Ananthu C V pushed to branch master at Debian Med / lefse
Commits: d69e3719 by Ananthu C V at 2024-12-04T23:43:02+05:30 Correct patch header metadata - - - - - ff8fbfbf by Ananthu C V at 2024-12-04T23:45:12+05:30 Fix typos in manpages - - - - - 367c4f00 by Ananthu C V at 2024-12-05T00:08:04+05:30 Add patch to fix syntaxwarnings (Closes: #1085666) - - - - - aa5c204d by Ananthu C V at 2024-12-05T00:08:15+05:30 Bump standards version to 4.7.0 (no changes needed) - - - - - 713d9c56 by Ananthu C V at 2024-12-05T00:19:12+05:30 Update changelog - - - - - 8 changed files: - debian/changelog - debian/control - debian/mans/lefse_plot_features.py.1 - debian/mans/lefse_plot_res.py.1 - debian/mans/lefse_run.py.1 - debian/patches/2to3.patch - debian/patches/series - + debian/patches/use-raw-strings.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +lefse (1.1.2-2) UNRELEASED; urgency=medium + + * Correct patch header metadata + * Fix typos in manpages + * Add patch to fix syntaxwarnings (Closes: #1085666) + * Bump standards version to 4.7.0 (no changes needed) + + -- Ananthu C V <[email protected]> Thu, 05 Dec 2024 00:18:51 +0530 + lefse (1.1.2-1) unstable; urgency=medium * Fix Homepage ===================================== debian/control ===================================== @@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools -Standards-Version: 4.6.0 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/lefse Vcs-Git: https://salsa.debian.org/med-team/lefse.git Homepage: https://github.com/SegataLab/lefse ===================================== debian/mans/lefse_plot_features.py.1 ===================================== @@ -65,7 +65,7 @@ unused the format for the output file .TP \fB\-f\fR {all,diff,one} -wheter to plot all features (all), only those +whether to plot all features (all), only those differentially abundant according to LEfSe or only one (the one given with \fB\-\-feature_name\fR) .TP ===================================== debian/mans/lefse_plot_res.py.1 ===================================== @@ -61,7 +61,7 @@ only for vertical histograms set the color of the background .TP \fB\-\-subclades\fR N_SCL -number of label levels to be dislayed (starting from +number of label levels to be displayed (starting from the leaves, \fB\-1\fR means all the levels, 1 is default ) .TP \fB\-\-max_feature_len\fR MAX_FEATURE_LEN ===================================== debian/mans/lefse_run.py.1 ===================================== @@ -45,7 +45,7 @@ max log ingluence of LDA coeff verbose execution (default 0) .TP \fB\-\-wilc\fR int -wheter to perform the Wicoxon step (default 1) +whether to perform the Wicoxon step (default 1) .TP \fB\-r\fR str select LDA or SVM for effect size (default LDA) ===================================== debian/patches/2to3.patch ===================================== @@ -1,7 +1,7 @@ Description: 2to3 to port from python2 to python3 Bug-Debian: https://bugs.debian.org/936836 Author: Shayan Doust <[email protected]> -Last-Update: Mon, 09 Sep 2019 21:01:50 +0200 +Last-Update: 2019-09-09 --- a/lefsebiom/AbundanceTable.py +++ b/lefsebiom/AbundanceTable.py ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ 2to3.patch +use-raw-strings.patch ===================================== debian/patches/use-raw-strings.patch ===================================== @@ -0,0 +1,23 @@ +Description: use raw strings for strings with escape sequences +Author: Ananthu C V <[email protected]> +Bug-Debian: https://bugs.debian.org/1085666 +Last-Update: 2024-12-04 +--- a/lefsebiom/AbundanceTable.py ++++ b/lefsebiom/AbundanceTable.py +@@ -386,3 +386,3 @@ + #Used to substitute . to - +- reSubPeriod = re.compile('\.') ++ reSubPeriod = re.compile(r'\.') + +--- a/lefse/lefse_format_input.py ++++ b/lefse/lefse_format_input.py +@@ -273,3 +273,3 @@ + +- for v in ["\|"]: ++ for v in [r"\|"]: + ret = [re.sub(v,".",f) for f in ret] +@@ -463,2 +463,2 @@ + if __name__ == '__main__': +- format_input() +\ No newline at end of file ++ format_input() View it on GitLab: https://salsa.debian.org/med-team/lefse/-/compare/5507a90038ca8fee55cb90391276c0c4323281a7...713d9c56c25d83f9f72fa00a3fafe88d43329e4c -- View it on GitLab: https://salsa.debian.org/med-team/lefse/-/compare/5507a90038ca8fee55cb90391276c0c4323281a7...713d9c56c25d83f9f72fa00a3fafe88d43329e4c You're receiving this email because of your account on salsa.debian.org.
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