From bb828de92d961f2b106f20da5c7616f062393af7 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 5 Feb 2024 09:49:43 +0100
Subject: [PATCH] [doc] Disable docstring summary wrapping with docformatter
---
.pre-commit-config.yaml | 3 +++
.../config/data/montgomery_shenzhen_indian/datamodule.py | 6 ++----
.../data/montgomery_shenzhen_indian_padchest/datamodule.py | 3 +--
.../data/montgomery_shenzhen_indian_padchest/default.py | 3 +--
.../data/montgomery_shenzhen_indian_tbx11k/datamodule.py | 3 +--
src/mednet/config/data/nih_cxr14_padchest/idiap.py | 3 +--
src/mednet/config/data/tbx11k/datamodule.py | 3 +--
src/mednet/engine/device.py | 3 +--
src/mednet/models/transforms.py | 6 ++----
src/mednet/scripts/click.py | 4 +---
src/mednet/scripts/predict.py | 3 +--
src/mednet/scripts/train_analysis.py | 3 +--
src/mednet/utils/resources.py | 3 +--
tests/conftest.py | 3 +--
14 files changed, 18 insertions(+), 31 deletions(-)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c74881a8..2c305176 100644
--- a/.pre-commit-config.yaml
+++ b/.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:
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
index 64b4d0f7..676fa8ef 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -1,8 +1,7 @@
# 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
----------
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index e30fac0a..2876af8f 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -1,8 +1,7 @@
# 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
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
index 07b695cc..7a0c7dce 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_padchest/default.py
@@ -1,8 +1,7 @@
# 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,
diff --git a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index dbda251e..8dd83198 100644
--- a/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -1,8 +1,7 @@
# 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
diff --git a/src/mednet/config/data/nih_cxr14_padchest/idiap.py b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
index aed16c8f..6ac62f99 100644
--- a/src/mednet/config/data/nih_cxr14_padchest/idiap.py
+++ b/src/mednet/config/data/nih_cxr14_padchest/idiap.py
@@ -1,8 +1,7 @@
# 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
diff --git a/src/mednet/config/data/tbx11k/datamodule.py b/src/mednet/config/data/tbx11k/datamodule.py
index 1efd1c02..dfb3038b 100644
--- a/src/mednet/config/data/tbx11k/datamodule.py
+++ b/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
diff --git a/src/mednet/engine/device.py b/src/mednet/engine/device.py
index 7f989523..c501f7f2 100644
--- a/src/mednet/engine/device.py
+++ b/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(",")]
diff --git a/src/mednet/models/transforms.py b/src/mednet/models/transforms.py
index 55312665..4ee73548 100644
--- a/src/mednet/models/transforms.py
+++ b/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__()
diff --git a/src/mednet/scripts/click.py b/src/mednet/scripts/click.py
index 7f8830d6..8cb7c392 100644
--- a/src/mednet/scripts/click.py
+++ b/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
diff --git a/src/mednet/scripts/predict.py b/src/mednet/scripts/predict.py
index 664da885..214b85e7 100644
--- a/src/mednet/scripts/predict.py
+++ b/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
diff --git a/src/mednet/scripts/train_analysis.py b/src/mednet/scripts/train_analysis.py
index cb240a6e..73e683a1 100644
--- a/src/mednet/scripts/train_analysis.py
+++ b/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
diff --git a/src/mednet/utils/resources.py b/src/mednet/utils/resources.py
index e1800778..8d95e121 100644
--- a/src/mednet/utils/resources.py
+++ b/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()
diff --git a/tests/conftest.py b/tests/conftest.py
index 5b9d4d47..bacef95e 100644
--- a/tests/conftest.py
+++ b/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
--
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