From 5362361d4e4232b92a548cc95ba6ce13f1e6c92e Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Fri, 8 Nov 2024 18:13:01 +0100 Subject: [PATCH 1/2] Support Python 3.13 --- .github/workflows/ci.yml | 4 ++-- CHANGES.rst | 5 +++++ tox.ini | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9e262ed6..9f640f19 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] include: - os: macos-13 python-version: "3.10" @@ -88,7 +88,7 @@ jobs: with: fetch-depth: 0 # required for setuptools_scm - name: Build wheels - uses: pypa/cibuildwheel@v2.17.0 + uses: pypa/cibuildwheel@v2.21.3 env: CIBW_BUILD: "cp*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64" CIBW_SKIP: "cp37-*" diff --git a/CHANGES.rst b/CHANGES.rst index d8bf3d47..99bbda17 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -2,6 +2,11 @@ Changelog ========= +unreleased +---------- + +* Added support for Python 3.13 + v1.2.2 (2024-10-04) ------------------- * :pr:`139`: Fix an error that occurred when decoding BAM records with missing diff --git a/tox.ini b/tox.ini index 3bee4262..ba091dc8 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -envlist = flake8,black,mypy,docs,py38,py39,py310,py311,py312 +envlist = flake8,black,mypy,docs,py38,py39,py310,py311,py312,py313 isolated_build = True [testenv] From 32aff0b07b03f1eb1ecc0a377e3139ce48e29e42 Mon Sep 17 00:00:00 2001 From: Marcel Martin Date: Fri, 8 Nov 2024 18:19:54 +0100 Subject: [PATCH 2/2] Drop support for Python 3.8 --- .github/workflows/ci.yml | 4 +--- CHANGES.rst | 1 + README.rst | 2 +- pyproject.toml | 2 +- tox.ini | 2 +- 5 files changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9f640f19..bb51fcf9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] include: - os: macos-13 python-version: "3.10" @@ -91,8 +91,6 @@ jobs: uses: pypa/cibuildwheel@v2.21.3 env: CIBW_BUILD: "cp*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64" - CIBW_SKIP: "cp37-*" - CIBW_TEST_SKIP: "cp38-macosx_*:arm64" - uses: actions/upload-artifact@v4 with: name: wheels-${{ matrix.os }} diff --git a/CHANGES.rst b/CHANGES.rst index 99bbda17..f0f256ef 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -6,6 +6,7 @@ unreleased ---------- * Added support for Python 3.13 +* Dropped support for Python 3.8 v1.2.2 (2024-10-04) ------------------- diff --git a/README.rst b/README.rst index d00c236d..9e01843a 100644 --- a/README.rst +++ b/README.rst @@ -16,7 +16,7 @@ dnaio processes FASTQ, FASTA and uBAM files =========================================== -``dnaio`` is a Python 3.8+ library for very efficient parsing and writing of FASTQ and also FASTA files. +``dnaio`` is a Python 3.9+ 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 `_ basecaller directly. diff --git a/pyproject.toml b/pyproject.toml index d26cdf19..9769c3fd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ classifiers = [ "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ] -requires-python = ">3.7" +requires-python = ">=3.9" dependencies = [ "xopen >= 1.4.0" ] diff --git a/tox.ini b/tox.ini index ba091dc8..a9c63396 100644 --- a/tox.ini +++ b/tox.ini @@ -1,5 +1,5 @@ [tox] -envlist = flake8,black,mypy,docs,py38,py39,py310,py311,py312,py313 +envlist = flake8,black,mypy,docs,py39,py310,py311,py312,py313 isolated_build = True [testenv]