pyproject.toml

[tool.poetry]
name = "neural-pipeline-search"
version = "v0.12.2"
description = "Neural Pipeline Search helps deep learning experts find the best neural pipeline."
authors = [
    "Danny Stoll <stolld@cs.uni-freiburg.de>",
    "Neeratyoy Mallik <mallik@cs.uni-freiburg.de>",
    "Simon Schrodi",
    "Eddie Bergman",
    "Maciej Janowski",
    "Samir Garibov",
    "Tarek Abou Chakra",
    "Daniel Rogalla",
    "Carl Hvarfner",
    "Binxin Ru",
    "Nils Kober",
    "Théophane Vallaeys",
    "Frank Hutter",
]
readme = "README.md"
license = "Apache-2.0"
homepage = "https://github.com/automl/neps"
repository = "https://github.com/automl/neps"
documentation = "https://automl.github.io/neps/"
keywords = [
    "Neural Pipeline Search",
    "Neural Architecture Search",
    "Hyperparameter Optimization",
    "AutoML",
]
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Developers",
  "Intended Audience :: Science/Research",
  "Natural Language :: English",
  "License :: OSI Approved :: Apache Software License",
  "Operating System :: POSIX :: Linux",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: MacOS",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
  "Topic :: System :: Distributed Computing",
]
packages = [{ include = "neps" }, { include = "neps_examples" }]


[tool.poetry.dependencies]
python = ">=3.10,<3.12"
ConfigSpace = "^0.7"
grakel = "^0.1"
numpy = "^1"
pandas = "^2"
networkx = "^2.6.3"
nltk = "^3.6.4"
scipy = ">=1.13.1"
torch = ">=2.0.1"
matplotlib = "^3"
more-itertools = "*"
portalocker = "^2"
seaborn = "^0.13"
pyyaml = "^6"
tensorboard = "^2"
typing-extensions = "*"
torchvision = ">=0.8.0"
ifbo = ">=0.3.10"
botorch = ">=0.12"
gpytorch = "1.13.0"

[tool.poetry.group.dev.dependencies]
ruff = "*"
pre-commit = "^3"
mypy = "^1"
pytest = "^7"
pytest-cases = "^3"
types-PyYAML = "^6"
mkdocs-material = "*"
mkdocs-autorefs = "*"
mkdocs-gen-files = "*"
mkdocstrings = { extras = ["python"], version = "*" }
mkdocs-literate-nav = "*"
mike = "*"
black = "*"                                           # This allows mkdocstrings to format signatures in the docs

[build-system]
requires = ["poetry-core>=1.1.0"]
build-backend = "poetry.core.masonry.api"

# TODO(eddiebergman): Include more of these as we go on in migration
# "tests",
# "neps_examples",
[tool.ruff]
target-version = "py310"
output-format = "full"
line-length = 90
src = ["neps"]

# TODO(eddiebergman): Include more of these as we go on in migration
exclude = [
    "neps/optimizers/multi_fidelity_prior/utils.py",
    "neps/search_spaces/architecture/**/*.py",
    "neps/search_spaces/yaml_search_space_utils.py",
    "neps/search_spaces/architecture",
    "neps/utils/run_args_from_yaml.py",
    "neps/api.py",
    "tests",
    "neps_examples",
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
    "docs",
]

[tool.ruff.lint]
# Extend what ruff is allowed to fix, even it it may break
# This is okay given we use it all the time and it ensures
# better practices. Would be dangerous if using for first
# time on established project.
extend-safe-fixes = ["ALL"]

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

select = [
    "A",
    # "ANN", # Handled by mypy
    "ARG",
    "B",
    "BLE",
    "COM",
    "C4",
    "D",
    # "DTZ",  # One day I should know how to utilize timezones and dates...
    "E",
    # "EXE", Meh
    "ERA",
    "F",
    "FBT",
    "I",
    # "ISC",  # Favours implicit string concatenation
    "INP",
    # "INT", # I don't understand this one
    "N",
    "NPY",
    "PD",
    "PLC",
    "PLE",
    "PLR",
    "PLW",
    "PIE",
    "PT",
    "PTH",
    # "PYI", # Specific to .pyi files for type stubs
    "Q",
    "PGH004",
    "RET",
    "RUF",
    "C90",
    "S",
    # "SLF",    # Private member accessed (sure, it's python)
    "SIM",
    # "TRY", # Good in principle, would take a lot of work to statisfy
    "T10",
    "T20",
    "TID",
    "TCH",
    "UP",
    "N",
    "W",
    "YTT",
]

