[med-svn] [Git][med-team/python-screed][master] 17 commits: d/watch: Convert to version 5
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Mar 7 08:06:24 GMT 2026
Andreas Tille pushed to branch master at Debian Med / python-screed
Commits:
873e1a35 by Karsten Schöke at 2026-03-03T07:55:01+01:00
d/watch: Convert to version 5
- - - - -
77178ce7 by Karsten Schöke at 2026-03-03T07:59:01+01:00
New upstream version 1.2.0
- - - - -
6a12ad4c by Karsten Schöke at 2026-03-03T07:59:07+01:00
Update upstream source from tag 'upstream/1.2.0'
Update to upstream version '1.2.0'
with Debian dir ad7c10e61b0bfbc2c273c0f8e8dc1d43381e8446
- - - - -
ac9b30bd by Karsten Schöke at 2026-03-03T08:04:54+01:00
Rediff patches
- - - - -
53f1fcb6 by Karsten Schöke at 2026-03-05T14:23:20+01:00
d/control: update BD
- - - - -
ce677370 by Karsten Schöke at 2026-03-05T14:24:01+01:00
reorganize testing to use Testsuite: autopkgtest-pkg-pybuild
- - - - -
a1e0f466 by Karsten Schöke at 2026-03-05T14:39:37+01:00
d/control Bump standards to 4.7.3
- - - - -
bcb77dcb by Karsten Schöke at 2026-03-05T14:45:26+01:00
remove obsolete python3-screed.lintian-overrides
- - - - -
33740ce9 by Karsten Schöke at 2026-03-05T14:56:29+01:00
add debian/python3-screed.doc-base file
- - - - -
095d5975 by Karsten Schöke at 2026-03-05T15:57:21+01:00
Added man page for screed.
- - - - -
9581cd18 by Karsten Schöke at 2026-03-05T16:01:47+01:00
Unnecessary top_level.txt file removed.
- - - - -
8af4f97c by Karsten Schöke at 2026-03-05T16:07:01+01:00
Remove forgotten template description from patch
- - - - -
06595fca by Karsten Schöke at 2026-03-05T16:11:03+01:00
add myself to debian copyrigth.
- - - - -
782d6875 by Karsten Schöke at 2026-03-05T16:12:51+01:00
Release prepared
- - - - -
af0fdd8d by Karsten Schöke at 2026-03-06T06:30:28+01:00
d/control: insert Testsuite: autopkgtest-pkg-pybuild
- - - - -
4f66f5ae by Karsten Schöke at 2026-03-06T11:43:19+01:00
d/watch: remove obsolete *versionmangle lines.
- - - - -
04630d55 by Andreas Tille at 2026-03-07T09:06:17+01:00
Merge branch 'karso/1.2.0' into 'master'
Karso/1.2.0
See merge request med-team/python-screed!1
- - - - -
22 changed files:
- .github/workflows/python.yml
- .readthedocs.yaml
- Makefile
- − debian/README.test
- debian/changelog
- debian/control
- debian/copyright
- debian/docs
- + debian/patches/exclude-tests-from-package.patch
- debian/patches/python3-tests
- debian/patches/series
- + debian/python3-screed.doc-base
- debian/python3-screed.lintian-overrides
- + debian/python3-screed.manpages
- debian/rules
- − debian/tests/control
- − debian/tests/run-unit-test
- debian/watch
- pyproject.toml
- − setup.cfg
- − setup.py
- tox.ini
Changes:
=====================================
.github/workflows/python.yml
=====================================
@@ -14,7 +14,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest, macos-latest]
- py: ["3.10", 3.9, 3.8]
+ py: ["3.11", "3.12", "3.13", "3.14"]
fail-fast: false
steps:
@@ -33,7 +33,7 @@ jobs:
echo "::set-output name=dir::$(pip cache dir)"
- name: pip cache
- uses: actions/cache at v3
+ uses: actions/cache at v4
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-v2-${{ hashFiles('**/setup.py') }}
@@ -46,7 +46,7 @@ jobs:
pip install tox tox-gh-actions
- name: tox cache
- uses: actions/cache at v3
+ uses: actions/cache at v4
with:
path: .tox/
key: ${{ runner.os }}-tox-v2-${{ hashFiles('**/setup.py') }}
@@ -59,8 +59,10 @@ jobs:
PYTHONDEVMODE: 1
- name: Upload Python coverage to codecov
- uses: codecov/codecov-action at v3
+ uses: codecov/codecov-action at v5
with:
flags: python
fail_ci_if_error: true
files: coverage.xml
+ env:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
=====================================
.readthedocs.yaml
=====================================
@@ -2,9 +2,9 @@ version: 2
# Set the version of Python and other tools you might need
build:
- os: ubuntu-22.04
+ os: ubuntu-24.04
tools:
- python: "3.10"
+ python: "3.14"
# Build documentation in the docs/ directory with Sphinx
sphinx:
=====================================
Makefile
=====================================
@@ -5,39 +5,39 @@
PYSOURCES=$(wildcard screed/*.py)
TESTSOURCES=$(wildcard screed/tests/*.py)
-SOURCES=$(PYSOURCES) setup.py
+SOURCES=$(PYSOURCES)
VERSION=$(shell git describe --tags --dirty | sed s/v//)
all:
- ./setup.py build
+ python -m build .
