* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] <20170218181854.49ea3b17@scratchpost.org> @ 2017-02-19 23:00 ` Marius Bakke [not found] ` <87bmtxkcqi.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> 1 sibling, 0 replies; 23+ messages in thread From: Marius Bakke @ 2017-02-19 23:00 UTC (permalink / raw) To: Danny Milosavljevic, guix-devel, Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 874 bytes --] Danny Milosavljevic <dannym@scratchpost.org> writes: > Hi, > > so we finally got to the bottom of the problem with python-oslosphinx. > It should be fixed now (the main fix is in python-pbr-minimal). Thanks a lot for this! > > @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? 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 :-) [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
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* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] ` <87bmtxkcqi.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> @ 2017-02-21 4:16 ` Leo Famulari [not found] ` <20170221041645.GC19762@jasmine> 1 sibling, 0 replies; 23+ messages in thread From: Leo Famulari @ 2017-02-21 4:16 UTC (permalink / raw) To: Marius Bakke; +Cc: guix-devel, 25177 [-- Attachment #1: Type: text/plain, Size: 1172 bytes --] On Mon, Feb 20, 2017 at 12:00:21AM +0100, Marius Bakke wrote: > Danny Milosavljevic <dannym@scratchpost.org> 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. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
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* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] ` <20170221041645.GC19762@jasmine> @ 2017-02-21 7:50 ` Ricardo Wurmus [not found] ` <87h93oyod0.fsf@elephly.net> 1 sibling, 0 replies; 23+ messages in thread From: Ricardo Wurmus @ 2017-02-21 7:50 UTC (permalink / raw) To: Leo Famulari; +Cc: guix-devel, 25177 Leo Famulari <leo@famulari.name> writes: > On Mon, Feb 20, 2017 at 12:00:21AM +0100, Marius Bakke wrote: >> Danny Milosavljevic <dannym@scratchpost.org> 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 -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 23+ messages in thread
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* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] ` <87h93oyod0.fsf@elephly.net> @ 2017-02-21 17:30 ` Ricardo Wurmus [not found] ` <87zihfxxi3.fsf@elephly.net> 1 sibling, 0 replies; 23+ messages in thread From: Ricardo Wurmus @ 2017-02-21 17:30 UTC (permalink / raw) To: Leo Famulari; +Cc: guix-devel, 25177 [-- Attachment #1: Type: text/plain, Size: 1925 bytes --] Ricardo Wurmus <rekado@elephly.net> writes: > Leo Famulari <leo@famulari.name> writes: > >> On Mon, Feb 20, 2017 at 12:00:21AM +0100, Marius Bakke wrote: >>> Danny Milosavljevic <dannym@scratchpost.org> 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. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-python-dendropy-Disable-failing-tests.patch --] [-- Type: text/x-patch, Size: 1140 bytes --] From 1ac5166df11766b47cd1ac723a464063a89afc96 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <rekado@elephly.net> 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 [-- Attachment #3: Type: text/plain, Size: 90 bytes --] -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply related [flat|nested] 23+ messages in thread
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* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] ` <87zihfxxi3.fsf@elephly.net> @ 2017-02-21 17:47 ` Leo Famulari 2017-02-21 22:15 ` Ricardo Wurmus ` (2 more replies) 0 siblings, 3 replies; 23+ messages in thread From: Leo Famulari @ 2017-02-21 17:47 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: guix-devel, 25177 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 <rekado@elephly.net> > 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 ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-21 17:47 ` Leo Famulari @ 2017-02-21 22:15 ` Ricardo Wurmus 2017-02-21 22:21 ` Ben Woodcroft [not found] ` <87wpcjxka7.fsf@elephly.net> 2 siblings, 0 replies; 23+ messages in thread From: Ricardo Wurmus @ 2017-02-21 22:15 UTC (permalink / raw) To: Leo Famulari; +Cc: guix-devel, 25177 Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >> 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. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-21 17:47 ` Leo Famulari 2017-02-21 22:15 ` Ricardo Wurmus @ 2017-02-21 22:21 ` Ben Woodcroft [not found] ` <87wpcjxka7.fsf@elephly.net> 2 siblings, 0 replies; 23+ messages in thread From: Ben Woodcroft @ 2017-02-21 22:21 UTC (permalink / raw) To: Leo Famulari, Ricardo Wurmus; +Cc: guix-devel, 25177 Hi Ricardo, On 22/02/17 03:47, Leo Famulari wrote: > 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 <rekado@elephly.net> >> 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 Me too, though perhaps it might be good to include a comment pointing to the GitHub issue you raised. Thanks for chasing this down - you beat me to the same conclusions. ben ^ permalink raw reply [flat|nested] 23+ messages in thread
