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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-01-01 16:37:08 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-01-01 16:47:47 +1000 |
| commit | 25d84d3122b8de29a67d69e8ff5de6660b8d44c5 (patch) | |
| tree | 24d8b90335b20d51c2ac3cecdeb128abacae5718 | |
| parent | 322a583fcfff9f5173ad388ee876aa29d9f8edcc (diff) | |
| download | patches-25d84d3122b8de29a67d69e8ff5de6660b8d44c5.tar patches-25d84d3122b8de29a67d69e8ff5de6660b8d44c5.tar.gz | |
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.
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 18 | ||||
| -rw-r--r-- | gnu/packages/patches/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 69633131e6..6ab1c1c488 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 b1d0c38a49..7a61de2eda 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 288a58b06f..0000000000 --- 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", |