diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 | ||||
| -rw-r--r-- | gnu/packages/patches/python-dendropy-fix-tests.patch | 41 |
2 files changed, 9 insertions, 60 deletions
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 - |