[Biopython-dev] Need guidance.

Thu Jul 6 20:04:00 UTC 2017

Another issue, perhaps more likely to be a real issue is that the test
in line 127 fails about 50% of the time, and I've seen occasional
failure in line 107.

Are the results of the tests non-deterministic? If so, would it be
advisable to make them fail much less often, e.g. once per billion runs
(this can usually be achieved by doing a probability calculation)?

That's the stack trace of the failing tests:

**********************************************************************
File "testseq.py", line 107, in __main__.testseq
Failed example:
    my_seq2.alphabet
Expected:
    IUPACProtein()
Got:
    HasStopCodon(IUPACProtein(), '*')
**********************************************************************
File "testseq.py", line 127, in __main__.testseq
Failed example:
    -5 < error < 5
Expected:
    False
Got:
    True
**********************************************************************

Adam

On Thu, Jul 6, 2017, at 08:46 PM, Adam Kurkiewicz wrote:
> Hi,
> 
> I've been just having a look at the pull request.
> 
> Please correct me if I'm wrong.
> 
> 1. At the moment one of the ways to run tests locally is to execute
> `python Tests/run_tests.py` from the project's main directory.
> 2. Adil's code will not be tested in this way.
> 3. In order to test Adil's code one has to `run python
> Scripts/testseq.py` from the main directory.
> 
> If that's the case, then it doesn't work on my machine (but I'm most
> likely missing something):
> 
> picrin at lamport:~/programming/biopython/adil$ which python
> /home/picrin/anaconda3/bin/python
> picrin at lamport:~/programming/biopython/adil$ python --version
> Python 3.6.0 :: Anaconda custom (64-bit)
> picrin at lamport:~/programming/biopython/adil$ python Scripts/testseq.py 
> Running doctests...
> **********************************************************************
> File "Scripts/testseq.py", line 65, in __main__.testseq
> Failed example:
>     from Scripts.testseq import testseq
> Exception raised:
>     Traceback (most recent call last):
>       File "/home/picrin/anaconda3/lib/python3.6/doctest.py", line 1330,
>       in __run
>         compileflags, 1), test.globs)
>       File "<doctest __main__.testseq[0]>", line 1, in <module>
>         from Scripts.testseq import testseq
>     ModuleNotFoundError: No module named 'Scripts.testseq'
> **********************************************************************
> 1 items had failures:
>    1 of  41 in __main__.testseq
> ***Test Failed*** 1 failures.
> Done
> 
> 
> Adam
> 
> On Tue, Jul 4, 2017, at 04:41 PM, Peter Cock wrote:
> > Could someone else please take a look at Adil's pull request,
> > particularly his doctest tweaks and import magic in order to
> > test the code under Scripts/ rather than under Bio/ as usual:
> > 
> > https://github.com/biopython/biopython/pull/1306
> > 
> > (I'd just like the reassurance of a second opinion here, as
> > the import stuff has a lot of subtleties.)
> > 
> > Many thanks,
> > 
> > Peter
> > 
> > 
> > On Thu, Jun 15, 2017 at 10:33 AM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> > > Hi Adil,
> > >
> > > You've certainly learnt lots about imports and doctests - and probably
> > > know more than me now.
> > >
> > > I think you've made a sensible choice in restricting the special cases
> > > to your new test_testseq.py while leaving run_tests.py and the
> > > existing doctests as they are.
> > >
> > > Biopython is likely to keep supporting Python 2.7 until the year 2020, see:
> > >
> > > http://mailman.open-bio.org/pipermail/biopython-dev/2016-December/021613.html
> > >
> > > Peter
> > >
> > > On Thu, Jun 15, 2017 at 5:43 AM, Adil Iqbal <aiqbal85 at gmail.com> wrote:
> > >> Hey, though I managed to solve the importing issue, in my conversation with
> > >> Peter, I realized I made a rather large decision without consulting the
> > >> community.
> > >>
> > >> In my current build, I am omitting all modules that are not part of the Bio
> > >> package from executing doctests in version 2.7.
> > >>
> > >> My reason for doing that is copy-pasted below this message. Please read it
> > >> for context.
> > >>
> > >> I realize that 'testseq' is the only module this change effects but is it
> > >> something that we should extend to future modules?
> > >>
> > >> Best,
> > >> Adil
> > >>
> > >> That method will certainly succeed in importing the ['testseq'] module. The
> > >> issue is that once the importing is complete, the doctests are run. And the
> > >> doctest also contain an import statement. The doctests cause an error in 2.7
> > >> because they are subject to the same importing limitations as
> > >> "run_tests.py". I will now describe these limitations below:
> > >>
> > >> Prior to 3.3, hierarchical importing (with "dot" notation) required a
> > >> directory to be initialized with a "__init__.py" file. With the introduction
> > >> of 3.3, hierarchical importing was generalized to all directories,
> > >> regardless of initialization. This is why my commits were passing all tests
> > >> except 2.7.
> > >>
> > >> Since we can't initialize folders carelessly, its best to remove the non-Bio
> > >> modules from the "run_tests.py" file just prior to version 3.3. All versions
> > >> of python after-and-including 3.3 don't require an extra "__init__.py" file,
> > >> so the doctests will run fine on 3.3, 3.4, 3.5, and 3.6. That's why the most
> > >> recent build passed the Travis CI test.
> > >>
> > >> I agree that my import methods were becoming overly-complicated. In the most
> > >> recent build, I've eliminated the complicated code in favor of just deleting
> > >> non-Bio files.The only complicated code left is limited to just the unit
> > >> test ("test_testseq.py").
> > >>
> > >> Thankfully, the unit test for 'testseq' runs all of the same tests that are
> > >> in the doctests, so we can be confident that 'testseq' is compatible with
> > >> all versions of python. In the future, if "biopython" decides to stop
> > >> supporting python 2.7, I would be happy to remove the last bit of
> > >> complicated code.
> > >>
> > >> TL:DR - In 2.7 only: Modules outside 'Bio' package can be imported from
> > >> "run_tests.py", however, their doctests will likely fail because they must
> > >> also contain import statements. It's best to remove them from doctesting in
> > >> earlier versions of python and allow the unit tests to confirm
> > >> compatibility. (Only for non-Bio files in only 2.7).
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Biopython-dev mailing list
> > >> Biopython-dev at mailman.open-bio.org
> > >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
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