Merge remote-tracking branch 'upstream/master' into ResourceWarning_unclosed_file

Author: effigies

.git-blame-ignore-revs

@@ -0,0 +1,12 @@
+# Thu Dec 29 22:53:17 2022 -0500 - [email protected] - STY: Reduce array().astype() and similar constructs
+bf298113da99079c9c7b5e1690e41879828cd472
+# Thu Dec 29 22:32:46 2022 -0500 - [email protected] - STY: pyupgrade --py37-plus
+4481a4c2640bd4be6e9c468e550d01aae448ab99
+# Fri Dec 30 11:01:19 2022 -0500 - [email protected] - STY: Run vanilla blue
+6b0ddd23b1da1df7ca9ae275673f82bfa20a754c
+# Thu Dec 29 21:46:13 2022 -0500 - [email protected] - STY: Manual, blue-compatible touchups
+263fca9bf6d4ca314a5a322b4824d6f53d0589df
+# Thu Dec 29 21:32:00 2022 -0500 - [email protected] - STY: isort
+0ab2856cac4d4baae7ab3e2f6d58421db55d807f
+# Thu Dec 29 21:30:29 2022 -0500 - [email protected] - STY: blue
+1a8dd302ff85b1136c81d492509b80e7748339f0

.github/workflows/misc.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
         install: ['pip']
-        check: ['style', 'doc']
+        check: ['style', 'doctest']
         pip-flags: ['']
         depends: ['REQUIREMENTS']
     env:

.gitignore

@@ -83,6 +83,7 @@ Thumbs.db
 # Things specific to this project #
 ###################################
 doc/source/reference
+doc/source/generated
 venv/
 .buildbot.patch
 .vscode

Makefile

@@ -78,6 +78,9 @@ distclean: clean
 $(WWW_DIR):
 	if [ ! -d $(WWW_DIR) ]; then mkdir -p $(WWW_DIR); fi
 
+.git-blame-ignore-revs:
+	git log --grep "\[git-blame-ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" \
+		> .git-blame-ignore-revs
 
 #
 # Tests
@@ -288,4 +291,4 @@ rm-orig:
 	# Remove .orig temporary diff files generated by git
 	find . -name "*.orig" -print | grep -v "fsaverage" | xargs rm
 
-.PHONY: orig-src pylint all build
+.PHONY: orig-src pylint all build .git-blame-ignore-revs

doc-requirements.txt

@@ -1,6 +1,7 @@
-# Requirements for building docs
+# Auto-generated by tools/update_requirements.py
 -r requirements.txt
-sphinx<3
+matplotlib >= 1.5.3
 numpydoc
+sphinx ~= 5.3
 texext
-matplotlib >=1.3.1
+tomli; python_version < "3.11"

doc/source/conf.py

@@ -19,10 +19,14 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+from pathlib import Path
 from runpy import run_path
-from configparser import ConfigParser
+
+try:
+    import tomllib
+except ImportError:
+    import tomli as tomllib
 
 # Check for external Sphinx extensions we depend on
 try:
@@ -41,11 +45,6 @@
     raise RuntimeError('Need nibabel on Python PATH; consider "make htmldoc" '
                        'from nibabel root directory')
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.append(os.path.abspath('../sphinxext'))
-
 # -- General configuration ----------------------------------------------------
 
 # We load the nibabel release info into a dict by explicit execution
@@ -56,15 +55,15 @@
     fobj.write(rel['long_description'])
 
 # Load metadata from setup.cfg
-config = ConfigParser()
-config.read(os.path.join('..', '..', 'setup.cfg'))
-metadata = config['metadata']
+with open(Path("../../pyproject.toml"), 'rb') as fobj:
+    pyproject = tomllib.load(fobj)
+authors = pyproject["project"]["authors"][0]
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.doctest',
-              #'sphinx.ext.intersphinx',
+              'sphinx.ext.intersphinx',
               'sphinx.ext.todo',
               'sphinx.ext.mathjax',
               'sphinx.ext.inheritance_diagram',
@@ -74,9 +73,10 @@
               'matplotlib.sphinxext.plot_directive',
               ]
 
