Subject: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

From: Ricardo Wurmus <[email-masked]>
Date: Wed, 22 Feb 2017 13:42:01 +0100

Ricardo Wurmus <[email-masked]> writes:

> Leo Famulari <[email-masked]> writes:
>
>> On Tue, Feb 21, 2017 at 06:30:12PM +0100, Ricardo Wurmus wrote:
>>> From 1ac5166df11766b47cd1ac723a464063a89afc96 Mon Sep 17 00:00:00 2001
>>> From: Ricardo Wurmus <[email-masked]>
>>> Date: Tue, 21 Feb 2017 18:28:21 +0100
>>> Subject: [PATCH] gnu: python-dendropy: Disable failing tests.
>>>
>>> * gnu/packages/bioinformatics.scm (python-dendropy): Disable two failing
>>> tests.
>>
>> LGTM
>
> The problem was fixed in the upstream commit 93f984b in response to my
> bug report:
>
>     https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453
>
> I believe we can just backport this fix instead of deleting the test.

Here’s a patch that fixes the tests by applying the changes of the
upstream commit.  If this is fine I’ll push it to the python-tests
branch.

>From 0959e057886f9d9ab83467f6280ceefa35d05972 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <[email-masked]>
Date: Tue, 21 Feb 2017 18:28:21 +0100
Subject: [PATCH] gnu: python-dendropy: Fix failing tests.

* gnu/packages/patches/python-dendropy-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    |  3 +-
 .../patches/python-dendropy-fix-tests.patch        | 41 ++++++++++++++++++++++
 3 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 0b9b5b1a1..ac22924c4 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -853,6 +853,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-search-paths.patch		\
   %D%/packages/patches/python-3.4-fix-tests.patch		\
   %D%/packages/patches/python-3.5-fix-tests.patch		\
+  %D%/packages/patches/python-dendropy-fix-tests.patch		\
   %D%/packages/patches/python-file-double-encoding-bug.patch	\
   %D%/packages/patches/python-fix-tests.patch			\
   %D%/packages/patches/python-parse-too-many-fields.patch	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5a1738b93..de6186de2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1981,7 +1981,8 @@ accessing bigWig files.")
        (uri (pypi-uri "DendroPy" version))
        (sha256
         (base32
-         "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))))
+         "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
+       (patches (search-patches "python-dendropy-fix-tests.patch"))))
     (build-system python-build-system)
     (home-page "http://packages.python.org/DendroPy/")
     (synopsis "Library for phylogenetics and phylogenetic computing")
diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch
new file mode 100644
index 000000000..30ab618ff
--- /dev/null
+++ b/gnu/packages/patches/python-dendropy-fix-tests.patch
@@ -0,0 +1,41 @@
+This patch fixes two test failures.  It was downloaded from:
+https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453
+
+From 93f984bba7a6c588a28ca87f4e557ce283809453 Mon Sep 17 00:00:00 2001
+From: jeetsukumaran <[email-masked]>
+Date: Tue, 21 Feb 2017 16:41:01 -0500
+Subject: [PATCH] Update to Python 3 container and iteration semantics
+
+---
+ dendropy/dataio/newickreader.py | 3 ++-
+ dendropy/datamodel/treemodel.py | 3 +++
+ 2 files changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/dendropy/dataio/newickreader.py b/dendropy/dataio/newickreader.py
+index 6dcf3c5..f978729 100644
+--- a/dendropy/dataio/newickreader.py
++++ b/dendropy/dataio/newickreader.py
+@@ -303,7 +303,8 @@ def tree_iter(self,
+                     taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
+             yield tree
+             if tree is None:
+-                raise StopIteration
++                # raise StopIteration
++                return
+ 
+     def _read(self,
+             stream,
+diff --git a/dendropy/datamodel/treemodel.py b/dendropy/datamodel/treemodel.py
+index 0ecfe31..73146f0 100644
+--- a/dendropy/datamodel/treemodel.py
++++ b/dendropy/datamodel/treemodel.py
+@@ -772,6 +772,9 @@ def __hash__(self):
+     def __eq__(self, other):
+         return self is other
+ 
++    def __lt__(self, other):
++        return id(self) < id(other)
++
+     ###########################################################################
+     ### Basic Structure
+ 
-- 
2.11.1

--
Ricardo

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