Alexandre Detiste pushed to branch master at Debian Med / python-cgecore
Commits: e4798232 by Alexandre Detiste at 2024-11-19T21:17:48+01:00 use dh-sequence-python3 - - - - - 65c32693 by Alexandre Detiste at 2024-11-19T21:24:16+01:00 Python 3.12 + 3.13 transition - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/python3.13.patch - + debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +python-cgecore (1.5.6+ds-2) unstable; urgency=medium + + * Team upload. + * Patch out regexp that causes SyntaxWarning's (Closes: #1085895) + * Patch out usage of "pipes" module removed from Py3.13 (Closes: #1084632) + * Use dh-sequence-python3 + + -- Alexandre Detiste <[email protected]> Tue, 19 Nov 2024 21:23:35 +0100 + python-cgecore (1.5.6+ds-1) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -5,7 +5,7 @@ Section: python Testsuite: autopkgtest-pkg-python Priority: optional Build-Depends: debhelper-compat (= 13), - dh-python, + dh-sequence-python3, python3, python3-setuptools, python3-biopython ===================================== debian/patches/python3.13.patch ===================================== @@ -0,0 +1,70 @@ +--- a/cgecore/cmdline.py ++++ b/cgecore/cmdline.py +@@ -6,7 +6,7 @@ + # This script is part of the CGE Pipeline structure + import sys, os + from subprocess import Popen, PIPE +-from pipes import quote ++from shlex import quote + from time import time, sleep + from datetime import timedelta + +--- a/cgecore/cgefinder.py ++++ b/cgecore/cgefinder.py +@@ -239,8 +239,8 @@ + align_homo = "".join(kma_results[db][hit]['homo_string']) + + # Extract only aligned sequences +- start = re.search("^-*(\w+)", align_query).start(1) +- end = re.search("\w+(-*)$", align_query).start(1) ++ start = re.search(r"^-*(\w+)", align_query).start(1) ++ end = re.search(r"\w+(-*)$", align_query).start(1) + + kma_results[db][hit]['sbjct_string'] = align_sbjct[start:end] + kma_results[db][hit]['query_string'] = align_query[start:end] +--- a/cgecore/utility.py ++++ b/cgecore/utility.py +@@ -134,7 +134,7 @@ + return inv_map + + class Reg: +- """ ++ r""" + NAME: Reg - Extended Regular Expression Handler + AUTHOR: Martin Thomsen + DESCRIPTION: +@@ -488,9 +488,9 @@ + path given as input + """ + # Sanity checkpoint +- src = re.sub('[^\w/\-\.\*]', '', src) +- dst = re.sub('[^\w/\-\.\*]', '', dst) +- if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: ++ src = re.sub(r'[^\w/\-\.\*]', '', src) ++ dst = re.sub(r'[^\w/\-\.\*]', '', dst) ++ if len(re.sub(r'[\W]', '', src)) < 5 or len(re.sub(r'[\W]', '', dst)) < 5: + debug.log("Error: Moving file failed. Provided paths are invalid! src='%s' dst='%s'"%(src, dst)) + else: + # Check destination +@@ -517,7 +517,7 @@ + debug.log("Moving File(s)...", "Move from %s"%src, "to %s"%dst) + for file_ in files: + # Check if file contains invalid symbols: +- invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_)) ++ invalid_chars = re.findall(r'[^\w/\-\.\*]', os.path.basename(file_)) + if invalid_chars: + debug.graceful_exit(("Error: File %s contains invalid " + "characters %s!" +@@ -536,9 +536,9 @@ + path given as input + """ + # Sanity checkpoint +- src = re.sub('[^\w/\-\.\*]', '', src) +- dst = re.sub('[^\w/\-\.\*]', '', dst) +- if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5: ++ src = re.sub(r'[^\w/\-\.\*]', '', src) ++ dst = re.sub(r'[^\w/\-\.\*]', '', dst) ++ if len(re.sub(r'[\W]', '', src)) < 5 or len(re.sub(r'[\W]', '', dst)) < 5: + debug.log("Error: Copying file failed. Provided paths are invalid! src='%s' dst='%s'"%(src, dst)) + else: + # Check destination ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +python3.13.patch ===================================== debian/rules ===================================== @@ -3,7 +3,7 @@ export PYBUILD_NAME=cgecore %: - dh $@ --with python3 --buildsystem=pybuild + dh $@ --buildsystem=pybuild override_dh_auto_clean: dh_auto_clean View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/80f95cd5fd2dcc44efd86fd806e4d753f9d75e7d...65c326937a1891ca06d94c2b78c6a065c7e97361 -- View it on GitLab: https://salsa.debian.org/med-team/python-cgecore/-/compare/80f95cd5fd2dcc44efd86fd806e4d753f9d75e7d...65c326937a1891ca06d94c2b78c6a065c7e97361 You're receiving this email because of your account on salsa.debian.org.
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