pyproject.toml

[build-system]
requires = ["flit_core==3.9.0"]
build-backend = "flit_core.buildapi"

[project]
name = "boilercv"
version = "2024.1.3"
description = "Computer vision routines suitable for nucleate pool boiling bubble analysis"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.11"
classifiers = [
  "License :: OSI Approved :: MIT License",
  # ? Also in CI (https://github.com/actions/python-versions/releases)
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  # "Programming Language :: Python :: 3.13",  # ? (via myst-nb) https://github.com/crate-py/rpds/issues/72
  # "Programming Language :: Python :: 3.14",  # ? Not yet beta (https://peps.python.org/pep-0745)
]
dependencies = [
  # TODO
  "context-models>=0.0.1",
  "matplotlib>=3.7.2",
  "numpy>=1.24.4",
  "numpydantic>=1.6.4",
  "pandas[hdf5,performance]>=2.2.2",
  "pillow>=10.3.0",
  "pydantic>=2.9.1",
  "pytz>=2023.3",
  "sympy>=1.12",
  "xarray[accel,io,parallel]>=2023.7.0",
  # ? https://github.com/softboiler/boilercv/issues/213
  "netcdf4>=1.6.5",
  "netcdf4!=1.7.1.post1 ; sys_platform == 'linux'",
]
[project.optional-dependencies]
# * Minimal CV flavor needed, but allow `boilercv` to coexist with different flavors
cv = ["opencv-python>=4.10.0.84"]
[project.urls]
Changes = "https://softboiler.github.io/boilercv/changelog.html"
Docs = "https://softboiler.github.io/boilercv"
Home = "https://github.com/softboiler/boilercv"
Tracker = "https://github.com/softboiler/boilercv/issues"
[[project.authors]]
name = "Blake Naccarato, Kwang Jin Kim"
email = "blake.naccarato@gmail.com"

[tool.uv]
override-dependencies = ["cachier @ ${PROJECT_ROOT}/packages/cachier"]
constraint-dependencies = [
  # ? Security
  "fiona>=1.10.1",
  "setuptools>=70.0.0",
  # ? https://nvd.nist.gov/vuln/detail/CVE-2024-37891
  # ? via sphinx
  "urllib3>=2.2.2",
]
dev-dependencies = [
  # TODO
  "pycine @ git+https://github.com/ottomatic-io/pycine@815cfca06cafc50745a43b2cd0168982225c6dca",
  # ? Workspaces
  "boilercine",
  "boilercore",
  "boilercv_pipeline",
  "context_models",
  "dev",
  # ? Path-sourced deps
  "cachier",
  # ? Dev
  "debugpy>=1.8.2",
  "dvc[gs]>=3.55.2",
  "fawltydeps>=0.16.0",
  "ipython>=8.26.0",
  "pandas-stubs~=2.2.2",
  "pipdeptree>=2.23.0",
  "pipx>=1.6.0",
  "pre-commit>=3.7.1",
  "pyright>=1.1.371",
  "ruff>=0.5.1",
  "rust-just>=1.36.0",
  "snakeviz>=2.2.0",
  "sourcery>=1.21.0",
  "towncrier>=23.11.0",
  # ? Docs
  "linkify-it-py>=2.0.3",
  "myst-nb>=1.1.1",
  "myst-parser>=3.0.1",
  "sphinx-autobuild>=2024.4.16",
  "sphinx-autodoc2>=0.5.0",
  "sphinx-book-theme>=1.1.3",
  "sphinx-design>=0.6.0",
  "sphinx-thebe>=0.3.1",
  "sphinx-tippy>=0.4.3",
  "sphinx-togglebutton>=0.3.2",
  "sphinxcontrib-bibtex>=2.6.2",
  "sphinxcontrib-mermaid>=0.9.2",
  "sphinxcontrib-towncrier>=0.4.0a0",
  # ? Tests
  "pytest-cov>=5.0.0",
  "pytest-custom-exit-code>=0.3.0",
  "pytest-github-actions-annotate-failures>=0.2.0",
  "pytest-plt>=1.1.1",
  "pytest-xdist[psutil,setproctitle]>=3.6.1",
]
[tool.uv.pip]
python-version = "3.11"
all-extras = true
[tool.uv.workspace]
members = ["packages/*"]
exclude = ["packages/cachier"]
[tool.uv.sources]
cachier = { path = "packages/cachier", editable = true }
dev = { workspace = true }
boilercine = { workspace = true }
boilercore = { workspace = true }
boilercv_pipeline = { workspace = true }
context_models = { workspace = true }

