Ananthu C V pushed to branch master at Debian Med / python-pyvcf
Commits: 8b11945d by Ananthu C V at 2024-11-26T21:15:29+05:30 Drop dependency on python3-pkg-resources (Closes: #1083698) - - - - - 66d364eb by Ananthu C V at 2024-11-26T21:22:45+05:30 Fix patch header format - - - - - bb181f70 by Ananthu C V at 2024-11-26T21:30:42+05:30 Use setuptools instead of deprecated distutils - - - - - aed7104e by Ananthu C V at 2024-11-26T21:37:15+05:30 Use raw strings to prevent invalid escape sequences in regex (Closes: 1079359) - - - - - f20be58d by Ananthu C V at 2024-11-26T21:43:56+05:30 Use execute_after target instead of overriding dh_install - - - - - af350088 by Ananthu C V at 2024-11-26T21:47:12+05:30 Bump standards version to 4.7.0 (no changes needed) - - - - - 2ab9de1a by Ananthu C V at 2024-11-26T21:50:09+05:30 Upload to unstable - - - - - 8 changed files: - debian/changelog - debian/control - debian/patches/quitechar.patch - + debian/patches/replace-distutils-with-setuptools.patch - + debian/patches/replace-pkg-resources-with-importlib.patch - debian/patches/series - + debian/patches/use-raw-strings-for-regex.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +python-pyvcf (0.6.8+git20170215.476169c-11) unstable; urgency=medium + + * Team upload. + * Drop dependency on python3-pkg-resources (Closes: #1083698) + * Fix patch header format + * Use setuptools instead of deprecated distutils + * Use raw strings to prevent invalid escape sequences + in regex (Closes: 1079359) + * Use execute_after target instead of overriding dh_install + * Bump standards version to 4.7.0 (no changes needed) + + -- Ananthu C V <[email protected]> Tue, 26 Nov 2024 21:49:45 +0530 + python-pyvcf (0.6.8+git20170215.476169c-10) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13), python3-setuptools, python3-pytest <!nocheck>, python3-pysam <!nocheck> -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git Homepage: https://github.com/jamescasbon/PyVCF ===================================== debian/patches/quitechar.patch ===================================== @@ -1,5 +1,5 @@ Author: Andreas Tille <[email protected]> -Last-Update: Mon, 14 Nov 2022 13:54:52 +0100 +Last-Update: 2022-11-14 Bug-Debian: https://bugs.debian.org/1024063 Description: Fix 'TypeError: "quotechar" must be a 1-character string' ===================================== debian/patches/replace-distutils-with-setuptools.patch ===================================== @@ -0,0 +1,10 @@ +Description: use setuptools instead of deprecated distutils +Author: Ananthu C V <[email protected]> +Last-Update: 2024-11-26 +--- a/setup.py ++++ b/setup.py +@@ -1,3 +1,2 @@ +-from setuptools import setup +-from distutils.extension import Extension ++from setuptools import setup, Extension + import sys ===================================== debian/patches/replace-pkg-resources-with-importlib.patch ===================================== @@ -0,0 +1,26 @@ +Description: replace deprecated pkg_resources usage with importlib.metadata +Author: Ananthu C V <[email protected]> +Bug-Debian: https://bugs.debian.org/1083698 +Last-Update: 2024-11-26 +--- a/scripts/vcf_filter.py ++++ b/scripts/vcf_filter.py +@@ -3,3 +3,3 @@ + import argparse +-import pkg_resources ++import importlib + +@@ -89,3 +89,3 @@ + # look for global extensions +- for p in pkg_resources.iter_entry_points('vcf.filters'): ++ for p in importlib.metadata.entry_points(group='vcf.filters'): + filt = p.load() +--- a/setup.py ++++ b/setup.py +@@ -10,3 +10,2 @@ + +-DEPENDENCIES = ['setuptools'] + +@@ -40,3 +39,2 @@ + test_suite='vcf.test.test_vcf.suite', +- install_requires=DEPENDENCIES, + entry_points = { ===================================== debian/patches/series ===================================== @@ -1,3 +1,6 @@ fix-setuptools.patch 2to3.patch quitechar.patch +replace-pkg-resources-with-importlib.patch +replace-distutils-with-setuptools.patch +use-raw-strings-for-regex.patch ===================================== debian/patches/use-raw-strings-for-regex.patch ===================================== @@ -0,0 +1,16 @@ +Description: use raw strings in regex to prevent invalid escape sequences +Author: Ananthu C V <[email protected]> +Bug-Debian: https://bugs.debian.org/1079359 +Last-Update: 2024-11-26 +--- a/vcf/parser.py ++++ b/vcf/parser.py +@@ -277,3 +277,3 @@ + self._row_pattern = re.compile(self._separator) +- self._alt_pattern = re.compile('[\[\]]') ++ self._alt_pattern = re.compile(r'[\[\]]') + +@@ -535,3 +535,3 @@ + orientation = (str[0] == '[' or str[0] == ']') +- remoteOrientation = (re.search('\[', str) is not None) ++ remoteOrientation = (re.search(r'\[', str) is not None) + if orientation: ===================================== debian/rules ===================================== @@ -16,8 +16,7 @@ export PYBUILD_BEFORE_TEST = mkdir {build_dir}/vcf; \ %: dh $@ --buildsystem=pybuild -override_dh_install: - dh_install +execute_after_dh_install: # move testdata to separate dir mkdir -p $(examplesdir) mv `find debian/python3-$(PYBUILD_NAME) -type d -name test | head -n 1` $(examplesdir) View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/-/compare/ee9f6539b94f9a2b1323a46b170c735790ef6b0d...2ab9de1a6ca10b4c5793a15928fe5d643c722a71 -- View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/-/compare/ee9f6539b94f9a2b1323a46b170c735790ef6b0d...2ab9de1a6ca10b4c5793a15928fe5d643c722a71 You're receiving this email because of your account on salsa.debian.org.
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