Pierre Gruet pushed to branch master at Debian Med / spades
Commits: 4b4994e2 by Pierre Gruet at 2024-12-16T21:27:35+01:00 Passing raw regex patterns in Python - - - - - dba0a18a by Pierre Gruet at 2024-12-16T21:28:41+01:00 Adding changelog entry of last upload to unstable - - - - - 3 changed files: - debian/changelog - + debian/patches/raw_regex_pattern.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -21,6 +21,13 @@ spades (4.0.0+dfsg1-1) experimental; urgency=medium -- Pierre Gruet <[email protected]> Wed, 02 Oct 2024 08:56:41 +0200 +spades (3.15.5+dfsg-8) unstable; urgency=medium + + * Team upload + * Fixing Python3 SyntaxWarning by using raw regex patterns (Closes: #1087093) + + -- Pierre Gruet <[email protected]> Sat, 14 Dec 2024 00:09:08 +0100 + spades (3.15.5+dfsg-7) unstable; urgency=medium * Replace distutils which is removed in Python3.12 ===================================== debian/patches/raw_regex_pattern.patch ===================================== @@ -0,0 +1,86 @@ +Description: passing regex patterns as raw strings to avoid SyntaxWarnings with + Python 3 +Author: Pierre Gruet <[email protected]> +Bug-Debian: https://bugs.debian.org/1087093 +Forwarded: no +Last-Update: 2024-12-14 + +--- a/src/projects/mts/scripts/common.py ++++ b/src/projects/mts/scripts/common.py +@@ -84,7 +84,7 @@ + return sample + "-" + res + + id_re = re.compile("\\d+") +-split_format = re.compile("^([\w.-]+)_\(\d+_\d+\)$") ++split_format = re.compile(r"^([\w.-]+)_\(\d+_\d+\)$") + + def extract_id(name): + bin_id = None +@@ -114,7 +114,7 @@ + + def contig_length(name): + # Length of contig split +- split = re.search("\((\d+)_(\d+)\)", name) ++ split = re.search(r"\((\d+)_(\d+)\)", name) + if split: + return int(split.group(2)) - int(split.group(1)) + #Default format +--- a/src/projects/mts/scripts/converters.py ++++ b/src/projects/mts/scripts/converters.py +@@ -41,7 +41,7 @@ + self.header(params[1:]) + self.format(params[0], params[1:]) + +-extract_num = re.compile("\d+") ++extract_num = re.compile(r"\d+") + + class BinningParser: + def __init__(self, sep=",", filter=None): +--- a/src/projects/mts/scripts/filter_nucmer.py ++++ b/src/projects/mts/scripts/filter_nucmer.py +@@ -32,9 +32,9 @@ + sys.exit(2) + + with open(nucmer_output_fn, "r") as nucmer_output: +- contig_data = re.compile("CONTIG: ([\w.-]+) \((\d+)bp\)") +- align_data = re.compile("Best alignment score: ([\d.]+)") +- split_format = re.compile("^([\w.-]+_)_(\d+_\d+)_$") #Replace brackets back ++ contig_data = re.compile(r"CONTIG: ([\w.-]+) \((\d+)bp\)") ++ align_data = re.compile(r"Best alignment score: ([\d.]+)") ++ split_format = re.compile(r"^([\w.-]+_)_(\d+_\d+)_$") #Replace brackets back + while True: + line = nucmer_output.readline() + if not line or line.startswith("Analyzing coverage"): +--- a/src/projects/mts/scripts/run_tsne.py ++++ b/src/projects/mts/scripts/run_tsne.py +@@ -83,7 +83,7 @@ + return points, names + + import re +-extract_num = re.compile("\d+") ++extract_num = re.compile(r"\d+") + + def run_tsne(features_file, colors_file, output_prefix + , filter_sample=[] +--- a/src/projects/mts/test.py ++++ b/src/projects/mts/test.py +@@ -123,7 +123,7 @@ + class mut: + res = 0 + +- re_num = re.compile("-?\d+(?:\.\d+)?") ++ re_num = re.compile(r"-?\d+(?:\.\d+)?") + def read_cell(str): + maybe_num = re_num.search(str) + if not maybe_num: +--- a/src/projects/spades/pipeline/spades_pipeline/support.py ++++ b/src/projects/spades/pipeline/spades_pipeline/support.py +@@ -485,7 +485,7 @@ + return text + + def natural_keys(text): +- return [atoi(c) for c in re.split("(\d+)", text)] ++ return [atoi(c) for c in re.split(r"(\d+)", text)] + + latest_dir = None + for dir_to_test in sorted(glob.glob(pattern), key=natural_keys, reverse=True): ===================================== debian/patches/series ===================================== @@ -26,3 +26,4 @@ use_debian_xxhash.patch use_debian_cuckoo.patch samtools_missing_source.patch deactivate_tests_with_no_data.patch +raw_regex_pattern.patch View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/18a83bef87fb0b17e299e404b4a9e7a295c18f75...dba0a18a8ae6f5b027bebc923ef4c1f97051abdd -- View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/18a83bef87fb0b17e299e404b4a9e7a295c18f75...dba0a18a8ae6f5b027bebc923ef4c1f97051abdd You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
