[med-svn] [Git][med-team/nibabel][master] 7 commits: Update copyright years for recent contributors
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 9 13:03:29 BST 2026
Andreas Tille pushed to branch master at Debian Med / nibabel
Commits:
1bcf83f1 by Andreas Tille at 2026-06-05T12:44:46+00:00
Update copyright years for recent contributors
- - - - -
64aff5ba by Andreas Tille at 2026-06-05T12:44:48+00:00
Apply consistent formatting to packaging files
Run `debputy reformat --style black` and `wrap-and-sort -vast` to enforce
uniform deb822 formatting with one item per line. This makes future
changes to dependencies and other lists easier to track in git diffs.
No functional changes.
- - - - -
7a493f82 by Andreas Tille at 2026-06-05T12:44:48+00:00
Fix issues found by Shellcheck
Apply all fixes suggested by Shellcheck that can be applied automatically in
a way that is unlikely to change functionality, only make the syntax more
robust to protect from unintentional use and side effect.
- - - - -
bf9833a1 by Andreas Tille at 2026-06-05T12:44:49+00:00
Fix spelling
Fix minor typos and spelling mistakes that can be automatically corrected.
No functional changes.
- - - - -
d55b7510 by Andreas Tille at 2026-09-09T13:43:42+02:00
Fix test failures with Python 3.15 Closes: #1146887
- - - - -
fe93ba4c by Andreas Tille at 2026-09-09T13:44:33+02:00
debhelper-compat = 14
- - - - -
a6b91363 by Andreas Tille at 2026-09-09T13:52:06+02:00
Upload to unstable
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/createmanpages
- + debian/patches/python3.15.patch
- debian/patches/series
- debian/python3-nibabel.install
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+nibabel (5.4.2-5) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Maximiliano Curia ]
+ * Fix test failures with Python 3.15
+ Closes: #1146887
+
+ [ Andreas Tille ]
+ * debhelper-compat = 14
+
+ -- Andreas Tille <tille at debian.org> Wed, 09 Sep 2026 13:44:37 +0200
+
nibabel (5.4.2-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,24 +7,24 @@ Uploaders:
Étienne Mollier <emollier at debian.org>,
Section: python
Build-Depends:
- debhelper-compat (= 13),
+ debhelper-compat (= 14),
dh-sequence-python3,
- pybuild-plugin-pyproject,
fuse3,
+ help2man,
+ libjs-mathjax,
+ pybuild-plugin-pyproject,
python3-all,
python3-hatch-vcs,
python3-hatchling,
+ python3-matplotlib,
python3-numpy,
+ python3-numpydoc,
+ python3-pytest <!nocheck>,
+ python3-pytest-httpserver <!nocheck>,
python3-scipy,
python3-setuptools,
- help2man,
python3-sphinx,
- python3-matplotlib,
python3-texext,
- libjs-mathjax,
- python3-numpydoc,
- python3-pytest <!nocheck>,
- python3-pytest-httpserver <!nocheck>,
Vcs-Browser: https://salsa.debian.org/med-team/nibabel
Vcs-Git: https://salsa.debian.org/med-team/nibabel.git
Homepage: https://nipy.org/nibabel/
@@ -32,13 +32,13 @@ Homepage: https://nipy.org/nibabel/
Package: python3-nibabel
Architecture: all
Depends:
- ${misc:Depends},
- ${python3:Depends},
python3-numpy,
python3-scipy,
+ ${misc:Depends},
+ ${python3:Depends},
Recommends:
- python3-pydicom,
fuse3,
+ python3-pydicom,
Suggests:
python-nibabel-doc,
Description: Python3 bindings to various neuroimaging data formats
@@ -53,9 +53,9 @@ Architecture: all
Multi-Arch: foreign
Section: doc
Depends:
- ${misc:Depends},
libjs-jquery,
libjs-mathjax,
+ ${misc:Depends},
Description: documentation for NiBabel
NiBabel provides read and write access to some common medical and
neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI,