install: FORCE
- ./setup.py build install
+ pip install -e .
install-dependencies: FORCE
pip install -e .[all]
develop: FORCE
- ./setup.py develop
+ pip install -e .
dist: dist/screed-$(VERSION).tar.gz
dist/screed-$(VERSION).tar.gz: $(SOURCES)
- ./setup.py sdist
+ python -m build --sdist .
clean: FORCE
- ./setup.py clean --all || true
+ pip uninstall screed || true
rm -rf build/
rm -rf coverage-debug .coverage coverage.xml
rm -rf doc/_build
rm -rf .eggs/ *.egg-info/ .cache/ __pycache__/ *.pyc */*.pyc */*/*.pyc
pep8: $(PYSOURCES) $(TESTSOURCES)
- pycodestyle --exclude=_version.py setup.py screed/
+ pycodestyle --exclude=_version.py screed/
pylint: FORCE
pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
- setup.py screed || true
+ screed || true
doc: FORCE
cd doc && make html
=====================================
debian/README.test deleted
=====================================
@@ -1,8 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-To run the unit tests provided by the package you can do
-
- sh run-unit-test
-
-in this directory.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+python-screed (1.2.0-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version 1.2.0
+ * d/watch: Convert to version 5
+ * Rediff patches
+ * d/control: update BD
+ * reorganize testing to use Testsuite: autopkgtest-pkg-pybuild
+ * d/control Bump standards to 4.7.3, drop obsolete
+ - Priority: optional
+ - Rules-Requires-Root: no
+ * add debian/python3-screed.doc-base file
+ * Added man page for screed.
+
+ -- Karsten Schöke <karsten.schoeke at geobasis-bb.de> Thu, 05 Mar 2026 16:11:46 +0100
+
python-screed (1.1.3-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -2,19 +2,19 @@ Source: python-screed
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe at debian.org>
Section: python
-Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
+ pybuild-plugin-pyproject,
python3-all,
python3-pytest,
python3-sphinx,
python3-setuptools,
python3-setuptools-scm
-Standards-Version: 4.6.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/python-screed
Vcs-Git: https://salsa.debian.org/med-team/python-screed.git
Homepage: https://screed.readthedocs.org
-Rules-Requires-Root: no
+Testsuite: autopkgtest-pkg-pybuild
Package: python3-screed
Architecture: all
=====================================
debian/copyright
=====================================
@@ -9,6 +9,7 @@ License: BSD-3-Clause
Files: debian/*
Copyright: 2015 Michigan State University <mcrusoe at msu.edu>
+ 2026 Karsten Schöke <karsten.schoeke at geobasis-bb.de>
License: BSD-3-Clause
License: BSD-3-Clause
=====================================
debian/docs
=====================================
@@ -1,3 +1 @@
-debian/README.test
-debian/tests/run-unit-test
build/html
=====================================
debian/patches/exclude-tests-from-package.patch
=====================================
@@ -0,0 +1,17 @@
+From: Karsten Schöke <karsten.schoeke at geobasis-bb.de>
+Date: Mar, 05 2026 13:08:51 +0100
+Subject: No tests included in the package
+Forwarded: not-needed
+
+--- python-screed-1.2.0.orig/pyproject.toml
++++ python-screed-1.2.0/pyproject.toml
+@@ -64,4 +64,8 @@ test = [
+ all = ["screed[test]"]
+
+ [tool.setuptools]
+-packages = ["screed"]
++include-package-data = false
++
++[tool.setuptools.packages.find]
++include = ["screed*"]
++exclude = ["screed.tests*"]
=====================================
debian/patches/python3-tests
=====================================
@@ -1,9 +1,18 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: use python3 for the tests
+From: "Michael R. Crusoe" <crusoe at debian.org>
+Date: Tue, 3 Mar 2026 08:04:11 +0100
+Subject: use python3 for the tests
+
Forwarded: not-needed
---- python-screed.orig/screed/tests/test_open.py
-+++ python-screed/screed/tests/test_open.py
-@@ -33,7 +33,7 @@
+---
+ screed/tests/test_open.py | 2 +-
+ screed/tests/test_shell.py | 4 ++--
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/screed/tests/test_open.py b/screed/tests/test_open.py
+index 3d880ce..b830509 100644
+--- a/screed/tests/test_open.py
++++ b/screed/tests/test_open.py
+@@ -33,7 +33,7 @@ def test_open_stdin():
Uses a subprocess with the data file directlyused as stdin."""
