[med-svn] [Git][med-team/python-dnaio][upstream] New upstream version 1.2.4

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / python-dnaio


Commits:
c52ac8d8 by Étienne Mollier at 2025-11-15T10:10:53+01:00
New upstream version 1.2.4
- - - - -


7 changed files:

- .github/workflows/ci.yml
- .readthedocs.yaml
- CHANGES.rst
- README.rst
- 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.


=====================================
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/-/commit/c52ac8d82696824ce83a08fe4c04462d0fb161bc

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View it on GitLab: https://salsa.debian.org/med-team/python-dnaio/-/commit/c52ac8d82696824ce83a08fe4c04462d0fb161bc
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