Merge pull request #1078 from nipy/rel/3.2.2

REL: 3.2.2

.github/CODE_OF_CONDUCT.md

@@ -30,15 +30,15 @@ implementation of methods, on finding technical solutions, establishing best pra
 otherwise. We are accepting of all who wish to take part in our activities, fostering an
 environment where anyone can participate and everyone can make a difference.
 
-#### Be collaborative!
+#### Collaborative
 
 Our work will be used by other people, and in turn we will depend on the work of others. When we
 make something for the benefit of others, we are willing to explain to others how it works, so that
 they can build on the work to make it even better. We are willing to provide constructive criticism
 on the work of others and accept criticism of our own work, as the experiences and skill sets of
 other members contribute to the whole of our efforts.
 
-#### Be inquisitive!
+#### Inquisitive
 
 Nobody knows everything! Asking questions early avoids many problems later, so questions are
 encouraged, though they may be directed to the appropriate forum. Those who are asked should be
@@ -51,7 +51,7 @@ efforts of others, keeping in mind that often-times the labor was completed simp
 the community. We are attentive in our communications, whether in person or online, and we are
 tactful when approaching differing views.
 
-#### Be careful in the words that you choose:
+#### Careful in the words we choose
 
 We value courtesy, kindness and inclusiveness in all our interactions. Therefore, we take
 responsibility for our own speech. In particular, we avoid:
@@ -66,7 +66,7 @@ responsibility for our own speech. In particular, we avoid:
  * Repeated harassment of others. In general, if someone asks you to stop, then stop.
  * Advocating for, or encouraging, any of the above behaviour.
 
-#### Try to be concise in communication
+#### Concise
 
 Keep in mind that what you write once will be read by many others. Writing a short email means
 people can understand the conversation as efficiently as possible. Even short emails should always

.mailmap

@@ -26,7 +26,8 @@ Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <e
 Cindee Madison <[email protected]> CindeeM <[email protected]>
 Cindee Madison <[email protected]> cindeem <[email protected]>
 Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
-Dimitri Papadopoulos Orfanos <[email protected]> Dimitri Papadopoulos <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
 Eric Larson <[email protected]> Eric89GXL <[email protected]>
 Eric Larson <[email protected]> larsoner <[email protected]>
 Fernando Pérez-García <[email protected]> Fernando <[email protected]>

.zenodo.json

@@ -141,10 +141,10 @@
       "orcid": "0000-0001-9791-4404"
     },
     {
-      "name": "Lepp\u00e4kangas, Jaakko"
+      "name": "S\u00f3lon, Anibal"
     },
     {
-      "name": "S\u00f3lon, Anibal"
+      "name": "Lepp\u00e4kangas, Jaakko"
     },
     {
       "name": "van den Bosch, Jasper J.F."
@@ -228,6 +228,11 @@
     {
       "name": "St-Jean, Samuel"
     },
+    {
+      "affiliation": "CEA",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990"
+    },
     {
       "name": "Panfilov, Egor",
       "orcid": "0000-0002-2500-6375"
@@ -286,6 +291,9 @@
     {
       "name": "Baratz, Zvi"
     },
+    {
+      "name": "Van, Andrew"
+    },
     {
       "affiliation": "Hospital for Sick Children",
       "name": "Darwin, Benjamin C"
@@ -298,11 +306,6 @@
     {
       "name": "Gauthier, Carl"
     },
-    {
-      "affiliation": "CEA",
-      "name": "Papadopoulos Orfanos, Dimitri",
-      "orcid": "0000-0002-1242-8990"
-    },
     {
       "name": "Solovey, Igor"
     },
@@ -326,6 +329,11 @@
       "affiliation": "National Technical University of Athens, Greece",
       "name": "Raktivan, Konstantinos"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "name": "Cal\u00e1bkov\u00e1, Mark\u00e9ta"
     },
@@ -346,6 +354,9 @@
     {
       "name": "Roos, Thomas"
     },
+    {
+      "name": "Hrn\u010diar, Tom\u00e1\u0161"
+    },
     {
       "affiliation": "National Institute of Mental Health and Neuro-Sciences, India",
       "name": "Reddam, Venkateswara Reddy",