filename1 = utils.get_test_data('test.fa')
@@ -12,9 +21,11 @@ Forwarded: not-needed
"import screed; print(list(screed.open('-')))"]
with open(filename1, 'rb') as data_file:
output = subprocess.Popen(command,
---- python-screed.orig/screed/tests/test_shell.py
-+++ python-screed/screed/tests/test_shell.py
-@@ -65,7 +65,7 @@
+diff --git a/screed/tests/test_shell.py b/screed/tests/test_shell.py
+index 7ab3ff2..7909001 100644
+--- a/screed/tests/test_shell.py
++++ b/screed/tests/test_shell.py
+@@ -65,7 +65,7 @@ class Test_fa_shell_module(test_fasta.Test_fasta):
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
@@ -23,7 +34,7 @@ Forwarded: not-needed
ret = subprocess.check_call(cmd, stdout=subprocess.PIPE)
assert ret == 0, ret
self.db = screed.ScreedDB(self._testfa)
-@@ -87,7 +87,7 @@
+@@ -87,7 +87,7 @@ class Test_fq_shell_module(test_fastq.Test_fastq):
self._testfq = utils.get_temp_filename('test.fastq')
shutil.copy(utils.get_test_data('test.fastq'), self._testfq)
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
python3-tests
+exclude-tests-from-package.patch
=====================================
debian/python3-screed.doc-base
=====================================
@@ -0,0 +1,9 @@
+Document: python-screed
+Title: Python Screed User Manual
+Author: Alex Nolley, C. Titus Brown
+Section: Programming/Python
+
+Format: HTML
+Index: /usr/share/doc/python3-screed/html/index.html
+Files: /usr/share/doc/python3-screed/html/*.html
+
=====================================
debian/python3-screed.lintian-overrides
=====================================
@@ -1,3 +1,2 @@
-# The duplicated compressed file is used intentionally since the test
-# should run on both compression methods
-compressed-duplicate [usr/lib/python3/dist-packages/screed/tests/*]
+# possible error in documentation
+typo-in-manual-page retriving retrieving [usr/share/man/man1/screed.1.gz:936]
=====================================
debian/python3-screed.manpages
=====================================
@@ -0,0 +1 @@
+build/man/screed.1
=====================================
debian/rules
=====================================
@@ -2,19 +2,15 @@
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
-export DH_VERBOSE=1
+#export DH_VERBOSE=1
export PYBUILD_NAME=screed
+export PYBUILD_TEST_ARGS={dir}/screed/tests
+export PYBUILD_AFTER_INSTALL=rm -fr {destdir}/usr/lib/python3*/dist-packages/screed-*/top_level.txt
+
%:
dh $@ --with sphinxdoc --buildsystem=pybuild
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- dh_auto_install
- PYBUILD_SYSTEM=custom \
- PYBUILD_TEST_ARGS="export PATH={destdir}/usr/usr/bin:$$PATH {interpreter} -m pytest -m 'not known_failing'"
-endif
-
-override_dh_auto_build:
- dh_auto_build
+execute_after_dh_auto_build:
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/ build/html
+ PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman doc/ build/man
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, python3-pytest
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,13 +0,0 @@
-#!/bin/sh -e
-
-pkg=python-screed
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-fi
-cd $AUTOPKGTEST_TMP
-
-for release in /usr/lib/python*/dist-packages/screed
-do
- cp -r ${release} .
