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pyproject.toml 27.96 KiB
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# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later

[build-system]
    requires = ["setuptools>=61.0.0", "wheel"]
    build-backend = "setuptools.build_meta"

[project]
name = "ptbench"
version = "1.0.0b0"
requires-python = ">=3.9"
description = "Benchmarks for training and evaluating deep models for the detection of active Pulmonary Tuberculosis from Chest X-Ray imaging."
dynamic = ["readme"]
license = {text = "GNU General Public License v3 (GPLv3)"}
authors = [
    {name = "Geoffrey Raposo", email = "geoffrey@raposo.ch"}
]
maintainers = [
    {name = "Andre Anjos", email = "andre.anjos@idiap.ch"}
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Topic :: Software Development :: Libraries :: Python Modules",
]
dependencies = [
   "clapper",
   "click",
   "numpy",
   "pandas",
   "scipy",
   "scikit-learn",
   "tqdm",
   "psutil",
   "tabulate",
   "matplotlib",
   "pillow",
   "torch>=1.8",
   "torchvision>=0.10",
   "pytorch-lightning",
   "tensorboard",
]

[project.urls]
documentation = "https://www.idiap.ch/software/biosignal/software/docs/biosignal/software/ptbench/main/sphinx/"
homepage = "https://pypi.org/project/ptbench"
repository = "https://gitlab.idiap.ch/biosignal/software/ptbench"
changelog = "https://gitlab.idiap.ch/biosignal/software/ptbench/-/releases"

[project.optional-dependencies]
qa = ["pre-commit"]
doc = [
    "sphinx",
    "furo",
    "sphinx-autodoc-typehints",
    "auto-intersphinx",
    "sphinx-copybutton",
    "sphinx-inline-tabs",
    "sphinx-click",
    ]
test = [
    "pytest",
    "pytest-cov",
    "coverage",
    ]

[project.scripts]
ptbench = "ptbench.scripts.cli:cli"

[project.entry-points."ptbench.config"]
# models
pasa = "ptbench.configs.models.pasa"
signs_to_tb = "ptbench.configs.models.signs_to_tb"
logistic_regression = "ptbench.configs.models.logistic_regression"
densenet_rs = "ptbench.configs.models_datasets.densenet_rs"
alexnet = "ptbench.configs.models.alexnet"
alexnet_pre = "ptbench.configs.models.alexnet_pretrained"
densenet = "ptbench.configs.models.densenet"
densenet_pre = "ptbench.configs.models.densenet_pretrained"
# montgomery dataset (and cross-validation folds)
montgomery = "ptbench.configs.datasets.montgomery.default"
montgomery_rgb = "ptbench.configs.datasets.montgomery.rgb"
montgomery_f0 = "ptbench.configs.datasets.montgomery.fold_0"
montgomery_f1 = "ptbench.configs.datasets.montgomery.fold_1"
montgomery_f2 = "ptbench.configs.datasets.montgomery.fold_2"
montgomery_f3 = "ptbench.configs.datasets.montgomery.fold_3"
montgomery_f4 = "ptbench.configs.datasets.montgomery.fold_4"
montgomery_f5 = "ptbench.configs.datasets.montgomery.fold_5"
montgomery_f6 = "ptbench.configs.datasets.montgomery.fold_6"
montgomery_f7 = "ptbench.configs.datasets.montgomery.fold_7"
montgomery_f8 = "ptbench.configs.datasets.montgomery.fold_8"
montgomery_f9 = "ptbench.configs.datasets.montgomery.fold_9"
montgomery_f0_rgb = "ptbench.configs.datasets.montgomery.fold_0_rgb"
montgomery_f1_rgb = "ptbench.configs.datasets.montgomery.fold_1_rgb"
montgomery_f2_rgb = "ptbench.configs.datasets.montgomery.fold_2_rgb"
montgomery_f3_rgb = "ptbench.configs.datasets.montgomery.fold_3_rgb"
montgomery_f4_rgb = "ptbench.configs.datasets.montgomery.fold_4_rgb"
montgomery_f5_rgb = "ptbench.configs.datasets.montgomery.fold_5_rgb"
montgomery_f6_rgb = "ptbench.configs.datasets.montgomery.fold_6_rgb"
montgomery_f7_rgb = "ptbench.configs.datasets.montgomery.fold_7_rgb"
