pyproject.toml

[build-system]
requires = ["setuptools>=76.1.0", "setuptools-scm>=8.0"]
build-backend = "setuptools.build_meta"


[project]
name = "emmiai-noether"
version = "2.0.0"
description = "Noether: A PyTorch-based Framework for Engineering AI"
authors = [{ name = "Emmi AI", email = "contact@emmi.ai" }]
license-files = ["LICENSE.txt"]
license = "LicenseRef-ENPL"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
    "setuptools",
    "wheel",
    # ---
    "loguru>=0.7.3",
    "einops>=0.8.1",
    "hydra-core>=1.3.2",
    "numpy==2.3.1",
    "torch==2.11.0",
    "pandas>=2.3.3",
    "h5py>=3.12.1",
    # ---
    "aistore>=1.13.5",
    "pyvista>=0.44.2",
    "rtree>=1.4.0",
    "trimesh>=4.6.6",
    # ---
    "boto3>=1.40.4",
    "huggingface-hub>=0.34.3",
    "typer>=0.16.0",
    "fsspec>=2025.5.1",
    "psutil>=5.9.0",
    # ---
]

[project.urls]
Source = "https://github.com/Emmi-AI/noether"
Docs = "https://noether-docs.emmi.ai/"


[tool.setuptools_scm]
write_to = "src/noether/_version.py"

[tool.setuptools.package-data]
"noether.scaffold" = ["template_files/**/*.py", "template_files/**/*.yaml", "template_files/**/*.toml"]

[project.scripts]
noether-train = "noether.training.cli.main_train:main"
noether-train-submit-job = "noether.training.cli.submit_job:main"
noether-eval = "noether.inference.cli.main_inference:main"
noether-data = "noether.io.cli.cli:app"
noether-dataset-stats = "noether.data.tools.calculate_statistics:main"
noether-init = "noether.scaffold.cli:app"
noether-development = "noether.training.cli.development:main"

# --- Centralized Development & Tooling Dependencies ---
# These are dependencies for developing the *entire* workspace.
# Install them with `uv sync --group dev --group docs` or `uv sync --all-groups`.
[dependency-groups]
dev = [
    { include-group = "docs" },
    "pre-commit>=4.2.0",
    "pytest>=8.3.5",
    "pytest-cov", # Added for code coverage
    "mypy[reports]>=1.15.0",
    "ruff>=0.11.0",
    "fixit>=2.1.0",
    "ipykernel>=6.30.0", # Useful for notebooks
    "types-docutils==0.22.0.20250822",
    "types-pyyaml>=6.0.12.20241230",
    "types-tqdm>=4.67.0.20250809",
    "docutils-stubs==0.0.22",
    "pytest-benchmark>=5.2.3",
    "wandb>=0.19.6",  # Added for testing WandB integration
]
docs = [
    "sphinx>=7.3",
    "furo==2025.7.19",
    "sphinx-autoapi>=3.6.0",
    "sphinx-autodoc-typehints",
    "sphinx-multiversion",
    "sphinx-design",
    "myst-parser",
    "autodoc-pydantic>=2.2.0",
    "sphinx-copybutton>=0.5.2",
    "roman-numerals-py==4.0.0", # pin because of https://github.com/sphinx-doc/sphinx/issues/14186
]


[[tool.uv.index]]
name = "torch-cpu"
url = "https://download.pytorch.org/whl/cpu"
explicit = true

[[tool.uv.index]]
name = "torch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true
 
[tool.uv.sources]
torch = [
    { index = "torch-cu128", marker = "sys_platform != 'darwin'" },
    { index = "torch-cpu", marker = "sys_platform == 'darwin'" },
]

[tool.coverage.run]
source = ["noether"]

[tool.coverage.report]
omit = [
    "src/noether/data/datasets/*",
    "src/noether/data/cli/*",
    "src/noether/training/cli/*",
    "src/noether/inference/cli/*",
    "src/noether/io/cli/*",
    "src/noether/scaffold/*",
    "src/noether/__init__.py",
    "src/noether/_version.py",
    "src/noether/core/scripts/*",
    "tests/*",
    "examples/*",
]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "if __name__ == \\'__main__\\':",
    "if __name__ == \"__main__\":",
    "@overload",
    "raise NotImplementedError",
    "\\.\\.\\.", # abstract method bodies
]

# mypy and ruff ran in the child packages will fall back to this configuration
[tool.mypy]
python_version = "3.12"
mypy_path = ["src"]
files = ["src"]
plugins = ["pydantic.mypy"]

ignore_missing_imports = true

check_untyped_defs = true
explicit_package_bases = true
namespace_packages = true
no_implicit_optional = true
strict = false
warn_return_any = true
warn_unused_ignores = false
show_error_codes = true
exclude = ["^_build/|^build/|^dist/|^docs/|^\\.venv/|template_files/"]

