[Biopython-dev] PAML test problems under Python 3.3.0

[Peter Cock]

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