From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. Date: Wed, 22 Feb 2017 13:42:01 +0100 Message-ID: <87lgsybdnq.fsf@elephly.net> References: <20170218181854.49ea3b17@scratchpost.org> <87bmtxkcqi.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> <20170221041645.GC19762@jasmine> <87h93oyod0.fsf@elephly.net> <87zihfxxi3.fsf@elephly.net> <20170221174756.GA6450@jasmine> <87wpcjxka7.fsf@elephly.net> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:42748) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cgWGA-0007QM-S3 for bug-guix@gnu.org; Wed, 22 Feb 2017 07:43:09 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cgWG6-00028P-Rj for bug-guix@gnu.org; Wed, 22 Feb 2017 07:43:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:51555) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cgWG6-00028I-O1 for bug-guix@gnu.org; Wed, 22 Feb 2017 07:43:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1cgWG6-0005jc-GU for bug-guix@gnu.org; Wed, 22 Feb 2017 07:43:02 -0500 Sender: "Debbugs-submit" Resent-Message-ID: In-reply-to: <87wpcjxka7.fsf@elephly.net> List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+gcggb-bug-guix=m.gmane.org@gnu.org Sender: "bug-Guix" To: Leo Famulari Cc: guix-devel@gnu.org, 25177@debbugs.gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Ricardo Wurmus writes: > Leo Famulari writes: > >> On Tue, Feb 21, 2017 at 06:30:12PM +0100, Ricardo Wurmus wrote: >>> From 1ac5166df11766b47cd1ac723a464063a89afc96 Mon Sep 17 00:00:00 2001 >>> From: Ricardo Wurmus >>> Date: Tue, 21 Feb 2017 18:28:21 +0100 >>> Subject: [PATCH] gnu: python-dendropy: Disable failing tests. >>> >>> * gnu/packages/bioinformatics.scm (python-dendropy): Disable two failing >>> tests. >> >> LGTM > > The problem was fixed in the upstream commit 93f984b in response to my > bug report: > > https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453 > > I believe we can just backport this fix instead of deleting the test. Here’s a patch that fixes the tests by applying the changes of the upstream commit. If this is fine I’ll push it to the python-tests branch. --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename=0001-gnu-python-dendropy-Fix-failing-tests.patch >From 0959e057886f9d9ab83467f6280ceefa35d05972 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: [PATCH] gnu: python-dendropy: Fix failing tests. * gnu/packages/patches/python-dendropy-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 3 +- .../patches/python-dendropy-fix-tests.patch | 41 ++++++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0b9b5b1a1..ac22924c4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -853,6 +853,7 @@ 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-fix-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 5a1738b93..de6186de2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1981,7 +1981,8 @@ accessing bigWig files.") (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) + (patches (search-patches "python-dendropy-fix-tests.patch")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch new file mode 100644 index 000000000..30ab618ff --- /dev/null +++ b/gnu/packages/patches/python-dendropy-fix-tests.patch @@ -0,0 +1,41 @@ +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 +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 + -- 2.11.1 --=-=-= Content-Type: text/plain -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net --=-=-=--