From 0c2dffdbf3e51db105e9a94401963a4ce76b0fb7 Mon Sep 17 00:00:00 2001
From: Zvi Baratz <z.baratz@gmail.com>
Date: Sat, 18 Feb 2023 10:54:27 +0200
Subject: [PATCH 1/3] DOC: Homogenized module-level docstring formatting

---
 nibabel/affines.py         |  5 ++---
 nibabel/brikhead.py        |  3 +--
 nibabel/data.py            |  4 +---
 nibabel/deprecated.py      |  3 +--
 nibabel/deprecator.py      |  3 +--
 nibabel/dft.py             |  3 +--
 nibabel/environment.py     |  4 +---
 nibabel/filebasedimages.py |  2 +-
 nibabel/fileslice.py       |  3 +--
 nibabel/fileutils.py       |  3 +--
 nibabel/imagestats.py      |  4 +---
 nibabel/mriutils.py        |  4 +---
 nibabel/onetime.py         |  3 +--
 nibabel/openers.py         |  3 +--
 nibabel/parrec.py          |  2 +-
 nibabel/processing.py      | 12 +++++++-----
 nibabel/quaternions.py     |  2 +-
 nibabel/tmpdirs.py         |  3 +--
 nibabel/tripwire.py        |  3 +--
 nibabel/viewers.py         |  2 +-
 nibabel/xmlutils.py        |  4 +---
 21 files changed, 28 insertions(+), 47 deletions(-)

diff --git a/nibabel/affines.py b/nibabel/affines.py
index 59b52e768e..d6c101ddd5 100644
--- a/nibabel/affines.py
+++ b/nibabel/affines.py
@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Utility routines for working with points and affine transforms
-"""
+"""Utility routines for working with points and affine transforms"""
 from functools import reduce
 
 import numpy as np
@@ -313,7 +312,7 @@ def voxel_sizes(affine):
 
 def obliquity(affine):
     r"""
-    Estimate the *obliquity* an affine's axes represent.
+    Estimate the *obliquity* an affine's axes represent
 
     The term *obliquity* is defined here as the rotation of those axes with
     respect to the cardinal axes.
diff --git a/nibabel/brikhead.py b/nibabel/brikhead.py
index f375b541dc..ee5f766722 100644
--- a/nibabel/brikhead.py
+++ b/nibabel/brikhead.py
@@ -6,8 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""
-Class for reading AFNI BRIK/HEAD datasets
+"""Class for reading AFNI BRIK/HEAD datasets
 
 See https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.attributes.html
 for information on what is required to have a valid BRIK/HEAD dataset.
diff --git a/nibabel/data.py b/nibabel/data.py
index 42826d2f67..7e2fe2af70 100644
--- a/nibabel/data.py
+++ b/nibabel/data.py
@@ -1,8 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Utilities to find files from NIPY data packages
-"""
+"""Utilities to find files from NIPY data packages"""
 import configparser
 import glob
 import os
diff --git a/nibabel/deprecated.py b/nibabel/deprecated.py
index c353071954..092370106e 100644
--- a/nibabel/deprecated.py
+++ b/nibabel/deprecated.py
@@ -1,5 +1,4 @@
-"""Module to help with deprecating objects and classes
-"""
+"""Module to help with deprecating objects and classes"""
 from __future__ import annotations
 
 import typing as ty
diff --git a/nibabel/deprecator.py b/nibabel/deprecator.py
index 3ef6b45066..779fdb462d 100644
--- a/nibabel/deprecator.py
+++ b/nibabel/deprecator.py
@@ -1,5 +1,4 @@
-"""Class for recording and reporting deprecations
-"""
+"""Class for recording and reporting deprecations"""
 from __future__ import annotations
 
 import functools
diff --git a/nibabel/dft.py b/nibabel/dft.py
index c805128951..7a49d49f52 100644
--- a/nibabel/dft.py
+++ b/nibabel/dft.py
@@ -7,8 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # Copyright (C) 2011 Christian Haselgrove
-"""DICOM filesystem tools
-"""
+"""DICOM filesystem tools"""
 