[tool.coverage.run]
branch = true
source = ["boilercv", "boilercv_pipeline", "dev", "tests"]

[tool.dev.env]
COVERAGE_CORE = "sysmon"
JUPYTER_PLATFORM_DIRS = "1"
PYDEVD_DISABLE_FILE_VALIDATION = "1"
PYTHONIOENCODING = "utf-8:strict"
PYTHONUTF8 = "1"
PYTHONWARNDEFAULTENCODING = "1"
PYTHONWARNINGS = "ignore"

[tool.fawltydeps]
deps = ["pyproject.toml"]
code = ["src"]
ignore_undeclared = ["_typeshed"]
ignore_unused = ["netcdf4"]
[tool.fawltydeps.custom_mapping]
context_models = ["context_models"]
pydantic = ["pydantic", "pydantic_core"]

[tool.pytest.ini_options]
addopts = """
    --strict-config
    --strict-markers
    --suppress-no-test-exit-code
    --color=yes
    -p no:legacypaths
    -r a
    -n auto
    --dist=loadfile
    --plots=tests/plots
""" # ? `-n 0` because test suite is currently faster in series
cache_dir = ".cache/.pytest_cache"
markers = "slow"
testpaths = "tests"
xfail_strict = true

[tool.towncrier]
directory = "changelog"
filename = "CHANGELOG.md"
template = "changelog/towncrier_template.md.jinja"
title_format = ""
issue_format = "[#{issue}](https://github.com/softboiler/boilercv/issues/{issue})"
underlines = ["", "", ""]
[[tool.towncrier.section]]
path = ""
[[tool.towncrier.type]]
directory = "breaking"
name = "Backwards-incompatible changes"
showcontent = true
[[tool.towncrier.type]]
directory = "deprecation"
name = "Deprecations"
showcontent = true
[[tool.towncrier.type]]
directory = "change"
name = "Changes"
showcontent = true