Changelog

@@ -25,6 +25,36 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+3.2.2 (Monday 7 February 2022)
+=================================
+
+Bug fix release in the 3.2.x series.
+
+Bug fixes
+---------
+* Reshape CIFTI-2 affines to 4x4 when encoded as row-major sequence (pr/1059)
+  (Andrew Van, reviewed by CM)
+* Suggest nibabel.save() on calls to deprecated giftiio.write() (pr/1055)
+  (Anibal Solon, reviewed by CM)
+* Various bugs and style issues detected by LGTM (pr/1043, pr/1048)
+  (Dimitri Papadopoulos, reviewed by CM)
+* Resolve unclosed file warning in GiftiImage (pr/1038) (Lea Waller, reviewed by CM)
+* Fix typos preventing deprecation warnings from being raised (pr/991)
+  (Jonathan Daniel, reviewed by MB)
+* Work around numpy SystemError to maintain expected error types (pr/1051) (CM)
+* Use more constrained mock when testing optpkg (pr/983) (CM, reviewed by YOH)
+
+Maintenance
+-----------
+* Add setuptools requirement to match usage (pr/1009)
+  (Tomáš Hrnčiar, reviewed by CM)
+* Fix grammar of headings in CoC (pr/996) (MB, reviewed by CM, Ariel Rokem)
+* Set minimum pydicom to 1.0.0 (pr/1050) (CM)
+* Submit coverage to codecov via pinned PyPI package (pr/1008) (CM)
+* Upgrade versioneer to 0.19 (pr/967) (CM)
+* Migrate to GitHub actions (pr/972) (CM, reviewed by Serge Koudoro)
+
+
 3.2.1 (Saturday 28 November 2020)
 =================================
 

doc/source/conf.py

@@ -92,7 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = f"2006-2020, {metadata['maintainer']} <{metadata['author_email']}>"
+copyright = f"2006-2022, {metadata['maintainer']} <{metadata['author_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

doc/source/index.rst

@@ -114,6 +114,9 @@ contributed code and discussion (in rough order of appearance):
 * Markéta Calábková
 * Carl Gauthier
 * Julian Klug
+* Lea Waller
+* Tomáš Hrnčiar
+* Andrew Van
 
 License reprise
 ===============

min-requirements.txt

@@ -1,3 +1,4 @@
 # Auto-generated by tools/update_requirements.py
 numpy ==1.14
 packaging ==14.3
+setuptools

nibabel/cifti2/cifti2.py

@@ -1156,8 +1156,7 @@ def get_index_map(self, index):
             a2md = self._get_indices_from_mim(v)
             if index in a2md:
                 return v
-        else:
-            raise Cifti2HeaderError("Index not mapped")
+        raise Cifti2HeaderError("Index not mapped")
 
     def _validate_new_mim(self, value):
         if value.applies_to_matrix_dimension is None:

nibabel/cifti2/parse_cifti2.py

@@ -538,7 +538,8 @@ def flush_chardata(self):
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             transform = self.struct_state[-1]
-            transform.matrix = np.loadtxt(c, dtype=np.float64)
+            matrix = np.loadtxt(c, dtype=np.float64)
+            transform.matrix = matrix.reshape(4, 4)
             c.close()
 
         elif self.write_to == 'Label':

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -41,6 +41,11 @@
 datafiles = [DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5, DATA_FILE6]
 
 
+def test_space_separated_affine():
+    img = ci.Cifti2Image.from_filename(
+        pjoin(NIBABEL_TEST_DATA, "row_major.dconn.nii"))
+
+
 def test_read_nifti2():
     # Error trying to read a CIFTI-2 image from a NIfTI2-only image.
     filemap = ci.Cifti2Image.make_file_map()

nibabel/cmdline/dicomfs.py

@@ -71,7 +71,7 @@ def get_paths(self):
         for study in dft.get_studies(self.dicom_path, self.followlinks):
             pd = paths.setdefault(study.patient_name_or_uid(), {})
             patient_info = 'patient information\n'
-            patient_info = f'name: {study.patient_name}\n'
+            patient_info += f'name: {study.patient_name}\n'
             patient_info += f'ID: {study.patient_id}\n'
             patient_info += f'birth date: {study.patient_birth_date}\n'
             patient_info += f'sex: {study.patient_sex}\n'
@@ -172,9 +172,9 @@ def open(self, path, flags):
                 elif isinstance(matched_path, tuple):
                     self.fhs[i] = matched_path[1]()
                 else:
-                    raise -errno.EFTYPE
+                    return -errno.EFTYPE
                 return FileHandle(i)
-        raise -errno.ENFILE
+        return -errno.ENFILE
 
     # not done
     def read(self, path, size, offset, fh):

nibabel/filebasedimages.py

@@ -202,7 +202,7 @@ def __init__(self, header=None, extra=None, file_map=None):
     def header(self):
         return self._header
 
-    def __getitem__(self):
+    def __getitem__(self, key):
         """ No slicing or dictionary interface for images
         """
         raise TypeError("Cannot slice image objects.")

nibabel/gifti/gifti.py

@@ -43,7 +43,7 @@ def from_dict(klass, data_dict):
 
     @deprecate_with_version(
         'get_metadata method deprecated. '
-        "Use the metadata property instead."
+        "Use the metadata property instead.",
         '2.1', '4.0')
     def get_metadata(self):
         return self.metadata
@@ -155,7 +155,7 @@ def __init__(self, key=0, red=None, green=None, blue=None, alpha=None):
 
