From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] gnu: Add python-dendropy. Date: Sat, 9 Jul 2016 00:04:36 +1000 Message-ID: <20160708140436.23475-1-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:46759) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bLWOj-0008JW-CW for guix-devel@gnu.org; Fri, 08 Jul 2016 10:04:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1bLWOe-0006VG-IJ for guix-devel@gnu.org; Fri, 08 Jul 2016 10:04:52 -0400 Received: from mail-pf0-x243.google.com ([2607:f8b0:400e:c00::243]:34863) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1bLWOe-0006V0-6v for guix-devel@gnu.org; Fri, 08 Jul 2016 10:04:48 -0400 Received: by mail-pf0-x243.google.com with SMTP id t190so7390739pfb.2 for ; Fri, 08 Jul 2016 07:04:47 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id d8sm5148286pfg.72.2016.07.08.07.04.43 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Fri, 08 Jul 2016 07:04:45 -0700 (PDT) List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * 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. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++ .../python-dendropy-exclude-failing-tests.patch | 21 +++++++++++++ 3 files changed, 56 insertions(+) create mode 100644 gnu/packages/patches/python-dendropy-exclude-failing-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 947d1b0..e95c6ae 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 03e7584..8f72816 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 thare 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 0000000..288a58b --- /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", -- 2.9.0