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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=60", "versioneer[toml]==0.29"]
build-backend = "setuptools.build_meta"
[tool.versioneer]
VCS = "git"
style = "pep440"
versionfile_source = "src/python_projector/_version.py" # CHANGE
versionfile_build = "python_projector/_version.py" # CHANGE
tag_prefix = "v"
parentdir_prefix = "python-projector-" # CHANGE
[project]
name = "python-projector" # CHANGE
dynamic = ["version", "dependencies", "optional-dependencies"]
description = "Python project template" # OPTIONALLY CHANGE
authors = [
{ name = "Kiyoon Kim" }, # OPTIONALLY CHANGE
]
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.11,<4"
classifiers = [
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"License :: OSI Approved :: Apache Software License",
]
keywords = ["development", "template"]
[project.urls]
"Homepage" = "https://github.com/deargen/workflows" # OPTIONALLY CHANGE
[project.scripts]
projector = "python_projector.cli:main" # CHANGE
[tool.setuptools]
license-files = []
[tool.setuptools.dynamic]
dependencies = {file = ["deps/requirements.in"]}
[tool.setuptools.package-data]
python_projector = ["scripts/**/*.sh", "scripts/**/*.py"] # CHANGE (name of the importing module name)
[tool.setuptools.packages.find]
where = ["src"]
[tool.projector.pip_compile]
requirements_in_dir = "deps"
requirements_out_dir = "deps/lock"
python_platforms = ["x86_64-manylinux_2_28", "aarch64-apple-darwin", "x86_64-apple-darwin"]
[tool.pytest.ini_options]
addopts = "--cov=python_projector" # CHANGE (name of the importing module name)
testpaths = ["tests"]
log_cli = true
log_cli_level = "INFO"
[tool.coverage.report]
omit = [
"src/python_projector/_version.py", # CHANGE
# OPTIONALLY ADD MORE LATER
]
[tool.pyright]
include = ["src"]
typeCheckingMode = "standard"
useLibraryCodeForTypes = true
autoImportCompletions = true
pythonVersion = "3.11"
# pythonPlatform = "Linux"
reportDuplicateImport = true
[tool.ruff]
# suppress INP001 on these directories
namespace-packages = [
"scripts",
"src/python_projector/scripts",
]
extend-exclude = [
"src/python_projector/_version.py", # CHANGE
]
[tool.ruff.lint]
# OPTIONALLY ADD MORE LATER
select = [
# flake8
"E",
"F",
"W",
"B", # Bugbear
"D", # Docstring
"D213", # Multi-line docstring summary should start at the second line (replace D212)
"N", # Naming
"C4", # flake8-comprehensions
"UP", # pyupgrade
"SIM", # simplify
"RUF", # ruff-specific
"RET501", # return
"RET502", # return
"RET503", # return
"PTH", # path
"NPY", # numpy
"PD", # pandas
"PYI", # type stubs for pyright/pylance
"PT", # pytest
"PIE", #
"LOG", # logging
"COM818", # comma misplaced
"COM819", # comma
"DTZ", # datetime
"YTT",
"ASYNC",
"FBT", # boolean trap
"A", # Shadowing python builtins
"EXE", # executable (shebang)
"FA", # future annotations
"ISC", # Implicit string concatenation
"ICN", # Import convention
"INP", # Implicit namespace package (no __init__.py)
"Q", # Quotes
"RSE", # raise
"SLOT", # __slots__
"PL", # Pylint
"TRY", # try
"FAST", # FastAPI
"AIR", # airflow
"DOC", # docstring
"TID", # tidy-imports
# Not important
"T10", # debug statements
"T20", # print statements
]
ignore = [
"E402", # Module level import not at top of file
"W293", # Blank line contains whitespace
"W291", # Trailing whitespace
"D10", # Missing docstring in public module / function / etc.
"D200", # One-line docstring should fit on one line with quotes
"D212", # Multi-line docstring summary should start at the first line
"D417", # require documentation for every function parameter.
"D401", # require an imperative mood for all docstrings.
"DOC201", # missing Return field in docstring
"PTH123", # Path.open should be used instead of built-in open
"PT006", # Pytest parameterize style
"N812", # Lowercase `functional` imported as non-lowercase `F` (import torch.nn.functional as F)
"NPY002", # legacy numpy random
"UP017", # datetime.timezone.utc -> datetime.UTC
"SIM108", # use ternary operator instead of if-else
"TRY003", # long message in except
"PLR2004", # magic value comparison
]
[tool.ruff.lint.per-file-ignores]
"__init__.py" = [
"F401", # Ignore seemingly unused imports (they're meant for re-export)
]
"src/python_projector/scripts/**/*.py" = [
"T20", # print statements
]
"[!s][!r][!c]*/**" = ["INP001"] # Implicit namespace package (no __init__.py) ignored not under src/
[tool.ruff.lint.pydocstyle]
convention = "google"
[tool.ruff.lint.pycodestyle]
# Black or ruff will enforce line length to be 88, except for docstrings and comments.
# We set it to 120 so we have more space for docstrings and comments.
max-line-length = 120
[tool.ruff.lint.isort]
# combine-as-imports = true
known-third-party = ["wandb"]
known-first-party = [
"rust_graph",
"bio_data_to_db",
"reduce_binary",
"apbs_binary",
"msms_binary",
"slack_helpers",
"biotest",
]
## Uncomment this if you want to use Python < 3.10
# required-imports = [
# "from __future__ import annotations",
# ]
# [tool.ruff.lint.flake8-tidy-imports]
# Ban certain modules from being imported at module level, instead requiring
# that they're imported lazily (e.g., within a function definition, if TYPE_CHECKING, etc.)
# banned-module-level-imports = ["torch"]
[tool.ruff.lint.flake8-tidy-imports.banned-api]
"pytorch_lightning".msg = "Use lightning.fabric instead"
"lightning.pytorch".msg = "Use lightning.fabric instead"
"lightning_fabric".msg = "Use lightning.fabric instead"
"accelerate".msg = "Use lightning.fabric instead"
"os.system".msg = "Use subprocess.run or subprocess.Popen instead"
"easydict".msg = "Use typing.TypedDict instead (also consider dataclasses and pydantic)"
[tool.ruff.lint.pylint]
max-args = 15
max-bool-expr = 10
max-statements = 100
max-returns = 6
max-public-methods = 30
max-nested-blocks = 10
max-locals = 30
max-branches = 24