- pytest -m 'not known_failing' screed
-done
=====================================
debian/watch
=====================================
@@ -1,3 +1,5 @@
-version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-screed-$1.tar.gz%"
-https://github.com/dib-lab/screed/tags (?:.*?/)?v?@ANY_VERSION@\.tar\.gz
+Version: 5
+
+Source: https://github.com/dib-lab/screed.git
+Matching-Pattern: refs/tags/v at ANY_VERSION@
+Mode: git
=====================================
pyproject.toml
=====================================
@@ -1,7 +1,7 @@
[build-system]
requires = [
"setuptools >= 48",
- "setuptools_scm[toml] >= 4, <6",
+ "setuptools_scm[toml] >= 9, <10",
"setuptools_scm_git_archive",
"wheel >= 0.29.0",
]
@@ -10,3 +10,58 @@ build-backend = 'setuptools.build_meta'
[tool.setuptools_scm]
write_to = "screed/version.py"
git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"
+
+[project]
+name = "screed"
+description = "a Python library for loading FASTA and FASTQ sequences"
+readme = "README.md"
+license = "BSD-3-Clause"
+license-files = [ "doc/LICENSE.rst" ]
+requires-python = ">=3.11"
+dynamic = [ "version" ]
+
+authors = [
+ { name = "Alex Nolley" },
+ { name = "C. Titus Brown" },
+]
+
+maintainers = [
+ { name = "C. Titus Brown", email = "titus at idyll.org" },
+ { name = "Luiz Irber", email="luiz at sourmash.bio" },
+]
+
+classifiers = [
+ "Development Status :: 5 - Production/Stable",
+ "Environment :: Console",
+ "Environment :: MacOS X",
+ "Intended Audience :: Science/Research",
+ "Natural Language :: English",
+ "Operating System :: POSIX :: Linux",
+ "Operating System :: MacOS :: MacOS X",
+ "Programming Language :: Python :: 3.14",
+ "Programming Language :: Python :: 3.13",
+ "Programming Language :: Python :: 3.12",
+ "Programming Language :: Python :: 3.11",
+ "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/dib-lab/screed"
+"Documentation" = "https://screed.readthedocs.io/"
+"Source" = "https://github.com/dib-lab/screed"
+"Tracker" = "https://github.com/dib-lab/screed/issues"
+"CI" = "https://github.com/dib-lab/screed/actions"
+
+[project.scripts]
+"screed" = "screed.__main__:main"
+
+[project.optional-dependencies]
+test = [
+ "pytest >= 6.2.2",
+ "pycodestyle",
+ "pytest-cov",
+]
+all = ["screed[test]"]
+
+[tool.setuptools]
+packages = ["screed"]
=====================================
setup.cfg deleted
=====================================
@@ -1,55 +0,0 @@
-[metadata]
-name = screed
-description = a Python library for loading FASTA and FASTQ sequences
-long_description = file: README.md
-long_description_content_type = text/markdown; charset=UTF-8
-url = https://github.com/dib-lab/screed
-author = Alex Nolley, C. Titus Brown
-author_email = ctbrown at ucdavis.edu,
-license = BSD 3-clause
-license_file = doc/LICENSE.rst
-classifiers =
- Development Status :: 5 - Production/Stable
- Environment :: Console
- Environment :: MacOS X
- Intended Audience :: Science/Research
- License :: OSI Approved :: BSD License
- Natural Language :: English
- Operating System :: POSIX :: Linux
- Operating System :: MacOS :: MacOS X
- Programming Language :: Python :: 3.7
- Programming Language :: Python :: 3.8
- Programming Language :: Python :: 3.9
- Topic :: Scientific/Engineering :: Bio-Informatics
-project_urls =
- Documentation = https://screed.readthedocs.io
- Source = https://github.com/dib-lab/screed
- Tracker = https://github.com/dib-lab/screed/issues
-
-[options]
-zip_safe = False
-packages = find:
-platforms = any
-include_package_data = True
-python_requires = >=3.7
-setup_requires =
- setuptools_scm
-
-[bdist_wheel]
-universal = 1
-
-[aliases]
-test=pytest
-
-[options.entry_points]
-console_scripts =
- screed = screed.__main__:main
-
-[options.extras_require]
-test =
- pytest >= 6.2.2
- pycodestyle
- pytest-cov
- importlib_resources;python_version<'3.9'
-all =
- %(test)s
=====================================
setup.py deleted
=====================================
@@ -1,5 +0,0 @@
-#!/usr/bin/env python
-import setuptools
-
-if __name__ == "__main__":
- setuptools.setup()
=====================================
tox.ini
=====================================
@@ -1,5 +1,5 @@
[tox]
-envlist = py38, py39, py310
+envlist = py311, py312, py313, py314
minversion = 3.12
isolated_build = true
skip_missing_interpreters = true
@@ -26,6 +26,7 @@ deps =
[gh-actions]
python =
- 3.8: py38
- 3.9: py39
- 3.10: py310
+ 3.11: py311
+ 3.12: py312
+ 3.13: py313
+ 3.14: py314
View it on GitLab: https://salsa.debian.org/med-team/python-screed/-/compare/35a6103a716ebb80a2f020b4a832238fe680353b...04630d5547a0d31be1b3fdcf11c299297c200b18
--
View it on GitLab: https://salsa.debian.org/med-team/python-screed/-/compare/35a6103a716ebb80a2f020b4a832238fe680353b...04630d5547a0d31be1b3fdcf11c299297c200b18
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