[med-svn] [Git][med-team/circlator][master] 4 commits: Fix Python3.12 string syntax Closes: #1085417

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / circlator


Commits:
eb5f83c0 by Andreas Tille at 2024-12-06T10:49:06+01:00
Fix Python3.12 string syntax Closes: #1085417

- - - - -
0a235ab2 by Andreas Tille at 2024-12-06T10:49:28+01:00
Standards-Version: 4.7.0 (routine-update)

- - - - -
63508b9b by Andreas Tille at 2024-12-06T10:50:43+01:00
routine-update: Ready to upload to unstable

- - - - -
c8cd26d2 by Andreas Tille at 2024-12-06T10:53:00+01:00
DEP3

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/python3.12-syntax.patch
- debian/patches/remove-distutils.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+circlator (1.5.6-12) unstable; urgency=medium
+
+  * Fix Python3.12 string syntax
+    Closes: #1085417
+  * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 06 Dec 2024 10:49:37 +0100
+
 circlator (1.5.6-11) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -18,7 +18,7 @@ Build-Depends: debhelper-compat (= 13),
                bwa <!nocheck>,
                prodigal <!nocheck>,
                canu <!nocheck>
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/circlator
 Vcs-Git: https://salsa.debian.org/med-team/circlator.git
 Homepage: https://sanger-pathogens.github.io/circlator/


=====================================
debian/patches/python3.12-syntax.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix Python3.12 string syntax
+Bug-Debian: https://bugs.debian.org/1085417
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-06-06
+
+--- a/circlator/dnaa.py
++++ b/circlator/dnaa.py
+@@ -15,7 +15,7 @@ class UniprotDownloader:
+     def __init__(self, min_gene_length=333, max_gene_length=500, uniprot_search='dnaa', header_regex='dnaa', header_regex_ignorecase=True):
+         self.min_gene_length = min_gene_length
+         self.max_gene_length = max_gene_length
+-        self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
++        self.uniprot_search = re.sub(r'\s+', '+', uniprot_search.strip())
+         if header_regex_ignorecase:
+             self.header_regex = re.compile(header_regex, re.IGNORECASE)
+         else:


=====================================
debian/patches/remove-distutils.patch
=====================================
@@ -1,3 +1,8 @@
+Author: Nilesh Patra
+Last-Update: 2023-12-03
+Description: Replace LooseVersion usage with packaging.version.parse
+Bug-Debian: https://bugs.debian.org/1056234
+
 --- a/circlator/program.py
 +++ b/circlator/program.py
 @@ -2,7 +2,7 @@


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ fix_canu_detection.patch
 switch-to-pytest.patch
 split_canu_tests
 remove-distutils.patch
+python3.12-syntax.patch



View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/270329badf9cc4cc4b8dd8bdc74872d7a11bbd0f...c8cd26d2e2037e040014d9ca506dc65d3d6caa7d

-- 
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/270329badf9cc4cc4b8dd8bdc74872d7a11bbd0f...c8cd26d2e2037e040014d9ca506dc65d3d6caa7d
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