[med-svn] [Git][med-team/pybigwig][master] 6 commits: Let wrap-and-sort tidy files
Stuart Prescott (@stuart)
gitlab at salsa.debian.org
Sun Dec 14 02:38:26 GMT 2025
Stuart Prescott pushed to branch master at Debian Med / pybigwig
Commits:
ccb0690b by Stuart Prescott at 2025-12-14T11:40:33+11:00
Let wrap-and-sort tidy files
- - - - -
ccfb83d8 by Stuart Prescott at 2025-12-14T11:42:13+11:00
Ensure python package picks up fixed libbigwig0 in testing
- - - - -
ea34c1ac by Stuart Prescott at 2025-12-14T13:12:14+11:00
Let quilt reformet gcc-14.patch to stop complaints
- - - - -
3199b011 by Stuart Prescott at 2025-12-14T13:12:14+11:00
Fix build-time and autopkgtest tests to actually run
build-time was using unittest discover which was not finding any tests.
autopkgtests was running test.py rather than running the tests in it so nothing
was actually being run
- - - - -
98f447cc by Stuart Prescott at 2025-12-14T13:12:14+11:00
Add patch to include test artifacts in the package
test.py is present but the data files it needs are not
- - - - -
38cb13f4 by Stuart Prescott at 2025-12-14T13:36:27+11:00
Add changelog for upload
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/gcc-14.patch
- + debian/patches/include-datafiles.patch
- debian/patches/series
- debian/rules
- debian/tests/control
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+pybigwig (0.3.23+dfsg-3) unstable; urgency=medium
+
+ * Team upload.
+ * Add versioned dependency on fixed libbigwig0 to ensure the fixed library
+ is used for testing.
+ * Fix build-time test discovery so that tests are actually run; skip tests
+ that need internet access.
+ * Fix autopkgtest tests to actually run the tests.
+ * Add patch to include data files needed for the tests in the package
+ alongside the test.py script.
+
+ -- Stuart Prescott <stuart at debian.org> Sun, 14 Dec 2025 13:11:52 +1100
+
pybigwig (0.3.23+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,17 +1,20 @@
Source: pybigwig
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Diane Trout <diane at ghic.org>
-Build-Depends: debhelper-compat (= 13),
- dh-sequence-python3,
- pybuild-plugin-pyproject,
- libcurl4-gnutls-dev,
- zlib1g-dev,
- libbigwig-dev (>= 0.4.8+dfsg-3~),
- python3-all,
- python3-all-dev,
- python3-numpy,
- python3-setuptools
+Uploaders:
+ Diane Trout <diane at ghic.org>,
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ libbigwig-dev (>= 0.4.8+dfsg-3~),
+ libcurl4-gnutls-dev,
+ pybuild-plugin-pyproject,
+ python3-all,
+ python3-all-dev,
+ python3-numpy,
+ python3-pytest,
+ python3-setuptools,
+ zlib1g-dev,
Standards-Version: 4.7.2
Vcs-Git: https://salsa.debian.org/med-team/pybigwig.git
Vcs-Browser: https://salsa.debian.org/med-team/pybigwig
@@ -21,7 +24,11 @@ Rules-Requires-Root: no
Package: python3-pybigwig
Architecture: any
-Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}
+Depends:
+ libbigwig0 (>= 0.4.8+dfsg-3~),
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
Description: Python 3 module for quick access to bigBed and bigWig files
This is a Python extension, written in C, for quick access to bigBed files,
and access to and creation of bigWig files.
=====================================
debian/copyright
=====================================
@@ -33,4 +33,3 @@ License: MIT
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -8,8 +8,8 @@ Forwarded: https://github.com/deeptools/pyBigWig/pull/151
Last-Update: 2024-07-22
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- pybigwig.orig/pyBigWig.c
-+++ pybigwig/pyBigWig.c
+--- a/pyBigWig.c
++++ b/pyBigWig.c
@@ -894,7 +894,7 @@
}
=====================================
debian/patches/include-datafiles.patch
=====================================
@@ -0,0 +1,12 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -38,6 +38,9 @@
+ include-package-data = true
+ packages = ["pyBigWigTest"]
+
++[tool.setuptools.package-data]
++"pyBigWigTest" = ["test.*"]
++
+ # Enable version inference from scm
+ [tool.setuptools_scm]
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
prepareForExternalLibBigWig.patch
gcc-14.patch
+include-datafiles.patch
=====================================
debian/rules
=====================================
@@ -6,6 +6,10 @@ include /usr/share/dpkg/buildflags.mk
#export DH_VERBOSE=1
export PYBUILD_NAME=pybigwig
+export PYBUILD_TEST_ARGS = \
+ -k 'not TestRemote and not testNumpyValues' \
+ -v pyBigWigTest/test.py
+
%:
dh $@ --buildsystem=pybuild
=====================================
debian/tests/control
=====================================
@@ -1,7 +1,10 @@
Test-Command: set -e
; for py in $(py3versions -r 2>/dev/null)
- ; do cd pyBigWigTest
- ; $py test.py
- ; cd ..
+ ; do $py -m pytest -v pyBigWigTest/test.py
; done
-Depends: python3-pybigwig, python3-all
+Depends:
+ python3-all,
+ python3-pybigwig,
+ python3-pytest,
+Restrictions:
+ needs-internet,
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/73671b598354859954477ff6d573edc335a3e79f...38cb13f479755aa60c5d5587052a8dca7dab0996
--
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/73671b598354859954477ff6d573edc335a3e79f...38cb13f479755aa60c5d5587052a8dca7dab0996
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