[Biopython-dev] PAML test problems under Python 3.3.0

[Brandon Invergo]

Yes no problem, I can take a look at it. I'm completely swamped at the
moment, though, so I might have to put it off for a couple of days. If
it's an emergency, let me know.

-brandon


Peter Cock <p.j.a.cock at googlemail.com> writes:

> Hi Brandon (et al),
>
> Could you have a look at the PAML unit tests under Python 3.3 please?
> I see a mix of failures and 'blocking' under a self-compiled Python 3.3.0
> on Mac OS X 10.8 (Mountain Lion):
>
> $ python3 test_PAML_yn00.py
> testAlignmentExists (__main__.ModTest) ... ok
> testAlignmentFileIsValid (__main__.ModTest) ... FAIL
> testAlignmentSpecified (__main__.ModTest) ... ok
> testCtlFileExistsOnRead (__main__.ModTest) ... ok
> testCtlFileExistsOnRun (__main__.ModTest) ... ok
> testCtlFileValidOnRead (__main__.ModTest) ... ERROR
> testCtlFileValidOnRun (__main__.ModTest) ... ok
> testOptionExists (__main__.ModTest) ... ok
> testOutputFileSpecified (__main__.ModTest) ... ok
> testOutputFileValid (__main__.ModTest) ... ok
> testParseAllVersions (__main__.ModTest) ... ok
> testResultsExist (__main__.ModTest) ... ok
> testResultsParsable (__main__.ModTest) ... ok
> testResultsValid (__main__.ModTest) ... ^C
>
> $ python3 test_PAML_codeml.py
> testAlignmentExists (__main__.ModTest) ... ok
> testAlignmentFileIsValid (__main__.ModTest) ... FAIL
> testAlignmentSpecified (__main__.ModTest) ... ok
> testCtlFileExistsOnRead (__main__.ModTest) ... ok
> testCtlFileExistsOnRun (__main__.ModTest) ... ok
> testCtlFileValidOnRead (__main__.ModTest) ... ERROR
> testCtlFileValidOnRun (__main__.ModTest) ... ok
> testOptionExists (__main__.ModTest) ... ok
> testOutputFileSpecified (__main__.ModTest) ... ok
> testOutputFileValid (__main__.ModTest) ... ok
> testPamlErrorsCaught (__main__.ModTest) ... ok
> testParseAA (__main__.ModTest) ... ok
> testParseAAPairwise (__main__.ModTest) ... ok
> testParseAllNSsites (__main__.ModTest) ... ok
> testParseBranchSiteA (__main__.ModTest) ... ok
> testParseCladeModelC (__main__.ModTest) ... ok
> testParseFreeRatio (__main__.ModTest) ... ok
> testParseNSsite3 (__main__.ModTest) ... ok
> testParseNgene2Mgene02 (__main__.ModTest) ... ok
> testParseNgene2Mgene1 (__main__.ModTest) ... ok
> testParseNgene2Mgene34 (__main__.ModTest) ... ok
> testParsePairwise (__main__.ModTest) ... ok
> testParseSEs (__main__.ModTest) ... ok
> testResultsExist (__main__.ModTest) ... ok
> testResultsParsable (__main__.ModTest) ... ok
> testResultsValid (__main__.ModTest) ... ^C
>
> $ python3 test_PAML_baseml.py
> testAlignmentExists (__main__.ModTest) ... ok
> testAlignmentFileIsValid (__main__.ModTest) ... FAIL
> testAlignmentSpecified (__main__.ModTest) ... ok
> testCtlFileExistsOnRead (__main__.ModTest) ... ok
> testCtlFileExistsOnRun (__main__.ModTest) ... ok
> testCtlFileValidOnRead (__main__.ModTest) ... ERROR
> testCtlFileValidOnRun (__main__.ModTest) ... ok
> testOptionExists (__main__.ModTest) ... ok
> testOutputFileSpecified (__main__.ModTest) ... ok
> testOutputFileValid (__main__.ModTest) ... ok
> testPamlErrorsCaught (__main__.ModTest) ... ok
> testParseAllVersions (__main__.ModTest) ... ok
> testParseAlpha1Rho1 (__main__.ModTest) ... ok
> testParseModel (__main__.ModTest) ... ok
> testParseNhomo (__main__.ModTest) ... ok
> testParseSEs (__main__.ModTest) ... ok
> testResultsExist (__main__.ModTest) ... ok
> testResultsParsable (__main__.ModTest) ... ok
> testResultsValid (__main__.ModTest) ... ^C
>
> If you've not tried this before, the procedure I'm using is:
>
> $ python3 setup.py build
> $ cd build/py3.3/Tests
> $ python3 test_PAML_baseml.py
> etc
>
> The key point is to run the tests directly (rather than
> just via 'python3 setup.py test') you must change
> director to the 2to3 converted folder under the build
> folder.
>
> By commenting out the test methods which seem to
> blocking, it seems some of the failures are to do with
> exception handling. I've not dug any further into this.
>
> Thanks,
>
> Peter