[tool.pyright]
stubPath = "typings/stubs"
exclude = [
  "**/node_modules",
  "**/__pycache__",
  "**/.*",
  ".cache",
  "typings",
  "packages/boilercine",
  "packages/boilercore",
  "packages/cachier",
]
ignore = [
  "**/node_modules",
  "**/__pycache__",
  "**/.*",
  ".cache",
  "typings",
  "packages/context_models",
]
typeCheckingMode = "strict"
# Default "true" in strict
analyzeUnannotatedFunctions = true
strictParameterNoneValue = true
enableTypeIgnoreComments = true
disableBytesTypePromotions = true
strictListInference = true
strictDictionaryInference = true
strictSetInference = true
# Default "false" in strict
deprecateTypingAliases = false
enableExperimentalFeatures = false
# Default "warning" in strict
reportMissingModuleSource = "warning"
# Default "error" in strict
reportMissingImports = "warning"
reportInvalidTypeForm = "none"                 # Works fine in BaseModels
reportUndefinedVariable = "warning"
reportAssertAlwaysTrue = "warning"
reportInvalidStringEscapeSequence = "warning"
reportInvalidTypeVarUse = "warning"
reportMissingTypeStubs = "none"                # Overeager
reportSelfClsParameterName = "warning"
reportUnsupportedDunderAll = "warning"
reportUnusedExpression = "none"                # Handled by Ruff
reportWildcardImportFromLibrary = "warning"
reportAbstractUsage = "warning"
reportArgumentType = "warning"
reportAssertTypeFailure = "warning"
reportAssignmentType = "warning"
reportAttributeAccessIssue = "warning"
reportCallIssue = "warning"
reportGeneralTypeIssues = "warning"
reportInconsistentOverload = "warning"
reportIndexIssue = "warning"
reportInvalidTypeArguments = "warning"
reportNoOverloadImplementation = "warning"
reportOperatorIssue = "warning"
reportOptionalSubscript = "warning"
reportOptionalMemberAccess = "warning"
reportOptionalCall = "warning"
reportOptionalIterable = "warning"
reportOptionalContextManager = "warning"
reportOptionalOperand = "warning"
reportRedeclaration = "warning"
reportReturnType = "warning"
reportTypedDictNotRequiredAccess = "warning"
reportPrivateImportUsage = "none"              # Flaky regarding "not exported"
reportUnboundVariable = "warning"
reportUnusedCoroutine = "none"                 # Handled by Ruff
reportUnusedExcept = "warning"
reportFunctionMemberAccess = "warning"
reportIncompatibleMethodOverride = "warning"
reportIncompatibleVariableOverride = "warning"
reportOverlappingOverload = "warning"
reportPossiblyUnboundVariable = "warning"
reportConstantRedefinition = "none"
reportDeprecated = "warning"
reportDuplicateImport = "warning"
reportIncompleteStub = "warning"
reportInconsistentConstructor = "warning"
reportInvalidStubStatement = "warning"
reportMatchNotExhaustive = "warning"
reportMissingParameterType = "none"
reportMissingTypeArgument = "warning"
reportPrivateUsage = "none"                    # Ruff checks this well enough
reportTypeCommentUsage = "warning"
reportUnknownArgumentType = "none"
reportUnknownLambdaType = "none"
reportUnknownMemberType = "none"
reportUnknownParameterType = "none"
reportUnknownVariableType = "none"
reportUnnecessaryCast = "warning"
reportUnnecessaryComparison = "warning"
reportUnnecessaryContains = "warning"
reportUnnecessaryIsInstance = "warning"
reportUnusedClass = "none"                     # Handled by Ruff
reportUnusedImport = "none"                    # Handled by Ruff
reportUnusedFunction = "none"                  # Handled by Ruff
reportUnusedVariable = "none"                  # Handled by Ruff
reportUntypedBaseClass = "none"
reportUntypedClassDecorator = "warning"
reportUntypedFunctionDecorator = "none"        # Often out of our control
reportUntypedNamedTuple = "warning"
# Default "none" in strict
reportCallInDefaultInitializer = "none"
reportImplicitOverride = "none"
reportImplicitStringConcatenation = "none"
reportImportCycles = "none"
reportMissingSuperCall = "none"
reportPropertyTypeMismatch = "none"
reportShadowedImports = "none"
reportUninitializedInstanceVariable = "warning" # Ensure we define instance vars
reportUnnecessaryTypeIgnoreComment = "none"
reportUnusedCallResult = "none"

