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authorRicardo Wurmus <rekado@elephly.net>2017-02-21 18:28:21 +0100
committerRicardo Wurmus <rekado@elephly.net>2017-02-24 23:44:31 +0100
commit1885bb0c08e943a2e0e37c5c0a83473c8af904d0 (patch)
treec28728da69e667716e0c38ecc8e7143eaf8d8db7
parentd6caebc4d63ac8e7ae5e82b1261557e1b6898c10 (diff)
downloadguix-1885bb0c08e943a2e0e37c5c0a83473c8af904d0.tar.gz
guix-1885bb0c08e943a2e0e37c5c0a83473c8af904d0.zip
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.
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm3
-rw-r--r--gnu/packages/patches/python-dendropy-fix-tests.patch41
3 files changed, 44 insertions, 1 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 63eb56cc51..899dc06b8e 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 5a1738b936..de6186de27 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 0000000000..30ab618ff1
--- /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 <jeetsukumaran@gmail.com>
+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
+