  ".git",
  ".ipynb_checkpoints",
  ".pyenv",
  ".pytest_cache",
  ".ruff_cache",
  ".svn",
  ".venv",
  ".vscode",
  "__pypackages__",
  "build",
  "dist",
  "site-packages",
  "venv",
  ".*",
  "README.*",
  "docs/examples/*",
  "autoscaler.py",
]

# Same as Black.
line-length = 88
indent-width = 4

# Assume Python 3.9
target-version = "py39"

[tool.ruff.lint]
select = [
  "E",  # pycodestyle
  "F",  # Pyflakes
  "UP", # pyupgrade
  "B",  # flake8-bugbear
  # "SIM",  # flake8-simplify
  "I", # isort
]

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

ignore = [
  "B905", # zip w/o explicit `strict=` (active if target-version>=3.10)
]

[tool.ruff.lint.per-file-ignores]
"dapper/da_methods/{ensemble,variational}.py" = [
  "B023", # Function definition does not bind loop variable
]
"tests/test_{example_2,data}.py" = [
  "E501", # "line too long"
  "W291", # "trailing whitespace"
]
"tests/test_plotting_nonempty.py" = [
  "E402", # Module level import not at top of file
]
"**/__init__.py" = [
  "F401", # "imported but unused"
  "E402", # "module level import not at top of file"
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"
docstring-code-format = false
docstring-code-line-length = "dynamic"