montgomery_f8_rgb = "ptbench.configs.datasets.montgomery.fold_8_rgb"
montgomery_f9_rgb = "ptbench.configs.datasets.montgomery.fold_9_rgb"
# extended montgomery dataset (with radiological signs)
montgomery_rs = "ptbench.configs.datasets.montgomery_RS.default"
montgomery_rs_f0 = "ptbench.configs.datasets.montgomery_RS.fold_0"
montgomery_rs_f1 = "ptbench.configs.datasets.montgomery_RS.fold_1"
montgomery_rs_f2 = "ptbench.configs.datasets.montgomery_RS.fold_2"
montgomery_rs_f3 = "ptbench.configs.datasets.montgomery_RS.fold_3"
montgomery_rs_f4 = "ptbench.configs.datasets.montgomery_RS.fold_4"
montgomery_rs_f5 = "ptbench.configs.datasets.montgomery_RS.fold_5"
montgomery_rs_f6 = "ptbench.configs.datasets.montgomery_RS.fold_6"
montgomery_rs_f7 = "ptbench.configs.datasets.montgomery_RS.fold_7"
montgomery_rs_f8 = "ptbench.configs.datasets.montgomery_RS.fold_8"
montgomery_rs_f9 = "ptbench.configs.datasets.montgomery_RS.fold_9"
# shenzhen dataset (and cross-validation folds)
shenzhen = "ptbench.configs.datasets.shenzhen.default"
shenzhen_rgb = "ptbench.configs.datasets.shenzhen.rgb"
shenzhen_f0 = "ptbench.configs.datasets.shenzhen.fold_0"
shenzhen_f1 = "ptbench.configs.datasets.shenzhen.fold_1"
shenzhen_f2 = "ptbench.configs.datasets.shenzhen.fold_2"
shenzhen_f3 = "ptbench.configs.datasets.shenzhen.fold_3"
shenzhen_f4 = "ptbench.configs.datasets.shenzhen.fold_4"
shenzhen_f5 = "ptbench.configs.datasets.shenzhen.fold_5"
shenzhen_f6 = "ptbench.configs.datasets.shenzhen.fold_6"
shenzhen_f7 = "ptbench.configs.datasets.shenzhen.fold_7"
shenzhen_f8 = "ptbench.configs.datasets.shenzhen.fold_8"
shenzhen_f9 = "ptbench.configs.datasets.shenzhen.fold_9"
shenzhen_f0_rgb = "ptbench.configs.datasets.shenzhen.fold_0_rgb"
shenzhen_f1_rgb = "ptbench.configs.datasets.shenzhen.fold_1_rgb"
shenzhen_f2_rgb = "ptbench.configs.datasets.shenzhen.fold_2_rgb"
shenzhen_f3_rgb = "ptbench.configs.datasets.shenzhen.fold_3_rgb"
shenzhen_f4_rgb = "ptbench.configs.datasets.shenzhen.fold_4_rgb"
shenzhen_f5_rgb = "ptbench.configs.datasets.shenzhen.fold_5_rgb"
shenzhen_f6_rgb = "ptbench.configs.datasets.shenzhen.fold_6_rgb"
shenzhen_f7_rgb = "ptbench.configs.datasets.shenzhen.fold_7_rgb"
shenzhen_f8_rgb = "ptbench.configs.datasets.shenzhen.fold_8_rgb"
shenzhen_f9_rgb = "ptbench.configs.datasets.shenzhen.fold_9_rgb"
# extended shenzhen dataset (with radiological signs)
shenzhen_rs = "ptbench.configs.datasets.shenzhen_RS.default"
shenzhen_rs_f0 = "ptbench.configs.datasets.shenzhen_RS.fold_0"
shenzhen_rs_f1 = "ptbench.configs.datasets.shenzhen_RS.fold_1"
shenzhen_rs_f2 = "ptbench.configs.datasets.shenzhen_RS.fold_2"
shenzhen_rs_f3 = "ptbench.configs.datasets.shenzhen_RS.fold_3"
shenzhen_rs_f4 = "ptbench.configs.datasets.shenzhen_RS.fold_4"
shenzhen_rs_f5 = "ptbench.configs.datasets.shenzhen_RS.fold_5"
shenzhen_rs_f6 = "ptbench.configs.datasets.shenzhen_RS.fold_6"
shenzhen_rs_f7 = "ptbench.configs.datasets.shenzhen_RS.fold_7"
shenzhen_rs_f8 = "ptbench.configs.datasets.shenzhen_RS.fold_8"
shenzhen_rs_f9 = "ptbench.configs.datasets.shenzhen_RS.fold_9"
# indian dataset (and cross-validation folds)
indian = "ptbench.configs.datasets.indian.default"
indian_rgb = "ptbench.configs.datasets.indian.rgb"
indian_f0 = "ptbench.configs.datasets.indian.fold_0"
indian_f1 = "ptbench.configs.datasets.indian.fold_1"
indian_f2 = "ptbench.configs.datasets.indian.fold_2"
indian_f3 = "ptbench.configs.datasets.indian.fold_3"
indian_f4 = "ptbench.configs.datasets.indian.fold_4"
indian_f5 = "ptbench.configs.datasets.indian.fold_5"
indian_f6 = "ptbench.configs.datasets.indian.fold_6"
