From 1885bb0c08e943a2e0e37c5c0a83473c8af904d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: 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. --- .../patches/python-dendropy-fix-tests.patch | 41 ++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch (limited to 'gnu/packages/patches') 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 +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 + -- cgit v1.2.3