Andreas Tille pushed to branch master at Debian Med / changeo
Commits: 4945e9d3 by Andreas Tille at 2024-12-05T17:38:00+01:00 Fix Python3.12 string syntax Closes: #1085416 - - - - - 1482ce4c by Andreas Tille at 2024-12-05T17:39:14+01:00 Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/python3.12-syntax.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +changeo (1.3.0-3) UNRELEASED; urgency=medium + + * Team upload. + * Fix Python3.12 string syntax + Closes: #1085416 + * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) + + -- Andreas Tille <[email protected]> Thu, 05 Dec 2024 17:35:49 +0100 + changeo (1.3.0-2) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -1,11 +1,11 @@ Source: changeo Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Steffen Moeller <[email protected]>, +Uploaders: Steffen Moeller <[email protected]> Section: science Testsuite: autopkgtest-pkg-python Priority: optional Build-Depends: debhelper-compat (= 13), - dh-python, + dh-sequence-python3, python3-all, python3-setuptools Standards-Version: 4.7.0 @@ -21,7 +21,7 @@ Depends: ${python3:Depends}, Recommends: python3-biopython, python3-pandas, python3-scipy, - python3-presto (>= 0.6.2), + python3-presto, python3-airr Description: Repertoire clonal assignment toolkit (Python 3) Change-O is a collection of tools for processing the output of V(D)J ===================================== debian/patches/python3.12-syntax.patch ===================================== @@ -0,0 +1,49 @@ +Description: Fix Python3.12 string syntax +Bug-Debian: https://bugs.debian.org/1085416 +Author: Andreas Tille <[email protected]> +Last-Update: 2024-12-05 + +--- a/changeo/Applications.py ++++ b/changeo/Applications.py +@@ -280,7 +280,7 @@ def getIgBLASTVersion(exec=default_igbla + printError('Running command: %s\n%s' % (' '.join(cmd), e.output)) + + # Extract version number +- match = re.search('(?<=Package: igblast )(\d+\.\d+\.\d+)', stdout_str) ++ match = re.search(r'(?<=Package: igblast )(\d+\.\d+\.\d+)', stdout_str) + version = match.group(0) + +- return version +\ No newline at end of file ++ return version +--- a/changeo/IO.py ++++ b/changeo/IO.py +@@ -526,8 +526,8 @@ class IMGTReader: + Returns: + dict : database entries for gene calls. + """ +- clean_regex = re.compile('(,)|(\(see comment\))') +- delim_regex = re.compile('\sor\s') ++ clean_regex = re.compile(r'(,)|(\(see comment\))') ++ delim_regex = re.compile(r'\sor\s') + + # Gene calls + v_str = summary['V-GENE and allele'] +@@ -953,7 +953,7 @@ class IgBLASTReader: + + # Extract column names from comments + f = next((x for x in chunk if x.startswith('# V-(D)-J rearrangement summary'))) +- f = re.search('summary for query sequence \((.+)\)\.', f).group(1) ++ f = re.search(r'summary for query sequence \((.+)\)\.', f).group(1) + columns = [summary_map[x.strip()] for x in f.split(',')] + + # Extract first row as a list +@@ -987,7 +987,7 @@ class IgBLASTReader: + + # Extract column names from comments + f = next((x for x in chunk if x.startswith('# Sub-region sequence details'))) +- f = re.search('sequence details \((.+)\)', f).group(1) ++ f = re.search(r'sequence details \((.+)\)', f).group(1) + columns = [cdr3_map[x.strip()] for x in f.split(',')] + + # Extract first CDR3 as a list and remove the CDR3 label ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ rm-setuptools.patch +python3.12-syntax.patch ===================================== debian/rules ===================================== @@ -4,7 +4,7 @@ export PYBUILD_NAME=changeo %: - dh $@ --with python3 --buildsystem=pybuild + dh $@ --buildsystem=pybuild override_dh_installman: # Trick to avoid manpage to assume files with extension .py is a language View it on GitLab: https://salsa.debian.org/med-team/changeo/-/compare/4f9816d8a7c8082777a3405158848b92b22c9b46...1482ce4cbace9d249caf7a5445363e87ebabe65c -- View it on GitLab: https://salsa.debian.org/med-team/changeo/-/compare/4f9816d8a7c8082777a3405158848b92b22c9b46...1482ce4cbace9d249caf7a5445363e87ebabe65c You're receiving this email because of your account on salsa.debian.org.
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