=====================================
debian/copyright
=====================================
@@ -18,8 +18,9 @@ License: BSD-3
Files: debian/*
-Copyright: 2006-2010, Michael Hanke <michael.hanke at gmail.com>
- 2011-, Yaroslav Halchenko <debian at onerussian.com>
+Copyright:
+ 2026 Andreas Tille <tille at debian.org>
+ 2026 Étienne Mollier <emollier at debian.org>
License: Expat
=====================================
debian/createmanpages
=====================================
@@ -1,13 +1,13 @@
#!/bin/sh
MANDIR=debian
-mkdir -p $MANDIR
+mkdir -p "${MANDIR}"
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
-PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+VERSION=$(dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//')
+NAME=$(grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1)
+PROGNAME=$(grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1)
AUTHOR=".SH AUTHOR\n \
-This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+This manpage was written by ${DEBFULLNAME} for the Debian distribution and\n \
can be used for any other usage of the program.\
"
@@ -15,11 +15,11 @@ can be used for any other usage of the program.\
# different from package short description change this here
progname=nib-conform
help2man --no-info --no-discard-stderr --help-option="-h" \
- --name="$NAME" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+ --name="${NAME}" \
+ --version-string="${VERSION}" "${progname}" > "${MANDIR}"/"${progname}".1
+echo "${AUTHOR}" >> "${MANDIR}"/"${progname}".1
-echo "$MANDIR/*.1" > debian/manpages
+echo "${MANDIR}/*.1" > debian/manpages
cat <<EOT
Please enhance the help2man output.
@@ -31,11 +31,11 @@ EOT
# different from package short description change this here
progname=nib-diff
help2man --no-info --no-discard-stderr --help-option="-h" \
- --name="$NAME" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+ --name="${NAME}" \
+ --version-string="${VERSION}" "${progname}" > "${MANDIR}"/"${progname}".1
+echo "${AUTHOR}" >> "${MANDIR}"/"${progname}".1
-echo "$MANDIR/*.1" > debian/manpages
+echo "${MANDIR}/*.1" > debian/manpages
cat <<EOT
Please enhance the help2man output.
@@ -47,11 +47,11 @@ EOT
# different from package short description change this here
progname=nib-tck2trk
help2man --no-info --no-discard-stderr --help-option="-h" \
- --name="$NAME" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+ --name="${NAME}" \
+ --version-string="${VERSION}" "${progname}" > "${MANDIR}"/"${progname}".1
+echo "${AUTHOR}" >> "${MANDIR}"/"${progname}".1
-echo "$MANDIR/*.1" > debian/manpages
+echo "${MANDIR}/*.1" > debian/manpages
cat <<EOT
Please enhance the help2man output.
@@ -63,11 +63,11 @@ EOT
# different from package short description change this here
progname=nib-trk2tck
help2man --no-info --no-discard-stderr --help-option="-h" \
- --name="$NAME" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+ --name="${NAME}" \
+ --version-string="${VERSION}" "${progname}" > "${MANDIR}"/"${progname}".1
+echo "${AUTHOR}" >> "${MANDIR}"/"${progname}".1
-echo "$MANDIR/*.1" > debian/manpages
+echo "${MANDIR}/*.1" > debian/manpages
cat <<EOT
Please enhance the help2man output.
=====================================
debian/patches/python3.15.patch
=====================================
@@ -0,0 +1,47 @@
+Description: Fix test failures with Python 3.15
+ In Python 3.15, gzip.GzipFile changed its default compresslevel from 9 to 6.
+ Allow DeterministicGzipFile to inherit the default compresslevel from GzipFile
+ when unspecified instead of hardcoding 9.
