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.
This commit is contained in:
Ben Woodcroft 2016-04-23 13:38:43 +10:00
parent c11f79a49e
commit ec2a67de88
No known key found for this signature in database
GPG key ID: E44DCCD146E0CCF4
3 changed files with 56 additions and 0 deletions

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@ -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 \

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@ -1446,6 +1446,40 @@ (define-public python2-pybigwig
(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")

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@ -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",