Étienne Mollier pushed to branch master at Debian Med / ivar
Commits: fa696fe8 by Étienne Mollier at 2021-09-16T21:54:15+02:00 update debian/source/lintian-overrides A change in the format of the detection of lines too long for a source code is causing a mismatched-override lintian warning (in addition to the error that cropped back up). - - - - - 2324e5be by Étienne Mollier at 2021-09-16T22:04:28+02:00 add privacy-breach.patch to point to local diagram The diagram shown was initially pulled from github. Thanks lintian for catching this! - - - - - f2c38ea2 by Étienne Mollier at 2021-09-16T22:31:45+02:00 ready to upload to unstable - - - - - 4 changed files: - debian/changelog - + debian/patches/privacy-breach.patch - debian/patches/series - debian/source/lintian-overrides Changes: ===================================== debian/changelog ===================================== @@ -1,10 +1,14 @@ -ivar (1.3.1+dfsg-2) UNRELEASED; urgency=medium +ivar (1.3.1+dfsg-2) unstable; urgency=medium - * add forward-build-options.patch; build ivar with Debian build options + * add forward-build-options.patch; build ivar with hardened build options * add gcc-11.patch; fixes ftbfs with Gcc 11 (Closes: #984067) * d/salsa-ci.yml: allow reproducible build test to fail, for the moment + * update d/s/lintian-overrides to match the new lintian semantics against the + false positive + * add privacy-breach.patch to point to the local diagram in cookbook.html, + instead of the github page - -- Étienne Mollier <[email protected]> Sat, 28 Aug 2021 11:17:19 +0200 + -- Étienne Mollier <[email protected]> Thu, 16 Sep 2021 22:22:30 +0200 ivar (1.3.1+dfsg-1) unstable; urgency=medium ===================================== debian/patches/privacy-breach.patch ===================================== @@ -0,0 +1,21 @@ +Description: fix privacy-breach-generic in cookbookpage.html + The document refers to a diagram hosted on github, but there is a local copy + readily available for use, so lets use this one. + . + The file layout is somewhat odd, so I refrained to forward upstream. +Author: Étienne Mollier <[email protected]> +Forwarded: not-needed +Last-Update: 2021-09-16 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- ivar.orig/docs/html/cookbookpage.html ++++ ivar/docs/html/cookbookpage.html +@@ -73,7 +73,7 @@ + <p>The two pipelines are distributed along with iVar and are present in the<a href="https://github.com/andersen-lab/ivar/tree/master/pipeline";>pipeline/</a> and <a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field";>pipeline_field/</a> fodlers respectively.</p> + <p>For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.</p> + <div class="fragment"><div class="line">in_dir = "<input fastq files>"</div><div class="line">out_dir = "<output directory>"</div><div class="line">bed = "<bed-file-with-primer-positions>"</div><div class="line">ref="<path to reference fasta>"</div></div><!-- fragment --><div class="image"> +-<img src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png"; width="500"/> ++<img src="./pipeline.png/pipeline.png" width="500"/> + </div> + <h3>Call iSNVs from samples with known reference sequence</h3> + <p><a href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb";>Link to Jupyter Notebook</a></p> ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ Fix-warning.patch forward-build-options.patch gcc-11.patch +privacy-breach.patch ===================================== debian/source/lintian-overrides ===================================== @@ -1,3 +1,2 @@ # False positive -ivar source: source-is-missing docs/html/menu.js line length is 695 characters (>512) - +ivar source: source-is-missing docs/html/menu.js line 26 is 695 characters long (>512) View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4 -- View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4 You're receiving this email because of your account on salsa.debian.org.
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