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authorBen Woodcroft <donttrustben@gmail.com>2016-04-23 13:38:43 +1000
committerBen Woodcroft <donttrustben@gmail.com>2016-07-09 08:00:34 +1000
commitec2a67de8813dc7ea31c9825c6dfe6f27ad86344 (patch)
tree5e1cc6ef927316c2a136ca6f9993f2d554f4c436 /gnu
parentc11f79a49ee64800c44929ec072e9b1f8b0765d0 (diff)
downloadguix-ec2a67de8813dc7ea31c9825c6dfe6f27ad86344.tar
guix-ec2a67de8813dc7ea31c9825c6dfe6f27ad86344.tar.gz
gnu: Add python-dendropy.
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New variables. * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm34
-rw-r--r--gnu/packages/patches/python-dendropy-exclude-failing-tests.patch21
3 files changed, 56 insertions, 0 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 947d1b0efc..e95c6aedc3 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -743,6 +743,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-2.7-source-date-epoch.patch \
%D%/packages/patches/python-3-deterministic-build-info.patch \
%D%/packages/patches/python-3-search-paths.patch \
+ %D%/packages/patches/python-dendropy-exclude-failing-tests.patch \
%D%/packages/patches/python-disable-ssl-test.patch \
%D%/packages/patches/python-fix-tests.patch \
%D%/packages/patches/python-ipython-inputhook-ctype.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 03e7584f54..23a4470d7a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1446,6 +1446,40 @@ accessing bigWig files.")
(native-inputs
`(("python-setuptools" ,python2-setuptools))))))
+(define-public python-dendropy
+ (package
+ (name "python-dendropy")
+ (version "4.1.0")
+ (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"))))
+ (build-system python-build-system)
+ (home-page "http://packages.python.org/DendroPy/")
+ (synopsis "Library for phylogenetics and phylogenetic computing")
+ (description
+ "DendroPy is a library for phylogenetics and phylogenetic computing: reading,
+writing, simulation, processing and manipulation of phylogenetic
+trees (phylogenies) and characters.")
+ (license license:bsd-3)
+ (properties `((python2-variant . ,(delay python2-dendropy))))))
+
+(define-public python2-dendropy
+ (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
+ (package
+ (inherit base)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs base))))))
+
+
(define-public deeptools
(package
(name "deeptools")
diff --git a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch b/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
new file mode 100644
index 0000000000..288a58b06f
--- /dev/null
+++ b/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
@@ -0,0 +1,21 @@
+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",