Merge pull request #1078 from nipy/rel/3.2.2

REL: 3.2.2

Author: effigies

.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()