[med-svn] [Git][med-team/changeo][master] 2 commits: Fix Python3.12 string syntax Closes: #1085416

[Andreas Tille (@tille)]

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 <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>,
+Uploaders: Steffen Moeller <moeller at debian.org>
 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 <tille at debian.org>
+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
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