pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "pypllr-gui"
version = "0.1.0"
description = "AI/ML Research -> Clinical Applications (Speech Pathology)"
readme = "README.md"
requires-python = ">=3.11"
license = {text = "MIT"}
authors = [
    {name = "Beckett Frey", email = "code@beckettfrey.com"}
]

dependencies = [
    "pyqt6>=6.9.1",
    "torch==2.8.0",
    "torchaudio==2.8.0",
    "pypllrcomputer @ git+https://github.com/BrainBehaviorAnalyticsLab/PyPLLRComputer.git@48a0c934e75f73235ba5a002538b8588fd6697e7",
    "wav2textgrid @ git+https://github.com/pkadambi/Wav2TextGrid.git@3862476185a7558d481f1ae1c9cbca2e48c825a0",
    "datasets>=4.3.0",
    "accelerate>=1.11.0",
    "keyring>=25.6.0",
    "pre-commit>=4.3.0",
    "pytest>=8.4.2",
    "pydantic>=2.12.3",
    "numba>=0.59.0",
    "pyyaml>=6.0.0",
    "rich>=14.2.0",
    "faster-whisper>=1.1.0",
    "alignment-comparison-plots==0.1.1",
]

[dependency-groups]
dev = [
    "pre-commit>=4.3.0",
    "pytest>=8.4.2",
    "pytest-asyncio>=1.3.0",
    "pytest-cov>=7.0.0",
    "pytest-qt>=4.4.0",
    "pre-commit>=4.3.0",
    "ruff>=0.14.0",
    "mypy>=1.18.2",
    "types-PyYAML>=6.0.0",
    "genbadge[coverage]>=1.1.3",
    "invoke>=2.2.0",
    "shred-guard>=1.1.0",
]
docs = [
    "pdoc>=16.0.0",
]
installation = [
    "pyinstaller>=5.10.1",
]

[project.urls]
Homepage = "https://github.com/BrainBehaviorAnalyticsLab/voxkit-desktop"
Repository = "https://github.com/BrainBehaviorAnalyticsLab/voxkit-desktop"
Issues = "https://github.com/BrainBehaviorAnalyticsLab/voxkit-desktop/issues"

[tool.ruff]
line-length = 100
target-version = "py310"
src = ["src"]

exclude = [
    ".git",
    ".mypy_cache",
    ".ruff_cache",
    ".venv",
    "venv",
    "build",
    "dist",
    "examples",
    "__pycache__",
    "main.py",
    "build.py",
    "example_startup_script.py",
    "test_imports.py",
    "coverage.svg"
]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "F",   # pyflakes
    "I",   # isort (import sorting)
    "S",   # bandit (security)
]

ignore = [
    "S101",   # Use of assert (OK in tests)
    "S301",   # Pickle usage (needed for ML)
]

fixable = ["ALL"]

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"]
"scripts/**/*.py" = ["S101","S603"] # Allow subprocess in scripts
"src/voxkit/services/**/*.py" = ["S603", "S108"] # Allow subprocess and temp dirs in services
"hooks/**/*.py" = ["E402"] # Allow imports after code in hooks
"src/voxkit/gui/pages/pipeline/evaluation_stacker.py" = ["S603", "S607"] # Allow subprocess in eval

[tool.ruff.lint.isort]
known-first-party = ["Wav2TextGrid"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.mypy]
python_version = "3.11"
ignore_missing_imports = true
check_untyped_defs = false
warn_return_any = true
warn_unused_configs = true
exclude = [
    "main.py",
    "build.py",
    "example_startup_script.py",
    "test_imports.py",
    "tests/"
]


[tool.coverage.run]
# Omit modules that are difficult, impractical, or low-value to test
omit = [
    # Engine implementations - OS/hardware-dependent external tool integrations
    "src/voxkit/engines/*_engine.py",

    # GUI layer - PyQt6 UI components are difficult to test reliably
    # Focus testing on business logic, not UI rendering
    # Use **/*.py to match all .py files recursively in subdirectories
    "src/voxkit/gui/components/**/*.py",
    "src/voxkit/gui/frameworks/**/*.py",
    "src/voxkit/gui/pages/**/*.py",
    "src/voxkit/gui/styles/**/*.py",
    "src/voxkit/gui/workers/**/*.py",
    "src/voxkit/gui/__init__.py",
    "src/voxkit/gui/utils.py",

    # External service integrations - subprocess/system calls
    "src/voxkit/services/**/*.py",

    # Startup routines that download external models (HuggingFace, MFA)
    "src/voxkit/config.py",
    "src/voxkit/config/startup_config.py",

    # Build and deployment scripts
    "build.py",
    "main.py",
    "_frozen_patch.py",

    # Test files themselves
    "tests/**/*.py",

    # Package initialization files (typically just imports)
    "src/voxkit/__init__.py",
]

[tool.coverage.report]
# Exclude common patterns that don't need coverage
exclude_lines = [
    # Standard pragmas
    "pragma: no cover",

    # Abstract methods and NotImplementedError
    "raise NotImplementedError",
    "raise NotImplemented",
    "@abstractmethod",
    "@abc.abstractmethod",

    # Type checking imports
    "if TYPE_CHECKING:",
    "if typing.TYPE_CHECKING:",

    # Defensive programming
    "assert False",
    "raise AssertionError",

    # Debugging/development code
    "if __name__ == \"__main__\":",
    "if 0:",
    "if False:",

    # Pass statements in abstract classes/protocols
    "pass",

    # Ellipsis in stub files or protocols
    '^\\.\\.\\.\\s*$',
]

# Report settings for clearer output
precision = 2
skip_empty = true
skip_covered = false

# Show missing line numbers in terminal output
show_missing = true

[tool.setuptools.packages.find]
where = ["src"]

[tool.shredguard]

[[tool.shredguard.patterns]]
regex = "\\b\\d{10}\\b|\\b\\d{3}[-.\\s]?\\d{3}[-.\\s]?\\d{4}\\b"
description = "Phone numbers (10 digits)"

[[tool.shredguard.patterns]]
regex = "\\d{3,5}_[MF]_+"
description = "Patient ID"