pyproject.toml

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
py-modules = ["dashboard", "external", "src", "cv", "run_dashboard", "submit", "train"]

[project]
name = "detect_kelp"
version = "0.0.1"
authors = [
    { name = "Emiel Witting", email = "emiel.witting@gmail.com" },
    { name = "Hugo de Heer", email = "hugodeheer1234@gmail.com" },
    { name = "Jasper van Selm", email = "jmvanselm@gmail.com" },
    { name = "Jeffrey Lim", email = "jeffrey-lim@outlook.com" },
    { name = "Tolga Kopar", email = "cahittolgakopar@gmail.com" },
]
description = "Team Epoch's solution to the \"Kelp Wanted: Segmenting Kelp Forests\" competition."
license = { file = "LICENSE" }
readme = "README.md"
requires-python = ">=3.10"
dependencies = [
    # Machine Learning Basics
    "numpy>=1.26.2",
    "pandas>=2.1.4",
    "scikit-learn>=1.4.0",
    "scikit-image>=0.22.0",
    "scipy>=1.11.4",
    "tqdm>=4.66.1",
    "polars>=0.19.19",

    # Reading Image Data
    "imagecodecs>=2023.9.18",
    "Pillow>=10.1.0",
    "opencv-python>=4.9.0.80",
    "tifffile>=2023.9.26",

    # Visualizations
    "seaborn>=0.13.0",
    "matplotlib>=3.8.2",
    "plotly>=5.18.0",

    # PyTorch
    "torch==2.1.2+cu118",
    "torchaudio==2.1.2+cu118",
    "torchvision==0.16.2+cu118",
    "torch-summary>=1.4.5",
    "open-clip-torch>=2.23.0",
    "einops>=0.7.0",
    "kornia>=0.7.1",
    "kornia-rs>=0.0.8",

    # Dash
    "dash>=2.14.2",
    "dash-bootstrap-components>=1.5.0",
    "dash-bootstrap-templates>=1.1.1",
    "rasterio>=1.3.9",

    # Dask
    "dask>=2023.12.0",
    "dask-glm>=0.3.2",
    "dask_image>=2023.8.1",
    "dask-ml>=2023.3.24",
    "bokeh>=3.3.2",
    "distributed>=2023.12.0",
    "fsspec>=2023.5.0",

    # Pretrained Models
    "segmentation-models-pytorch>=0.3.3",
    "catboost>=1.2.2",
    "sentence-transformers>=2.2.2",
    "monai>=1.3.0",
    "xgboost>=2.0.3",
    "lightgbm>=4.2.0",

    # Data Augmentation
    "albumentations>=1.3.1",

    # Sphinx
    "Sphinx>=7.2.6",
    "sphinx-autodoc-typehints>=1.25.2",
    "sphinxawesome-theme>=5.0.0",
    "myst-parser>=2.0.0",
    "pygit2>=1.13.3",

    # pre-commit & MyPy
    "pre-commit>=3.6.0",
    "mypy>=1.7.1",
    "typing_extensions>=4.9.0",
    "annotated-types>=0.6.0",
    "pandas-stubs>=2.1.1.230928",
    "traitlets>=5.14.1",

    # Hydra
    "hydra-core>=1.3.2",

    # Weights & Biases
    "wandb>=0.16.2",
    "randomname>=0.2.1",

    # Logging
    "coloredlogs>=15.0.1",

    # Notebooks
    "notebook>=7.0.6",
    "jupyter>=1.0.0",
    "ipykernel>=6.27.1",

    # Other
    "pyngrok>=7.0.3",
    "zarr>=2.16.1",
]


[tool.mypy]
exclude = ["external/", "venv/", ".cache"]
allow_untyped_calls = true
disable_error_code = ["import-untyped"]
python-version = "3.10"

[tool.ruff]
extend-exclude = ["external/*"]
line-length = 175
fix = true
show-fixes = true
select = [
    "ALL",  # Every check supported by Ruff
]
ignore = [
    # pydocstyle (D)
    "D203",  # 1 blank line required before class docstring
    "D213",  # Multi-line docstring summary should start at the second line
     # eradicate (ERA)
    "ERA001",  # Found commented-out code
    # Pylint (PL)
    "PLR0913", # Too many arguments for function
    "PLR2004",  # Magic value used in comparison, consider replacing with a constant variable
    # flake8-annotations (ANN)
    "ANN101",  # Missing type annotation for self in method
    # flake8-errmsg (EM)
    "EM101",  # Exception must not use a string literal, assign to variable first
    "EM102",  # Exception must not use an f-string literal, assign to variable first
    # flake8-future-annotations (FA)
    "FA",  # Missing from __future__ import annotations
    # flake8-fixme (FIX)
    "FIX001",  # Line contains FIXME
    "FIX002",  # Line contains TODO
    "FIX003",  # Line contains XXX
    "FIX004",  # Line contains HACK
    # pep8-naming (N)
    "N803",  # Argument name should be lowercase. Variable name "X" is very common in machine learning.
    "N806",  # Variable in function should be lowercase. Variable name "X" is very common in machine learning.
    # flake8-use-pathlib (PTH)
    "PTH",  # Use pathlib instead of os.path. Dask does not seem to like pathlib.
    # flake8-quotes (Q)
    "Q000",  # Single quotes found but double quotes preferred
    # flake8-simplify (SIM)
    "SIM108",  # Use ternary operator instead of `if`-`else`-block
    # flake8-type-checking (TCH)
    "TCH001",  # Move application import into a type-checking block. Breaks Sphinx autodoc (https://github.com/sphinx-doc/sphinx/issues/11225).
    "TCH002",  # Move third-party import into a type-checking block. Breaks Sphinx autodoc (https://github.com/sphinx-doc/sphinx/issues/11225).
    "TCH003",  # Move standard library import into a type-checking block. Breaks Sphinx autodoc (https://github.com/sphinx-doc/sphinx/issues/11225).
    # flake8-todos (TD)
    "TD003",  # Missing issue link on the line following this TODO
    # tryceratops (TRY)
    "TRY003",  # Avoid specifying long messages outside the exception class
]

[tool.ruff.format]
docstring-code-format = true