03/04: gnu: python-dendropy: Update to 4.4.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9e0c135c39b5f1fa2c5c9cd4a1e50ccee75cc31e
Author: Ben Woodcroft <address@hidden>
Date:   Sun Jul 29 22:44:37 2018 +1000

    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.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    | 28 +++++----------
 .../patches/python-dendropy-fix-tests.patch        | 41 ----------------------
 3 files changed, 9 insertions(+), 61 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index af25477..c58eec7 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 4d84b90..7509f07 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 30ab618..0000000
--- 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 <address@hidden>
-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
-