[med-svn] [Git][med-team/srst2][master] 3 commits: syntax-warning.patch: new: fix Python SyntaxWarning.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Dec 5 21:14:16 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / srst2
Commits:
9f437180 by Étienne Mollier at 2024-12-05T22:12:20+01:00
syntax-warning.patch: new: fix Python SyntaxWarning.
Closes: #1087097
- - - - -
ceb8e8d0 by Étienne Mollier at 2024-12-05T22:12:56+01:00
d/patches/*: normalize last update timestamp.
- - - - -
6003ad0d by Étienne Mollier at 2024-12-05T22:13:50+01:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- debian/patches/2to3.patch
- debian/patches/add_usr_bin_python_to_scripts.patch
- debian/patches/check_command_line_arguments.patch
- debian/patches/fix_grep_call.patch
- debian/patches/fix_test.patch
- debian/patches/series
- + debian/patches/syntax-warning.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+srst2 (0.2.0-13) unstable; urgency=medium
+
+ * syntax-warning.patch: new: fix Python SyntaxWarning. (Closes: #1087097)
+ * d/patches/*: normalize last update timestamp.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 05 Dec 2024 22:13:26 +0100
+
srst2 (0.2.0-12) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,7 +1,7 @@
Description: Use 2to3 to port from Python2 to Python3
Bug-Debian: https://bugs.debian.org/938560
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 11 Dec 2019 15:20:13 +0100
+Last-Update: 2019-12-11
Bug-Upstream: https://github.com/katholt/srst2/issues/122
--- a/README.md
=====================================
debian/patches/add_usr_bin_python_to_scripts.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 31 May 2016 15:02:45 +0200
+Last-Update: 2016-05-31
Description: Add missing interpreter line
--- a/database_clustering/VFDBgenus.py
=====================================
debian/patches/check_command_line_arguments.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 07 Dec 2015 14:37:55 +0100
+Last-Update: 2015-12-07
Description: Check command line arguments before processing
--- a/database_clustering/get_all_vfdb.sh
=====================================
debian/patches/fix_grep_call.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 01 Mar 2017 09:15:07 +0100
+Last-Update: 2017-03-01
Bug-Debian: https://bugs.debian.org/856479
Description: Do not fail if search string contains special shell characters
=====================================
debian/patches/fix_test.patch
=====================================
@@ -1,5 +1,5 @@
Author: Ryan Wick <rrwick at gmail.com>
-Last-Update: Mon Aug 22 16:25:02 2016 +1000
+Last-Update: 2016-08-22
Origin: Upstream commit cd93cde1f2e4639db426e8b57b6ec5d278c0d02f
Description: Update test for recent version
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ fix_test.patch
fix_grep_call.patch
2to3.patch
biopython-1.78.patch
+syntax-warning.patch
=====================================
debian/patches/syntax-warning.patch
=====================================
@@ -0,0 +1,69 @@
+Description: fix Python SyntaxWarning.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087097
+Forwarded: no
+Last-Update: 2024-12-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- srst2.orig/database_clustering/VFDB_cdhit_to_csv.py
++++ srst2/database_clustering/VFDB_cdhit_to_csv.py
+@@ -50,7 +50,7 @@
+ for record in SeqIO.parse(open(args.infile, "r"), "fasta"):
+ full_name = record.description
+ genus = full_name.split("[")[-1].split()[0]
+- in_brackets = re.findall('\((.*?)\)', full_name)
++ in_brackets = re.findall(r'\((.*?)\)', full_name)
+ seqID = full_name.split("(")[0]
+ if in_brackets[0].startswith('gi:'):
+ gene = in_brackets[1]
+--- srst2.orig/database_clustering/align_plot_tree_min3.py
++++ srst2/database_clustering/align_plot_tree_min3.py
+@@ -25,7 +25,7 @@
+ #alignment()
+
+
+-r('''
++r(r'''
+ require(ape, quietly=TRUE)
+
+ all_files = list.files("/home/UNIMELB/hdashnow/resistance_database/by_gene",
+--- srst2.orig/scripts/getmlst.py
++++ srst2/scripts/getmlst.py
+@@ -178,7 +178,7 @@
+
+ print("\n For SRST2, remember to check what separator is being used in this allele database")
+ head = os.popen('head -n 1 ' + species_all_fasta_filename).read().rstrip()
+- m = re.match('>(.*)([_-])(\d*)',head).groups()
++ m = re.match(r'>(.*)([_-])(\d*)',head).groups()
+ if len(m)==3:
+ print()
+ print(" Looks like --mlst_delimiter '" + m[1] + "'")
+--- srst2.orig/scripts/srst2.py
++++ srst2/scripts/srst2.py
+@@ -87,7 +87,7 @@
+
+ # Mapping parameters for bowtie2
+ parser.add_argument('--stop_after', type=str, required=False, help='Stop mapping after this number of reads have been mapped (otherwise map all)')
+- parser.add_argument('--other', type=str, help='Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False)
++ parser.add_argument('--other', type=str, help=r'Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False)
+
+ # Filtering parameters for initial SAM file
+ parser.add_argument('--max_unaligned_overlap', type=int, default=10, help='Read discarded from alignment if either of its ends has unaligned '+\
+@@ -96,7 +96,7 @@
+ # Samtools parameters
+ parser.add_argument('--mapq', type=int, default=1, help='Samtools -q parameter (default 1)')
+ parser.add_argument('--baseq', type=int, default=20, help='Samtools -Q parameter (default 20)')
+- parser.add_argument('--samtools_args', type=str, help='Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False)
++ parser.add_argument('--samtools_args', type=str, help=r'Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False)
+
+ # Reporting options
+ parser.add_argument('--output', type=str, required=True, help='Prefix for srst2 output files')
+@@ -238,7 +238,7 @@
+ continue
+ flag = int(fields[1])
+ flag = (flag - 256) if (flag & 256) else flag
+- m = re.search("NM:i:(\d+)\s",line)
++ m = re.search(r"NM:i:(\d+)\s",line)
+ if m != None:
+ num_mismatch = m.group(1)
+ if int(num_mismatch) <= int(max_mismatch):
View it on GitLab: https://salsa.debian.org/med-team/srst2/-/compare/1a8f060ac05d2cc20f3b39a4a8842d2fcec88454...6003ad0d74213a7a61ec68b5d59cdfb5047577ba
--
View it on GitLab: https://salsa.debian.org/med-team/srst2/-/compare/1a8f060ac05d2cc20f3b39a4a8842d2fcec88454...6003ad0d74213a7a61ec68b5d59cdfb5047577ba
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