 
 import contextlib
diff --git a/nibabel/environment.py b/nibabel/environment.py
index 6f331eed5a..a828ccb865 100644
--- a/nibabel/environment.py
+++ b/nibabel/environment.py
@@ -1,8 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Settings from the system environment relevant to NIPY
-"""
+"""Settings from the system environment relevant to NIPY"""
 
 import os
 from os.path import join as pjoin
diff --git a/nibabel/filebasedimages.py b/nibabel/filebasedimages.py
index 556d8b75e5..6e4ea86135 100644
--- a/nibabel/filebasedimages.py
+++ b/nibabel/filebasedimages.py
@@ -6,7 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Common interface for any image format--volume or surface, binary or xml."""
+"""Common interface for any image format--volume or surface, binary or xml"""
 from __future__ import annotations
 
 import io
diff --git a/nibabel/fileslice.py b/nibabel/fileslice.py
index 87cac05a4a..816f1cdaf6 100644
--- a/nibabel/fileslice.py
+++ b/nibabel/fileslice.py
@@ -1,5 +1,4 @@
-"""Utilities for getting array slices out of file-like objects
-"""
+"""Utilities for getting array slices out of file-like objects"""
 
 import operator
 from functools import reduce
diff --git a/nibabel/fileutils.py b/nibabel/fileutils.py
index da44fe51a9..1defbc62f7 100644
--- a/nibabel/fileutils.py
+++ b/nibabel/fileutils.py
@@ -6,8 +6,7 @@
 #   copyright and license terms.
 #
 # ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Utilities for reading and writing to binary file formats
-"""
+"""Utilities for reading and writing to binary file formats"""
 
 
 def read_zt_byte_strings(fobj, n_strings=1, bufsize=1024):
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 6f1b68178b..36fbddee0e 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -6,9 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""
-Functions for computing image statistics
-"""
+"""Functions for computing image statistics"""
 
 import numpy as np
 
diff --git a/nibabel/mriutils.py b/nibabel/mriutils.py
index d993d26a21..09067cc1e9 100644
--- a/nibabel/mriutils.py
+++ b/nibabel/mriutils.py
@@ -6,9 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""
-Utilities for calculations related to MRI
-"""
+"""Utilities for calculations related to MRI"""
 
 __all__ = ['calculate_dwell_time']
 
diff --git a/nibabel/onetime.py b/nibabel/onetime.py
index 7c723d4c83..e365e81f74 100644
--- a/nibabel/onetime.py
+++ b/nibabel/onetime.py
@@ -1,5 +1,4 @@
-"""
-Descriptor support for NIPY.
+"""Descriptor support for NIPY
 
 Utilities to support special Python descriptors [1,2], in particular the use of
 a useful pattern for properties we call 'one time properties'.  These are
diff --git a/nibabel/openers.py b/nibabel/openers.py
index d75839fe1a..d11c8834a4 100644
--- a/nibabel/openers.py
+++ b/nibabel/openers.py
@@ -6,8 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Context manager openers for various fileobject types
-"""
+"""Context manager openers for various fileobject types"""
 
 import gzip
 import warnings
diff --git a/nibabel/parrec.py b/nibabel/parrec.py
index 7c594dcb45..086f2a79d2 100644
--- a/nibabel/parrec.py
+++ b/nibabel/parrec.py
@@ -8,7 +8,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # Disable line length checking for PAR fragments in module docstring
 # flake8: noqa E501
-"""Read images in PAR/REC format.
+"""Read images in PAR/REC format
 
 This is yet another MRI image format generated by Philips scanners. It is an
 ASCII header (PAR) plus a binary blob (REC).
diff --git a/nibabel/processing.py b/nibabel/processing.py
index c7bd3888de..6027575d47 100644
--- a/nibabel/processing.py
+++ b/nibabel/processing.py
@@ -6,13 +6,15 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Image processing functions for:
+"""Image processing functions
 
-* smoothing
-* resampling
-* converting sd to and from FWHM
+Image processing functions for:
 
-Smoothing and resampling routines need scipy
+    * smoothing
+    * resampling
+    * converting SD to and from FWHM
+
+Smoothing and resampling routines need scipy.
 """
 
 import numpy as np
diff --git a/nibabel/quaternions.py b/nibabel/quaternions.py
index 04c570c84b..9732bc5c63 100644
--- a/nibabel/quaternions.py
+++ b/nibabel/quaternions.py
@@ -7,7 +7,7 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """
-Functions to operate on, or return, quaternions.
+Functions to operate on, or return, quaternions
 