     @deprecate_with_version(
         'get_rgba method deprecated. '
-        "Use the rgba property instead."
+        "Use the rgba property instead.",
         '2.1', '4.0')
     def get_rgba(self):
         return self.rgba
@@ -523,7 +523,7 @@ def print_summary(self):
 
     @deprecate_with_version(
         'get_metadata method deprecated. '
-        "Use the metadata property instead."
+        "Use the metadata property instead.",
         '2.1', '4.0')
     def get_metadata(self):
         return self.meta.metadata
@@ -877,8 +877,8 @@ def to_file_map(self, file_map=None):
         """
         if file_map is None:
             file_map = self.file_map
-        f = file_map['image'].get_prepare_fileobj('wb')
-        f.write(self.to_xml())
+        with file_map['image'].get_prepare_fileobj('wb') as f:
+            f.write(self.to_xml())
 
     @classmethod
     def from_file_map(klass, file_map, buffer_size=35000000):

nibabel/gifti/giftiio.py

@@ -34,7 +34,7 @@ def read(filename):
 
 
 @deprecate_with_version('giftiio.write function deprecated. '
-                        "Use nibabel.load() instead.",
+                        "Use nibabel.save() instead.",
                         '2.1', '4.0')
 def write(image, filename):
     """ Save the current image to a new file

nibabel/gifti/tests/test_gifti.py

@@ -6,6 +6,8 @@
 
 import numpy as np
 
+from nibabel.tmpdirs import InTemporaryDirectory
+
 from ... import load
 from .. import (GiftiImage, GiftiDataArray, GiftiLabel,
                 GiftiLabelTable, GiftiMetaData, GiftiNVPairs,
@@ -40,7 +42,7 @@ def test_agg_data():
 
     assert_array_equal(surf_gii_img.agg_data('pointset'), point_data)
     assert_array_equal(surf_gii_img.agg_data('triangle'), triangle_data)
-    assert_array_equal(func_gii_img.agg_data('time series'), func_data) 
+    assert_array_equal(func_gii_img.agg_data('time series'), func_data)
     assert_array_equal(shape_gii_img.agg_data('shape'), shape_data)
 
     assert surf_gii_img.agg_data('time series') == ()
@@ -443,3 +445,11 @@ def test_darray_dtype_coercion_failures():
         da_copy = gii_copy.darrays[0]
         assert np.dtype(da_copy.data.dtype) == np.dtype(darray_dtype)
         assert_array_equal(da_copy.data, da.data)
+
+
+def test_gifti_file_close():
+    gii = load(test_data('gifti', 'ascii.gii'))
+    with pytest.WarningsRecorder() as record:
+        with InTemporaryDirectory():
+            gii.to_filename('test.gii')
+    assert not any(isinstance(r.message, ResourceWarning) for r in record.list)

nibabel/pydicom_compat.py

@@ -23,7 +23,6 @@
 # Module has (apparently) unused imports; stop flake8 complaining
 # flake8: noqa
 
-import numpy as np
 from .deprecated import deprecate_with_version
 
 have_dicom = True

nibabel/volumeutils.py

@@ -1551,7 +1551,7 @@ class BinOpener(Opener):
     __doc__ = Opener.__doc__
 
     @deprecate_with_version('BinOpener class deprecated. '
-                            "Please use Opener class instead."
+                            "Please use Opener class instead.",
                             '2.1', '4.0')
     def __init__(self, *args, **kwargs):
         return super(BinOpener, self).__init__(*args, **kwargs)

nisext/py3builder.py

@@ -1,9 +1,6 @@
 """ distutils utilities for porting to python 3 within 2-compatible tree """
 
 
-import sys
-import re
-
 try:
     from distutils.command.build_py import build_py_2to3
 except ImportError:

requirements.txt

@@ -1,3 +1,4 @@
 # Auto-generated by tools/update_requirements.py
 numpy >=1.14
 packaging >=14.3
+setuptools

setup.cfg

@@ -32,6 +32,7 @@ python_requires = >=3.6
 install_requires =
     numpy >=1.14
     packaging >=14.3
+    setuptools
 zip_safe = False
 packages = find:
 
@@ -58,6 +59,7 @@ style =
 test =
     coverage
     pytest !=5.3.4
+    pytest <7 ; python_version == "3.6"
     pytest-cov
     pytest-doctestplus !=0.9.0
 all =

setup.py

@@ -10,7 +10,6 @@
 """Build helper."""
 
 import sys
-import os
 
 from setuptools import setup
 import versioneer

tools/make_tarball.py

@@ -4,8 +4,6 @@
 
 import commands
 import os
-import sys
-import shutil
 
 from  toollib import *
 

tools/mpkg_wrapper.py

@@ -16,8 +16,6 @@
 __docformat__ = 'restructuredtext'
 
 import sys
-import setuptools
-import bdist_mpkg
 
 def main():
     del sys.argv[0]