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* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. [not found] ` <87wpcjxka7.fsf@elephly.net> @ 2017-02-22 12:42 ` Ricardo Wurmus 2017-02-22 12:57 ` Marius Bakke 2017-02-24 22:20 ` Marius Bakke 0 siblings, 2 replies; 23+ messages in thread From: Ricardo Wurmus @ 2017-02-22 12:42 UTC (permalink / raw) To: Leo Famulari; +Cc: guix-devel, 25177 [-- Attachment #1: Type: text/plain, Size: 899 bytes --] Ricardo Wurmus <rekado@elephly.net> writes: > Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >>> 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. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-python-dendropy-Fix-failing-tests.patch --] [-- Type: text/x-patch, Size: 3761 bytes --] From 0959e057886f9d9ab83467f6280ceefa35d05972 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus <rekado@elephly.net> 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 <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 + -- 2.11.1 [-- Attachment #3: Type: text/plain, Size: 89 bytes --] -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply related [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-22 12:42 ` Ricardo Wurmus @ 2017-02-22 12:57 ` Marius Bakke 2017-02-24 22:20 ` Marius Bakke 1 sibling, 0 replies; 23+ messages in thread From: Marius Bakke @ 2017-02-22 12:57 UTC (permalink / raw) To: Ricardo Wurmus, Leo Famulari; +Cc: guix-devel, 25177 [-- Attachment #1: Type: text/plain, Size: 1018 bytes --] Ricardo Wurmus <rekado@elephly.net> writes: > Ricardo Wurmus <rekado@elephly.net> writes: > >> Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >>>> 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. LGTM, thank you! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-22 12:42 ` Ricardo Wurmus 2017-02-22 12:57 ` Marius Bakke @ 2017-02-24 22:20 ` Marius Bakke 2017-02-24 22:29 ` Ricardo Wurmus 2017-02-27 11:46 ` Marius Bakke 1 sibling, 2 replies; 23+ messages in thread From: Marius Bakke @ 2017-02-24 22:20 UTC (permalink / raw) To: Ricardo Wurmus, Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 1749 bytes --] Ricardo Wurmus <rekado@elephly.net> writes: > Ricardo Wurmus <rekado@elephly.net> writes: > >> Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >>>> 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. I tried this patch, and guess the reason it was not pushed is because dendropy now has a different failure. Can you look into it? Currently, I can build all of 'guix package -A python' on amd64, and have fixed the few i686 problems on Hydra. Except for these three: python-dendropy python-openid python-axolotl Given that the two latter packages have security implications I would rather leave them broken, than ignoring the test failures. They don't have any in-tree users. I don't always break packages wittingly, but when I do, it's on 'master'. Should we do a final Hydra round, or just merge it to the master branch first? The 'python-tests' branch haven't been synced in a while, so many substitutes will be out of date. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-24 22:20 ` Marius Bakke @ 2017-02-24 22:29 ` Ricardo Wurmus 2017-02-24 22:36 ` Marius Bakke 2017-02-27 11:46 ` Marius Bakke 1 sibling, 1 reply; 23+ messages in thread From: Ricardo Wurmus @ 2017-02-24 22:29 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177 Marius Bakke <mbakke@fastmail.com> writes: > Ricardo Wurmus <rekado@elephly.net> writes: > >> Ricardo Wurmus <rekado@elephly.net> writes: >> >>> Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >>>>> 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. > > I tried this patch, and guess the reason it was not pushed is because > dendropy now has a different failure. Can you look into it? Oh? I didn’t get an error building it on the “python-tests” branch on x86_64. Could you show me the error messages you get? (I didn’t build