 The module also includes functions for the closely related angle, axis
 pair as a specification for rotation.
diff --git a/nibabel/tmpdirs.py b/nibabel/tmpdirs.py
index 3074fca6f2..7fe47e6510 100644
--- a/nibabel/tmpdirs.py
+++ b/nibabel/tmpdirs.py
@@ -6,8 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""Contexts for *with* statement providing temporary directories
-"""
+"""Contexts for *with* statement providing temporary directories"""
 import os
 import tempfile
 from contextlib import contextmanager
diff --git a/nibabel/tripwire.py b/nibabel/tripwire.py
index d0c3d4c50c..fa45e73382 100644
--- a/nibabel/tripwire.py
+++ b/nibabel/tripwire.py
@@ -1,5 +1,4 @@
-"""Class to raise error for missing modules or other misfortunes
-"""
+"""Class to raise error for missing modules or other misfortunes"""
 from typing import Any
 
 
diff --git a/nibabel/viewers.py b/nibabel/viewers.py
index 9dad3dd17f..5138610fe4 100644
--- a/nibabel/viewers.py
+++ b/nibabel/viewers.py
@@ -14,7 +14,7 @@
 
 
 class OrthoSlicer3D:
-    """Orthogonal-plane slice viewer.
+    """Orthogonal-plane slice viewer
 
     OrthoSlicer3d expects 3- or 4-dimensional array data.  It treats
     4D data as a sequence of 3D spatial volumes, where a slice over the final
diff --git a/nibabel/xmlutils.py b/nibabel/xmlutils.py
index 8e0b18fb6e..9b47d81381 100644
--- a/nibabel/xmlutils.py
+++ b/nibabel/xmlutils.py
@@ -6,9 +6,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-"""
-Thin layer around xml.etree.ElementTree, to abstract nibabel xml support.
-"""
+"""Thin layer around xml.etree.ElementTree, to abstract nibabel xml support"""
 
 from io import BytesIO
 from xml.etree.ElementTree import Element, SubElement, tostring  # noqa

From e7dc5fee1d847504c6c764b1030cc91af9953f48 Mon Sep 17 00:00:00 2001
From: Zvi Baratz <z.baratz@gmail.com>
Date: Sat, 18 Feb 2023 11:04:58 +0200
Subject: [PATCH 2/3] DOC: Removed spacing between module docstrings and
 imports

---
 nibabel/arraywriters.py    | 1 -
 nibabel/ecat.py            | 1 -
 nibabel/environment.py     | 1 -
 nibabel/eulerangles.py     | 1 -
 nibabel/fileholders.py     | 1 -
 nibabel/filename_parser.py | 1 -
 nibabel/fileslice.py       | 1 -
 nibabel/imageclasses.py    | 1 -
 nibabel/imageglobals.py    | 1 -
 nibabel/imagestats.py      | 1 -
 nibabel/loadsave.py        | 1 -
 nibabel/nifti2.py          | 1 -
 nibabel/openers.py         | 1 -
 nibabel/orientations.py    | 2 --
 nibabel/parrec.py          | 1 -
 nibabel/processing.py      | 1 -
 nibabel/quaternions.py     | 1 -
 nibabel/rstutils.py        | 1 -
 nibabel/spaces.py          | 1 -
 nibabel/viewers.py         | 1 -
 nibabel/xmlutils.py        | 1 -
 21 files changed, 22 deletions(-)

diff --git a/nibabel/arraywriters.py b/nibabel/arraywriters.py
index 5a0b04925e..bdd2d548f8 100644
--- a/nibabel/arraywriters.py
+++ b/nibabel/arraywriters.py
@@ -28,7 +28,6 @@ def __init__(self, array, out_dtype=None)
 something else to make sense of conversions between float and int, or between
 larger ints and smaller.
 """
-
 import numpy as np
 
