[med-svn] [Git][med-team/python-biopython][master] 2 commits: Ignore some failing test

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-biopython


Commits:
bb94263d by Andreas Tille at 2019-11-19T16:46:25Z
Ignore some failing test

- - - - -
e22d8659 by Andreas Tille at 2019-11-19T18:12:32Z
exclude docstring tests - thanks to Peter Cock

- - - - -


3 changed files:

- + debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
- + debian/patches/exclude_docstring_tests.patch
- debian/patches/series


Changes:

=====================================
debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
=====================================
@@ -0,0 +1,30 @@
+From 5af680b5043c9f160a19e4bb0deab0ccc271280d Mon Sep 17 00:00:00 2001
+From: Peter Cock <p.j.a.cock at googlemail.com>
+Date: Tue, 19 Nov 2019 09:59:16 +0000
+Subject: [PATCH] Ignore C modules with no docstrings
+   Does not work as expected
+
+---
+ Tests/run_tests.py | 9 +++++++++
+ 1 file changed, 9 insertions(+)
+
+diff --git a/Tests/run_tests.py b/Tests/run_tests.py
+index 15503f65d5..084df08afc 100644
+--- a/Tests/run_tests.py
++++ b/Tests/run_tests.py
+@@ -358,6 +358,15 @@ def runTest(self, name):
+                 except MissingPythonDependencyError:
+                     sys.stderr.write("skipped, missing Python dependency\n")
+                     return True
++                except ValueError as e:
++                    if str(e).startswith("module ") and str(e).endswith("has no docstrings"):
++                        # Seen with some C modules via Debian build testing
++                        sys.stderr.write("skipped, has no docstrings\n")
++                        return True
++                    sys.stderr.write("FAIL, ValueError\n")
++                    result.stream.write("ERROR while importing %s: %s\n" % (name, e))
++                    result.printErrors()
++                    return False
+                 except ImportError as e:
+                     sys.stderr.write("FAIL, ImportError\n")
+                     result.stream.write("ERROR while importing %s: %s\n" % (name, e))


=====================================
debian/patches/exclude_docstring_tests.patch
=====================================
@@ -0,0 +1,20 @@
+From: Peter Cock <p.j.a.cock at googlemail.com>
+Last-Update: Tue, 19 Nov 2019 10:03:25 +0000
+Bug-Debian: https://bugs.debian.org/944242
+Description: Test issues with BioPython 1.75
+
+--- a/Tests/run_tests.py
++++ b/Tests/run_tests.py
+@@ -148,9 +148,9 @@ except ImportError:
+ 
+ # Skip Bio.Seq doctest under Python 2, see http://bugs.python.org/issue7490
+ # Can't easily write exceptions with consistent class name in python 2 and 3
+-if sys.version_info[0] == 2:
+-    EXCLUDE_DOCTEST_MODULES.append("Bio.Seq")
+-    EXCLUDE_DOCTEST_MODULES.append("Bio.Phylo")
++#if sys.version_info[0] == 2:
++#    EXCLUDE_DOCTEST_MODULES.append("Bio.Seq")
++#    EXCLUDE_DOCTEST_MODULES.append("Bio.Phylo")
+ 
+ 
+ def find_modules(path):


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,5 @@ remove_mathml-qname.patch
 privacy_breach.patch
 reportlab3.5.patch
 python_3.8_iteration_fix.patch
+# 5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
+exclude_docstring_tests.patch



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/3dbc41144094f7a25205d0a4445f68e95609ccce...e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/3dbc41144094f7a25205d0a4445f68e95609ccce...e22d86592d4c29c723297d3d5eb9cc63aa6f8fb8
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191119/bca05705/attachment-0001.html>