[Biopython-dev] Need guidance.

Thu Jul 6 19:46:15 UTC 2017

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
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython-dev