From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. Date: Tue, 21 Feb 2017 18:30:12 +0100 Message-ID: <87zihfxxi3.fsf__21360.7747726657$1487701285$gmane$org@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> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37486) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cgEHK-0002VY-0w for bug-guix@gnu.org; Tue, 21 Feb 2017 12:31:07 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cgEHG-0006Ht-S9 for bug-guix@gnu.org; Tue, 21 Feb 2017 12:31:06 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:50949) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cgEHG-0006Hh-OM for bug-guix@gnu.org; Tue, 21 Feb 2017 12:31:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1cgEHF-0006W2-VW for bug-guix@gnu.org; Tue, 21 Feb 2017 12:31:01 -0500 Sender: "Debbugs-submit" Resent-Message-ID: In-reply-to: <87h93oyod0.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 Mon, Feb 20, 2017 at 12:00:21AM +0100, Marius Bakke wrote: >>> Danny Milosavljevic writes: >>> > @Leo: Can you please start a new evaluation of python-tests? >>> >>> I pushed some other fixes recently and built most of `guix package -A >>> python`, so I think we're ready for a new evaluation. I suggest we do a >>> new evaluation on 'master' after fixing the most critical packages so we >>> can include this in 'core-updates'. How does that sound? >> >> I just started a new evaluation of the branch. >> >>> These packages are known to fail still: >>> >>> python-dendropy >>> python2-fastlmm >>> python2-bandit >>> python-openid >>> python-axolotl >>> >>> + Many of the python2 variants of the openstack family libraries (oslo >>> etc), which seems to have a unittest2 version mismatch. Should be >>> easy to fix, but let's get some substitutes first :-) >> >> I think we should set '#:tests? #f' in these packages and build and >> merge the branch. >> >> If these remaining test suite failures indicate that the packages are >> broken, they will be equally broken with the test suites disabled. But >> overall we will benefit from fixing this bug in python-build-system. > > I agree. > > Only two tests (out of 820) for python-dendropy fail: > > + test_fixed_species_tree_fitting (dendropy.test.test_multispeciescoalescent.MultispeciesCoalescentBasicTestCase) > + test1 (dendropy.test.test_multispeciescoalescent.MultispeciesCoalescentFixedSingleTreesCalculationTestCase) > > Both fail with > > TypeError: unorderable types: Edge() < Edge() > > I think it’s worth building the package anyway after disabling these two > tests. I reported the test failures upstream: > > https://github.com/jeetsukumaran/DendroPy/issues/77 Attached is a patch to delete the failing tests for DendroPy. --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename=0001-gnu-python-dendropy-Disable-failing-tests.patch >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. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1738b93..8295479a2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1983,6 +1983,13 @@ accessing bigWig files.") (base32 "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-broken-tests + (lambda _ + (delete-file "dendropy/test/test_multispeciescoalescent.py") + #t))))) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") (description -- 2.11.1 --=-=-= Content-Type: text/plain -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net --=-=-=--