 from .casting import (
diff --git a/nibabel/ecat.py b/nibabel/ecat.py
index f1a40dd27c..23a58f752e 100644
--- a/nibabel/ecat.py
+++ b/nibabel/ecat.py
@@ -42,7 +42,6 @@
 GPL and some of the header files are adapted from CTI files (called CTI code
 below).  It's not clear what the licenses are for these files.
 """
-
 import warnings
 from numbers import Integral
 
diff --git a/nibabel/environment.py b/nibabel/environment.py
index a828ccb865..09aaa6320f 100644
--- a/nibabel/environment.py
+++ b/nibabel/environment.py
@@ -1,7 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Settings from the system environment relevant to NIPY"""
-
 import os
 from os.path import join as pjoin
 
diff --git a/nibabel/eulerangles.py b/nibabel/eulerangles.py
index b1d187e8c1..13dc059644 100644
--- a/nibabel/eulerangles.py
+++ b/nibabel/eulerangles.py
@@ -82,7 +82,6 @@
 ``y``, followed by rotation around ``x``, is known (confusingly) as
 "xyz", pitch-roll-yaw, Cardan angles, or Tait-Bryan angles.
 """
-
 import math
 from functools import reduce
 
diff --git a/nibabel/fileholders.py b/nibabel/fileholders.py
index f2ec992da5..691d31ecff 100644
--- a/nibabel/fileholders.py
+++ b/nibabel/fileholders.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Fileholder class"""
-
 from copy import copy
 
 from .openers import ImageOpener
diff --git a/nibabel/filename_parser.py b/nibabel/filename_parser.py
index 77949a6791..c4e47ee72c 100644
--- a/nibabel/filename_parser.py
+++ b/nibabel/filename_parser.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Create filename pairs, triplets etc, with expected extensions"""
-
 import os
 import pathlib
 
diff --git a/nibabel/fileslice.py b/nibabel/fileslice.py
index 816f1cdaf6..fe7d6bba54 100644
--- a/nibabel/fileslice.py
+++ b/nibabel/fileslice.py
@@ -1,5 +1,4 @@
 """Utilities for getting array slices out of file-like objects"""
-
 import operator
 from functools import reduce
 from mmap import mmap
diff --git a/nibabel/imageclasses.py b/nibabel/imageclasses.py
index ac27a6ecac..e2dbed129d 100644
--- a/nibabel/imageclasses.py
+++ b/nibabel/imageclasses.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Define supported image classes and names"""
-
 from .analyze import AnalyzeImage
 from .brikhead import AFNIImage
 from .cifti2 import Cifti2Image
diff --git a/nibabel/imageglobals.py b/nibabel/imageglobals.py
index 81a1742809..551719a7ee 100644
--- a/nibabel/imageglobals.py
+++ b/nibabel/imageglobals.py
@@ -23,7 +23,6 @@
 
 Use ``logger.level = 1`` to see all messages.
 """
-
 import logging
 
 error_level = 40
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 36fbddee0e..38dc9d3f16 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Functions for computing image statistics"""
-
 import numpy as np
 
 from nibabel.imageclasses import spatial_axes_first
diff --git a/nibabel/loadsave.py b/nibabel/loadsave.py
index 6c1981ca77..f12b81b30b 100644
--- a/nibabel/loadsave.py
+++ b/nibabel/loadsave.py
@@ -8,7 +8,6 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # module imports
 """Utilities to load and save image objects"""
-
 import os
 
 import numpy as np
diff --git a/nibabel/nifti2.py b/nibabel/nifti2.py
index 9c898b47ba..8d9b81e1f9 100644
--- a/nibabel/nifti2.py
+++ b/nibabel/nifti2.py
@@ -12,7 +12,6 @@
 
     https://www.nitrc.org/forum/message.php?msg_id=3738
 """
-
 import numpy as np
 
 from .analyze import AnalyzeHeader
diff --git a/nibabel/openers.py b/nibabel/openers.py
index d11c8834a4..5f2bb0cde7 100644
--- a/nibabel/openers.py
+++ b/nibabel/openers.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Context manager openers for various fileobject types"""
-
 import gzip
 import warnings
 from bz2 import BZ2File
diff --git a/nibabel/orientations.py b/nibabel/orientations.py
index f9e1ea028c..075cbd4ffd 100644
--- a/nibabel/orientations.py
+++ b/nibabel/orientations.py
@@ -7,8 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Utilities for calculating and applying affine orientations"""
-
-
 import numpy as np
 import numpy.linalg as npl
 
