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]

[-- 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 --]

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

[Leo Famulari]

[-- 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 --]

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

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

[Ricardo Wurmus]

[-- 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

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]

[-- 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

Re: 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.

[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