indian_f7 = "ptbench.configs.datasets.indian.fold_7"
indian_f8 = "ptbench.configs.datasets.indian.fold_8"
indian_f9 = "ptbench.configs.datasets.indian.fold_9"
indian_f0_rgb = "ptbench.configs.datasets.indian.fold_0_rgb"
indian_f1_rgb = "ptbench.configs.datasets.indian.fold_1_rgb"
indian_f2_rgb = "ptbench.configs.datasets.indian.fold_2_rgb"
indian_f3_rgb = "ptbench.configs.datasets.indian.fold_3_rgb"
indian_f4_rgb = "ptbench.configs.datasets.indian.fold_4_rgb"
indian_f5_rgb = "ptbench.configs.datasets.indian.fold_5_rgb"
indian_f6_rgb = "ptbench.configs.datasets.indian.fold_6_rgb"
indian_f7_rgb = "ptbench.configs.datasets.indian.fold_7_rgb"
indian_f8_rgb = "ptbench.configs.datasets.indian.fold_8_rgb"
indian_f9_rgb = "ptbench.configs.datasets.indian.fold_9_rgb"
# extended indian dataset (with radiological signs)
indian_rs = "ptbench.configs.datasets.indian_RS.default"
indian_rs_f0 = "ptbench.configs.datasets.indian_RS.fold_0"
indian_rs_f1 = "ptbench.configs.datasets.indian_RS.fold_1"
indian_rs_f2 = "ptbench.configs.datasets.indian_RS.fold_2"
indian_rs_f3 = "ptbench.configs.datasets.indian_RS.fold_3"
indian_rs_f4 = "ptbench.configs.datasets.indian_RS.fold_4"
indian_rs_f5 = "ptbench.configs.datasets.indian_RS.fold_5"
indian_rs_f6 = "ptbench.configs.datasets.indian_RS.fold_6"
indian_rs_f7 = "ptbench.configs.datasets.indian_RS.fold_7"
indian_rs_f8 = "ptbench.configs.datasets.indian_RS.fold_8"
indian_rs_f9 = "ptbench.configs.datasets.indian_RS.fold_9"
# TBX11K simplified dataset split 1 (and cross-validation folds)
tbx11k_simplified = "ptbench.configs.datasets.tbx11k_simplified.default"
tbx11k_simplified_rgb = "ptbench.configs.datasets.tbx11k_simplified.rgb"
tbx11k_simplified_f0 = "ptbench.configs.datasets.tbx11k_simplified.fold_0"
tbx11k_simplified_f1 = "ptbench.configs.datasets.tbx11k_simplified.fold_1"
tbx11k_simplified_f2 = "ptbench.configs.datasets.tbx11k_simplified.fold_2"
tbx11k_simplified_f3 = "ptbench.configs.datasets.tbx11k_simplified.fold_3"
tbx11k_simplified_f4 = "ptbench.configs.datasets.tbx11k_simplified.fold_4"
tbx11k_simplified_f5 = "ptbench.configs.datasets.tbx11k_simplified.fold_5"
tbx11k_simplified_f6 = "ptbench.configs.datasets.tbx11k_simplified.fold_6"
tbx11k_simplified_f7 = "ptbench.configs.datasets.tbx11k_simplified.fold_7"
tbx11k_simplified_f8 = "ptbench.configs.datasets.tbx11k_simplified.fold_8"
tbx11k_simplified_f9 = "ptbench.configs.datasets.tbx11k_simplified.fold_9"
tbx11k_simplified_f0_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_0_rgb"
tbx11k_simplified_f1_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_1_rgb"
tbx11k_simplified_f2_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_2_rgb"
tbx11k_simplified_f3_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_3_rgb"
tbx11k_simplified_f4_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_4_rgb"
tbx11k_simplified_f5_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_5_rgb"
tbx11k_simplified_f6_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_6_rgb"
tbx11k_simplified_f7_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_7_rgb"
tbx11k_simplified_f8_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_8_rgb"
tbx11k_simplified_f9_rgb = "ptbench.configs.datasets.tbx11k_simplified.fold_9_rgb"
# extended TBX11K simplified dataset split 1 (with radiological signs)
tbx11k_simplified_rs = "ptbench.configs.datasets.tbx11k_simplified_RS.default"
tbx11k_simplified_rs_f0 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_0"
tbx11k_simplified_rs_f1 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_1"
