[med-svn] [Git][med-team/pybigwig][master] 6 commits: New upstream version 0.3.25+dfsg
Diane Trout (@diane)
gitlab at salsa.debian.org
Thu Jan 15 05:10:52 GMT 2026
Diane Trout pushed to branch master at Debian Med / pybigwig
Commits:
94f5cdf5 by Diane Trout at 2026-01-14T20:31:43-08:00
New upstream version 0.3.25+dfsg
- - - - -
cbc2c8f1 by Diane Trout at 2026-01-14T20:31:43-08:00
Update upstream source from tag 'upstream/0.3.25+dfsg'
Update to upstream version '0.3.25+dfsg'
with Debian dir b5b08dc0caffb0e3f978617893d02944da93666c
- - - - -
4925d6eb by Diane Trout at 2026-01-14T20:33:09-08:00
New upstream release
- - - - -
853466ff by Diane Trout at 2026-01-14T20:33:22-08:00
Update homepage url
- - - - -
380171b8 by Diane Trout at 2026-01-14T21:10:00-08:00
Remove gcc-14.patch, upstream found another solution.
- - - - -
b68536e3 by Diane Trout at 2026-01-14T21:10:19-08:00
Add python3-numpy-dev to Build-Depends
- - - - -
8 changed files:
- .github/workflows/build.yml
- debian/changelog
- debian/control
- − debian/patches/gcc-14.patch
- debian/patches/series
- pyBigWig.c
- pyBigWig.h
- pyproject.toml
Changes:
=====================================
.github/workflows/build.yml
=====================================
@@ -45,7 +45,7 @@ jobs:
- name: Build sdist
run: |
python -m build --sdist
- - uses: actions/upload-artifact at v3
+ - uses: actions/upload-artifact at v6
with:
name: pyBigWig-build
path: |
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+pybigwig (0.3.25+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Update homepage url
+ * Remove gcc-14.patch, upstream found another solution.
+ * Add python3-numpy-dev to Build-Depends
+
+ -- Diane Trout <diane at ghic.org> Wed, 14 Jan 2026 20:32:14 -0800
+
pybigwig (0.3.23+dfsg-5) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Build-Depends:
python3-all,
python3-all-dev,
python3-numpy,
+ python3-numpy-dev,
python3-pytest,
python3-setuptools,
zlib1g-dev,
@@ -19,7 +20,7 @@ Standards-Version: 4.7.2
Vcs-Git: https://salsa.debian.org/med-team/pybigwig.git
Vcs-Browser: https://salsa.debian.org/med-team/pybigwig
Section: science
-Homepage: https://github.com/dpryan79/pyBigWig
+Homepage: https://github.com/deeptools/pyBigWig
Rules-Requires-Root: no
Package: python3-pybigwig
=====================================
debian/patches/gcc-14.patch deleted
=====================================
@@ -1,30 +0,0 @@
-Description: cast string arrays to constant pointers.
- This fixes build failure with gcc 14, since incompatible pointer types
- are now fatal.
-
-Author: Étienne Mollier <emollier at debian.org>
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075407
-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/
---- a/pyBigWig.c
-+++ b/pyBigWig.c
-@@ -894,7 +894,7 @@
- }
-
- //Create the chromosome list
-- bw->cl = bwCreateChromList(chroms, lengths, n);
-+ bw->cl = bwCreateChromList((const char * const*)chroms, lengths, n);
- if(!bw->cl) {
- PyErr_SetString(PyExc_RuntimeError, "Received an error in bwCreateChromList");
- goto error;
-@@ -1248,7 +1248,7 @@
- if(PyErr_Occurred()) goto error;
- }
-
-- rv = bwAddIntervals(bw, cchroms, ustarts, uends, fvalues, n);
-+ rv = bwAddIntervals(bw, (const char * const*)cchroms, ustarts, uends, fvalues, n);
- if(!rv) {
- self->lastTid = bwGetTid(bw, cchroms[n-1]);
- self->lastStart = uends[n-1];
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
prepareForExternalLibBigWig.patch
-gcc-14.patch
include-datafiles.patch
=====================================
pyBigWig.c
=====================================
@@ -612,7 +612,8 @@ static PyObject *pyBwGetValues(pyBigWigFile_t *self, PyObject *args) {
if(!hasEntries(self->bw)) {
#ifdef WITHNUMPY
if(outputNumpy == Py_True) {
- return PyArray_SimpleNew(0, NULL, NPY_FLOAT);
+ const npy_intp arr[1] = {0};
+ return PyArray_SimpleNew(1, arr, NPY_FLOAT);
} else {
#endif
return PyList_New(0);
@@ -894,7 +895,7 @@ PyObject *pyBwAddHeader(pyBigWigFile_t *self, PyObject *args, PyObject *kwds) {
}
//Create the chromosome list
- bw->cl = bwCreateChromList(chroms, lengths, n);
+ bw->cl = bwCreateChromList((const char* const*) chroms, lengths, n);
if(!bw->cl) {
PyErr_SetString(PyExc_RuntimeError, "Received an error in bwCreateChromList");
goto error;
@@ -1248,7 +1249,7 @@ int PyAddIntervals(pyBigWigFile_t *self, PyObject *chroms, PyObject *starts, PyO
if(PyErr_Occurred()) goto error;
}
- rv = bwAddIntervals(bw, cchroms, ustarts, uends, fvalues, n);
+ rv = bwAddIntervals(bw, (const char * const*) cchroms, ustarts, uends, fvalues, n);
if(!rv) {
self->lastTid = bwGetTid(bw, cchroms[n-1]);
self->lastStart = uends[n-1];
=====================================
pyBigWig.h
=====================================
@@ -2,7 +2,7 @@
#include <structmember.h>
#include "bigWig.h"
-#define pyBigWigVersion "0.3.23"
+#define pyBigWigVersion "0.3.25"
typedef struct {
PyObject_HEAD
=====================================
pyproject.toml
=====================================
@@ -20,7 +20,7 @@ classifiers = [
description = "A package for accessing bigWig files using libBigWig"
keywords = ["bioinformatics", "bigWig", "bigBed"]
name = "pyBigWig"
-version = "0.3.23"
+version = "0.3.25"
readme = "README.md"
requires-python = ">=3.9"
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/462ef3efda727f1d5a728adf1033aa849c153f62...b68536e3ad1836eda3cbc912f9f21b5fe5c82d29
--
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/462ef3efda727f1d5a728adf1033aa849c153f62...b68536e3ad1836eda3cbc912f9f21b5fe5c82d29
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