[med-svn] [Git][med-team/python-pyspoa][master] 3 commits: New upstream version 0.3.2
Aryan Karamtoth (@SpaciousCoder78)
gitlab at salsa.debian.org
Tue Dec 9 06:16:23 GMT 2025
Aryan Karamtoth pushed to branch master at Debian Med / python-pyspoa
Commits:
cfb16b39 by Aryan Karamtoth at 2025-12-09T11:37:33+05:30
New upstream version 0.3.2
- - - - -
54ddd62e by Aryan Karamtoth at 2025-12-09T11:37:33+05:30
Update upstream source from tag 'upstream/0.3.2'
Update to upstream version '0.3.2'
with Debian dir 04f26196d7eb7b2c36b6010246473fff1a077639
- - - - -
7b3ec960 by Aryan Karamtoth at 2025-12-09T11:46:02+05:30
New upstream version 0.3.2
- - - - -
11 changed files:
- .gitlab-ci.yml
- CHANGELOG.md
- Makefile
- build-wheels.sh
- conda/meta.yaml
- debian/changelog
- debian/control
- debian/copyright
- pyproject.toml
- pyspoa.cpp
- setup.py
Changes:
=====================================
.gitlab-ci.yml
=====================================
@@ -5,7 +5,7 @@ include:
- "push-conda.yaml"
- "snippets.yaml"
-image: ${UBUNTUIMAGE}:20.04
+image: ${UBUNTUIMAGE}:24.04
variables:
GIT_SUBMODULE_STRATEGY: recursive
@@ -15,7 +15,7 @@ variables:
.prep-image: &prep-image |
export DEBIAN_FRONTEND=noninteractive
apt update -qq
- apt install -y --no-install-recommends gcc autoconf libtool automake make curl wget zlib1g-dev git
+ apt install -y --no-install-recommends build-essential autoconf libtool automake curl wget zlib1g-dev git
.minimal-python: &minimal-python |
export DEBIAN_FRONTEND=noninteractive
@@ -32,7 +32,7 @@ test:
stage: test
parallel:
matrix:
- - PYENV_VERSION: ["3.8", "3.9", "3.10", "3.11"]
+ - PYENV_VERSION: ["3.10", "3.11", "3.12", "3.13", "3.14"]
script:
- *prep-image
- !reference [.install, pyenv]
@@ -40,6 +40,7 @@ test:
- make test
+
deploy-checks:
stage: prerelease
variables:
@@ -68,6 +69,19 @@ conda:
- *prep-image
- *conda-before-script
+test-conda-build:
+ extends:
+ - .deploy-conda-linux
+ stage: prerelease
+ variables:
+ RECIPEPATH: "../conda"
+ UPLOAD: "no"
+ before_script:
+ - *prep-image
+ - *conda-before-script
+ rules:
+ - when: always
+
conda-arm:
extends:
- .deploy-conda-linux-arm
@@ -77,6 +91,19 @@ conda-arm:
- *prep-image
- *conda-before-script
+test-conda-arm-build:
+ extends:
+ - .deploy-conda-linux-arm
+ stage: prerelease
+ variables:
+ RECIPEPATH: "../conda"
+ UPLOAD: "no"
+ before_script:
+ - *prep-image
+ - *conda-before-script
+ rules:
+ - when: always
+
conda-mac:
extends:
- .deploy-conda-mac
@@ -85,6 +112,18 @@ conda-mac:
before_script:
- *conda-before-script
+test-conda-mac-build:
+ extends:
+ - .deploy-conda-mac
+ stage: prerelease
+ variables:
+ RECIPEPATH: "../conda"
+ UPLOAD: "no"
+ before_script:
+ - *conda-before-script
+ rules:
+ - when: always
+
conda-mac-arm:
extends:
- .deploy-conda-mac-arm
@@ -93,6 +132,17 @@ conda-mac-arm:
before_script:
- *conda-before-script
+test-conda-mac-arm-build:
+ extends:
+ - .deploy-conda-mac-arm
+ stage: prerelease
+ variables:
+ RECIPEPATH: "../conda"
+ UPLOAD: "no"
+ before_script:
+ - *conda-before-script
+ rules:
+ - when: always
### Python
# The selection of wheels built here is mainly driven by the matrix
@@ -123,15 +173,6 @@ bld:py-sdist:
