[qa] Changes to docformatter; Update minimum Python version to 3.9

src/ptbench/data/mc_ch_in_pc/default.py

 # Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Aggregated dataset composed of Montgomery, Shenzhen, Indian and Padchest
 datasets."""
 

src/ptbench/data/padchest/__init__.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Padchest dataset for computer-aided diagnosis.
 
 A large chest x-ray image dataset with multi-label annotated reports.

src/ptbench/data/padchest/cardiomegaly_idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Padchest cardiomegaly (idiap protocol) dataset for computer-aided diagnosis.
 
 The first 40 images with cardiomegaly.

src/ptbench/data/padchest/idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Padchest (idiap protocol) dataset for computer-aided diagnosis.
 
 * See :py:mod:`ptbench.data.padchest` for dataset details

src/ptbench/data/padchest/no_tb_idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Padchest tuberculosis (no TB idiap protocol) dataset for computer-aided
 diagnosis.
 

src/ptbench/data/padchest/tb_idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Padchest tuberculosis (idiap protocol) dataset for computer-aided diagnosis.
 
 The 125 healthy images are the first 125 padchest images with the following

src/ptbench/data/tbpoc/__init__.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for computer-aided diagnosis.
 
 * Reference: [TB-POC-2018]_

src/ptbench/data/tbpoc/fold_0.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 0)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_1.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 1)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_2.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 2)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_3.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 3)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_4.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 4)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_5.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 5)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_6.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 6)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_7.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 7)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_8.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 8)
 
 * Split reference: none (stratified kfolding)

src/ptbench/data/tbpoc/fold_9.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """TB-POC dataset for TB detection (cross validation fold 9)
 
 * Split reference: none (stratified kfolding)

src/ptbench/engine/evaluator.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """Defines functionality for the evaluation of predictions."""
 
 import logging
 import os
 import re
 
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import numpy
@@ -292,7 +292,6 @@ def run(
         ),
     )
     data_df = data_df.set_index("index")
-
     """# Save evaluation csv
     if output_folder is not None:
         fullpath = os.path.join(output_folder, f"{name}.csv")
@@ -353,7 +352,6 @@ def run(
     axes.spines["right"].set_visible(False)
     axes.spines["top"].set_visible(False)
     axes.spines["left"].set_position(("data", -0.015))
-
     """if f1_thresh is not None and eer_thresh is not None:
         # get the closest possible threshold we have
         index = int(round(steps * f1_thresh))

src/ptbench/models/normalizer.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """A network model that prefixes a subtract/divide step to any other module."""
 
 import torch

src/ptbench/models/transforms.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-
 """A transform that turns grayscale images to RGB."""
 
 import torch