ignore = [
  "D104",    # Missing docstring in public package
  "D105",    # Missing docstring in magic mthod
  "D203",    # 1 blank line required before class docstring
  "D205",    # 1 blank line between summary and description
  "D401",    # First line of docstring should be in imperative mood
  "N806",    # Variable X in function should be lowercase
  "E731",    # Do not assign a lambda expression, use a def
  "A003",    # Shadowing a builtin
  "S101",    # Use of assert detected.
  "W292",    # No newline at end of file
  "PLC1901", # "" can be simplified to be falsey
  "TCH003",  # Move stdlib import into TYPE_CHECKING
  "B010",    # Do not use `setattr`
  "PD901",   # Use a better name than 'df'
  "PD011",   # Use .to_numpy() instead of .values  (triggers on report.values)
  "PD008",   # Use `.loc` instead of `.at`. If speed is important, use NumPy.
  "COM812",  # Require trailing commas, recommended to ignore due to ruff formatter
  "PLR2004", # No magic numbers inline
  "N817",    # CamelCase import as (ignore for ConfigSpace)
  "N999",    # Invalid name for module
  "NPY002",  # Replace legacy `np.random.choice` call with `np.random.Generator`
  "N803",    # Arguments should start with a lower case letter.
  "S311",    # Standard pseudo-random generators are not suitable for cryptographic purposes
]


# Exclude a variety of commonly ignored directories.
[tool.ruff.lint.per-file-ignores]
"tests/*.py" = [
    "S101",
    "D101",
    "D102",
    "D103",
    "ANN001",
    "ANN201",
    "FBT001",
    "D100",
    "PD901", #  X is a bad variable name. (pandas)
    "TCH",
    "N803",
    "C901", # Too complex
]
"__init__.py" = ["I002"]
"neps_examples/*" = [
    "INP001",
    "I002",
    "E741",
    "D101",
    "D103",
    "T20",
    "D415",
    "ERA001",
    "E402",
    "E501",
]
"docs/*" = ["INP001"]
# TODO
"neps/optimizers/**.py" = [
  "D", # Documentation of everything
  "ARG002", # Unused arguments, bunch of them in inits
  "PLR0913", # Too many arguments...
]


[tool.ruff.lint.isort]
known-first-party = ["neps"]
known-third-party = []
required-imports = ["from __future__ import annotations"]
no-lines-before = ["future"]
combine-as-imports = true
extra-standard-library = ["typing_extensions"]
force-wrap-aliases = true

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

[tool.ruff.lint.pylint]
max-args = 10 # Changed from default of 5

[tool.pytest.ini_options]
addopts = "--basetemp ./tests_tmpdir -m 'not ci_examples'"
markers = [
    "ci_examples",
    "core_examples",
    "regression_all",
    "runtime",
    "neps_api",
    "summary_csv",
]
filterwarnings = "ignore::DeprecationWarning:torch.utils.tensorboard.*:"

[tool.mypy]
python_version = "3.10"  # Match minimum supported version
packages = ["neps"]
show_error_codes = true

namespace_packages = true
explicit_package_bases = true

follow_imports = "normal"

ignore_missing_imports = true

warn_unused_configs = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true

disallow_untyped_defs = true       # All functions must have types
disallow_untyped_decorators = true # ... even decorators
disallow_incomplete_defs = true    # ...all types

no_implicit_optional = true
check_untyped_defs = true

# TODO(eddiebergman): Improve coverage on these modules
[[tool.mypy.overrides]]
module = [
    "neps.api",
    "neps.search_spaces.architecture.*",
    "neps.utils.run_args_from_yaml",
    "neps.optimizers.multi_fidelity.successive_halving",
    "neps.optimizers.multi_fidelity.sampling_policy",
    "neps.optimizers.multi_fidelity.promotion_policy",
    "neps.optimizers.bayesian_optimization.acquisition_functions.ei",
    "neps.optimizers.bayesian_optimization.acquisition_functions.prior_weighted",
    "neps.optimizers.bayesian_optimization.acquisition_functions.ucb",
    "neps.optimizers.bayesian_optimization.acquisition_functions.base_acquisition",
    "neps.optimizers.bayesian_optimization.acquisition_functions.weighted_acquisition",
    "requests.*",
]
ignore_errors = true

[tool.poetry.scripts]
neps = "neps.utils.cli:main"