02/02: gnu: python-dendropy: Update to 4.2.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 25d84d3122b8de29a67d69e8ff5de6660b8d44c5
Author: Ben Woodcroft <address@hidden>
Date:   Sun Jan 1 16:37:08 2017 +1000

    gnu: python-dendropy: Update to 4.2.0.
    
    * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
    [source]: Remove patch.
    (python2-dendropy)[source]: Use the same source as python-dendropy.
    * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
    file.
    * gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |    1 -
 gnu/packages/bioinformatics.scm                    |   18 ++---------------
 .../python-dendropy-exclude-failing-tests.patch    |   21 --------------------
 3 files changed, 2 insertions(+), 38 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 6963313..6ab1c1c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -814,7 +814,6 @@ 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-exclude-failing-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 b1d0c38..7a61de2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1930,19 +1930,14 @@ accessing bigWig files.")
 (define-public python-dendropy
   (package
     (name "python-dendropy")
-    (version "4.1.0")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "DendroPy" version))
        (sha256
         (base32
-         "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"))
-       ;; There are two known test failures that will be fixed in the next
-       ;; release after 4.1.0.
-       ;; https://github.com/jeetsukumaran/DendroPy/issues/48
-       (patches (search-patches
-                 "python-dendropy-exclude-failing-tests.patch"))))
+         "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))))
     (build-system python-build-system)
     (home-page "http://packages.python.org/DendroPy/";)
     (synopsis "Library for phylogenetics and phylogenetic computing")
@@ -1957,15 +1952,6 @@ trees (phylogenies) and characters.")
   (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
     (package
       (inherit base)
-      ;; Do not use same source as 'python-dendropy' because the patched
-      ;; failing tests do not occur on Python 2.
-      (source
-       (origin
-         (method url-fetch)
-         (uri (pypi-uri "DendroPy" (package-version base)))
-         (sha256
-          (base32
-           "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"))))
       (arguments
        `(#:python ,python-2
          #:phases
diff --git a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch 
b/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
deleted file mode 100644
index 288a58b..0000000
--- a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/dendropy/test/test_phylogenetic_distance_matrix.py 
b/dendropy/test/test_phylogenetic_distance_matrix.py
-index 10c05f5..a18ba52 100644
---- a/dendropy/test/test_phylogenetic_distance_matrix.py
-+++ b/dendropy/test/test_phylogenetic_distance_matrix.py
-@@ -793,7 +793,7 @@ class PdmUpgmaTree(PdmTreeChecker, unittest.TestCase):
-                     expected_tree=expected_tree)
- 
- class NodeToNodeDistancesTest(unittest.TestCase):
--
-+    @unittest.expectedFailure
-     def test_distances(self):
-         ## get distances from ape
-         # library(ape)
-@@ -825,6 +825,7 @@ class NodeToNodeDistancesTest(unittest.TestCase):
-                     e = reference_table[nd1.label, nd2.label]
-                     self.assertAlmostEqual(d, e)
- 
-+    @unittest.expectedFailure
-     def test_mrca(self):
-         test_runs = [
-                 "hiv1.newick",