Merge remote-tracking branch 'upstream/master' into rel/23.2.0

Author: effigies

.github/workflows/pre-release.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
         install: ['pip']
         check: ['tests']
         pip-flags: ['PRE_PIP_FLAGS']

.github/workflows/stable.yml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
         install: ['pip']
         check: ['tests']
         pip-flags: ['']

docker/files/freesurfer7.3.2-exclude.txt

@@ -766,8 +766,6 @@ freesurfer/lib/tktools
 freesurfer/lib/vtk
 freesurfer/matlab
 freesurfer/mni-1.4
-freesurfer/mni/bin/autocrop
-freesurfer/mni/bin/check_scale
 freesurfer/mni/bin/correct_field
 freesurfer/mni/bin/crispify
 freesurfer/mni/bin/dcm2mnc
@@ -783,7 +781,6 @@ freesurfer/mni/bin/make_phantom
 freesurfer/mni/bin/make_template
 freesurfer/mni/bin/mincaverage
 freesurfer/mni/bin/mincbbox
-freesurfer/mni/bin/mincblur
 freesurfer/mni/bin/minccalc
 freesurfer/mni/bin/mincchamfer
 freesurfer/mni/bin/mincconcat
@@ -801,7 +798,6 @@ freesurfer/mni/bin/mincmakevector
 freesurfer/mni/bin/mincmath
 freesurfer/mni/bin/minc_modify_header
 freesurfer/mni/bin/mincpik
-freesurfer/mni/bin/mincresample
 freesurfer/mni/bin/mincreshape
 freesurfer/mni/bin/mincstats
 freesurfer/mni/bin/minctoecat
@@ -827,7 +823,6 @@ freesurfer/mni/bin/sharpen_volume
 freesurfer/mni/bin/spline_smooth
 freesurfer/mni/bin/transformtags
 freesurfer/mni/bin/upet2mnc
-freesurfer/mni/bin/volume_cog
 freesurfer/mni/bin/volume_hist
 freesurfer/mni/bin/volume_stats
 freesurfer/mni/bin/voxeltoworld

docs/_static/OHBM2017-poster.png

@@ -285,7 +285,7 @@ mid-thickness surface mesh::
     func/
       sub-<subject_label>_[specifiers]_space-T1w_desc-aparcaseg_dseg.nii.gz
       sub-<subject_label>_[specifiers]_space-T1w_desc-aseg_dseg.nii.gz
-      sub-<subject_label>_[specifiers]_space-<space_label>_hemi-[LR]_bold.func.gii
+      sub-<subject_label>_[specifiers]_hemi-[LR]_space-<space_label>_bold.func.gii
 
 Surface output spaces include ``fsnative`` (full density subject-specific mesh),
 ``fsaverage`` and the down-sampled meshes ``fsaverage6`` (41k vertices) and
@@ -375,6 +375,8 @@ to perform more advanced denoising or alternative combination strategies.
    slice as reference).
    Alternatively, you could manually adjust the volume onsets (e.g. as mentioned in
    the example above from [0, 2, 4] to [1, 3, 5]) or the event onsets accordingly.
+   In contrast to volume onsets, event onsets need to be shifted *backward* by half a TR,
+   for example, from [5, 10, 15] to [4, 9, 14].
 
    Further information on this issue is found at
    `this blog post (with thanks to Russell Poldrack and Jeanette Mumford)

docs/_static/OHBM2017-poster_thumb.png

@@ -1,24 +1,24 @@
 """
-This script comes from scikit-learn:
+This vendored script comes from scikit-learn:
 https://github.com/scikit-learn/scikit-learn/blob/master/doc/sphinxext/github_link.py
 """
-from operator import attrgetter
 import inspect
-import subprocess
 import os
+import subprocess
 import sys
 from functools import partial
+from operator import attrgetter
 
-REVISION_CMD = 'git rev-parse --short HEAD'
+REVISION_CMD = "git rev-parse --short HEAD"
 
 
 def _get_git_revision():
     try:
         revision = subprocess.check_output(REVISION_CMD.split()).strip()
     except (subprocess.CalledProcessError, OSError):
-        print('Failed to execute git to get revision')
+        print("Failed to execute git to get revision")
         return None
-    return revision.decode('utf-8')
+    return revision.decode("utf-8")
 
 
 def _linkcode_resolve(domain, info, package, url_fmt, revision):
@@ -30,25 +30,26 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     >>> _linkcode_resolve('py', {'module': 'tty',
     ...                          'fullname': 'setraw'},
     ...                   package='tty',
-    ...                   url_fmt='https://hg.python.org/cpython/file/'
+    ...                   url_fmt='http://hg.python.org/cpython/file/'
     ...                           '{revision}/Lib/{package}/{path}#L{lineno}',
     ...                   revision='xxxx')
-    'https://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
+    'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
     """
 
     if revision is None:
         return
-    if domain not in ('py', 'pyx'):
+    if domain not in ("py", "pyx"):
         return
-    if not info.get('module') or not info.get('fullname'):
+    if not info.get("module") or not info.get("fullname"):
         return
 
-    class_name = info['fullname'].split('.')[0]
-    if type(class_name) != str:
-        # Python 2 only
-        class_name = class_name.encode('utf-8')
-    module = __import__(info['module'], fromlist=[class_name])
-    obj = attrgetter(info['fullname'])(module)
+    class_name = info["fullname"].split(".")[0]
+    module = __import__(info["module"], fromlist=[class_name])
+    obj = attrgetter(info["fullname"])(module)
+
+    # Unwrap the object to get the correct source
+    # file in case that is wrapped by a decorator
+    obj = inspect.unwrap(obj)
 
     try:
         fn = inspect.getsourcefile(obj)
@@ -62,14 +63,12 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     if not fn:
         return
 
-    fn = os.path.relpath(fn,
-                         start=os.path.dirname(__import__(package).__file__))
+    fn = os.path.relpath(fn, start=os.path.dirname(__import__(package).__file__))
     try:
         lineno = inspect.getsourcelines(obj)[1]
     except Exception:
-        lineno = ''
-    return url_fmt.format(revision=revision, package=package,
-                          path=fn, lineno=lineno)
+        lineno = ""
+    return url_fmt.format(revision=revision, package=package, path=fn, lineno=lineno)
 
 
 def make_linkcode_resolve(package, url_fmt):
@@ -84,5 +83,6 @@ def make_linkcode_resolve(package, url_fmt):
                                    '{path}#L{lineno}')
     """
     revision = _get_git_revision()
-    return partial(_linkcode_resolve, revision=revision, package=package,
-                   url_fmt=url_fmt)
+    return partial(
+        _linkcode_resolve, revision=revision, package=package, url_fmt=url_fmt
+    )