[med-svn] [Git][med-team/python-dnaio][master] 6 commits: New upstream version 1.2.4
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Nov 15 09:23:48 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / python-dnaio
Commits:
c52ac8d8 by Étienne Mollier at 2025-11-15T10:10:53+01:00
New upstream version 1.2.4
- - - - -
0e6643c3 by Étienne Mollier at 2025-11-15T10:10:53+01:00
Update upstream source from tag 'upstream/1.2.4'
Update to upstream version '1.2.4'
with Debian dir bb91ed3b14be80158e948bd5a39e373e9484e331
- - - - -
3cef73fb by Étienne Mollier at 2025-11-15T10:11:42+01:00
d/copyright: drop the old FSF mail address.
- - - - -
41b000d1 by Étienne Mollier at 2025-11-15T10:12:56+01:00
d/watch: convert to v5 Github watch file.
- - - - -
9bf5964f by Étienne Mollier at 2025-11-15T10:19:54+01:00
d/s/lintian-overrides: new: explain why the missing Priority field.
- - - - -
9383b1a9 by Étienne Mollier at 2025-11-15T10:23:17+01:00
d/changelog: ready for upload to unstable.
- - - - -
11 changed files:
- .github/workflows/ci.yml
- .readthedocs.yaml
- CHANGES.rst
- README.rst
- debian/changelog
- debian/copyright
- + debian/source/lintian-overrides
- debian/watch
- pyproject.toml
- src/dnaio/_core.pyx
- tox.ini
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -50,11 +50,9 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest, windows-latest]
- python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+ python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
include:
- - os: macos-13
- python-version: "3.10"
- - os: macos-14
+ - os: macos-latest
python-version: "3.10"
steps:
- uses: actions/checkout at v4
@@ -77,14 +75,14 @@ jobs:
timeout-minutes: 15
strategy:
matrix:
- os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+ os: [ubuntu-latest, windows-latest, macos-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout at v4
with:
fetch-depth: 0 # required for setuptools_scm
- name: Build wheels
- uses: pypa/cibuildwheel at v2.21.3
+ uses: pypa/cibuildwheel at v3.2.1
env:
CIBW_BUILD: "cp*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64"
- uses: actions/upload-artifact at v4
@@ -107,7 +105,7 @@ jobs:
path: dist/
merge-multiple: true
- name: Publish to PyPI
- uses: pypa/gh-action-pypi-publish at v1.5.1
+ uses: pypa/gh-action-pypi-publish at release/v1
with:
password: ${{ secrets.pypi_password }}
#password: ${{ secrets.test_pypi_password }}
=====================================
.readthedocs.yaml
=====================================
@@ -3,6 +3,8 @@ build:
os: "ubuntu-22.04"
tools:
python: "3.11"
+sphinx:
+ configuration: "doc/conf.py"
python:
install:
- requirements: doc/requirements.txt
=====================================
CHANGES.rst
=====================================
@@ -2,6 +2,12 @@
Changelog
=========
+v1.2.4 (2025-10-12)
+-------------------
+
+* Added support for Python 3.14 (including the free-threaded "3.14t" variant)
+* Dropped support for Python 3.9
+
v1.2.3 (2024-11-12)
-------------------
=====================================
README.rst
=====================================
@@ -16,7 +16,7 @@
dnaio processes FASTQ, FASTA and uBAM files
===========================================
-``dnaio`` is a Python 3.9+ library for very efficient parsing and writing of FASTQ and also FASTA files.
+``dnaio`` is a Python 3 library for very efficient parsing and writing of FASTQ and also FASTA files.
Since ``dnaio`` version 1.1.0, support for efficiently parsing uBAM files has been implemented.
This allows reading ONT files from the `dorado <https://github.com/nanoporetech/dorado>`_
basecaller directly.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-dnaio (1.2.4-1) unstable; urgency=medium
+
+ * New upstream version 1.2.4
+ * d/copyright: drop the old FSF mail address.
+ * d/watch: convert to v5 Github watch file.
+ * d/s/lintian-overrides: new: explain why the missing Priority field.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 15 Nov 2025 10:20:08 +0100
+
python-dnaio (1.2.3-2) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -42,11 +42,5 @@ License: GPL-2+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
- You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- .
- For other licensing arrangements, please contact Daniel J. Schaid.
- .
On a Debian system, the GNU GPL license version 2 is distributed in the
file /usr/share/common-licenses/GPL-2.
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,5 @@
+# See the discussion on d-devel for the rationale[1], this override is
+# probably going to be temporary.
+#
+# [1]: https://lists.debian.org/debian-devel/2024/12/msg00328.html
+recommended-field (in section for source) Priority [debian/control:*]
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="uversionmangle=s/rc/~rc/,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/marcelm/dnaio/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Template: Github
+Owner: marcelm
+Project: dnaio
+Uversionmangle: s/rc/~rc/
+Dversionmangle: auto
=====================================
pyproject.toml
=====================================
@@ -1,5 +1,5 @@
[build-system]
-requires = ["setuptools >= 52", "setuptools_scm >= 6.2", "Cython >= 0.29.20"]
+requires = ["setuptools >= 78", "setuptools_scm >= 6.2", "Cython >= 3.1"]
build-backend = "setuptools.build_meta"
[project]
@@ -10,16 +10,15 @@ authors = [
]
description = "Read and write FASTA and FASTQ files efficiently"
readme = "README.rst"
-license = {text = "MIT"}
+license = "MIT"
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
- "License :: OSI Approved :: MIT License",
"Programming Language :: Cython",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
dependencies = [
"xopen >= 1.4.0"
]
@@ -46,17 +45,18 @@ write_to = "src/dnaio/_version.py"
testpaths = ["tests"]
[tool.cibuildwheel.windows.environment]
-CFLAGS = "-g0 -DNDEBUG"
+CFLAGS = "-O3 -DNDEBUG"
[tool.cibuildwheel.macos.environment]
-CFLAGS = "-g0 -DNDEBUG"
+CFLAGS = "-O3 -DNDEBUG"
[tool.cibuildwheel.linux.environment]
-CFLAGS = "-g0 -DNDEBUG"
+CFLAGS = "-O3 -DNDEBUG"
[tool.cibuildwheel]
test-requires = "pytest"
test-command = ["cd {project}", "pytest tests"]
+build-verbosity = 1
[[tool.cibuildwheel.overrides]]
select = "*-win*"
=====================================
src/dnaio/_core.pyx
=====================================
@@ -1,4 +1,5 @@
# cython: language_level=3, emit_code_comments=False
+# cython: freethreading_compatible = True
from cpython.buffer cimport PyBUF_SIMPLE, PyObject_GetBuffer, PyBuffer_Release
from cpython.bytes cimport PyBytes_FromStringAndSize, PyBytes_AS_STRING, PyBytes_GET_SIZE, PyBytes_CheckExact
=====================================
tox.ini
=====================================
@@ -1,5 +1,5 @@
[tox]
-envlist = flake8,black,mypy,docs,py39,py310,py311,py312,py313
+envlist = flake8,black,mypy,docs,py310,py311,py312,py313,py314
isolated_build = True
[testenv]
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/a64b31b1d8a845f858e0cdee058c476f9a1162c1...9383b1a909727475010772064021cf7e900db31f
--
View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/compare/a64b31b1d8a845f858e0cdee058c476f9a1162c1...9383b1a909727475010772064021cf7e900db31f
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