-# the following doesn't work with sphinx < 1.0, but will make a separate
-# sphinx-autogen run obsolete in the future
-#autosummary_generate = True
+# Autosummary always wants to use a `generated/` directory.
+# We generate with `make api-stamp`
+# This could change in the future
+autosummary_generate = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -92,7 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = f"2006-2022, {metadata['maintainer']} <{metadata['author_email']}>"
+copyright = f"2006-2022, {authors['name']} <{authors['email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -272,7 +272,7 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/3/': None}
 
 # Config of plot_directive
 plot_include_source = True

doc/source/devel/biaps/biap_0003.rst

@@ -199,8 +199,8 @@ The base level header will usually also have image metadata fields giving
 information about the whole image. A field is an "image metadata field" if it
 is defined at the top level of the header.  For example::
 
->>> hdr = dict(nipy_header_version='1.0',
-...            Manufacturer="SIEMENS")
+      >>> hdr = dict(nipy_header_version='1.0',
+      ...            Manufacturer="SIEMENS")
 
 All image metadata fields are optional.
 
@@ -635,7 +635,7 @@ Use case
 ^^^^^^^^
 
 When doing motion correction on a 4D image, we calculate the required affine
-transformation from |--| say |--| the second image to the first image; the
+transformation from, say, the second image to the first image; the
 third image to the first image; etc. If there are N volumes in the 4D image,
 we would need to store N-1 affine transformations.  If we have registered to
 the mean volume of the volume series instead of one of the volumes in the

doc/source/devel/biaps/biap_0004.rst

@@ -221,6 +221,7 @@ Improving access to varying meta data through the Nifti
 
 Currently, when accessing varying meta data through the `get_meta` method 
 you can only get one value at a time::
+
     >>> echo_times = [nii.get_meta('EchoTime', (0, 0, 0, idx)) 
                       for idx in xrange(data.shape[-1])]
 

doc/source/devel/biaps/biap_0006.rst

@@ -193,7 +193,7 @@ In NIfTI:
 
 We saw above that the MGH format refers to a volume (in our sense) as a
 *frame*.  ECAT has the same usage - a frame is a 3D volume. The fmristat
-software uses frame in the same sense |--| e.g. `line 32 of example.m
+software uses frame in the same sense, e.g., `line 32 of example.m
 <https://github.com/matthew-brett/fmristat/blob/master/fmristat/example.m#L32>`_.
 
 Unfortunately DICOM appears to use "frame" to mean a 2D slice.  For example,

doc/source/devel/devdiscuss.rst

@@ -22,3 +22,7 @@ progress.
     spm_use
     modified_images
     data_pkg_design
+    data_pkg_discuss
+    data_pkg_uses
+    scaling
+    bv_formats

doc/source/devel/image_design.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 ########################
 The nibabel image object
 ########################

doc/source/installing_data.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. _installing-data:
 
 Installing data packages

doc/source/old/ioimplementation.rst

@@ -1,5 +1,7 @@
 .. -*- mode: rst -*-
 
+:orphan:
+
 ##################################################
 Relationship between images and io implementations
 ##################################################

doc/tools/build_modref_templates.py

@@ -83,6 +83,7 @@ def abort(error):
                                         r'\.info.*$',
                                         r'\.pkg_info.*$',
                                         r'\.py3k.*$',
+                                        r'\._version.*$',
                                         ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)

nibabel/__init__.py

@@ -9,8 +9,9 @@
 
 import os
 
-from .pkg_info import __version__
 from .info import long_description as __doc__
+from .pkg_info import __version__
+
 __doc__ += """
 Quickstart
 ==========
@@ -38,32 +39,39 @@
 
