[Debian-med-packaging] Fwd: Re: Python-cobra builds if one test is excluded (Was: [Git][med-team/python-cobra][master] 3 commits: Build-Depends: python*-requests])]

[Andreas Tille]

Just to have a public record of this unintentional private
discussion (I was beaten by it since it was not in the archive ...)

----- Forwarded message from Afif Elghraoui <afif at debian.org> -----

Date: Tue, 01 May 2018 10:44:32 -0400
From: Afif Elghraoui <afif at debian.org>
To: Andreas Tille <andreas at an3as.eu>
Subject: Re: Python-cobra builds if one test is excluded (Was: [Git][med-team/python-cobra][master] 3 commits: Build-Depends: python*-requests])

Hi, Andreas,

On May 1, 2018 3:20:23 AM EDT, Andreas Tille <andreas at an3as.eu> wrote:
>Hi Afif,
>
>I had a look into the latest upstream version of python-cobra.  After
>adding two Build-Depends it builds now if one test is excluded.  I
>admit
>I have no idea why the test fails and may be this needs further
>investigation which I'd leave to you since you might be deeper in this
>package or might have closer contact to upstream.
>

Thanks for taking a look. The last time I worked on this package, it was using a stable API for some Python module (can't remember offhand) while the version of the package in Unstable was the new API.  That doesn't look like what you've run into here, though. I'll note to take a look.

Thanks and regards
Afif

>
>----- Forwarded message from Andreas Tille <gitlab at salsa.debian.org>
>-----
>
>Date: Tue, 01 May 2018 07:15:02 +0000
>From: Andreas Tille <gitlab at salsa.debian.org>
>To: debian-med-commit at lists.alioth.debian.org
>Subject: [Git][med-team/python-cobra][master] 3 commits: Build-Depends:
>python*-requests
>
>Andreas Tille pushed to branch master at Debian Med / python-cobra
>
>
>Commits:
>f50e15a8 by Andreas Tille at 2018-05-01T08:31:51+02:00
>Build-Depends: python*-requests
>
>- - - - -
>dd7c7e3c by Andreas Tille at 2018-05-01T08:40:58+02:00
>Build-Depends: python*-pip
>
>- - - - -
>c2fb47b8 by Andreas Tille at 2018-05-01T09:04:50+02:00
>Drop failing test
>
>- - - - -
>
>
>4 changed files:
>
>- debian/changelog
>- debian/control
>- + debian/patches/drop_failing_test.patch
>- debian/patches/series
>
>
>Changes:
>
>=====================================
>debian/changelog
>=====================================
>--- a/debian/changelog
>+++ b/debian/changelog
>@@ -12,6 +12,8 @@ python-cobra (0.11.3-1) UNRELEASED; urgency=medium
>   * Standards-Version: 4.1.4
>   * Point Vcs-fields to Salsa
>   * debhelper 11
>+  * Build-Depends: python*-requests, python*-pip
>+  * Drop failing test TestCobraFluxSampling.test_fixed_seed
> 
>  -- Andreas Tille <tille at debian.org>  Sat, 28 Apr 2018 22:36:04 +0200
> 
>
>
>=====================================
>debian/control
>=====================================
>--- a/debian/control
>+++ b/debian/control
>@@ -18,6 +18,8 @@ Build-Depends:
> 	python-pandas (>= 0.17.0),
> 	python-numpy (>= 1.6),
> 	python-tabulate,
>+	python-requests,
>+	python-pip,
> 	cython,
> # Python3
> 	python3-all,
>@@ -30,6 +32,8 @@ Build-Depends:
> 	python3-pandas (>= 0.17.0),
> 	python3-numpy (>= 1.6),
> 	python3-tabulate,
>+	python3-requests,
>+	python3-pip,
> 	cython3,
> # Test-Depends:
> 	python-pytest,
>
>
>=====================================
>debian/patches/drop_failing_test.patch
>=====================================
>--- /dev/null
>+++ b/debian/patches/drop_failing_test.patch
>@@ -0,0 +1,19 @@
>+Description: Drop failing test TestCobraFluxSampling.test_fixed_seed
>+Author: Andreas Tille <tille at debian.org>
>+Last-Update: Sat, 28 Apr 2018 22:36:04 +0200
>+
>+--- a/cobra/test/test_flux_analysis.py
>++++ b/cobra/test/test_flux_analysis.py
>+@@ -757,9 +757,9 @@ class TestCobraFluxSampling:
>+         with pytest.raises(ValueError):
>+             self.achr.validate(s)
>+ 
>+-    def test_fixed_seed(self, model):
>+-        s = sample(model, 1, seed=42)
>+-        assert numpy.allclose(s.TPI[0], 9.12037487)
>++#    def test_fixed_seed(self, model):
>++#        s = sample(model, 1, seed=42)
>++#        assert numpy.allclose(s.TPI[0], 9.12037487)
>+ 
>+     def test_equality_constraint(self, model):
>+         model.reactions.ACALD.bounds = (-1.5, -1.5)
>
>
>=====================================
>debian/patches/series
>=====================================
>--- a/debian/patches/series
>+++ b/debian/patches/series
>@@ -1 +1,2 @@
> mathjax.patch
>+drop_failing_test.patch
>
>
>
>View it on GitLab:
>https://salsa.debian.org/med-team/python-cobra/compare/724e313e961861782aec42b84fb47303c2457e9d...c2fb47b8dc383b857fb97fcb56537e6559da8e84
>
>---
>View it on GitLab:
>https://salsa.debian.org/med-team/python-cobra/compare/724e313e961861782aec42b84fb47303c2457e9d...c2fb47b8dc383b857fb97fcb56537e6559da8e84
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>----- End forwarded message -----


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