python2-dendropy.) -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-24 22:29 ` Ricardo Wurmus @ 2017-02-24 22:36 ` Marius Bakke 0 siblings, 0 replies; 23+ messages in thread From: Marius Bakke @ 2017-02-24 22:36 UTC (permalink / raw) To: Ricardo Wurmus; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 2785 bytes --] Ricardo Wurmus <rekado@elephly.net> writes: > Marius Bakke <mbakke@fastmail.com> writes: > >> Ricardo Wurmus <rekado@elephly.net> writes: >> >>> Ricardo Wurmus <rekado@elephly.net> writes: >>> >>>> Leo Famulari <leo@famulari.name> 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 <rekado@elephly.net> >>>>>> 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. >> >> I tried this patch, and guess the reason it was not pushed is because >> dendropy now has a different failure. Can you look into it? > > Oh? I didn’t get an error building it on the “python-tests” branch on > x86_64. Could you show me the error messages you get? > > (I didn’t build python2-dendropy.) Strange. Here python2-dendropy builds fine, but python-dendropy fails: ====================================================================== FAIL: test_collection_comments_and_annotations (dendropy.test.test_dataio_nexml_reader_tree_list.NexmlStandardTreeParsingTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/guix-build-python-dendropy-4.2.0.drv-0/DendroPy-4.2.0/dendropy/test/test_dataio_nexml_reader_tree_list.py", line 60, in test_collection_comments_and_annotations expected_metadata) File "/tmp/guix-build-python-dendropy-4.2.0.drv-0/DendroPy-4.2.0/dendropy/test/support/standard_file_test_trees.py", line 127, in compare_annotations_to_json_metadata_dict self.assertEqual(item_annotations_as_dict, expected_metadata) AssertionError: {'$_demivotary_#_monumentlike': 31, 'mangan[226 chars]alse} != {'Merycoidodon_%_$_permeant': 'envyingly247[236 chars]'31'} Diff is 711 characters long. Set self.maxDiff to None to see it. ---------------------------------------------------------------------- Ran 840 tests in 263.965s FAILED (failures=1) phase `check' failed after 266.1 seconds builder for `/gnu/store/af6rm6s8g3cid461pvhl1j0fsyp06ifq-python-dendropy-4.2.0.drv' failed with exit code 1 [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-24 22:20 ` Marius Bakke 2017-02-24 22:29 ` Ricardo Wurmus @ 2017-02-27 11:46 ` Marius Bakke 2017-02-27 20:20 ` Leo Famulari 1 sibling, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-02-27 11:46 UTC (permalink / raw) To: Ricardo Wurmus, Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 450 bytes --] Marius Bakke <mbakke@fastmail.com> writes: > I don't always break packages wittingly, but when I do, it's on > 'master'. Should we do a final Hydra round, or just merge it to the > master branch first? The 'python-tests' branch haven't been synced in a > while, so many substitutes will be out of date. I've synced this branch with 'master'. Please start a final Hydra evaluation. I will merge this in a day or two unless there are major problems! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-27 11:46 ` Marius Bakke @ 2017-02-27 20:20 ` Leo Famulari 2017-02-28 16:15 ` Marius Bakke 0 siblings, 1 reply; 23+ messages in thread From: Leo Famulari @ 2017-02-27 20:20 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 552 bytes --] On Mon, Feb 27, 2017 at 12:46:58PM +0100, Marius Bakke wrote: > Marius Bakke <mbakke@fastmail.com> writes: > > > I don't always break packages wittingly, but when I do, it's on > > 'master'. Should we do a final Hydra round, or just merge it to the > > master branch first? The 'python-tests' branch haven't been synced in a > > while, so many substitutes will be out of date. > > I've synced this branch with 'master'. Please start a final Hydra > evaluation. I will merge this in a day or two unless there are major > problems! Done! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-27 20:20 ` Leo Famulari @ 2017-02-28 16:15 ` Marius Bakke 2017-03-01 15:36 ` Leo Famulari 0 siblings, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-02-28 16:15 UTC (permalink / raw) To: Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 677 bytes --] Leo Famulari <leo@famulari.name> writes: > On Mon, Feb 27, 2017 at 12:46:58PM +0100, Marius Bakke wrote: >> Marius Bakke <mbakke@fastmail.com> writes: >> >> > I don't always break packages wittingly, but when I do, it's on >> > 'master'. Should we do a final Hydra round, or just merge it to the >> > master branch first? The 'python-tests' branch haven't been synced in a >> > while, so many substitutes will be out of date. >> >> I've synced this branch with 'master'. Please start a final Hydra >> evaluation. I will merge this in a day or two unless there are major >> problems! > > Done! It seems the evaluation timed out. Can you give it another go? [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-02-28 16:15 ` Marius Bakke @ 2017-03-01 15:36 ` Leo Famulari 2017-03-01 17:36 ` Marius Bakke 0 siblings, 1 reply; 23+ messages in thread From: Leo Famulari @ 2017-03-01 15:36 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 134 bytes --] On Tue, Feb 28, 2017 at 05:15:59PM +0100, Marius Bakke wrote: > It seems the evaluation timed out. Can you give it another go? Done! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-01 15:36 ` Leo Famulari @ 2017-03-01 17:36 ` Marius Bakke 2017-03-01 17:44 ` Marius Bakke 0 siblings, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-03-01 17:36 UTC (permalink / raw) To: Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 220 bytes --] Leo Famulari <leo@famulari.name> writes: > On Tue, Feb 28, 2017 at 05:15:59PM +0100, Marius Bakke wrote: >> It seems the evaluation timed out. Can you give it another go? > > Done! Aaand hydra is out of disk space. :( [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-01 17:36 ` Marius Bakke @ 2017-03-01 17:44 ` Marius Bakke 2017-03-02 22:22 ` Leo Famulari 0 siblings, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-03-01 17:44 UTC (permalink / raw) To: Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 510 bytes --] Marius Bakke <mbakke@fastmail.com> writes: > Leo Famulari <leo@famulari.name> writes: > >> On Tue, Feb 28, 2017 at 05:15:59PM +0100, Marius Bakke wrote: >>> It seems the evaluation timed out. Can you give it another go? >> >> Done! > > Aaand hydra is out of disk space. :( This branch diverges quite a bit from master due to the 'python-build-system' change. I would recommend building out this branch and merge it before restarting 'master' after GC. The mirror have most master substitutes cached anyway. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-01 17:44 ` Marius Bakke @ 2017-03-02 22:22 ` Leo Famulari 2017-03-02 23:31 ` Marius Bakke 0 siblings, 1 reply; 23+ messages in thread From: Leo Famulari @ 2017-03-02 22:22 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 457 bytes --] On Wed, Mar 01, 2017 at 06:44:34PM +0100, Marius Bakke wrote: > Marius Bakke <mbakke@fastmail.com> writes: > > > Leo Famulari <leo@famulari.name> writes: > > > >> On Tue, Feb 28, 2017 at 05:15:59PM +0100, Marius Bakke wrote: > >>> It seems the evaluation timed out. Can you give it another go? > >> > >> Done! > > > > Aaand hydra is out of disk space. :( Finally, the evaluation is running :) https://hydra.gnu.org/jobset/gnu/python-tests [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-02 22:22 ` Leo Famulari @ 2017-03-02 23:31 ` Marius Bakke 2017-03-02 23:42 ` Leo Famulari 0 siblings, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-03-02 23:31 UTC (permalink / raw) To: Leo Famulari; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 1394 bytes --] Leo Famulari <leo@famulari.name> writes: > On Wed, Mar 01, 2017 at 06:44:34PM +0100, Marius Bakke wrote: >> Marius Bakke <mbakke@fastmail.com> writes: >> >> > Leo Famulari <leo@famulari.name> writes: >> > >> >> On Tue, Feb 28, 2017 at 05:15:59PM +0100, Marius Bakke wrote: >> >>> It seems the evaluation timed out. Can you give it another go? >> >> >> >> Done! >> > >> > Aaand hydra is out of disk space. :( > > Finally, the evaluation is running :) > > https://hydra.gnu.org/jobset/gnu/python-tests Thanks for starting it without me having to nag about it! You dodged a salty bullet there ;-) So far so good. The comparison against 'master' is broken, it's using an age-old master evaluation: https://hydra.gnu.org/eval/109515?compare=master Similarly, comparisons against the previous run shows some builds from back in December that have been fixed (like python-cov-core): https://hydra.gnu.org/eval/109515?full=1#tabs-still-fail This is likely why I could not reproduce any of the listed failures back in December! We should have just merged it, about half of the problems stems from adding/updating broken packages after that.. 153 commits! Anyway, this bug has been a massive pain and I'm going to merge it tomorrow so I can get on with life. The 'master' jobset should be started afterwards; perhaps you can merge and