python-tests: python-oslosphinx fixed. Please evaluate.

python-tests: python-oslosphinx fixed. Please evaluate.

[Danny Milosavljevic]

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).

@Leo: Can you please start a new evaluation of python-tests?

Re: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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 :-)

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Re: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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.

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Re: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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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


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-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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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


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-- 
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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

Re: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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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


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--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Re: bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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 --]

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

[-- 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 --]

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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.

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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!

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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!

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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?

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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!

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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. :(

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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.

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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?

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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.

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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!

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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!

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ben Woodcroft]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Ricardo Wurmus]

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

bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Leo Famulari]

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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.

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bug#25177: python-tests: python-oslosphinx fixed. Please evaluate.

[Marius Bakke]

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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 :-)

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