[med-svn] [Git][med-team/ivar][master] 3 commits: update debian/source/lintian-overrides

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  Sat, 28 Aug 2021 11:17:19 +0200
+ -- Étienne Mollier <emollier at debian.org>  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 <emollier at debian.org>
+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
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