start the evaluation? [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-02 23:31 ` Marius Bakke @ 2017-03-02 23:42 ` Leo Famulari 2017-03-03 16:52 ` Marius Bakke 0 siblings, 1 reply; 23+ messages in thread From: Leo Famulari @ 2017-03-02 23:42 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177 [-- Attachment #1: Type: text/plain, Size: 1105 bytes --] On Fri, Mar 03, 2017 at 12:31:51AM +0100, Marius Bakke wrote: > Thanks for starting it without me having to nag about it! You dodged a > salty bullet there ;-) > > So far so good. The comparison against 'master' is broken, it's using an > age-old master evaluation: > > https://hydra.gnu.org/eval/109515?compare=master > > Similarly, comparisons against the previous run shows some builds from > back in December that have been fixed (like python-cov-core): > > https://hydra.gnu.org/eval/109515?full=1#tabs-still-fail > > This is likely why I could not reproduce any of the listed failures back > in December! We should have just merged it, about half of the problems > stems from adding/updating broken packages after that.. 153 commits! Bah! Well, thanks for seeing it through to the end. > Anyway, this bug has been a massive pain and I'm going to merge it > tomorrow so I can get on with life. The 'master' jobset should be > started afterwards; perhaps you can merge and start the evaluation? Okay, let me know when you push the merge and I'll start the evaluation. [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-02 23:42 ` Leo Famulari @ 2017-03-03 16:52 ` Marius Bakke 2017-03-03 17:51 ` Leo Famulari 0 siblings, 1 reply; 23+ messages in thread From: Marius Bakke @ 2017-03-03 16:52 UTC (permalink / raw) To: Leo Famulari; +Cc: 25177-done [-- Attachment #1: Type: text/plain, Size: 364 bytes --] Leo Famulari <leo@famulari.name> writes: >> Anyway, this bug has been a massive pain and I'm going to merge it >> tomorrow so I can get on with life. The 'master' jobset should be >> started afterwards; perhaps you can merge and start the evaluation? > > Okay, let me know when you push the merge and I'll start the evaluation. Merged! Closing this bug. Hooray! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 487 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
* bug#25177: python-tests: python-oslosphinx fixed. Please evaluate. 2017-03-03 16:52 ` Marius Bakke @ 2017-03-03 17:51 ` Leo Famulari 0 siblings, 0 replies; 23+ messages in thread From: Leo Famulari @ 2017-03-03 17:51 UTC (permalink / raw) To: Marius Bakke; +Cc: 25177-done [-- Attachment #1: Type: text/plain, Size: 488 bytes --] On Fri, Mar 03, 2017 at 05:52:34PM +0100, Marius Bakke wrote: > Leo Famulari <leo@famulari.name> writes: > > >> Anyway, this bug has been a massive pain and I'm going to merge it > >> tomorrow so I can get on with life. The 'master' jobset should be > >> started afterwards; perhaps you can merge and start the evaluation? > > > > Okay, let me know when you push the merge and I'll start the evaluation. > > Merged! Closing this bug. Hooray! Thank you for working on this! [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --] ^ permalink raw reply [flat|nested] 23+ messages in thread
end of thread, other threads:[~2017-03-03 17:52 UTC | newest] Thread overview: 23+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- [not found] <20170218181854.49ea3b17@scratchpost.org> 2017-02-19 23:00 ` bug#25177: python-tests: python-oslosphinx fixed. Please evaluate Marius Bakke [not found] ` <87bmtxkcqi.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> 2017-02-21 4:16 ` Leo Famulari [not found] ` <20170221041645.GC19762@jasmine> 2017-02-21 7:50 ` Ricardo Wurmus [not found] ` <87h93oyod0.fsf@elephly.net> 2017-02-21 17:30 ` Ricardo Wurmus [not found] ` <87zihfxxi3.fsf@elephly.net> 2017-02-21 17:47 ` Leo Famulari 2017-02-21 22:15 ` Ricardo Wurmus 2017-02-21 22:21 ` Ben Woodcroft [not found] ` <87wpcjxka7.fsf@elephly.net> 2017-02-22 12:42 ` Ricardo Wurmus 2017-02-22 12:57 ` Marius Bakke 2017-02-24 22:20 ` Marius Bakke 2017-02-24 22:29 ` Ricardo Wurmus 2017-02-24 22:36 ` Marius Bakke 2017-02-27 11:46 ` Marius Bakke 2017-02-27 20:20 ` Leo Famulari 2017-02-28 16:15 ` Marius Bakke 2017-03-01 15:36 ` Leo Famulari 2017-03-01 17:36 ` Marius Bakke 2017-03-01 17:44 ` Marius Bakke 2017-03-02 22:22 ` Leo Famulari 2017-03-02 23:31 ` Marius Bakke 2017-03-02 23:42 ` Leo Famulari 2017-03-03 16:52 ` Marius Bakke 2017-03-03 17:51 ` Leo Famulari
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