[tool.ruff]
cache-dir = ".cache/.ruff_cache"
extend-exclude = [
  "typings",
  "packages/boilercine",
  "packages/boilercore",
  "packages/cachier",
  "packages/context_models",
]
extend-include = ["*.ipynb"]
src = ["src", "docs", "pipeline", "scripts", "tests"]
output-format = "grouped"
fix = true
preview = true
show-fixes = true
[tool.ruff.lint]
fixable = ["ALL"]
select = [
  "ALL",  # Select all rules
  "D417", # Explicitly enable parameter check even when using Numpy docstrings
]
unfixable = [
  "PIE790", # Don't remove `pass`/`...`, overridden in pre-commit
]
extend-safe-fixes = [
  "F401", # Allow autofix for unused imports even in `__init__.py`
]
ignore = [
  "ANN",     # Don't require type annotations
  "ARG005",  # Allow unused lambda argument. For consistency across df pipelines.
  "C408",    # Allow dict calls
  "COM",     # Allow magic commas and magic missing commas
  "CPY001",  # Don't check for copyright
  "D105",    # Allow missing docstring for magic methods
  "DTZ",     # Timezones are important, but only contextually necessary.
  "E501",    # Don't check line length. Black handles this.
  "EM",      # Don't check for exception message issues
  "ERA",     # False positives. Don't get rid of commented out code.
  "FBT",     # Allow boolean "traps"
  "FIX002",  # Allow TODOs
  "FLY002",  # Allow different string representations
  "FURB118", # Incorrectly applies `itemgetter`
  "FURB140", # Don't replace comprehensions with starmap
  "G0",      # Allow f-strings, etc. in Loguru logging
  "ICN",     # Don't require these ad-hoc "conventional" import names
  "INP001",  # False positives. Checks for packages missing `__init__.py`
  "ISC",     # False positives. Implicit string concatenation is fine.
  "PD009",   # Allow `df.iat`.
  "PD011",   # Allow use of `.values`. False positives.
  "PD013",   # Allow `stack` instead of `melt`. They're not a direct swap.
  "PD101",   # Allow use of nunique(). False positives
  "PD901",   # Allow `df` variable name. We are all consenting adults here.
  "PD011",   # Allow use of `.values`. False positives.
  "PLR6201", # Don't require set literal for membership checks
  "PGH003",  # Until black stops wrapping special ignores, let's allow bare
  "PIE804",  # Allow dict unpack even if unnecessary, consisent for df.assign{**...}
  "PLC0105", # Dont enforce Hungarian notation for `TypeVar` variance
  "PLC2701", # Allow private name imports
  "PLR0913", # Allow more than five function arguments
  "PLR0914", # Allow lots of local variables
  "PLR0917", # Allow more than five positional arguments
  "PLR1704", # Allow redefining arguments, often for sanitization
  "PLR2004", # Allow magic values. This check is too sensitive
  "PLR6201", # Don't require set literal for membership checks
  "PLR6301", # Allow methods that don't reference self, may be overridden
  "PLW0108", # Don't warn about unnecessary lambda. Often needed in pandas chains
  "PLW0642", # Allow reassignment to `cls` and `self`
  "PLW2901", # For loop variable
  "RET",     # Return checks are flaky, Sourcery does fine analysing these paths
  "S301",    # Don't warn about pickling.
  "S403",    # Don't warn about pickle-like modules.
  "S404",    # Don't warn about subprocess.
  "TCH",     # Type checking linter doesn't play nicely with pydantic
  "TD",      # Disable to-do validation. Too pedantic for now.
  "TRY003",  # Allow long exception messages
  "W2",      # Allow whitespace issues. Fixed automatically by black.
]
[tool.ruff.lint.isort]
split-on-trailing-comma = false
[tool.ruff.format]
skip-magic-trailing-comma = true
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.extend-per-file-ignores]
"**/*.ipynb" = [
  "B018", # Allow "useless" expressions, which do suppress outputs in notebooks
  "E703", # Allow semicolons to suppress outputs in notebooks
  "F821", # Allow undefined names, such as `display`
  "S101", # Allow assert
  "T201", # Allow print in notebooks
]
"docs/**.ipynb" = [
  "E402", # Need to allow imports below patches in docs notebooks
]
"packages/_dev/dev/tools/add_changes.py" = [
  "S603", # Allow shell expressions here
  "S607", # Allow shell expressions here
]
"packages/pipeline/boilercv_pipeline/sync_dvc/dvc.py" = [
  "D1", # Don't require docstrings
]
"packages/pipeline/boilercv_pipeline/models/generated/types/**/*.py" = [
  "D10",    # Allow missing docstrings in generated types
  "PYI047", # Allow unused private generated types
  "SLF001", # Allow private member access in generated types
]
"**/manual/**/*.py" = [
  "D10", # Allow missing docstrings in stage implementations
]
"**/stages/**/*.py" = [
  "D10",    # Allow missing docstrings in stage implementations
  "RUF012", # Disable this heuristic for Pydantic models with defaults
]
"tests/**" = [
  "ARG001", # Allow unused arguments
  "S101",   # Allow assert
  "SIM300", # Allow constants (expectations) on the RHS
  "SLF001", # Allow private member access in tests
]
"tests/test_morphs.py" = [
  "D101", # Allow not documenting a test class
  "D103", # Allow not documenting a test function
  "E302", # Allow manual spacing of test classes close to their headings
  "E305", # Allow manual spacing of test classes close to their headings
]