 # module imports
 from . import analyze as ana
-from . import spm99analyze as spm99
-from . import spm2analyze as spm2
+from . import ecat, mriutils
 from . import nifti1 as ni1
-from . import ecat
+from . import spm2analyze as spm2
+from . import spm99analyze as spm99
+from . import streamlines, viewers
+
+# isort: split
+
 # object imports
-from .fileholders import FileHolder, FileHolderError
-from .loadsave import load, save
-from .arrayproxy import is_proxy
 from .analyze import AnalyzeHeader, AnalyzeImage
-from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage
-from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
-from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
-from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
-from .minc1 import Minc1Image
-from .minc2 import Minc2Image
+from .arrayproxy import is_proxy
 from .cifti2 import Cifti2Header, Cifti2Image
-from .gifti import GiftiImage
+from .fileholders import FileHolder, FileHolderError
 from .freesurfer import MGHImage
-from .funcs import (squeeze_image, concat_images, four_to_three,
-                    as_closest_canonical)
-from .orientations import (io_orientation, flip_axis, OrientationError,
-                           apply_orientation, aff2axcodes)
+from .funcs import as_closest_canonical, concat_images, four_to_three, squeeze_image
+from .gifti import GiftiImage
 from .imageclasses import all_image_classes
-from . import mriutils
-from . import streamlines
-from . import viewers
+from .loadsave import load, save
+from .minc1 import Minc1Image
+from .minc2 import Minc2Image
+from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
+from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
+from .orientations import (
+    OrientationError,
+    aff2axcodes,
+    apply_orientation,
+    flip_axis,
+    io_orientation,
+)
+from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
+from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage
+
+# isort: split
 
 from .pkg_info import get_pkg_info as _get_pkg_info
 
@@ -72,9 +80,15 @@ def get_info():
     return _get_pkg_info(os.path.dirname(__file__))
 
 
-def test(label=None, verbose=1, extra_argv=None,
-         doctests=False, coverage=False, raise_warnings=None,
-         timer=False):
+def test(
+    label=None,
+    verbose=1,
+    extra_argv=None,
+    doctests=False,
+    coverage=False,
+    raise_warnings=None,
+    timer=False,
+):
     """
     Run tests for nibabel using pytest
 
@@ -107,29 +121,30 @@ def test(label=None, verbose=1, extra_argv=None,
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     import pytest
+
     args = []
 
     if label is not None:
-        raise NotImplementedError("Labels cannot be set at present")
+        raise NotImplementedError('Labels cannot be set at present')
 
     verbose = int(verbose)
     if verbose > 0:
-        args.append("-" + "v" * verbose)
+        args.append('-' + 'v' * verbose)
     elif verbose < 0:
-        args.append("-" + "q" * -verbose)
+        args.append('-' + 'q' * -verbose)
 
     if extra_argv:
         args.extend(extra_argv)
     if doctests:
-        args.append("--doctest-modules")
+        args.append('--doctest-modules')
     if coverage:
-        args.extend(["--cov", "nibabel"])
+        args.extend(['--cov', 'nibabel'])
     if raise_warnings is not None:
-        raise NotImplementedError("Warning filters are not implemented")
+        raise NotImplementedError('Warning filters are not implemented')
     if timer:
-        raise NotImplementedError("Timing is not implemented")
+        raise NotImplementedError('Timing is not implemented')
 
-    args.extend(["--pyargs", "nibabel"])
+    args.extend(['--pyargs', 'nibabel'])
 
     return pytest.main(args=args)
 
@@ -157,9 +172,10 @@ def bench(label=None, verbose=1, extra_argv=None):
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     from pkg_resources import resource_filename
-    config = resource_filename("nibabel", "benchmarks/pytest.benchmark.ini")
+
+    config = resource_filename('nibabel', 'benchmarks/pytest.benchmark.ini')
     args = []
     if extra_argv is not None:
         args.extend(extra_argv)
-    args.extend(["-c", config])
+    args.extend(['-c', config])
     return test(label, verbose, extra_argv=args)