- wheelhouse-final/*.whl
-wheels-2014:
- extends: .many-linux
- image: "quay.io/pypa/manylinux2014_x86_64"
- parallel:
- matrix:
- - PYWHEEL: [7, 8, 9]
- FLAVOUR: ["2014"]
-
-
wheels-arm-2014:
extends: .many-linux
tags:
@@ -139,7 +180,7 @@ wheels-arm-2014:
image: "quay.io/pypa/manylinux2014_aarch64"
parallel:
matrix:
- - PYWHEEL: [8, 9, 10]
+ - PYWHEEL: [10]
FLAVOUR: ["2014"]
@@ -148,7 +189,7 @@ wheels-2_28:
image: "quay.io/pypa/manylinux_2_28_x86_64"
parallel:
matrix:
- - PYWHEEL: [8, 9, 10, 11]
+ - PYWHEEL: [10, 11, 12, 13, 14]
FLAVOUR: ["2_28"]
@@ -159,7 +200,7 @@ wheels-arm-2_28:
image: "quay.io/pypa/manylinux_2_28_aarch64"
parallel:
matrix:
- - PYWHEEL: [8, 9, 10, 11]
+ - PYWHEEL: [10, 11, 12, 13, 14]
FLAVOUR: ["2_28"]
@@ -172,3 +213,5 @@ deploy:pypi:
- twine upload --non-interactive wheelhouse-final/pyspoa*.whl dist/pyspoa*.tar.gz
rules:
- if: '$CI_COMMIT_TAG =~ /^v[[:digit:]]+\.[[:digit:]]+\.[[:digit:]]+$/'
+
+
=====================================
CHANGELOG.md
=====================================
@@ -4,6 +4,28 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [v0.3.2]
+
+### Added
+- Python 3.13 and 3.14 binaries now available.
+### Removed
+- Deprecate Python<=3.9
+
+## [v0.3.1]
+
+### Fixed
+- Conda builds
+### Added
+- Pre-release build tests for conda
+
+## [v0.3.0]
+
+### Added
+- Python 3.12 support
+### Removed
+- Deprecate Python 3.7
+
## [v0.2.1]
### Changed
- Default argument for `min_coverage` to `None`
=====================================
Makefile
=====================================
@@ -19,7 +19,7 @@ test: install
${IN_VENV} && python tests/test_pyspoa.py
sdist: venv/bin/activate
- ${IN_VENV} && python setup.py sdist
+ ${IN_VENV} && pip install setuptools && python setup.py sdist
IN_BUILD=. ./pypi_build/bin/activate
pypi_build/bin/activate:
=====================================
build-wheels.sh
=====================================
@@ -37,12 +37,7 @@ ls /opt/python/
# Compile wheels
for minor in $@; do
- if [[ "${minor}" == "8" ]] || [[ "${minor}" == "9" ]] || \
- [[ "${minor}" == "10" ]] || [[ "${minor}" == "11" ]]; then
- PYBIN="/opt/python/cp3${minor}-cp3${minor}/bin"
- else
- PYBIN="/opt/python/cp3${minor}-cp3${minor}m/bin"
- fi
+ PYBIN="/opt/python/cp3${minor}-cp3${minor}/bin"
"${PYBIN}/python3" -m pip install --upgrade pip
"${PYBIN}/python3" -m pip install cmake==3.27.1 scikit-build
"${PYBIN}"/pip wheel --no-dependencies . -w ./wheelhouse/
@@ -58,12 +53,7 @@ done
# Install + test packages
for minor in $@; do
- if [[ "${minor}" == "8" ]] || [[ "${minor}" == "9" ]] || \
- [[ "${minor}" == "10" ]] || [[ "${minor}" == "11" ]]; then
- PYBIN="/opt/python/cp3${minor}-cp3${minor}/bin"
- else
- PYBIN="/opt/python/cp3${minor}-cp3${minor}m/bin"
- fi
+ PYBIN="/opt/python/cp3${minor}-cp3${minor}/bin"
"${PYBIN}"/pip install "${PACKAGE_NAME}" --no-index -f ./wheelhouse
"${PYBIN}"/python3 tests/test_pyspoa.py
done
=====================================
conda/meta.yaml
=====================================
@@ -14,7 +14,7 @@ requirements:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- make