[[tool.mypy.overrides]]
module = [
    "torch_geometric.*",
    "torch_scatter.*",
    "aistore.*",
    "boto3.*",
    #    "pyvista.*",
    #    "trimesh.*",
    #    "rtree.*"
]



[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]
addopts = ["--import-mode=importlib", "-m", "not benchmark"]


[tool.ruff]
exclude = [
    ".eggs",
    ".git",
    ".ipynb_checkpoints",
    ".pytest_cache",
    ".ruff_cache",
    ".vscode",
    "__pypackages__",
    "_build",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "archive",
]
line-length = 120

[tool.ruff.format]
docstring-code-format = true
quote-style = "double"

[tool.ruff.lint]
# NOTE: Synchronize the ignores with .flake8
ignore = [
    "G004", # "Logging statement uses f-string" is not an issue for the current ML pipeline
    # these ignores are from flake8-bugbear; please fix!
    "B007",
    "B008",
    "B017",
    "B018",   # Useless expression
    "B023",
    "B028",   # No explicit `stacklevel` keyword argument found
    "E402",
    "C408",   # C408 ignored because we like the dict keyword argument syntax
    "C409",   # prefer [] over list()
    "C410",   # prefer () over tuple()
    "E501",   # E501 is not flexible enough, we're using B950 instead
    "E721",
    "E731",   # Assign lambda expression
    "E741",
    "EXE001",
    "F405",
    "F841",
    # these ignores are from flake8-logging-format; please fix!
    "G101",
    # these ignores are from ruff NPY; please fix!
    "NPY002",
    # these ignores are from ruff PERF; please fix!
    "PERF203",
    "PERF401",
    "PERF403",
    # these ignores are from PYI; please fix!
    "PYI024",
    "PYI036",
    "PYI041",
    "PYI056",
    "SIM102",
    "SIM103",
    "SIM112", # flake8-simplify code styles
    "SIM113", # please fix
    "SIM105", # these ignores are from flake8-simplify. please fix or ignore with commented reason
    "SIM108", # SIM108 ignored because we prefer if-else-block instead of ternary expression
    "SIM110",
    "SIM114", # Combine `if` branches using logical `or` operator
    "SIM115",
    "SIM116", # Disable Use a dictionary instead of consecutive `if` statements
    "SIM117",
    "SIM118",
    "UP006",  # keep-runtime-typing
    "UP007",  # keep-runtime-typing
    "TC001",
    "TC002",
    "TC003",
]
select = [
    "B",
    "B904",   # Re-raised error without specifying the cause via the from keyword
    "C4",
    "G",
    "E",
    "EXE",
    "F",
    "SIM1",
    "SIM911",
    "W",
    # Not included in flake8
    "FURB",
    "LOG",
    "NPY",
    "PERF",
    "PGH004",
    "PIE790",
    "PIE794",
    "PIE800",
    "PIE804",
    "PIE807",
    "PIE810",
    "PLC0131", # type bivariance
    "PLC0132", # type param mismatch
    "PLC0205", # string as __slots__
    "PLC3002", # unnecessary-direct-lambda-call
    "PLE",
    "PLR0133", # constant comparison
    "PLR0206", # property with params
    "PLR1722", # use sys exit
    "PLR1736", # unnecessary list index
    "PLW0129", # assert on string literal
    "PLW0133", # useless exception statement
    "PLW0406", # import self
    "PLW0711", # binary op exception
    "PLW1509", # preexec_fn not safe with threads
    "PLW2101", # useless lock statement
    "PLW3301", # nested min max
    "PT006",
    "PT022",
    "PT023",
    "PT024",
    "PT025",
    "PT026",
    "PYI",
    "Q003",    # avoidable escaped quote
    "Q004",    # unnecessary escaped quote
    "RSE",
    "RUF008",  # mutable dataclass default
    "RUF015",  # access first ele in constant time
    "RUF016",  # type error non-integer index
    "RUF017",
    "RUF018",  # no assignment in assert
    "RUF019",  # unnecessary-key-check
    "RUF024",  # from keys mutable
    "RUF026",  # default factory kwarg
    "TCH",
    "TRY002",  # ban vanilla raise (todo fix NOQAs)
    "TRY203",
    "TRY401",  # verbose-log-message
    "UP",
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]

[tool.fixit]
enable = [".ci.rules"]
disable = ["fixit.rules:RewriteToLiteral"]