[med-svn] [Git][med-team/quast][master] Attempt to let test suite pass

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / quast


Commits:
d3b5a64c by Andreas Tille at 2020-06-26T13:06:30+02:00
Attempt to let test suite pass

- - - - -


4 changed files:

- debian/control
- + debian/patches/cgi_escape.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -11,7 +11,9 @@ Build-Depends: debhelper-compat (= 13),
                python3-simplejson,
                busco,
                minimap2,
-               tigr-glimmer
+               tigr-glimmer,
+               python3-matplotlib <!nocheck>,
+               python3-joblib <!nocheck>
 #               hmmer,
 #               bwa,
 #               bedtools,
@@ -41,7 +43,9 @@ Depends: ${shlibs:Depends},
          bedtools,
          barrnap,
          busco,
-         tigr-glimmer
+         tigr-glimmer,
+         python-matplotlib,
+         python3-joblib
 Description: Quality Assessment Tool for Genome Assemblies
  QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST
  project.  It can works both with and without a given reference genome.


=====================================
debian/patches/cgi_escape.patch
=====================================
@@ -0,0 +1,52 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 26 Jun 2020 11:35:10 +0200
+Origin: https://github.com/posativ/isso/issues/603
+Description: cgi.escape seems to be removed in Python 3.8. Use html.escape instead.
+
+--- a/quast_libs/site_packages/jsontemplate/jsontemplate.py
++++ b/quast_libs/site_packages/jsontemplate/jsontemplate.py
+@@ -47,7 +47,7 @@ import re
+ import sys
+ 
+ # For formatters
+-import cgi  # cgi.escape
++import html  # html.escape
+ try:
+     from urllib  import urlencode, quote_plus
+ except:
+@@ -555,7 +555,7 @@ def _ToString(x):
+ 
+ 
+ def _HtmlAttrValue(x):
+-  return cgi.escape(x, quote=True)
++  return html.escape(x, quote=True)
+ 
+ 
+ def _AbsUrl(relative_url, context, unused_args):
+@@ -580,7 +580,7 @@ def _AbsUrl(relative_url, context, unuse
+ # This is a *public* constant, so that callers can use it construct their own
+ # formatter lookup dictionaries, and pass them in to Template.
+ _DEFAULT_FORMATTERS = {
+-    'html': cgi.escape,
++    'html': html.escape,
+ 
+     # The 'htmltag' name is deprecated.  The html-attr-value name is preferred
+     # because it can be read with "as":
+@@ -607,7 +607,7 @@ _DEFAULT_FORMATTERS = {
+ 
+     # Just show a plain URL on an HTML page (without anchor text).
+     'plain-url': lambda x: '<a href="%s">%s</a>' % (
+-        cgi.escape(x, quote=True), cgi.escape(x)),
++        html.escape(x, quote=True), html.escape(x)),
+ 
+     # A context formatter
+     'AbsUrl': _AbsUrl,
+@@ -840,7 +840,7 @@ def CompileTemplate(
+ 
+     more_formatters:
+         Something that can map format strings to formatter functions.  One of:
+-          - A plain dictionary of names -> functions  e.g. {'html': cgi.escape}
++          - A plain dictionary of names -> functions  e.g. {'html': html.escape}
+           - A higher-order function which takes format strings and returns
+             formatter functions.  Useful for when formatters have parsed
+             arguments.


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 noBwa.patch
 adjustPythonImportPaths.patch
 pathonPaths.patch
+cgi_escape.patch


=====================================
debian/rules
=====================================
@@ -17,3 +17,8 @@ override_dh_auto_clean:
 override_dh_install:
 	dh_install
 	find debian -name LICENSE.txt -delete
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	PATH=$PATH:. ./setup.py test
+endif



View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/d3b5a64c82200499364b40b6fb95d4227ebd98c4

-- 
View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/d3b5a64c82200499364b40b6fb95d4227ebd98c4
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