tbx11k_simplified_rs_f2 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_2"
tbx11k_simplified_rs_f3 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_3"
tbx11k_simplified_rs_f4 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_4"
tbx11k_simplified_rs_f5 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_5"
tbx11k_simplified_rs_f6 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_6"
tbx11k_simplified_rs_f7 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_7"
tbx11k_simplified_rs_f8 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_8"
tbx11k_simplified_rs_f9 = "ptbench.configs.datasets.tbx11k_simplified_RS.fold_9"
# TBX11K simplified dataset split 2 (and cross-validation folds)
tbx11k_simplified_v2 = "ptbench.configs.datasets.tbx11k_simplified_v2.default"
tbx11k_simplified_v2_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.rgb"
tbx11k_simplified_v2_f0 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_0"
tbx11k_simplified_v2_f1 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_1"
tbx11k_simplified_v2_f2 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_2"
tbx11k_simplified_v2_f3 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_3"
tbx11k_simplified_v2_f4 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_4"
tbx11k_simplified_v2_f5 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_5"
tbx11k_simplified_v2_f6 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_6"
tbx11k_simplified_v2_f7 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_7"
tbx11k_simplified_v2_f8 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_8"
tbx11k_simplified_v2_f9 = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_9"
tbx11k_simplified_v2_f0_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_0_rgb"
tbx11k_simplified_v2_f1_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_1_rgb"
tbx11k_simplified_v2_f2_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_2_rgb"
tbx11k_simplified_v2_f3_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_3_rgb"
tbx11k_simplified_v2_f4_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_4_rgb"
tbx11k_simplified_v2_f5_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_5_rgb"
tbx11k_simplified_v2_f6_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_6_rgb"
tbx11k_simplified_v2_f7_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_7_rgb"
tbx11k_simplified_v2_f8_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_8_rgb"
tbx11k_simplified_v2_f9_rgb = "ptbench.configs.datasets.tbx11k_simplified_v2.fold_9_rgb"
# extended TBX11K simplified dataset split 2 (with radiological signs)
tbx11k_simplified_v2_rs = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.default"
tbx11k_simplified_v2_rs_f0 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_0"
tbx11k_simplified_v2_rs_f1 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_1"
tbx11k_simplified_v2_rs_f2 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_2"
tbx11k_simplified_v2_rs_f3 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_3"
tbx11k_simplified_v2_rs_f4 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_4"
tbx11k_simplified_v2_rs_f5 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_5"
tbx11k_simplified_v2_rs_f6 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_6"
tbx11k_simplified_v2_rs_f7 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_7"
tbx11k_simplified_v2_rs_f8 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_8"
tbx11k_simplified_v2_rs_f9 = "ptbench.configs.datasets.tbx11k_simplified_v2_RS.fold_9"
# montgomery-shenzhen aggregated dataset
mc_ch = "ptbench.configs.datasets.mc_ch.default"
