Bug#738962: [Debian-med-packaging] Bug#738962: python-csb: More issues with the tests
Hi Dmitry, On 15/02/14 10:13, Dmitry Shachnev wrote: Hi Tomas, Alternatively, you can make binary packages suggest/recommend them, but then you will need to add those packages as dependencies in debian/tests/control. I understand, thank you for the explanation. The Git looks out of date (it does not even include the latest release), where did you update the code? I'm sorry, I was working locally while trying to understand what's going on. I've now updated the sources. Note: this failure seems to only happen on i386 and not amd64. I'll contact upstream and see if they can take care of the i386 failure For running the tests, I personally use just adt-virt-null runner in a clean environment, but probably using something like adt-virt-schroot will be an easier solution. See this message for some instructions: https://lists.debian.org/debian-devel/2014/01/msg00507.html I've successfully set up the schroot. When running the command as follows adt-run python-csb_1.2.3+dfsg-1_all.deb --- adt-virt-schroot csb-amd64 I get a very short output from adt-run saying that the build and the tests are done. I have my doubts about it though, because it returns almost immediately. I am attaching a patch that addresses 1), 2) and 5), and also adds a dependency on python3-all to ensure that tests are run for all supported Python 3 versions. That patch will make the tests green on ci.debian.net, but will not fix the real failure (3). Thank you for the patch, I've applied it to the sources. I didn't know about ci.debian.net, that's a great resource to have handy. Cheers, Tomás -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#738962: python-csb: More issues with the tests
Dear Dmitry, thank you very much for your feedback. Please bear with me and my probably basic questions. This is my first packaging effort in Debian. On 14/02/14 11:18, Dmitry Shachnev wrote: 1) python-csb should depend on python-numpy and python-scipy (and python3-csb should depend on python3-numpy and python3-scipy). These dependencies are specified in REQUIRES field in setup.py and, as I understand, the package is mostly useless without these dependencies. The tests also need numpy to succeed. I see your point. Right now, build-depends is set to: debhelper (= 9),python-all,python3-all,python-epydoc,python-numpy,python-scipy,python-matplotlib And the test dependencies python-csb,python3-csb,python-unittest2,python-numpy I'm a bit confused about the dependencies and referencing to the source or binary packages, and whether they're missing from only the tests or also from the main package. Where should the references to the binary package python3-numpy and -scipy be added? 2) In debian/tests/build, Makefile-style variables are used. I think that was blindly copied from debian/rules, and not really needed. Also, you use python instead of $python, so in fact the test is ran three times for python2.7. I would write the command like this: for py in $(pyversions -i) $(py3versions -i); do PYTHONWARNINGS=d $py test/app.py --generated-resources /tmp --verbosity 2 done Note that I also increased verbosity to get the more understandable output in case of failures. Thank you very much for your suggestion. I've updated the code accordingly. 3) One of the tests fails (at least with Python 2.7): 4) The tests failures are ignored. When the test fails for python2.7, the next tests are run. After I figure out the correct setup for the tests I'll try to reproduce 3) and 4), and will probably get back to you with more questions ;) 5) Some test is printed into stderr, for example the deprecation warnings and names of the tests. Autopkgtest considers that as a failure by default, to allow stderr you need to add this line to debian/tests/control: Restrictions: allow-stderr Is the addition of this restriction a good idea, or should I rather try to get upstream to change the behaviour? Once again, thank you for your detailed observations. They are extremely helpful. Cheers, Tomás -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#735883: Bug fix commit for python-csb
Since I haven't been able to reproduce the bug locally yet and it's already been a couple of weeks, I went ahead and applied the fix that's been suggested by various developers so the package is not held back anymore. If anyone could check the package and upload, I'd be grateful. Best, Tomás -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#735883: Unrreproducible bug in autopkg test
Dear Matthias, As suggested by Paul, I'm contacting you in my quest to reproduce this error before submitting what should be the fix (my innocent mind assumed you would be aware of the thread as the submitter). If I try to run the adt-run command without sudo, I get a dpkg permission denied. Is there anything I can do to test this and make it fail as reported? I'm trying to learn about the test framework for reference in future packages I hope to maintain. Thank you! Tomás -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#735883: auto_test failing for python-csb
Hi Andreas, Right, I had missed that spot. Before applying the fix, however, I'd like to replicate the error and make sure it's fixed locally, both to make sure it'll work, and to learn about the test system in the process. I've been trying to get the tests to fail in the way it's reported, but I haven't been able to. By doing some research I ended up with this command: sudo adt-run --user=a_normal_user --no-built-binaries --built-tree=. --- adt-virt-null but still the tests run without any problems. Is there a way to replicate the test exactly as it is run when uploaded? Thanks! Tomás On 21/01/14 09:07, Andreas Tille wrote: Hi Tomás, On Sat, Jan 18, 2014 at 05:45:31PM +0100, Tomás Di Domenico wrote: Greegins, all. A bug that I had marked as closed has been reopened (or rather, re-reported) [1]. It seems like when running the tests as specified in debian/rules/override_dh_auto_test,the test suite tries to write to a forbidden location. The issue is that upon our request, after having faced the same problem in a previous release, upstream has added a parameter to specify the write directory. I added this parameter to the auto_test command, and it works perfectly when I run git-buildpackage. It also succeeds when running the test command manually (just to confirm, I do get the reported error if I leave out the new parameter). The issue is solved for *building* the package. I'm a bit at a loss here. I don't quite understand what could be causing the tests to try and write somewhere else than where the --generated-resources arguments is indicating. The bug report (in CC - it always makes sense to keep the reporter and readers of the bug report informed) is about autopkgtest which is some test suite which runs on all packages that have set XS-Testsuite: autopkgtest in d/control. So I think to fix the bug you need to pass the very same option you used in override_dh_auto_test in debian/tests/build as well to fix the problem. Hope this helps Andreas. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#695311: ITP: python3-csb -- Python framework for structural bioinformatics
Package: wnpp Severity: wishlist Owner: Debian Med group debian-...@lists.debian.org * Package name: python3-csb Version : 1.1.0 Upstream Author : Michael Habeck michael.hab...@tuebingen.mpg.de * URL : http://csb.codeplex.com/ * License : MIT Programming Lang: Python Description : Python framework for structural bioinformatics Computational Structural Biology Toolbox (CSB) is a Python class library for reading, storing and analyzing biomolecular structures in a variety of formats, with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#692032: ITP: python-csb -- Python framework for structural bioinformatics
Package: wnpp Severity: wishlist Owner: Debian Med group debian-...@lists.debian.org * Package name: python-csb Version : 1.1.0 Upstream Author : Michael Habeck michael.hab...@tuebingen.mpg.de * URL : http://csb.codeplex.com/ * License : MIT Programming Lang: Python Description : Python framework for structural bioinformatics Computational Structural Biology Toolbox (CSB) is a Python class library for reading, storing and analyzing biomolecular structures in a variety of formats, with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
