[med-svn] [Git][med-team/python-biopython][master] 3 commits: forward phyml test patch upstream

Fri Sep 11 22:25:04 BST 2020


Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
f22b5861 by Étienne Mollier at 2020-09-11T00:16:53+02:00
forward phyml test patch upstream

- - - - -
083b8a55 by Étienne Mollier at 2020-09-11T22:49:21+02:00
add spelling-error-in-binaries.patch

- - - - -
68e959e2 by Étienne Mollier at 2020-09-11T23:18:30+02:00
added privacy_breach_ie9.patch

- - - - -


4 changed files:

- + debian/patches/privacy_breach_ie9.patch
- debian/patches/series
- + debian/patches/spelling-error-in-binaries.patch
- debian/patches/stabilize-phyml-test.patch


Changes:

=====================================
debian/patches/privacy_breach_ie9.patch
=====================================
@@ -0,0 +1,22 @@
+Description: fix privacy breach with html5shiv
+ Actually the script called is commented out, except when reading the page with
+ Internet Explorer 9.  This patch makes sure the script is not called at all,
+ even if it is very unlikely that HTML document installed in Debian will ever
+ be read with this browser.
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Forwarded: not-needed
+Last-Update: 2020-09-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Doc/cookbook/Restriction/Restriction.html
++++ python-biopython/Doc/cookbook/Restriction/Restriction.html
+@@ -75,9 +75,6 @@
+     code span.vs { color: #4070a0; } /* VerbatimString */
+     code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
+   </style>
+-  <!--[if lt IE 9]>
+-    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
+-  <![endif]-->
+ </head>
+ <body>
+ <h1 id="working-with-restriction-enzymes">Working with restriction enzymes</h1>


=====================================
debian/patches/series
=====================================
@@ -1,5 +1,7 @@
 remove_mathml-qname.patch
 privacy_breach.patch
+privacy_breach_ie9.patch
 blastdbv4-impl.patch
 fix-use-of-unversionned-python.patch
 stabilize-phyml-test.patch
+spelling-error-in-binaries.patch


=====================================
debian/patches/spelling-error-in-binaries.patch
=====================================
@@ -0,0 +1,20 @@
+Description: fix lintian message spelling-error-in-binary
+ As a side note, lintian reports another spelling error "algorith" in another
+ binary, but the matching source code does not show any such issue in strings,
+ so it might have been a string sliced at a bad place by the compiler.
+Author: Étienne Mollier <etienne.mollier at mailoo.org>
+Forwarded: no
+Last-Update: 2020-09-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-biopython.orig/Bio/Cluster/clustermodule.c
++++ python-biopython/Bio/Cluster/clustermodule.c
+@@ -2132,7 +2132,7 @@
+ "\n"
+ " - transpose: if equal to 0: the distances between rows are\n"
+ "   calculated;\n"
+-"   if equal to 1, the distances beteeen columns are calculated.\n"
++"   if equal to 1, the distances between columns are calculated.\n"
+ "\n"
+ " - dist: specifies the distance function to be used:\n"
+ "\n"


=====================================
debian/patches/stabilize-phyml-test.patch
=====================================
@@ -5,8 +5,8 @@ Description: stabilize the test involving phyml
  environment variable PHYMLCPUS, allows one to avoid the message "No protocol
  specified" in the error output, which interferes with the version test.
 Author: Étienne Mollier <etienne.mollier at mailoo.org>
-Forwarded: no
-Last-Update: 2020-09-10
+Forwarded: https://github.com/biopython/biopython/pull/3268
+Last-Update: 2020-09-11
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 --- python-biopython.orig/Tests/test_phyml_tool.py



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/891939b0eb21c2cc0bddbc7738dbe5f7ba377221...68e959e2deccce41315988c2744262db15065ddc
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