[doc] Disable docstring summary wrapping with docformatter

.pre-commit-config.yaml

@@ -18,6 +18,9 @@ repos:
     rev: v1.7.5
     hooks:
       - id: docformatter
+        args: [
+          --wrap-summaries=0,
+      ]
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:

src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py

 # Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian
-datasets."""
+"""Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets."""
 
 from ....data.datamodule import ConcatDataModule
 from ..indian.datamodule import RawDataLoader as IndianLoader
@@ -14,8 +13,7 @@ from ..shenzhen.datamodule import make_split as make_shenzhen_split
 
 
 class DataModule(ConcatDataModule):
-    """Aggregated DataModule composed of Montgomery, Shenzhen and Indian
-    datasets.
+    """Aggregated DataModule composed of Montgomery, Shenzhen and Indian datasets.
 
     Parameters
     ----------

src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py

 # Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and PadChest
-datasets."""
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and PadChest datasets."""
 
 from ....data.datamodule import ConcatDataModule
 from ..indian.datamodule import RawDataLoader as IndianLoader

src/mednet/config/data/montgomery_shenzhen_indian_padchest/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."""
+"""Aggregated dataset composed of Montgomery, Shenzhen, Indian and Padchest datasets."""
 
 from mednet.config.data.montgomery_shenzhen_indian_padchest.datamodule import (
     DataModule,

src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py

 # Copyright © 2022 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k
-datasets."""
+"""Aggregated DataModule composed of Montgomery, Shenzhen, Indian, and TBX11k datasets."""
 
 from ....data.datamodule import ConcatDataModule
 from ..indian.datamodule import RawDataLoader as IndianLoader

src/mednet/config/data/nih_cxr14_padchest/idiap.py

 # SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
-"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized)
-datasets (no-tb-idiap split)."""
+"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest (normalized) datasets (no-tb-idiap split)."""
 
 from mednet.config.data.nih_cxr14_padchest.datamodule import DataModule
 

src/mednet/config/data/tbx11k/datamodule.py

@@ -119,8 +119,7 @@ class BoundingBoxes(collections.abc.Sequence[BoundingBox]):
 # explained at:
 # https://pytorch.org/docs/stable/data.html#torch.utils.data.default_collate
 def _collate_boundingboxes_fn(batch, *, collate_fn_map=None):
-    """Custom collate_fn() for pytorch dataloaders that ignores BoundingBoxes
-    objects."""
+    """Custom collate_fn() for pytorch dataloaders that ignores BoundingBoxes objects."""
     return batch
 
 

src/mednet/engine/device.py

@@ -21,8 +21,7 @@ SupportedPytorchDevice: typing.TypeAlias = typing.Literal[
 
 
 def _split_int_list(s: str) -> list[int]:
-    """Split a list of integers encoded in a string (e.g. "1,2,3") into a
-    Python list of integers (e.g. ``[1, 2, 3]``)."""
+    """Split a list of integers encoded in a string (e.g. "1,2,3") into a Python list of integers (e.g. ``[1, 2, 3]``)."""
     return [int(k.strip()) for k in s.split(",")]
 
 

src/mednet/models/transforms.py

@@ -95,8 +95,7 @@ def rgb_to_grayscale(img: torch.Tensor) -> torch.Tensor:
 
 
 class RGB(torch.nn.Module):
-    """Wrapper class around :py:func:`.grayscale_to_rgb` to be used as a model
-    transform."""
+    """Wrapper class around :py:func:`.grayscale_to_rgb` to be used as a model transform."""
 
     def __init__(self):
         super().__init__()
@@ -106,8 +105,7 @@ class RGB(torch.nn.Module):
 
 
 class Grayscale(torch.nn.Module):
-    """Wrapper class around :py:func:`rgb_to_grayscale` to be used as a model
-    transform."""
+    """Wrapper class around :py:func:`rgb_to_grayscale` to be used as a model transform."""
 
     def __init__(self):
         super().__init__()

src/mednet/scripts/click.py

@@ -8,9 +8,7 @@ from clapper.click import ConfigCommand as _BaseConfigCommand
 
 
 class ConfigCommand(_BaseConfigCommand):
-    """A click command-class that has the properties of
-    :py:class:`clapper.click.ConfigCommand` and adds verbatim epilog
-    formatting."""
+    """A click command-class that has the properties of :py:class:`clapper.click.ConfigCommand` and adds verbatim epilog formatting."""
 
     def format_epilog(
         self, _: click.core.Context, formatter: click.formatting.HelpFormatter

src/mednet/scripts/predict.py

@@ -125,8 +125,7 @@ def predict(
     parallel,
     **_,
 ) -> None:
-    """Run inference (generates scores) on all input images, using a pre-
-    trained model."""
+    """Run inference (generates scores) on all input images, using a pre-trained model."""
 
     import json
     import shutil

src/mednet/scripts/train_analysis.py

@@ -134,8 +134,7 @@ def train_analysis(
     logdir: pathlib.Path,
     output: pathlib.Path,
 ) -> None:
-    """Create a plot for each metric in the training logs and saves them in a
-    .pdf file."""
+    """Create a plot for each metric in the training logs and saves them in a .pdf file."""
 
     import matplotlib.pyplot as plt
 

src/mednet/utils/resources.py

@@ -582,8 +582,7 @@ class ResourceMonitor:
                     self.data[k] = 0.0
 
     def __exit__(self, *_) -> None:
-        """Stop the monitoring process and returns the summary of
-        observations."""
+        """Stop the monitoring process and returns the summary of observations."""
 
         self.stop_event.set()
         self.monitor.join()

tests/conftest.py

@@ -76,8 +76,7 @@ def temporary_basedir(tmp_path_factory):
 
 
 def pytest_sessionstart(session: pytest.Session) -> None:
-    """Preset the session start to ensure the Montgomery dataset is always
-    available."""
+    """Preset the session start to ensure the Montgomery dataset is always available."""
 
     from mednet.utils.rc import load_rc