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authorBen Woodcroft <donttrustben@gmail.com>2018-07-29 22:44:37 +1000
committerBen Woodcroft <donttrustben@gmail.com>2018-07-29 22:53:10 +1000
commit9e0c135c39b5f1fa2c5c9cd4a1e50ccee75cc31e (patch)
tree5fa0a3d6f41d8354d017cbec60d00d1836c1a70c /gnu
parent19601e895b816afc033a155a9309037ec21fd3ed (diff)
downloadguix-9e0c135c39b5f1fa2c5c9cd4a1e50ccee75cc31e.tar
guix-9e0c135c39b5f1fa2c5c9cd4a1e50ccee75cc31e.tar.gz
gnu: python-dendropy: Update to 4.4.0.
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): Update to 4.4.0. [source]: Use GitHub URI. Remove patch. [properties]: Remove field. (python2-dendropy)[arguments]: Run tests with setup.py. [native-inputs]: Remove 'python2-nose. * gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Delete it.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/bioinformatics.scm28
-rw-r--r--gnu/packages/patches/python-dendropy-fix-tests.patch41
3 files changed, 9 insertions, 61 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index af25477466..c58eec7bad 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1064,7 +1064,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-3-fix-tests.patch \
%D%/packages/patches/python-axolotl-AES-fix.patch \
%D%/packages/patches/python-cairocffi-dlopen-path.patch \
- %D%/packages/patches/python-dendropy-fix-tests.patch \
%D%/packages/patches/python-fix-tests.patch \
%D%/packages/patches/python-genshi-add-support-for-python-3.4-AST.patch \
%D%/packages/patches/python-genshi-buildable-on-python-2.7.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4d84b90f1e..7509f07d4a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1971,15 +1971,18 @@ accessing bigWig files.")
(define-public python-dendropy
(package
(name "python-dendropy")
- (version "4.2.0")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "DendroPy" version))
+ ;; Source from GitHub so that tests are included.
+ (uri
+ (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
- (patches (search-patches "python-dendropy-fix-tests.patch"))))
+ "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn"))))
(build-system python-build-system)
(home-page "http://packages.python.org/DendroPy/")
(synopsis "Library for phylogenetics and phylogenetic computing")
@@ -1987,23 +1990,10 @@ accessing bigWig files.")
"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))))))
+ (license license:bsd-3)))
(define-public python2-dendropy
- (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
- (package
- (inherit base)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- ;; There is currently a test failure that only happens on some
- ;; systems, and only using "setup.py test"
- (lambda _ (zero? (system* "nosetests")))))))
- (native-inputs `(("python2-nose" ,python2-nose)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-dendropy))
(define-public python-py2bit
(package
diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch
deleted file mode 100644
index 30ab618ff1..0000000000
--- a/gnu/packages/patches/python-dendropy-fix-tests.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-This patch fixes two test failures. It was downloaded from:
-https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453
-
-From 93f984bba7a6c588a28ca87f4e557ce283809453 Mon Sep 17 00:00:00 2001
-From: jeetsukumaran <jeetsukumaran@gmail.com>
-Date: Tue, 21 Feb 2017 16:41:01 -0500
-Subject: [PATCH] Update to Python 3 container and iteration semantics
-
----
- dendropy/dataio/newickreader.py | 3 ++-
- dendropy/datamodel/treemodel.py | 3 +++
- 2 files changed, 5 insertions(+), 1 deletion(-)
-
-diff --git a/dendropy/dataio/newickreader.py b/dendropy/dataio/newickreader.py
-index 6dcf3c5..f978729 100644
---- a/dendropy/dataio/newickreader.py
-+++ b/dendropy/dataio/newickreader.py
-@@ -303,7 +303,8 @@ def tree_iter(self,
- taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
- yield tree
- if tree is None:
-- raise StopIteration
-+ # raise StopIteration
-+ return
-
- def _read(self,
- stream,
-diff --git a/dendropy/datamodel/treemodel.py b/dendropy/datamodel/treemodel.py
-index 0ecfe31..73146f0 100644
---- a/dendropy/datamodel/treemodel.py
-+++ b/dendropy/datamodel/treemodel.py
-@@ -772,6 +772,9 @@ def __hash__(self):
- def __eq__(self, other):
- return self is other
-
-+ def __lt__(self, other):
-+ return id(self) < id(other)
-+
- ###########################################################################
- ### Basic Structure
-