mc_ch_rgb = "ptbench.configs.datasets.mc_ch.rgb"
mc_ch_f0 = "ptbench.configs.datasets.mc_ch.fold_0"
mc_ch_f1 = "ptbench.configs.datasets.mc_ch.fold_1"
mc_ch_f2 = "ptbench.configs.datasets.mc_ch.fold_2"
mc_ch_f3 = "ptbench.configs.datasets.mc_ch.fold_3"
mc_ch_f4 = "ptbench.configs.datasets.mc_ch.fold_4"
mc_ch_f5 = "ptbench.configs.datasets.mc_ch.fold_5"
mc_ch_f6 = "ptbench.configs.datasets.mc_ch.fold_6"
mc_ch_f7 = "ptbench.configs.datasets.mc_ch.fold_7"
mc_ch_f8 = "ptbench.configs.datasets.mc_ch.fold_8"
mc_ch_f9 = "ptbench.configs.datasets.mc_ch.fold_9"
mc_ch_f0_rgb = "ptbench.configs.datasets.mc_ch.fold_0_rgb"
mc_ch_f1_rgb = "ptbench.configs.datasets.mc_ch.fold_1_rgb"
mc_ch_f2_rgb = "ptbench.configs.datasets.mc_ch.fold_2_rgb"
mc_ch_f3_rgb = "ptbench.configs.datasets.mc_ch.fold_3_rgb"
mc_ch_f4_rgb = "ptbench.configs.datasets.mc_ch.fold_4_rgb"
mc_ch_f5_rgb = "ptbench.configs.datasets.mc_ch.fold_5_rgb"
mc_ch_f6_rgb = "ptbench.configs.datasets.mc_ch.fold_6_rgb"
mc_ch_f7_rgb = "ptbench.configs.datasets.mc_ch.fold_7_rgb"
mc_ch_f8_rgb = "ptbench.configs.datasets.mc_ch.fold_8_rgb"
mc_ch_f9_rgb = "ptbench.configs.datasets.mc_ch.fold_9_rgb"
# extended montgomery-shenzhen aggregated dataset
# (with radiological signs)
mc_ch_rs = "ptbench.configs.datasets.mc_ch_RS.default"
mc_ch_rs_f0 = "ptbench.configs.datasets.mc_ch_RS.fold_0"
mc_ch_rs_f1 = "ptbench.configs.datasets.mc_ch_RS.fold_1"
mc_ch_rs_f2 = "ptbench.configs.datasets.mc_ch_RS.fold_2"
mc_ch_rs_f3 = "ptbench.configs.datasets.mc_ch_RS.fold_3"
mc_ch_rs_f4 = "ptbench.configs.datasets.mc_ch_RS.fold_4"
mc_ch_rs_f5 = "ptbench.configs.datasets.mc_ch_RS.fold_5"
mc_ch_rs_f6 = "ptbench.configs.datasets.mc_ch_RS.fold_6"
mc_ch_rs_f7 = "ptbench.configs.datasets.mc_ch_RS.fold_7"
mc_ch_rs_f8 = "ptbench.configs.datasets.mc_ch_RS.fold_8"
mc_ch_rs_f9 = "ptbench.configs.datasets.mc_ch_RS.fold_9"
# montgomery-shenzhen-indian aggregated dataset
mc_ch_in = "ptbench.configs.datasets.mc_ch_in.default"
mc_ch_in_rgb = "ptbench.configs.datasets.mc_ch_in.rgb"
mc_ch_in_f0 = "ptbench.configs.datasets.mc_ch_in.fold_0"
mc_ch_in_f1 = "ptbench.configs.datasets.mc_ch_in.fold_1"
mc_ch_in_f2 = "ptbench.configs.datasets.mc_ch_in.fold_2"
mc_ch_in_f3 = "ptbench.configs.datasets.mc_ch_in.fold_3"
mc_ch_in_f4 = "ptbench.configs.datasets.mc_ch_in.fold_4"
mc_ch_in_f5 = "ptbench.configs.datasets.mc_ch_in.fold_5"
mc_ch_in_f6 = "ptbench.configs.datasets.mc_ch_in.fold_6"
mc_ch_in_f7 = "ptbench.configs.datasets.mc_ch_in.fold_7"
mc_ch_in_f8 = "ptbench.configs.datasets.mc_ch_in.fold_8"
mc_ch_in_f9 = "ptbench.configs.datasets.mc_ch_in.fold_9"
mc_ch_in_f0_rgb = "ptbench.configs.datasets.mc_ch_in.fold_0_rgb"
mc_ch_in_f1_rgb = "ptbench.configs.datasets.mc_ch_in.fold_1_rgb"
mc_ch_in_f2_rgb = "ptbench.configs.datasets.mc_ch_in.fold_2_rgb"
mc_ch_in_f3_rgb = "ptbench.configs.datasets.mc_ch_in.fold_3_rgb"
mc_ch_in_f4_rgb = "ptbench.configs.datasets.mc_ch_in.fold_4_rgb"
mc_ch_in_f5_rgb = "ptbench.configs.datasets.mc_ch_in.fold_5_rgb"
mc_ch_in_f6_rgb = "ptbench.configs.datasets.mc_ch_in.fold_6_rgb"
mc_ch_in_f7_rgb = "ptbench.configs.datasets.mc_ch_in.fold_7_rgb"
mc_ch_in_f8_rgb = "ptbench.configs.datasets.mc_ch_in.fold_8_rgb"
mc_ch_in_f9_rgb = "ptbench.configs.datasets.mc_ch_in.fold_9_rgb"
# extended montgomery-shenzhen-indian aggregated dataset
# (with radiological signs)
mc_ch_in_rs = "ptbench.configs.datasets.mc_ch_in_RS.default"
mc_ch_in_rs_f0 = "ptbench.configs.datasets.mc_ch_in_RS.fold_0"
mc_ch_in_rs_f1 = "ptbench.configs.datasets.mc_ch_in_RS.fold_1"
mc_ch_in_rs_f2 = "ptbench.configs.datasets.mc_ch_in_RS.fold_2"
