pyproject.toml

[build-system]
requires = ["setuptools>=42", "setuptools-git-versioning", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "alab_gpss"
description = "Code to operate the GPSS"
#readme = "README.md"
keywords = ["self-driving labs", "autonomous", "synthesis", "materials", "inorganic", "solid-state"]
authors = [
    { name = "Yuxing Fei", email = "yuxingfei@berkeley.edu" },
]
dynamic = ["version"]
classifiers = [
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.10",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering",
]
requires-python = ">=3.10"
dependencies = [
    "alab-control@git+https://github.com/CederGroupHub/alab_control",
    "alab-management@git+https://github.com/CederGroupHub/alab_management",
    "uvicorn",
    "fastapi",
    "ReactionCompleter@git+https://github.com/idocx/ReactionCompleter",
    "material_parser@git+https://github.com/idocx/MaterialParser",
    "easy-biologic>=0.4.0",
    "keyboard>=0.13.5",
    "qrcode==8.2",
    "dara-xrd>=1.1.4",
    "impedance>=1.7.1",
    "asgiref>=3.8.1",
    "ipykernel>=7.1.0",
    "plotly>=5.24.0",
    "kaleido>=1.1.0",
    "litellm>=1.80.0",
    "nbformat>=5.10.4",
    "numpy>=2",
    "openai-agents>=0.6.0",
    "pandas>=2.3.3",
    "pydantic>=2.8.2",
    "pymatgen>=2025.10.7",
    "pymongo>=3.1",
    "Flask>=3.0.0",
    "botorch>=0.16.1",
    "scikit-learn>=1.7.2",
    "gpytorch>=1.14.3",
    "uncertainties>=3.2.3",
    "json-repair>=0.55.0",
    "matminer",
    "networkx>=3.4.2",
    "bson>=0.5.10",
    "requests>=2.32.5",
    "seaborn>=0.13.2",
]

[project.optional-dependencies]
strict = [
    "alab-control@git+https://github.com/CederGroupHub/alab_control",
    "alab-management@git+https://github.com/CederGroupHub/alab_management",
    "uvicorn==0.34.1",
    "fastapi==0.115.12",
    "easy-biologic==0.4.0",
]
tests = [
    "pytest==8.0.1",
    "pytest-cov==4.1.0",
]

[tool.versioningit.vcs]
method = "git"
default-tag = "0.0.1"

[tool.coverage.run]
include = ["src/*"]
parallel = true
branch = false

[tool.coverage.paths]
source = ["src/"]

[tool.coverage.report]
show_missing = true
skip_covered = true
exclude_also = [
    '\#\s*pragma: no cover',
    '^\s*assert False(,|$)',
    'if typing.TYPE_CHECKING:',
    '^\s*@overload( |$)',
    'if TYPE_CHECKING:',
]

[tool.mypy]
ignore_missing_imports = true
namespace_packages = true
explicit_package_bases = true
no_implicit_optional = false
follow_imports = "skip"
disable_error_code = "annotation-unchecked"

[tool.ruff]
target-version = "py39"
lint.select = [
    "B", # flake8-bugbear
    "C4", # flake8-comprehensions
    "D", # pydocstyle
    "E", # pycodestyle error
    "EXE", # flake8-executable
    "F", # pyflakes
    "FA", # flake8-future-annotations
    "FBT003", # boolean-positional-value-in-call
    "FLY", # flynt
    "I", # isort
    "ICN", # flake8-import-conventions
    "ISC", # flake8-implicit-str-concat
    "PD", # pandas-vet
    "PERF", # perflint
    "PIE", # flake8-pie
    "PL", # pylint
    "PT", # flake8-pytest-style
    "PYI", # flakes8-pyi
    "Q", # flake8-quotes
    "RET", # flake8-return
    "RSE", # flake8-raise
    "RUF", # Ruff-specific rules
    "SIM", # flake8-simplify
    "SLOT", # flake8-slots
    "TCH", # flake8-type-checking
    "TID", # flake8-tidy-imports
    "UP", # pyupgrade
    "W", # pycodestyle warning
    "YTT", # flake8-2020
]
lint.ignore = [
    "B023", # Function definition does not bind loop variable
    "B028", # No explicit stacklevel keyword argument found
    "B904", # Within an except clause, raise exceptions with ...
    "C408", # unnecessary-collection-call
    "D105", # Missing docstring in magic method
    "D205", # 1 blank line required between summary line and description
    "D212", # Multi-line docstring summary should start at the first line
    "PD011", # pandas-use-of-dot-values
    "PD901", # pandas-df-variable-name
    "PERF203", # try-except-in-loop
    "PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)
    "PLR", # pylint-refactor
    "PLW2901", # Outer for loop variable overwritten by inner assignment target
    "PT004", # pytest-missing-fixture-name-underscore
    "PT006", # pytest-parametrize-names-wrong-type
    "PT013", # pytest-incorrect-pytest-import
    "PYI024", # collections-named-tuple (TODO should maybe fix these)
    "RUF012", # Disable checks for mutable class args. This is a non-problem.
    "RUF013", # implicit-optional
    "SIM105", # Use contextlib.suppress(OSError) instead of try-except-pass
    "PLE0704", # Checks for bare raise statements outside of exception handlers
]
lint.pydocstyle.convention = "google"
lint.isort.known-first-party = ["alab_one"]
line-length = 120

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"tests/**" = ["ANN201", "D", "S101"]

[tool.setuptools.package-data]
alab_one = ["py.typed"]

[tool.setuptools-git-versioning]
enabled = true