[med-svn] [Git][med-team/pybigwig][master] 7 commits: New upstream version 0.3.23+dfsg
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Nov 3 15:55:49 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / pybigwig
Commits:
ed57b37b by Étienne Mollier at 2024-11-03T16:39:44+01:00
New upstream version 0.3.23+dfsg
- - - - -
ef135104 by Étienne Mollier at 2024-11-03T16:39:44+01:00
Update upstream source from tag 'upstream/0.3.23+dfsg'
Update to upstream version '0.3.23+dfsg'
with Debian dir 8b718cfcf44bd1670ef4f2efd7a0f5591dd01ac5
- - - - -
84920aa6 by Étienne Mollier at 2024-11-03T16:41:51+01:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
db146ad9 by Étienne Mollier at 2024-11-03T16:45:54+01:00
d/{control,rules}: migrate to dh-sequence-python3.
- - - - -
fa3a37ee by Étienne Mollier at 2024-11-03T16:49:56+01:00
d/control: migrate to pyproject.
- - - - -
285ffe58 by Étienne Mollier at 2024-11-03T16:54:13+01:00
gcc-14.patch: fill missing Forwarded field.
- - - - -
4c818629 by Étienne Mollier at 2024-11-03T16:55:24+01:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- .environmentLinux.yaml
- .github/workflows/build.yml
- .github/workflows/pypi.yml
- debian/changelog
- debian/control
- debian/patches/gcc-14.patch
- debian/rules
- pyBigWig.h
- pyproject.toml
Changes:
=====================================
.environmentLinux.yaml
=====================================
@@ -7,7 +7,7 @@ dependencies:
- gcc_linux-64
- curl
- zlib
- - python 3.8
+ - python = 3.9
- pip
- numpy
- - nose
+ - pytest
\ No newline at end of file
=====================================
.github/workflows/build.yml
=====================================
@@ -1,5 +1,7 @@
name: Test
-on: pull_request
+on:
+ pull_request:
+ push:
jobs:
testLinux:
@@ -14,11 +16,11 @@ jobs:
with:
activate-environment: foo
environment-file: .environmentLinux.yaml
- python-version: 3.8
+ python-version: 3.9
auto-activate-base: false
- run: |
pip install .
- nosetests -sv
+ pytest pyBigWigTest/test.py
test-builds:
runs-on: ubuntu-latest
@@ -30,7 +32,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python at v4
with:
- python-version: '3.7'
+ python-version: '3.9'
- name: Install build prerequisites
run: |
python -m pip install --upgrade build numpy
=====================================
.github/workflows/pypi.yml
=====================================
@@ -11,7 +11,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python at v4
with:
- python-version: '3.7'
+ python-version: '3.9'
- name: Install build prerequisites
if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
run: |
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+pybigwig (0.3.23+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 0.3.23+dfsg
+ * d/control: declare compliance to standards version 4.7.0.
+ * d/{control,rules}: migrate to dh-sequence-python3.
+ * d/control: migrate to pyproject.
+ * gcc-14.patch: fill missing Forwarded field.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 03 Nov 2024 16:55:13 +0100
+
pybigwig (0.3.22+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -3,7 +3,8 @@ 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-python,
+ dh-sequence-python3,
+ pybuild-plugin-pyproject,
libcurl4-gnutls-dev,
zlib1g-dev,
libbigwig-dev,
@@ -11,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-all-dev,
python3-numpy,
python3-setuptools
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Git: https://salsa.debian.org/med-team/pybigwig.git
Vcs-Browser: https://salsa.debian.org/med-team/pybigwig
Section: science
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -4,7 +4,7 @@ Description: cast string arrays to constant pointers.
Author: Étienne Mollier <emollier at debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075407
-Forwarded:
+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/
=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ include /usr/share/dpkg/buildflags.mk
export PYBUILD_NAME=pybigwig
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_auto_install:
dh_auto_install
=====================================
pyBigWig.h
=====================================
@@ -2,7 +2,7 @@
#include <structmember.h>
#include "bigWig.h"
-#define pyBigWigVersion "0.3.22"
+#define pyBigWigVersion "0.3.23"
typedef struct {
PyObject_HEAD
=====================================
pyproject.toml
=====================================
@@ -1,6 +1,6 @@
[build-system]
build-backend = "setuptools.build_meta"
-requires = ["oldest-supported-numpy", "setuptools", "setuptools-scm"]
+requires = ["numpy >= 2.0.0", "setuptools", "setuptools-scm"]
[project]
authors = [{name = "Devon P. Ryan", email = "dryan79 at gmail.com"}]
@@ -11,7 +11,7 @@ classifiers = [
"Programming Language :: C",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
- "Programming Language :: Python :: 3.7",
+ "Programming Language :: Python :: 3.9",
"Programming Language :: Python :: Implementation :: CPython",
"Operating System :: POSIX",
"Operating System :: Unix",
@@ -20,9 +20,9 @@ classifiers = [
description = "A package for accessing bigWig files using libBigWig"
keywords = ["bioinformatics", "bigWig", "bigBed"]
name = "pyBigWig"
-version = "0.3.22"
+version = "0.3.23"
readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.9"
[project.license]
text = "MIT"
@@ -41,9 +41,9 @@ packages = ["pyBigWigTest"]
# Enable version inference from scm
[tool.setuptools_scm]
-# Target only minimum CPython version 3.7 on linux for wheel build
+# Target only minimum CPython version 3.9 on linux for wheel build
[tool.cibuildwheel]
-skip = "pp* cp36-* *-manylinux_i686 *_ppc64le *_s390x *-musllinux_x86_64 *-musllinux_i686"
+skip = "pp* cp38-* *-manylinux_i686 *_ppc64le *_s390x *-musllinux_x86_64 *-musllinux_i686"
[tool.cibuildwheel.linux]
manylinux-x86_64-image = "manylinux2014"
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/871ca16b3dcd372a5caa181b0c27636bf83b71ed...4c818629dbd4cb5d5927934f4c067cf1a9827de2
--
View it on GitLab: https://salsa.debian.org/med-team/pybigwig/-/compare/871ca16b3dcd372a5caa181b0c27636bf83b71ed...4c818629dbd4cb5d5927934f4c067cf1a9827de2
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