mc_ch_in_rs_f3 = "ptbench.configs.datasets.mc_ch_in_RS.fold_3"
mc_ch_in_rs_f4 = "ptbench.configs.datasets.mc_ch_in_RS.fold_4"
mc_ch_in_rs_f5 = "ptbench.configs.datasets.mc_ch_in_RS.fold_5"
mc_ch_in_rs_f6 = "ptbench.configs.datasets.mc_ch_in_RS.fold_6"
mc_ch_in_rs_f7 = "ptbench.configs.datasets.mc_ch_in_RS.fold_7"
mc_ch_in_rs_f8 = "ptbench.configs.datasets.mc_ch_in_RS.fold_8"
mc_ch_in_rs_f9 = "ptbench.configs.datasets.mc_ch_in_RS.fold_9"
# montgomery-shenzhen-indian-tbx11k aggregated dataset
mc_ch_in_11k = "ptbench.configs.datasets.mc_ch_in_11k.default"
mc_ch_in_11k_rgb = "ptbench.configs.datasets.mc_ch_in_11k.rgb"
mc_ch_in_11k_f0 = "ptbench.configs.datasets.mc_ch_in_11k.fold_0"
mc_ch_in_11k_f1 = "ptbench.configs.datasets.mc_ch_in_11k.fold_1"
mc_ch_in_11k_f2 = "ptbench.configs.datasets.mc_ch_in_11k.fold_2"
mc_ch_in_11k_f3 = "ptbench.configs.datasets.mc_ch_in_11k.fold_3"
mc_ch_in_11k_f4 = "ptbench.configs.datasets.mc_ch_in_11k.fold_4"
mc_ch_in_11k_f5 = "ptbench.configs.datasets.mc_ch_in_11k.fold_5"
mc_ch_in_11k_f6 = "ptbench.configs.datasets.mc_ch_in_11k.fold_6"
mc_ch_in_11k_f7 = "ptbench.configs.datasets.mc_ch_in_11k.fold_7"
mc_ch_in_11k_f8 = "ptbench.configs.datasets.mc_ch_in_11k.fold_8"
mc_ch_in_11k_f9 = "ptbench.configs.datasets.mc_ch_in_11k.fold_9"
mc_ch_in_11k_f0_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_0_rgb"
mc_ch_in_11k_f1_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_1_rgb"
mc_ch_in_11k_f2_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_2_rgb"
mc_ch_in_11k_f3_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_3_rgb"
mc_ch_in_11k_f4_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_4_rgb"
mc_ch_in_11k_f5_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_5_rgb"
mc_ch_in_11k_f6_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_6_rgb"
mc_ch_in_11k_f7_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_7_rgb"
mc_ch_in_11k_f8_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_8_rgb"
mc_ch_in_11k_f9_rgb = "ptbench.configs.datasets.mc_ch_in_11k.fold_9_rgb"
# extended montgomery-shenzhen-indian-tbx11k aggregated dataset
# (with radiological signs)
mc_ch_in_11k_rs = "ptbench.configs.datasets.mc_ch_in_11k_RS.default"
mc_ch_in_11k_rs_f0 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_0"
mc_ch_in_11k_rs_f1 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_1"
mc_ch_in_11k_rs_f2 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_2"
mc_ch_in_11k_rs_f3 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_3"
mc_ch_in_11k_rs_f4 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_4"
mc_ch_in_11k_rs_f5 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_5"
mc_ch_in_11k_rs_f6 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_6"
mc_ch_in_11k_rs_f7 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_7"
mc_ch_in_11k_rs_f8 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_8"
mc_ch_in_11k_rs_f9 = "ptbench.configs.datasets.mc_ch_in_11k_RS.fold_9"
# montgomery-shenzhen-indian-tbx11kv2 aggregated dataset
mc_ch_in_11kv2 = "ptbench.configs.datasets.mc_ch_in_11kv2.default"
mc_ch_in_11kv2_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.rgb"
mc_ch_in_11kv2_f0 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_0"
mc_ch_in_11kv2_f1 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_1"
mc_ch_in_11kv2_f2 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_2"
mc_ch_in_11kv2_f3 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_3"
mc_ch_in_11kv2_f4 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_4"
mc_ch_in_11kv2_f5 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_5"