- - cmake
+ - cmake <4
host:
- python
- pip
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-pyspoa (0.3.2-1) UNRELEASED; urgency=medium
+
+ * Package Adoption
+ * Added gbp.conf
+ * Standards-Version: 4.7.2
+
+ -- Aryan Karamtoth <spaciouscoder78 at disroot.org> Tue, 09 Dec 2025 11:39:22 +0530
+
python-pyspoa (0.2.1-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -2,7 +2,7 @@ Source: python-pyspoa
Section: python
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Nilesh Patra <nilesh at debian.org>,
+Uploaders: Aryan Karamtoth <spaciouscoder78 at disroot.org>
Testsuite: autopkgtest-pkg-python
Build-Depends:
debhelper-compat (= 13),
@@ -11,7 +11,7 @@ Build-Depends:
python3-setuptools,
libspoa-dev,
python3-pybind11
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/python-pyspoa
Vcs-Git: https://salsa.debian.org/med-team/python-pyspoa.git
Homepage: https://github.com/nanoporetech/pyspoa
=====================================
debian/copyright
=====================================
@@ -3,7 +3,7 @@ Upstream-Name: pyspoa
Source: https://github.com/nanoporetech/pyspoa/releases
Files: *
-Copyright: 2020 Oxford Nanopore Technologies
+Copyright: 2020-2025 Oxford Nanopore Technologies
License: BSD-4-Clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
@@ -35,7 +35,8 @@ License: BSD-4-Clause
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Files: debian/*
-Copyright: 2020 Nilesh Patra <nilesh at debian.org>
+Copyright: 2020-2025 Nilesh Patra <nilesh at debian.org>
+ 2025 Aryan Karamtoth <spaciouscoder78 at disroot.org>
License: Expat
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
=====================================
pyproject.toml
=====================================
@@ -1,3 +1,3 @@
[build-system]
-requires = ["cmake", "pybind11", "setuptools", "wheel", "scikit-build"]
+requires = ["cmake<4", "pybind11", "setuptools", "wheel", "scikit-build"]
build-backend = "setuptools.build_meta"
=====================================
pyspoa.cpp
=====================================
@@ -11,7 +11,7 @@ auto poa(std::vector<std::string> sequences, int algorithm, bool genmsa,
{
// set min_coverage to the default of the SPOA CLI (-1) if None
int min_cov = -1;
- if (min_coverage != pybind11::none()) {
+ if (!min_coverage.is(pybind11::none())) {
min_cov = min_coverage.cast<int>();
}
auto alignment_engine = spoa::AlignmentEngine::Create(
=====================================
setup.py
=====================================
@@ -139,7 +139,7 @@ with open('README.md', encoding='utf-8') as f:
setup(
name='pyspoa',
- version='0.2.1',
+ version='0.3.2',
author='Oxford Nanoporetech Technologies, Ltd.',
author_email='support at nanoporetech.com',
url='https://github.com/nanoporetech/pyspoa',
View it on GitLab: https://salsa.debian.org/med-team/python-pyspoa/-/compare/9cc1fac8182eebb581e3daa54e4187a7bf89ef3f...7b3ec9603ad489e62484e83843018c619cc58640
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyspoa/-/compare/9cc1fac8182eebb581e3daa54e4187a7bf89ef3f...7b3ec9603ad489e62484e83843018c619cc58640
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