01/01: gnu: python-dendropy: Fix failing tests.

[Ricardo Wurmus]

rekado pushed a commit to branch python-tests
in repository guix.

commit 1885bb0c08e943a2e0e37c5c0a83473c8af904d0
Author: Ricardo Wurmus <address@hidden>
Date:   Tue Feb 21 18:28:21 2017 +0100

    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(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 63eb56c..899dc06 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 5a1738b..de6186d 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 0000000..30ab618
--- /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 <address@hidden>
+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
+