mc_ch_in_11kv2_f6 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_6"
mc_ch_in_11kv2_f7 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_7"
mc_ch_in_11kv2_f8 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_8"
mc_ch_in_11kv2_f9 = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_9"
mc_ch_in_11kv2_f0_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_0_rgb"
mc_ch_in_11kv2_f1_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_1_rgb"
mc_ch_in_11kv2_f2_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_2_rgb"
mc_ch_in_11kv2_f3_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_3_rgb"
mc_ch_in_11kv2_f4_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_4_rgb"
mc_ch_in_11kv2_f5_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_5_rgb"
mc_ch_in_11kv2_f6_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_6_rgb"
mc_ch_in_11kv2_f7_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_7_rgb"
mc_ch_in_11kv2_f8_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_8_rgb"
mc_ch_in_11kv2_f9_rgb = "ptbench.configs.datasets.mc_ch_in_11kv2.fold_9_rgb"
# extended montgomery-shenzhen-indian-tbx11kv2 aggregated dataset
# (with radiological signs)
mc_ch_in_11kv2_rs = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.default"
mc_ch_in_11kv2_rs_f0 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_0"
mc_ch_in_11kv2_rs_f1 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_1"
mc_ch_in_11kv2_rs_f2 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_2"
mc_ch_in_11kv2_rs_f3 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_3"
mc_ch_in_11kv2_rs_f4 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_4"
mc_ch_in_11kv2_rs_f5 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_5"
mc_ch_in_11kv2_rs_f6 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_6"
mc_ch_in_11kv2_rs_f7 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_7"
mc_ch_in_11kv2_rs_f8 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_8"
mc_ch_in_11kv2_rs_f9 = "ptbench.configs.datasets.mc_ch_in_11kv2_RS.fold_9"
# tbpoc dataset (and cross-validation folds)
tbpoc_f0 = "ptbench.configs.datasets.tbpoc.fold_0"
tbpoc_f1 = "ptbench.configs.datasets.tbpoc.fold_1"
tbpoc_f2 = "ptbench.configs.datasets.tbpoc.fold_2"
tbpoc_f3 = "ptbench.configs.datasets.tbpoc.fold_3"
tbpoc_f4 = "ptbench.configs.datasets.tbpoc.fold_4"
tbpoc_f5 = "ptbench.configs.datasets.tbpoc.fold_5"
tbpoc_f6 = "ptbench.configs.datasets.tbpoc.fold_6"
tbpoc_f7 = "ptbench.configs.datasets.tbpoc.fold_7"
tbpoc_f8 = "ptbench.configs.datasets.tbpoc.fold_8"
tbpoc_f9 = "ptbench.configs.datasets.tbpoc.fold_9"
tbpoc_f0_rgb = "ptbench.configs.datasets.tbpoc.fold_0_rgb"
tbpoc_f1_rgb = "ptbench.configs.datasets.tbpoc.fold_1_rgb"
tbpoc_f2_rgb = "ptbench.configs.datasets.tbpoc.fold_2_rgb"
tbpoc_f3_rgb = "ptbench.configs.datasets.tbpoc.fold_3_rgb"
tbpoc_f4_rgb = "ptbench.configs.datasets.tbpoc.fold_4_rgb"
tbpoc_f5_rgb = "ptbench.configs.datasets.tbpoc.fold_5_rgb"
tbpoc_f6_rgb = "ptbench.configs.datasets.tbpoc.fold_6_rgb"
tbpoc_f7_rgb = "ptbench.configs.datasets.tbpoc.fold_7_rgb"
tbpoc_f8_rgb = "ptbench.configs.datasets.tbpoc.fold_8_rgb"
tbpoc_f9_rgb = "ptbench.configs.datasets.tbpoc.fold_9_rgb"
# extended tbpoc dataset (with radiological signs)
tbpoc_rs_f0 = "ptbench.configs.datasets.tbpoc_RS.fold_0"
tbpoc_rs_f1 = "ptbench.configs.datasets.tbpoc_RS.fold_1"
tbpoc_rs_f2 = "ptbench.configs.datasets.tbpoc_RS.fold_2"
tbpoc_rs_f3 = "ptbench.configs.datasets.tbpoc_RS.fold_3"
tbpoc_rs_f4 = "ptbench.configs.datasets.tbpoc_RS.fold_4"