+Author: Maximiliano Curia <maxy at debian.org>
+Bug-Debian: https://bugs.debian.org/1146887
+Forwarded: no
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+Index: nibabel/nibabel/_compression.py
+===================================================================
+--- nibabel.orig/nibabel/_compression.py
++++ nibabel/nibabel/_compression.py
+@@ -82,7 +82,7 @@ class DeterministicGzipFile(gzip.GzipFil
+ self,
+ filename: str | None = None,
+ mode: Mode | None = None,
+- compresslevel: int = 9,
++ compresslevel: int | None = None,
+ fileobj: io.FileIO | None = None,
+ mtime: int = 0,
+ ):
+@@ -99,19 +99,22 @@ class DeterministicGzipFile(gzip.GzipFil
+ raise TypeError('Must define either fileobj or filename')
+ # Cast because GzipFile.myfileobj has type io.FileIO while open returns ty.IO
+ fileobj = self.myfileobj = ty.cast('io.FileIO', open(filename, modestr))
++ kwargs = {}
++ if compresslevel is not None:
++ kwargs['compresslevel'] = compresslevel
+ super().__init__(
+ filename='',
+ mode=modestr,
+- compresslevel=compresslevel,
+ fileobj=fileobj,
+ mtime=mtime,
++ **kwargs,
+ )
+
+
+ def gzip_open(
+ filename: str,
+ mode: Mode = 'rb',
+- compresslevel: int = 9,
++ compresslevel: int | None = None,
+ mtime: int = 0,
+ keep_open: bool = False,
+ ) -> gzip.GzipFile:
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ skip-test-removalschedule.patch
skip-armel-test-nan2zero.patch
python3.14.patch
ignore_ordering_failure_in_test_for_i386.patch
+python3.15.patch
=====================================
debian/python3-nibabel.install
=====================================
@@ -1,2 +1,2 @@
-usr/lib/python3*
usr/bin
+usr/lib/python3*
=====================================
debian/rules
=====================================
@@ -34,7 +34,7 @@ endif
execute_after_dh_auto_install:
find $(NIBABEL_MODULE_DIR) -type f -name .gitignore -delete
-## immediately useable documentation
+## immediately usable documentation
## and exemplar data (they are small excerpts anyway)
COMPRESS_EXCLUDE_EXTS := .py .html .css .jpg .txt .js .json .rtc .par .bin
override_dh_compress:
=====================================
debian/tests/control
=====================================
@@ -1,8 +1,11 @@
-Tests: run-unit-test
-Depends: @,
- python3-all,
- python3-pytest,
- python3-numpy,
- python3-scipy,
- python3-pytest-httpserver
-Restrictions: allow-stderr
+Tests:
+ run-unit-test,
+Depends:
+ python3-all,
+ python3-numpy,
+ python3-pytest,
+ python3-pytest-httpserver,
+ python3-scipy,
+ @,
+Restrictions:
+ allow-stderr,
=====================================
debian/tests/run-unit-test
=====================================
@@ -9,13 +9,13 @@ set -efu
SKIP_TEST="not nipype.interfaces.io.BIDSDataGrabber"
arch=$(dpkg-architecture -qDEB_HOST_ARCH)
# skip tests
-if [ "$arch" = "s390x" ]; then
- SKIP_TEST=$SKIP_TEST" and not test_legacy_underscore_content"
+if [[ "${arch}" = "s390x" ]]; then
+ SKIP_TEST=${SKIP_TEST}" and not test_legacy_underscore_content"
fi
for py in $(py3versions --supported)
do
- $py -m pytest -k "$SKIP_TEST" -v nibabel
+ ${py} -m pytest -k "${SKIP_TEST}" -v nibabel
done
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/compare/71b82bdcce6e08af24b3fe30315b8ee2bc3bcfc6...a6b913632b31c9567e2b0bae8ed98193216d0429
--
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/compare/71b82bdcce6e08af24b3fe30315b8ee2bc3bcfc6...a6b913632b31c9567e2b0bae8ed98193216d0429
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