[med-svn] [Git][med-team/python-pyvcf][master] 7 commits: Drop dependency on python3-pkg-resources (Closes: #1083698)
Ananthu C V (@weepingclown)
gitlab at salsa.debian.org
Tue Nov 26 16:33:57 GMT 2024
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 <weepingclown at disroot.org> 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 <tille at debian.org>
-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 <weepingclown at debian.org>
+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 <weepingclown at debian.org>
+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 <weepingclown at debian.org>
+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
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