tbpoc_rs_f5 = "ptbench.configs.datasets.tbpoc_RS.fold_5"
tbpoc_rs_f6 = "ptbench.configs.datasets.tbpoc_RS.fold_6"
tbpoc_rs_f7 = "ptbench.configs.datasets.tbpoc_RS.fold_7"
tbpoc_rs_f8 = "ptbench.configs.datasets.tbpoc_RS.fold_8"
tbpoc_rs_f9 = "ptbench.configs.datasets.tbpoc_RS.fold_9"
# hivtb dataset (and cross-validation folds)
hivtb_f0 = "ptbench.configs.datasets.hivtb.fold_0"
hivtb_f1 = "ptbench.configs.datasets.hivtb.fold_1"
hivtb_f2 = "ptbench.configs.datasets.hivtb.fold_2"
hivtb_f3 = "ptbench.configs.datasets.hivtb.fold_3"
hivtb_f4 = "ptbench.configs.datasets.hivtb.fold_4"
hivtb_f5 = "ptbench.configs.datasets.hivtb.fold_5"
hivtb_f6 = "ptbench.configs.datasets.hivtb.fold_6"
hivtb_f7 = "ptbench.configs.datasets.hivtb.fold_7"
hivtb_f8 = "ptbench.configs.datasets.hivtb.fold_8"
hivtb_f9 = "ptbench.configs.datasets.hivtb.fold_9"
hivtb_f0_rgb = "ptbench.configs.datasets.hivtb.fold_0_rgb"
hivtb_f1_rgb = "ptbench.configs.datasets.hivtb.fold_1_rgb"
hivtb_f2_rgb = "ptbench.configs.datasets.hivtb.fold_2_rgb"
hivtb_f3_rgb = "ptbench.configs.datasets.hivtb.fold_3_rgb"
hivtb_f4_rgb = "ptbench.configs.datasets.hivtb.fold_4_rgb"
hivtb_f5_rgb = "ptbench.configs.datasets.hivtb.fold_5_rgb"
hivtb_f6_rgb = "ptbench.configs.datasets.hivtb.fold_6_rgb"
hivtb_f7_rgb = "ptbench.configs.datasets.hivtb.fold_7_rgb"
hivtb_f8_rgb = "ptbench.configs.datasets.hivtb.fold_8_rgb"
hivtb_f9_rgb = "ptbench.configs.datasets.hivtb.fold_9_rgb"
# extended hivtb dataset (with radiological signs)
hivtb_rs_f0 = "ptbench.configs.datasets.hivtb_RS.fold_0"
hivtb_rs_f1 = "ptbench.configs.datasets.hivtb_RS.fold_1"
hivtb_rs_f2 = "ptbench.configs.datasets.hivtb_RS.fold_2"
hivtb_rs_f3 = "ptbench.configs.datasets.hivtb_RS.fold_3"
hivtb_rs_f4 = "ptbench.configs.datasets.hivtb_RS.fold_4"
hivtb_rs_f5 = "ptbench.configs.datasets.hivtb_RS.fold_5"
hivtb_rs_f6 = "ptbench.configs.datasets.hivtb_RS.fold_6"
hivtb_rs_f7 = "ptbench.configs.datasets.hivtb_RS.fold_7"
hivtb_rs_f8 = "ptbench.configs.datasets.hivtb_RS.fold_8"
hivtb_rs_f9 = "ptbench.configs.datasets.hivtb_RS.fold_9"
# montgomery-shenzhen-indian-padchest aggregated dataset
mc_ch_in_pc = "ptbench.configs.datasets.mc_ch_in_pc.default"
mc_ch_in_pc_rgb = "ptbench.configs.datasets.mc_ch_in_pc.rgb"
# extended montgomery-shenzhen-indian-padchest aggregated dataset
# (with radiological signs)
mc_ch_in_pc_rs = "ptbench.configs.datasets.mc_ch_in_pc_RS.default"
# NIH CXR14 (relabeled)
nih_cxr14 = "ptbench.configs.datasets.nih_cxr14_re.default"
nih_cxr14_cm = "ptbench.configs.datasets.nih_cxr14_re.cardiomegaly"
# NIH CXR14 / PadChest aggregated dataset
nih_cxr14_pc_idiap = "ptbench.configs.datasets.nih_cxr14_re_pc.idiap"
# PadChest
padchest_idiap = "ptbench.configs.datasets.padchest.idiap"
padchest_tb_idiap = "ptbench.configs.datasets.padchest.tb_idiap"
padchest_no_tb_idiap = "ptbench.configs.datasets.padchest.no_tb_idiap"
padchest_tb_idiap_rgb = "ptbench.configs.datasets.padchest.tb_idiap_rgb"
padchest_cm_idiap = "ptbench.configs.datasets.padchest.cardiomegaly_idiap"
# extended PadChestTB dataset (with radiological signs)
padchest_tb_idiap_rs = "ptbench.configs.datasets.padchest_RS.tb_idiap"

[tool.setuptools]
zip-safe = true
package-dir = {"" = "src"}

[tool.setuptools.dynamic]
readme = {file = "README.md"}

[tool.distutils.bdist_wheel]
universal = true

[tool.isort]
profile = "black"
line_length = 80
order_by_type = true
lines_between_types = 1

[tool.black]
line-length = 80

[tool.pytest.ini_options]
addopts = [
    "--cov=ptbench",
    "--cov-report=term-missing",
    "--import-mode=append",
]
junit_logging = "all"
junit_log_passing_tests = false