diff --git a/nibabel/parrec.py b/nibabel/parrec.py
index 086f2a79d2..22219382c8 100644
--- a/nibabel/parrec.py
+++ b/nibabel/parrec.py
@@ -121,7 +121,6 @@
 utility via the option "--strict-sort".  The dimension info can be exported
 to a CSV file by adding the option "--volume-info".
 """
-
 import re
 import warnings
 from collections import OrderedDict
diff --git a/nibabel/processing.py b/nibabel/processing.py
index 6027575d47..d634ce7086 100644
--- a/nibabel/processing.py
+++ b/nibabel/processing.py
@@ -16,7 +16,6 @@
 
 Smoothing and resampling routines need scipy.
 """
-
 import numpy as np
 import numpy.linalg as npl
 
diff --git a/nibabel/quaternions.py b/nibabel/quaternions.py
index 9732bc5c63..ec40660607 100644
--- a/nibabel/quaternions.py
+++ b/nibabel/quaternions.py
@@ -25,7 +25,6 @@
 >>> vec = np.array([1, 2, 3]).reshape((3,1)) # column vector
 >>> tvec = np.dot(M, vec)
 """
-
 import math
 
 import numpy as np
diff --git a/nibabel/rstutils.py b/nibabel/rstutils.py
index cb40633e54..625a2af477 100644
--- a/nibabel/rstutils.py
+++ b/nibabel/rstutils.py
@@ -2,7 +2,6 @@
 
 * Make ReST table given array of values
 """
-
 import numpy as np
 
 
diff --git a/nibabel/spaces.py b/nibabel/spaces.py
index d06a39b0ed..e5b87171df 100644
--- a/nibabel/spaces.py
+++ b/nibabel/spaces.py
@@ -19,7 +19,6 @@
   mapping), or
 * a length 2 sequence with the same information (shape, affine).
 """
-
 from itertools import product
 
 import numpy as np
diff --git a/nibabel/viewers.py b/nibabel/viewers.py
index 5138610fe4..f2b32a1fd9 100644
--- a/nibabel/viewers.py
+++ b/nibabel/viewers.py
@@ -3,7 +3,6 @@
 Includes version of OrthoSlicer3D code originally written by our own
 Paul Ivanov.
 """
-
 import weakref
 
 import numpy as np
diff --git a/nibabel/xmlutils.py b/nibabel/xmlutils.py
index 9b47d81381..31637b5e0c 100644
--- a/nibabel/xmlutils.py
+++ b/nibabel/xmlutils.py
@@ -7,7 +7,6 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Thin layer around xml.etree.ElementTree, to abstract nibabel xml support"""
-
 from io import BytesIO
 from xml.etree.ElementTree import Element, SubElement, tostring  # noqa
 from xml.parsers.expat import ParserCreate

From 7903364b86bb4d592e60895f36f2a085379f58b6 Mon Sep 17 00:00:00 2001
From: Zvi Baratz <z.baratz@gmail.com>
Date: Sat, 18 Feb 2023 11:14:36 +0200
Subject: [PATCH 3/3] DOC: Minor docstring formatting fixes to functions

---
 nibabel/affines.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/nibabel/affines.py b/nibabel/affines.py
index d6c101ddd5..05fdd7bb58 100644
--- a/nibabel/affines.py
+++ b/nibabel/affines.py
@@ -99,7 +99,7 @@ def apply_affine(aff, pts, inplace=False):
 
 
 def to_matvec(transform):
-    """Split a transform into its matrix and vector components.
+    """Split a transform into its matrix and vector components
 
     The transformation must be represented in homogeneous coordinates and is
     split into its rotation matrix and translation vector components.
@@ -311,8 +311,7 @@ def voxel_sizes(affine):
 
 
 def obliquity(affine):
-    r"""
-    Estimate the *obliquity* an affine's axes represent
+    r"""Estimate the *obliquity* an affine's axes represent
 
     The term *obliquity* is defined here as the rotation of those axes with
     respect to the cardinal axes.